1
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Hogan BLM. Bud, branch, breathe! Building a mammalian lung over space and time. Dev Biol 2025; 522:64-75. [PMID: 40107482 DOI: 10.1016/j.ydbio.2025.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Revised: 03/12/2025] [Accepted: 03/16/2025] [Indexed: 03/22/2025]
Abstract
Many mammalian organs, such as the mammary and lachrymal glands, kidney and lungs develop by the process known as branching morphogenesis. An essential feature of this process is the reciprocal interaction between the inner branched tubular epithelium and the surrounding mesenchyme to optimize the final amount of epithelial tissue that is generated for specific functions. To achieve this expansion the initial epithelial population undergoes repeated rounds of bud formation, branch outgrowth and tip bifurcations, with each repertoire requiring dynamic changes in cell behavior. The process of branching morphogenesis was first studied experimentally by Grobstein and others who showed that the embryonic epithelium did not develop without so-called inductive signals from the mesenchyme. However, it was not known whether this activity was uniformly distributed throughout the mesoderm or localized to specific regions. The mouse lung was seen as a powerful system in which to investigate such questions since its early branching is highly stereotypic, both in vivo and in culture. This advantage was exploited by two young scientists, Alescio and Cassini, who used grafting techniques with explanted embryonic mouse lungs. They showed that mesenchyme from around distal buds could induce ectopic buds in the trachea and other non-branching regions of the epithelium. At the same time, distal regions denuded of their mesoderm failed to develop further. They speculated that inductive factors that promote bud formation and continued outgrowth in competent endoderm are specifically localized within the distal mesenchyme, establishing a conceptual framework for future experimentation. Since then, advances in many areas of biology and bioengineering have enabled the identification of gene regulatory networks, signaling pathways and biomechanical properties that mediate lung branching morphogenesis. However, a quantitative model of how these parameters are coordinated over space and time to control the pattern and scale of branching and the overall size of the lung, still remains elusive.
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Affiliation(s)
- Brigid L M Hogan
- Department of Cell Biology, Duke University Medical School, Durham, NC, 27710, USA.
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2
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Sakurai M, Hosokawa S, Yamaguchi Y, Kirimura S, Ihara K, Ohashi K, Furukawa T, Sasano T, Kashimada K, Ishii T. Cyclopamine Attenuates Pulmonary Arterial Hypertension Development: Implications of Hedgehog Signaling Involvement for the Pathophysiology. FASEB J 2025; 39:e70628. [PMID: 40353829 DOI: 10.1096/fj.202403350r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 03/24/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
Abstract
Pulmonary arterial hypertension (PAH) is one of the most severe pulmonary diseases. Although combination therapies of the key drugs have improved survival rates, unmet needs remain in its management. We examined the effects of cyclopamine, a Hedgehog (HH) signaling inhibitor, as a potential novel therapeutic approach for PAH. C57BL/6J male mice were exposed to 10% oxygen for 3 weeks to induce pulmonary hypertension. One week after hypoxia exposure, these mice were treated with cyclopamine or vehicle. Cyclopamine significantly attenuated right ventricular (RV) systolic pressure (H + C: 31 mmHg vs. H: 38 mmHg, p < 0.01) and RV hypertrophy (H + C: 0.28 vs. H: 0.37, p < 0.01). The fully muscularized small pulmonary arteries significantly decreased with cyclopamine (H + C: 30% vs. H: 80%, p < 0.01), suggesting a mediation by vascular remodeling inhibition. In vitro, human pulmonary arterial smooth muscle cells (HPASMC) exposed to hypoxia revealed that the inhibitory action of cyclopamine was limited to hypoxia-promoted cell proliferation. In single-cell RNA sequencing analysis of mice lungs treated with cyclopamine, the signaling pathways of vascular smooth muscle contraction and cGMP-PKG, that is, key regulators in PAH development through vascular remodeling, were suppressed in cells with the characteristics of vascular endothelial and smooth muscle cells. RNA sequencing analysis of hypoxia-exposed hPASMCs revealed that the pathways related to extracellular matrix regulation were particularly recovered. Our animal model-based data revealed that HH signaling inhibition would improve PAH development by suppressing pulmonary vascular remodeling.
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MESH Headings
- Animals
- Veratrum Alkaloids/pharmacology
- Hedgehog Proteins/metabolism
- Male
- Mice
- Signal Transduction/drug effects
- Mice, Inbred C57BL
- Humans
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/drug effects
- Pulmonary Arterial Hypertension/drug therapy
- Pulmonary Arterial Hypertension/metabolism
- Pulmonary Artery/drug effects
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/drug therapy
- Hypoxia
- Hypertrophy, Right Ventricular/metabolism
- Hypertrophy, Right Ventricular/drug therapy
- Vascular Remodeling/drug effects
- Cell Proliferation/drug effects
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Affiliation(s)
- Makito Sakurai
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
| | - Susumu Hosokawa
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
- Department of Pediatrics, Japanese Red Cross Musashino Hospital, Tokyo, Japan
| | - Yohei Yamaguchi
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
| | - Susumu Kirimura
- Department of Pathology, Institute of Science Tokyo, Tokyo, Japan
| | - Kensuke Ihara
- Department of Cardiovascular Medicine, Institute of Science Tokyo, Tokyo, Japan
| | - Kenichi Ohashi
- Department of Human Pathology, Institute of Science Tokyo, Tokyo, Japan
| | - Tetsushi Furukawa
- Department of Bio-Informational Pharmacology, Medical Research Institute, Institute of Science Tokyo, Tokyo, Japan
| | - Tetsuo Sasano
- Department of Cardiovascular Medicine, Institute of Science Tokyo, Tokyo, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
- Department of Pediatric Endocrinology, National Center for Child Health and Development, Tokyo, Japan
| | - Taku Ishii
- Department of Pediatrics and Developmental Biology, Institute of Science Tokyo, Tokyo, Japan
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3
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Lin Y, Chen J, Tan J, Yu Z, Pi R, Xiong J, Ding Y, Chen M, Bai X. Pericytes in the Pulmonary Microenvironment: Guardians or Adversaries? Lung 2025; 203:65. [PMID: 40448710 DOI: 10.1007/s00408-025-00820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Accepted: 05/11/2025] [Indexed: 06/02/2025]
Abstract
Pericytes, specialized mural cells residing within the basement membrane of pulmonary microvessels, participate in various biological processes, including vascular homeostasis, immunomodulation, and tissue repair. However, these beneficial physiological roles can be detrimental under pathological conditions. Numerous pulmonary fibrosis models have demonstrated pericyte differentiation into scar-forming myofibroblasts, leading to collagen deposition and matrix remodeling, thereby contributing to tissue fibrosis. Similarly, pericytes play crucial roles in inflammatory diseases. This review aims to explore the dual roles of pericytes in the lung and the underlying mechanisms of their role conversion, providing insights for developing therapeutic strategies targeting these cells.
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Affiliation(s)
- Yan Lin
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiaqi Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiale Tan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zihang Yu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ruozheng Pi
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingrong Xiong
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yi Ding
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| | - Minfeng Chen
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, China.
| | - Xue Bai
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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4
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Qu N, Daoud A, Kechele DO, Cleary CE, Múnera JO. Differentiation of human pluripotent stem cells into urothelial organoids via transient activation of WNT signaling. iScience 2025; 28:112398. [PMID: 40322079 PMCID: PMC12049843 DOI: 10.1016/j.isci.2025.112398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 10/15/2024] [Accepted: 04/07/2025] [Indexed: 05/08/2025] Open
Abstract
The cloaca is a transient structure that forms in the terminal hindgut giving rise to the rectum dorsally and the urogenital sinus ventrally. Similarly, human hindgut cultures derived from human pluripotent stem cells generate human colonic organoids (HCOs) which also contain co-developing urothelial tissue. In this study, our goal was to identify pathways involved in cloacal patterning and apply this to human hindgut cultures. RNA sequencing (RNA-seq) data comparing dorsal versus ventral cloaca in e10.5 mice revealed that WNT signaling was elevated in the ventral versus dorsal cloaca. Inhibition of WNT signaling in hindgut cultures maintained their differentiation toward colonic organoids. WNT activation promoted differentiation toward human urothelial organoids (HUOs). HUOs contained developmental stage specific cell types present in mammalian urothelial tissue including co-developing mesenchyme. Therefore, HUOs offer a powerful in vitro model for dissecting the regulatory pathways that control the dynamic emergence of stage specific cell types within the human urothelium.
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Affiliation(s)
- Na Qu
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Abdelkader Daoud
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Cassie E. Cleary
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jorge O. Múnera
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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5
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Song JY, Wehbe F, Wong AK, Hall BM, Vander Heiden JA, Brightbill HD, Arron JR, Garfield DA, Dey A, Rock JR. YAP/TAZ activity in PDGFRα-expressing alveolar fibroblasts modulates AT2 proliferation through Wnt4. Cell Rep 2025; 44:115645. [PMID: 40333185 DOI: 10.1016/j.celrep.2025.115645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 03/06/2025] [Accepted: 04/11/2025] [Indexed: 05/09/2025] Open
Abstract
The Hippo pathway, mediated by its transcriptional effectors Yes-associated protein 1 (YAP) and WW-domain-containing transcription regulator 1 (TAZ), is crucial in maintaining lung homeostasis and facilitating injury repair. While its roles in epithelial cells are well established, its regulatory effects on lung fibroblasts remain less understood. We engineered a mouse model for the inducible knockdown of YAP/TAZ and showed that fibroblast-specific knockdown enhances PDGFRα+ alveolar fibroblasts' support for alveolar-epithelial-stem-cell-derived organoids in vitro. Single-cell profiling revealed changes in fibroblast subpopulations, including the emergence of a Wnt4+ enriched subpopulation. Epigenomic analyses revealed shifts in transcription factor motif enrichment in both fibroblasts and epithelial cells due to fibroblast YAP/TAZ suppression. Further computational and in vivo analyses confirmed increased Wnt signaling and Wnt4 expression in PDGFRα-lineage+ fibroblasts, which enhanced SPC+ alveolar type 2 (AT2) cell proliferation. These findings highlight a mechanistic role of YAP/TAZ in PDGFRα+ alveolar fibroblasts in supporting AT2 cell maintenance and proliferation via Wnt4 secretion.
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Affiliation(s)
- Jane Y Song
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Fabien Wehbe
- Data & Analytics Chapter-Computational Science, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aaron K Wong
- Department of Immunology and Infectious Diseases, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ben M Hall
- Department of Immunology and Infectious Diseases, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Vander Heiden
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Immunology and Infectious Diseases, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - David A Garfield
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason R Rock
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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6
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Klinkhammer K, Warren R, Knopp J, Nguyen T, De Langhe SP. Epithelial-mesenchymal cell competition coordinates fate transitions across tissue compartments during lung development and fibrosis. RESEARCH SQUARE 2025:rs.3.rs-6189965. [PMID: 40343336 PMCID: PMC12060972 DOI: 10.21203/rs.3.rs-6189965/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/11/2025]
Abstract
Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. In this study, we reveal that lung mesenchymal Yap levels and fitness antagonize epithelial Yap levels and stemness during lung development and repair following bleomycin injury. Elevated mesenchymal Yap signaling and fitness antagonize epithelial Yap levels and stemness, accelerating alveolar epithelial differentiation while impairing branching during lung development or bronchiolization after bleomycin injury. Conversely, mesenchymal Snail/Slug sequesters Yap/Taz to direct an adipogenic differentiation program towards alveolar fibroblast 1 (AF1) during both lung development and the resolution of pulmonary fibrosis. On the other hand, Yap/Myc-Tead binding instructs a myogenic differentiation program. Through our experiments and modeling, we identify tissue-scale mechanical cooperation as a pivotal factor in orchestrating organ formation and regeneration.
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Affiliation(s)
- Kylie Klinkhammer
- Department of Medicine, Division of Pulmonary and Critical Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Rachel Warren
- Department of Medicine, Division of Pulmonary and Critical Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Joseph Knopp
- Department of Medicine, Division of Pulmonary and Critical Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Toan Nguyen
- Department of Medicine, Division of Pulmonary and Critical Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Stijn P. De Langhe
- Department of Medicine, Division of Pulmonary and Critical Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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7
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Hirsch TI, Tsikis ST, Fligor SC, Pan AS, Wang SZ, Quigley M, Dadi S, Kishikawa H, Mitchell PD, Niaudet C, Bielenberg DR, Puder M. Systemic heparin administration impairs lung development in neonatal mice. Sci Rep 2025; 15:15273. [PMID: 40312554 PMCID: PMC12046039 DOI: 10.1038/s41598-025-99831-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 04/23/2025] [Indexed: 05/03/2025] Open
Abstract
Preterm infants born in the saccular stage of lung development are at risk for developing bronchopulmonary dysplasia (BPD). Oxygen toxicity and volutrauma are identified as major contributors of BPD. Despite mitigation of these risks preterm infants continue to be affected by chronic lung disease. Heparin is commonly administered to preterm infants and is known to interfere with angiogenesis, a critical element of lung development. We previously demonstrated, in a murine model, that compensatory lung growth after left pneumonectomy is inhibited by heparin administration. Based on these results, we hypothesized that heparin would interfere with lung development in neonatal mice, which are born during the saccular phase of lung development. Newborn C57BL/6J mice received either therapeutic unfractionated heparin (UFH), low molecular weight heparin (LMWH) or normal saline (control) for the first week of life. At one month, both UFH and LMWH produced an emphysematous lung phenotype. Late administration of heparin, after the saccular phase did not impact lung function or growth. This data establishes the negative effects of UFH and LMWH during the critical period of postnatal lung development. Based on this work, clinical studies on the impact of heparin on lung development of newborn and preterm infants are warranted.
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Affiliation(s)
- Thomas I Hirsch
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Savas T Tsikis
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Scott C Fligor
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Amy Shei Pan
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Sarah Z Wang
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Mikayla Quigley
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA
| | - Srujan Dadi
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hiroko Kishikawa
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul D Mitchell
- Biostatistics and Research Design Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Colin Niaudet
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Diane R Bielenberg
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark Puder
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Fegan 3, Boston, MA, 02115, USA.
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8
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Mercer J, Saether E, King T, Maul H, Kennedy HP, Erickson-Owens D, Andersson O, Rabe H. How Delayed Cord Clamping Saves Newborn Lives. CHILDREN (BASEL, SWITZERLAND) 2025; 12:585. [PMID: 40426764 PMCID: PMC12110096 DOI: 10.3390/children12050585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2025] [Revised: 04/23/2025] [Accepted: 04/28/2025] [Indexed: 05/29/2025]
Abstract
Interest in the subject of umbilical cord clamping is long-standing. New evidence reveals that placental transfusion, facilitated by delayed cord clamping (DCC), reduces death and need for blood transfusions for preterm infants without evidence of harm. Even a brief delay in clamping the cord shows improved survival and well-being, but waiting at least two minutes is even better. We propose that three major benefits from DCC contribute to reduced mortality of preterm infants: (1) benefits from the components of blood; (2) assistance from the continued circulation of blood; and (3) the essential mechanical interactions that result from the enhanced volume of blood. The enhanced blood volume generates mechanical forces within the microcirculation that support the newborn's metabolic and cardiovascular stability and secure short- and long-term organ health. Several unique processes prime preterm and term newborns to receive the full placental transfusion, not to be misinterpreted as extra blood or over-transfusion. Disrupting cord circulation before the newborn's lung capillary bed has been fully recruited and the lungs can replace the placenta as a respiratory, gas-exchanging organ may be harmful. Early cord clamping also denies the newborn a full quota of iron-rich red blood cells as well as valuable stem cells for regeneration, repair, and seeding of a strong immune system. We propose that delayed cord clamping and intact-cord stabilization have the potential to save lives by protecting many neonates from hypovolemia, inflammation, and ischemia.
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Affiliation(s)
- Judith Mercer
- College of Nursing, University of Rhode Island, Kingston, RI 02881, USA;
| | | | - Tekoa King
- School of Nursing, University of California, San Francisco, CA 94143, USA;
| | - Holger Maul
- Department of Obstetrics and Gynecology of the Asklepios Kliniken Barmbek, Wandsbek and Nord-Heidberg, 22039 Hamburg, Germany;
| | | | | | - Ola Andersson
- Department of Neonatology, Skåne University Hospital, 22185 Malmo/Lund, Sweden;
- Department of Clinical Sciences, Pediatrics/Neonatology, Lund University, 22362 Lund, Sweden
| | - Heike Rabe
- Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9QG, UK;
- Department of Neonatology, University Hospitals Sussex NHS Foundation Trust, Royal Sussex County Hospital, Brighton BN2 5BE, UK
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9
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Muthumalage T, Sarles E, Wang Q, Hensel E, Hill T, Rahman I, Robinson R, Stroup AM, Thongphanh K, Miller LA. In Vitro assessments of ENDS toxicity in the respiratory tract: Are we there yet? NAM JOURNAL 2025; 1:100016. [PMID: 40264558 PMCID: PMC12013380 DOI: 10.1016/j.namjnl.2025.100016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
Abstract
Approximately 4.6 % of U.S. adults over the age of 18 use e-cigarettes, which are a type of electronic nicotine delivery system (ENDS). Over 2.5 million U.S. middle and high school students also use both disposable and/or flavored ENDS products. The health impacts of ENDS use by adults and adolescents are considered a controversial topic in the social media partially due to misperceptions surrounding ENDS toxicity compared to that of combustible cigarettes. There is growing evidence that ENDS, particularly their product composition and design, individual and combined ingredients, and produced aerosols, are toxic to human health. Animal studies have been critical for defining the pathophysiologic outcomes resulting from ENDS use. However, in vitro approaches using human cells can measure the potential toxicity of ENDS e-liquids and aerosols on a shorter timeline and are in keeping with recent statements to replace, reduce and refine the use of animals in biomedical research and regulatory decision making. This review examines current research related to cell culture models of the respiratory tract and exposure methodologies for ENDS use and compares known in vivo parameters of injury and inflammation associated with ENDS to different in vitro systems developed to replicate the inhaled toxicant outcomes. The design and interpretation of exposure methodologies and technological gaps in the evaluation of ENDS aerosols are also discussed. Given the ongoing evolution and popularity of ENDS products, in vitro assessments for measuring respiratory tract injury and inflammation resulting from ENDS use provide a critical scientific platform for rapid evaluation of potential inhalation toxicity in tobacco regulatory science.
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Affiliation(s)
| | - Emma Sarles
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Qixin Wang
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Edward Hensel
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Thomas Hill
- Office of Science, Center for Tobacco Products, US Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Risa Robinson
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Andrea M. Stroup
- Behavioral Health and Health Policy Practice, Westat, Rockville, MD, 20850, USA
| | - Krista Thongphanh
- California National Primate Research Center, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis 95616, USA
| | - Lisa A. Miller
- California National Primate Research Center, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis 95616, USA
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10
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Mohr-Allen SR, Gleghorn JP, Varner VD. Fluid secretion and luminal pressure control lateral branching morphogenesis in the embryonic avian lung. Dev Biol 2025; 520:251-263. [PMID: 39870322 DOI: 10.1016/j.ydbio.2025.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 12/20/2024] [Accepted: 01/23/2025] [Indexed: 01/29/2025]
Abstract
During lung development, the embryonic airway originates as a wishbone-shaped epithelial tube, which undergoes a series of branching events to build the bronchial tree. This process depends crucially on cell proliferation and is thought to involve distinct branching modes: lateral branching, wherein daughter branches emerge along the length of a parent branch, and bifurcations, wherein the tip of a parent branch splits to form two new daughter branches. The developing airway is fluid-filled, and previous studies have shown that altered luminal pressure can influence rates of branching morphogenesis. However, it is not clear if altered tissue mechanics influence patterns of proliferation along the embryonic airway epithelium nor if individual branching modes are affected differently by changes in luminal pressure. Here, we focused on mechanisms of lateral branching and used as a model system the embryonic avian lung, which forms exclusively via this branching mode during early development. We used microinjected fluid droplets or pharmacological modulators of fluid secretion to alter luminal fluid pressure either locally or globally within cultured embryonic lungs. Somewhat surprisingly, we found both local and global increases in luminal pressure to suppress the formation of new lateral branches while also promoting increased epithelial proliferation. In a consistent manner, decreased luminal pressure led to an increase in lateral branching morphogenesis. Morphometric analysis of airway branching patterns revealed that altered luminal pressure shifts the overall branching program, rather than simply changing rates of morphogenesis. Taken together, these results highlight the importance of mechanical forces during airway branching and suggest that different branching modes may be affected differently by luminal fluid pressure.
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Affiliation(s)
- Shelby R Mohr-Allen
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA; Department of Biomedical Engineering, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jason P Gleghorn
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Victor D Varner
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA; Department of Biomedical Engineering, UT Southwestern Medical Center, Dallas, TX, USA.
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11
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Qadir AS, Das S, Nedunchezian S, Masuhara K, Desai TJ, Rehman J, Kadur Murthy P, Tsukasaki Y, Shao L, Malik AB. Physiological Modeling of the Vascularized Human Lung Organoid. Am J Respir Cell Mol Biol 2025; 72:354-363. [PMID: 39514019 PMCID: PMC12005031 DOI: 10.1165/rcmb.2024-0413ma] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024] Open
Abstract
Human lung organoids (hLOs) derived from induced pluripotent stem cells (iPSCs) are of great interest, as they inform lung development, such as differentiation of lung epithelial subtypes in the distal alveolar unit. An unaddressed question is whether introducing endothelial cells (ECs) and vascularization provides a better representation of hLOs. Here we describe a method in which vessels become integrated with hLOs. hLOs were generated by combining human iPSC-derived lung progenitor cells (LPs) with ECs at varying LP:EC ratios. At the optimal combination of both cells, we observed vessel infiltration of hLOs compared to without ECs. Red blood cells were seen in hLOs implanted into kidney capsules of NOD/SCID mice. Both human and mouse ECs conjoined to form chimeric vessels in hLOs. The vascularized hLOs showed alveolar type II epithelial (ATII) cells and ATI cells, although there was no difference in 1:1 ATII/ATI ratio. We observed primitive airway sacs with alveolar epithelial cells lining the lumen of vascularized hLOs. Electron microscopy revealed surfactant production in ATII cells of vascularized hLOs in contrast to absence of vessels. The vascularized hLOs also mounted a robust inflammatory response characterized by influx of mouse neutrophils after challenging mice with LPS. Thus, interactions of ECs with LPs generated vascularized hLOs that induced ATII and ATI differentiation, although not reaching to the ratio of 1:9 seen in mature human lungs. hLOs also showed the LPS induced inflammatory response upon transplantation into recipient mice. Our results show the potential of vascularized hLOs for studying human lung development and inflammatory lung injury.
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Affiliation(s)
- Abdul S. Qadir
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
| | - Sukanta Das
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
| | - Swathi Nedunchezian
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
| | - Kaori Masuhara
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
| | - Tushar J. Desai
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California; and
| | - Jalees Rehman
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, Illinois
| | | | - Yoshikazu Tsukasaki
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
| | - Lijian Shao
- Department of Pharmacology and Regenerative Medicine
- Cell Biologic Inc., Chicago, Illinois
| | - Asrar B. Malik
- Department of Pharmacology and Regenerative Medicine
- The Center for Lung and Vascular Biology, and
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12
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Ke X, van Soldt B, Vlahos L, Zhou Y, Qian J, George J, Capdevila C, Glass I, Yan K, Califano A, Cardoso WV. Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate. Dev Cell 2025; 60:819-836.e7. [PMID: 39667932 PMCID: PMC11945641 DOI: 10.1016/j.devcel.2024.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 08/07/2024] [Accepted: 11/17/2024] [Indexed: 12/14/2024]
Abstract
Transitional cell states are at the crossroads of crucial developmental and regenerative events, yet little is known about how these states emerge and influence outcomes. The alveolar and airway epithelia arise from distal lung multipotent progenitors, which undergo cell fate transitions to form these distinct compartments. The identification and impact of cell states in the developing lung are poorly understood. Here, we identified a population of Icam1/Nkx2-1 epithelial progenitors harboring a transitional state program remarkably conserved in humans and mice during lung morphogenesis and regeneration. Lineage-tracing and functional analyses reveal their role as progenitors to both airways and alveolar cells and the requirement of this transitional program to make distal lung progenitors competent to undergo airway cell fate specification. The identification of a common progenitor cell state in vastly distinct processes suggests a unified program reiteratively regulating outcomes in development and regeneration.
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Affiliation(s)
- Xiangyi Ke
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin van Soldt
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yizhuo Zhou
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Pulmonary & Allergy Critical Care, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun Qian
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joel George
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Disease, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Claudia Capdevila
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Disease, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ian Glass
- Birth Defects Research Laboratory (BDRL), University of Washington, Seattle, WA 98105, USA
| | - Kelley Yan
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Disease, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wellington V Cardoso
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Pulmonary & Allergy Critical Care, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA.
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13
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Liu X, Lam SM, Zheng Y, Mo L, Li M, Sun T, Long X, Peng S, Zhang X, Mei M, Shui G, Bao S. Palmitoyl-carnitine Regulates Lung Development by Promoting Pulmonary Mesenchyme Proliferation. RESEARCH (WASHINGTON, D.C.) 2025; 8:0620. [PMID: 40104443 PMCID: PMC11914330 DOI: 10.34133/research.0620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 01/20/2025] [Accepted: 01/29/2025] [Indexed: 03/20/2025]
Abstract
Disruption of acylcarnitine homeostasis results in life-threatening outcomes in humans. Carnitine-acylcarnitine translocase deficiency (CACTD) is a scarce autosomal recessive genetic disease and may result in patients' death due to heart arrest or respiratory insufficiency. However, the reasons and mechanism of CACTD inducing respiratory insufficiency have never been elucidated. Herein, we employed lipidomic techniques to create comprehensive lipidomic maps of entire lungs throughout both prenatal and postnatal developmental stages in mice. We found that the acylcarnitines manifested notable variations and coordinated the expression levels of carnitine-acylcarnitine translocase (Cact) across these lung developmental stages. Cact-null mice were all dead with a symptom of respiratory distress and exhibited failed lung development. Loss of Cact resulted in an accumulation of palmitoyl-carnitine (C16-acylcarnitine) in the lungs and promoted the proliferation of mesenchymal progenitor cells. Mesenchymal cells with elevated C16-acylcarnitine levels displayed minimal changes in energy metabolism but, upon investigation, revealed an interaction with sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (Samhd1), leading to decreased protein abundance and enhanced cell proliferation. Thus, our findings present a mechanism addressing respiratory distress in CACTD, offering a valuable reference point for both the elucidation of pathogenesis and the exploration of treatment strategies for neonatal respiratory distress.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Respiratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Zheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lesong Mo
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhan Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Long
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Peng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinwei Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Mei
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, Beijing, China
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14
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Hutchins NT, Meziane M, Lu C, Mitalipova M, Fischer D, Li P. Reconstructing signaling histories of single cells via perturbation screens and transfer learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.16.643448. [PMID: 40166200 PMCID: PMC11957020 DOI: 10.1101/2025.03.16.643448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Manipulating the signaling environment is an effective approach to alter cellular states for broad-ranging applications, from engineering tissues to treating diseases. Such manipulation requires knowing the signaling states and histories of the cells in situ , for which high-throughput discovery methods are lacking. Here, we present an integrated experimental-computational framework that learns signaling response signatures from a high-throughput in vitro perturbation atlas and infers combinatorial signaling activities in in vivo cell types with high accuracy and temporal resolution. Specifically, we generated signaling perturbation atlas across diverse cell types/states through multiplexed sequential combinatorial screens on human pluripotent stem cells. Using the atlas to train IRIS, a neural network-based model, and predicting on mouse embryo scRNAseq atlas, we discovered global features of combinatorial signaling code usage over time, identified biologically meaningful heterogeneity of signaling states within each cell type, and reconstructed signaling histories along diverse cell lineages. We further demonstrated that IRIS greatly accelerates the optimization of stem cell differentiation protocols by drastically reducing the combinatorial space that needs to be tested. This framework leads to the revelation that different cell types share robust signal response signatures, and provides a scalable solution for mapping complex signaling interactions in vivo to guide targeted interventions.
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15
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Ansari SS, Dillard ME, Ghonim M, Zhang Y, Stewart DP, Canac R, Moskowitz IP, Wright WC, Daly CA, Pruett-Miller SM, Steinberg J, Wang YD, Chen T, Thomas PG, Bridges JP, Ogden SK. Receptor Allostery Promotes Context-Dependent Sonic Hedgehog Signaling During Embryonic Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.28.635336. [PMID: 39975106 PMCID: PMC11838287 DOI: 10.1101/2025.01.28.635336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Sonic Hedgehog (SHH) signaling functions in temporal- and context-dependent manners to pattern diverse tissues during embryogenesis. The signal transducer Smoothened (SMO) is activated by sterols, oxysterols, and arachidonic acid (AA) through binding pockets in its extracellular cysteine-rich domain (CRD) and 7-transmembrane (7TM) bundle. In vitro analyses suggest SMO signaling is allosterically enhanced by combinatorial ligand binding to these pockets but in vivo evidence of SMO allostery is lacking. Herein, we map an AA binding pocket at the top of the 7TM bundle and show that its disruption attenuates SHH and sterol-stimulated SMO induction. A knockin mouse model of compromised AA binding reveals that homozygous mutant mice are cyanotic, exhibit high perinatal lethality, and show congenital heart disease. Surviving mutants demonstrate pulmonary maldevelopment and fail to thrive. Neurodevelopment is unaltered in these mice, suggesting that context-dependent allosteric regulation of SMO signaling allows for precise tuning of pathway activity during cardiopulmonary development.
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Affiliation(s)
- Shariq S. Ansari
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Miriam E. Dillard
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mohamed Ghonim
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yan Zhang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel P. Stewart
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robin Canac
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Ivan P. Moskowitz
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christina A. Daly
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeffrey Steinberg
- Center for In Vivo Imaging and Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Paul G. Thomas
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - James P. Bridges
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Medicine, Division of Pulmonary Sciences and Critical Care, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Stacey K. Ogden
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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16
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Negretti NM, Son Y, Crooke P, Plosa EJ, Benjamin JT, Jetter CS, Bunn C, Mignemi N, Marini J, Hackett AN, Ransom M, Garg S, Nichols D, Guttentag SH, Pua HH, Blackwell TS, Zacharias W, Frank DB, Kozub JA, Mahadevan-Jansen A, Krystofiak E, Kropski JA, Wright CV, Millis B, Sucre JM. Epithelial outgrowth through mesenchymal rings drives lung alveologenesis. JCI Insight 2025; 10:e187876. [PMID: 39773701 PMCID: PMC11949025 DOI: 10.1172/jci.insight.187876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 01/06/2025] [Indexed: 01/11/2025] Open
Abstract
Determining how alveoli are formed and maintained is critical to understanding lung organogenesis and regeneration after injury. To study the cellular dynamics of this critical stage of lung development, we have used scanned oblique-plane illumination microscopy of living lung slices to observe alveologenesis in real time at high resolution over several days. Contrary to the prevailing notion that alveologenesis occurs by airspace subdivision via ingrowing septa, we found that alveoli form by ballooning epithelial outgrowth supported by contracting mesenchymal ring structures. Systematic analysis has produced a computational model of finely timed cellular structural changes that drive normal alveologenesis. With this model, we can now quantify how perturbing known regulatory intercellular signaling pathways and cell migration processes affects alveologenesis. In the future, this paradigm and platform can be leveraged for mechanistic studies and screening for therapies to promote lung regeneration.
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Affiliation(s)
| | | | | | | | | | | | | | - Nicholas Mignemi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - John Marini
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | | | | | | | - Heather H. Pua
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy S. Blackwell
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Medicine, and
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
| | - William Zacharias
- Department of Pediatrics, Cincinnati Children’s Hospital, Cincinnati, Ohio, USA
| | - David B. Frank
- Department of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John A. Kozub
- Department of Bioengineering
- Vanderbilt Biophotonics Center, and
- Department of Physics, Vanderbilt University, Nashville, Tennessee, USA
| | - Anita Mahadevan-Jansen
- Department of Bioengineering
- Vanderbilt Biophotonics Center, and
- Department of Surgery, Neurological Surgery and Otolaryngology, and
| | - Evan Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan A. Kropski
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Medicine, and
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
- Biodevelopmental Origins of Lung Disease (BOLD) Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher V.E. Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Biodevelopmental Origins of Lung Disease (BOLD) Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Bryan Millis
- Vanderbilt Biophotonics Center, and
- Biodevelopmental Origins of Lung Disease (BOLD) Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer M.S. Sucre
- Department of Pediatrics
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Biodevelopmental Origins of Lung Disease (BOLD) Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
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17
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Zhu Z, Cheng Y, Liu X, Ding W, Liu J, Ling Z, Wu L. Advances in the Development and Application of Human Organoids: Techniques, Applications, and Future Perspectives. Cell Transplant 2025; 34:9636897241303271. [PMID: 39874083 PMCID: PMC11775963 DOI: 10.1177/09636897241303271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/10/2024] [Accepted: 11/11/2024] [Indexed: 01/30/2025] Open
Abstract
Organoids are three-dimensional (3D) cell cultures derived from human pluripotent stem cells or adult stem cells that recapitulate the cellular heterogeneity, structure, and function of human organs. These microstructures are invaluable for biomedical research due to their ability to closely mimic the complexity of native tissues while retaining human genetic material. This fidelity to native organ systems positions organoids as a powerful tool for advancing our understanding of human biology and for enhancing preclinical drug testing. Recent advancements have led to the successful development of a variety of organoid types, reflecting a broad range of human organs and tissues. This progress has expanded their application across several domains, including regenerative medicine, where organoids offer potential for tissue replacement and repair; disease modeling, which allows for the study of disease mechanisms and progression in a controlled environment; drug discovery and evaluation, where organoids provide a more accurate platform for testing drug efficacy and safety; and microecological research, where they contribute to understanding the interactions between microbes and host tissues. This review provides a comprehensive overview of the historical development of organoid technology, highlights the key achievements and ongoing challenges in the field, and discusses the current and emerging applications of organoids in both laboratory research and clinical practice.
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Affiliation(s)
- Zhangcheng Zhu
- Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xia Liu
- Department of Intensive Care Unit, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenwen Ding
- Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiaming Liu
- Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lingbin Wu
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
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18
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Frenette B, Guéno J, Houde N, Landry-Truchon K, Giguère A, Ashok T, Ryckman A, Morton BR, Mansfield JH, Jeannotte L. Loss of Hoxa5 function affects Hox gene expression in different biological contexts. Sci Rep 2024; 14:30903. [PMID: 39730789 DOI: 10.1038/s41598-024-81867-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 11/29/2024] [Indexed: 12/29/2024] Open
Abstract
Hoxa5 plays numerous roles in development, but its downstream molecular effects are mostly unknown. We applied bulk RNA-seq assays to characterize the transcriptional impact of the loss of Hoxa5 gene function in seven different biological contexts, including developing respiratory and musculoskeletal tissues that present phenotypes in Hoxa5 mouse mutants. This global analysis revealed few common transcriptional changes, suggesting that HOXA5 acts mainly via the regulation of context-specific effectors. However, Hox genes themselves appeared as potentially conserved targets of HOXA5 across tissues. Notably, a trend toward reduced expression of HoxA genes was observed in Hoxa5 null mutants in several tissue contexts. Comparative analysis of epigenetic marks along the HoxA cluster in lung tissue from two different Hoxa5 mutant mouse lines revealed limited effect of either mutation indicating that Hoxa5 gene targeting did not significantly perturb the chromatin landscape of the surrounding HoxA cluster. Combined with the shared impact of the two Hoxa5 mutant alleles on phenotype and Hox expression, these data argue against the contribution of local cis effects to Hoxa5 mutant phenotypes and support the notion that the HOXA5 protein acts in trans in the control of Hox gene expression.
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Affiliation(s)
- Béatrice Frenette
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
| | - Josselin Guéno
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
| | - Nicolas Houde
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Kim Landry-Truchon
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Anthony Giguère
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Theyjasvi Ashok
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Abigail Ryckman
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Brian R Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Jennifer H Mansfield
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA.
| | - Lucie Jeannotte
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada.
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19
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Qi C, Li A, Su F, Wang Y, Zhou L, Tang C, Feng R, Mao R, Chen M, Chen L, Koppelman GH, Bourgonje AR, Zhou H, Hu S. An atlas of the shared genetic architecture between atopic and gastrointestinal diseases. Commun Biol 2024; 7:1696. [PMID: 39719505 DOI: 10.1038/s42003-024-07416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 12/18/2024] [Indexed: 12/26/2024] Open
Abstract
Comorbidity among atopic diseases (ADs) and gastrointestinal diseases (GIDs) has been repeatedly demonstrated by epidemiological studies, whereas the shared genetic liability remains largely unknown. Here we establish an atlas of the shared genetic architecture between 10 ADs or related traits and 11 GIDs, comprehensively investigating the comorbidity-associated genomic regions, cell types, genes and genetically predicted causality. Although distinct genetic correlations between AD-GID are observed, including 14 genome-wide and 28 regional correlations, genetic factors of Crohn's disease (CD), ulcerative colitis (UC), celiac disease and asthma subtypes are converged on CD4+ T cells consistently across relevant tissues. Fourteen genes are associated with comorbidities, with three genes are known treatment targets, showing probabilities for drug repurposing. Lower expressions of WDR18 and GPX4 in PBMC CD4+ T cells predict decreased risk of CD and asthma, which could be novel drug targets. MR unveils certain ADs led to higher risk of GIDs or vice versa. Taken together, here we show distinct genetic correlations between AD-GID pairs, but the correlated genomic loci converge on the dysregulation of CD4+ T cells. Inhibiting WDR18 and GPX4 expressions might be candidate therapeutic strategies for CD and asthma. Estimated causality indicates potential guidance for preventing comorbidity.
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Affiliation(s)
- Cancan Qi
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - An Li
- Department of Periodontology, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Fengyuan Su
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yu Wang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Longyuan Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ce Tang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, Guangxi, China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Gerard H Koppelman
- University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Centre Groningen, Beatrix Children's Hospital, Department of Paediatric Pulmonology and Paediatric Allergology, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Hongwei Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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Clarke DM, Kirkham MN, Beck LB, Campbell C, Alcorn H, Bikman BT, Arroyo JA, Reynolds PR. Temporal RAGE Over-Expression Disrupts Lung Development by Modulating Apoptotic Signaling. Curr Issues Mol Biol 2024; 46:14453-14463. [PMID: 39727995 DOI: 10.3390/cimb46120867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 12/06/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024] Open
Abstract
Receptors for advanced glycation end products (RAGE) are multiligand cell surface receptors found most abundantly in lung tissue. This study sought to evaluate the role of RAGE in lung development by using a transgenic (TG) mouse model that spatially and temporally controlled RAGE overexpression. Histological imaging revealed that RAGE upregulation from embryonic day (E) 15.5 to E18.5 led to a thickened alveolar parenchyma and reduced alveolar surface area, while RAGE overexpression from E0 to E18.5 caused a significant loss of tissue and decreased architecture. Mitochondrial dysfunction was a hallmark of RAGE-mediated disruption, with decreased levels of anti-apoptotic BCL-W and elevated pro-apoptotic BID, SMAC, and HTRA2, indicating compromised mitochondrial integrity and increased intrinsic apoptotic activity. Extrinsic apoptotic signaling was similarly dysregulated, as evidenced by the increased expression of TNFRSF21, Fas/FasL, and Trail R2 in E0-18.5 RAGE TG mice. Additionally, reductions in IGFBP-3 and IGFBP-4, coupled with elevated p53 and decreased p27 expression, highlighted disruptions in the cell survival and cycle regulatory pathways. Despite the compensatory upregulation of inhibitors of apoptosis proteins (cIAP-2, XIAP, and Survivin), tissue loss and structural damage persisted. These findings underscore RAGE's role as a pivotal modulator of lung development. Specifically, the timing of RAGE upregulation significantly impacts lung development by influencing pathways that cause distinct histological phenotypes. This research may foreshadow how RAGE signaling plausibly contributes to developmental lung diseases.
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Affiliation(s)
- Derek M Clarke
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Madison N Kirkham
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Logan B Beck
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Carrleigh Campbell
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Hayden Alcorn
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Benjamin T Bikman
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Juan A Arroyo
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Paul R Reynolds
- Department of Cell Biology and Physiology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
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21
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Young K, Benny M, Schmidt A, Wu S. Unveiling the Emerging Role of Extracellular Vesicle-Inflammasomes in Hyperoxia-Induced Neonatal Lung and Brain Injury. Cells 2024; 13:2094. [PMID: 39768185 PMCID: PMC11674922 DOI: 10.3390/cells13242094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 11/26/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025] Open
Abstract
Extremely premature infants are at significant risk for developing bronchopulmonary dysplasia (BPD) and neurodevelopmental impairment (NDI). Although BPD is a predictor of poor neurodevelopmental outcomes, it is currently unknown how BPD contributes to brain injury and long-term NDI in pre-term infants. Extracellular vesicles (EVs) are small, membrane-bound structures released from cells into the surrounding environment. EVs are involved in inter-organ communication in diverse pathological processes. Inflammasomes are large, multiprotein complexes that are part of the innate immune system and are responsible for triggering inflammatory responses and cell death. Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is pivotal in inflammasome assembly and activating inflammatory caspase-1. Activated caspase-1 cleaves gasdermin D (GSDMD) to release a 30 kD N-terminal domain that can form membrane pores, leading to lytic cell death, also known as pyroptosis. Activated caspase-1 can also cleave pro-IL-1β and pro-IL-18 to their active forms, which can be rapidly released through the GSDMD pores to induce inflammation. Recent evidence has emerged that activation of inflammasomes is associated with neonatal lung and brain injury, and inhibition of inflammasomes reduces hyperoxia-induced neonatal lung and brain injury. Additionally, multiple studies have demonstrated that hyperoxia stimulates the release of lung-derived EVs that contain inflammasome cargos. Adoptive transfer of these EVs into the circulation of normal neonatal mice and rats induces brain inflammatory injury. This review focuses on EV-inflammasomes' roles in mediating lung-to-brain crosstalk via EV-dependent and EV-independent mechanisms critical in BPD, brain injury, and NDI pathogenesis. EV-inflammasomes will be discussed as potential therapeutic targets for neonatal lung and brain injury.
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Affiliation(s)
| | | | | | - Shu Wu
- Division of Neonatology, Department of Pediatrics, Batchelor Children Research Institute, University of Miami School of Medicine, Miami, FL 33136, USA; (K.Y.); (M.B.); (A.S.)
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22
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Chen Y, Liang R, Li Y, Jiang L, Ma D, Luo Q, Song G. Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application. Signal Transduct Target Ther 2024; 9:340. [PMID: 39627201 PMCID: PMC11615378 DOI: 10.1038/s41392-024-02030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/04/2024] [Accepted: 10/17/2024] [Indexed: 12/06/2024] Open
Abstract
The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Rui Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Yong Li
- Hepatobiliary Pancreatic Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, PR China
| | - Lingli Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Di Ma
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Qing Luo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Guanbin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China.
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23
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Wang Y, Zhang J, Shao C. Cytological changes in radiation-induced lung injury. Life Sci 2024; 358:123188. [PMID: 39481833 DOI: 10.1016/j.lfs.2024.123188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/20/2024] [Accepted: 10/27/2024] [Indexed: 11/03/2024]
Abstract
Radiation-induced lung injury (RILI) is a prevalent complication associated with radiotherapy for thoracic tumors. Based on the pathological progression, it can be categorized into two stages: early radiation pneumonitis and late radiation pulmonary fibrosis. The occurrence of RILI not only constrains the therapeutic dose that can be administered to the tumor target area but also significantly impairs patients' health and quality of life, thereby limiting the efficacy and applicability of radiotherapy. To effectively prevent and mitigate the development of RILI, it is crucial to disclose its underlying mechanisms. This review aims to elucidate the specific mechanisms involved in RILI and to examine the roles of various cell types, including lung parenchymal cells and different immune cells. The functions and interactions of lung epithelial cells, pulmonary vascular endothelial cells, a variety of immune cells, and fibroblasts during different stages of inflammation, tissue repair, and fibrosis following radiation-induced lung injury are analyzed. A comprehensive understanding of the dynamic changes in these cellular components is anticipated to offer new strategies for the prevention of RILI.
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Affiliation(s)
- Yun Wang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai 200032, China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai 200032, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai 200032, China.
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24
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Lin X, Zhou M, Wang H. A rat model establishment of bronchopulmonary dysplasia-related lung & brain injury within 28 days after birth. BMC Neurosci 2024; 25:73. [PMID: 39609737 PMCID: PMC11603889 DOI: 10.1186/s12868-024-00912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 11/19/2024] [Indexed: 11/30/2024] Open
Abstract
PURPOSE Lung injury associated with bronchopulmonary dysplasia (BPD) and its related neurodevelopmental disorders have garnered increasing attention in the context of premature infants. Establishing a reliable animal model is essential for delving into the underlying mechanisms of these conditions. METHODS Newborn rats were randomly assigned to two groups: the hyperoxia-induced BPD group and the normoxia (NO) group. For the BPD group, they were nurtured in a hyperoxic environment with a high oxygen inspired fraction (0.85) from birth until day 14 within 28 days postnatally. In contrast, the NO group consisted of newborn rats that were nurtured in a normoxic environment with a standard oxygen inspired fraction (0.21) for 28 days postnatally. Various pathological sections of both lung and brain tissues were examined. TUNEL staining, immunofluorescence assays, and functional tests were performed, and the results were meticulously analyzed to assess the impact of hyperoxia environments on the developing organs. RESULTS In the newborn rats of the BPD group, a significant reduction in alveolar number coupled with enlargement was observed, alongside severe fibrosis, collagen deposition, and constriction of bronchi and vascular lumens. This was accompanied by an accumulation of inflammatory cells and a marked deterioration in lung function compared to the NO group (P < 0.05). Additionally, a decrease in neuronal count, an increase in neuronal apoptosis, proliferation of neuroglia cells, and demyelination were noted, and poorer performance in the Morris water maze test within the BPD group (P < 0.05). CONCLUSION The BPD-rats model was established successfully. Lung injury in the BPD group evident across the bronchi to the alveoli and pulmonary vessels, which was associated with deteriorated lung function at postnatal day 14. Concurrently, brain injury extended from the cerebral cortex to the hippocampus, which was associated with impaired performance in orientation navigation and spatial probe tests at postnatal day 28.
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Affiliation(s)
- Xin Lin
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Neonatology, Fujian Maternity and Child Health Hospital/College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Key Laboratory of Birth Defects and Related Disease of Women and Children (Sichuan University), Ministry of Education, Sichuan University, No. 20, Section 3, South Renmin Road, Chengdu, Sichuan Province, 610041, China
| | - Meicen Zhou
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Disease of Women and Children (Sichuan University), Ministry of Education, Sichuan University, No. 20, Section 3, South Renmin Road, Chengdu, Sichuan Province, 610041, China
| | - Hua Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Disease of Women and Children (Sichuan University), Ministry of Education, Sichuan University, No. 20, Section 3, South Renmin Road, Chengdu, Sichuan Province, 610041, China.
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25
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Liu J, Luo D, Huang H, Mu R, Yuan J, Jiang M, Lin C, Xiang H, Lin X, Song H, Zhang Y. Hippo cooperates with p53 to regulate lung airway mucous cell metaplasia. Dis Model Mech 2024; 17:dmm052074. [PMID: 39428818 PMCID: PMC11603118 DOI: 10.1242/dmm.052074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/12/2024] [Indexed: 10/22/2024] Open
Abstract
Airway mucous cell metaplasia is a significant feature of many chronic airway diseases, such as chronic obstructive pulmonary disease, cystic fibrosis and asthma. However, the mechanisms underlying this process remain poorly understood. Here, we employed in vivo mouse genetic models to demonstrate that Hippo and p53 (encoded by Trp53) cooperate to modulate the differentiation of club cells into goblet cells. We revealed that ablation of Mst1 (Stk4) and Mst2 (Stk3), encoding the core components of Hippo signaling, significantly reduces mucous metaplasia in the lung airways in a lipopolysaccharide (LPS)-induced lung inflammation murine model while promoting club cell proliferation in a Yap (Yap1)-dependent manner. Additionally, we showed that deleting Mst1/2 is sufficient to suppress p53 deficiency-mediated goblet cell metaplasia. Finally, single-cell RNA-sequencing analysis revealed downregulation of YAP and p53 signaling in goblet cells in human airways. These findings underscore the important role of Hippo and p53 signaling in regulating airway mucous metaplasia.
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Affiliation(s)
- Jiangying Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haidi Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rongzi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianghong Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Jiang
- Center for Genetic Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310030, Zhejiang, China
| | - Chuwen Lin
- Department of Histology and Embryology, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
| | - Honggang Xiang
- Department of General Surgery, Pudong New Area People's Hospital, Shanghai 201299, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University Shanghai, Shanghai 200438, China
| | - Haihan Song
- Central Lab, Shanghai Key Laboratory of Pathogenic Fungi Medical Testing, Shanghai Pudong New Area People's Hospital, Shanghai 201299, China
- Department of Immunology, DICAT National Biomedical Computation Centre, Vancouver, BC V6B 5A6, Canada
| | - Yongchun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Inner Mongolia Research Institute, Shenzhen Research Institute, Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of General Surgery, Pudong New Area People's Hospital, Shanghai 201299, China
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26
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Sariyar S, Sountoulidis A, Hansen JN, Marco Salas S, Mardamshina M, Martinez Casals A, Ballllosera Navarro F, Andrusivova Z, Li X, Czarnewski P, Lundeberg J, Linnarsson S, Nilsson M, Sundström E, Samakovlis C, Lundberg E, Ayoglu B. High-parametric protein maps reveal the spatial organization in early-developing human lung. Nat Commun 2024; 15:9381. [PMID: 39477961 PMCID: PMC11525936 DOI: 10.1038/s41467-024-53752-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 10/22/2024] [Indexed: 11/02/2024] Open
Abstract
The respiratory system, including the lungs, is essential for terrestrial life. While recent research has advanced our understanding of lung development, much still relies on animal models and transcriptome analyses. In this study conducted within the Human Developmental Cell Atlas (HDCA) initiative, we describe the protein-level spatiotemporal organization of the lung during the first trimester of human gestation. Using high-parametric tissue imaging with a 30-plex antibody panel, we analyzed human lung samples from 6 to 13 post-conception weeks, generating data from over 2 million cells across five developmental timepoints. We present a resource detailing spatially resolved cell type composition of the developing human lung, including proliferative states, immune cell patterns, spatial arrangement traits, and their temporal evolution. This represents an extensive single-cell resolved protein-level examination of the developing human lung and provides a valuable resource for further research into the developmental roots of human respiratory health and disease.
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Affiliation(s)
- Sanem Sariyar
- Science for Life Laboratory, Solna, Sweden
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Solna, Sweden
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jan Niklas Hansen
- Science for Life Laboratory, Solna, Sweden
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sergio Marco Salas
- Science for Life Laboratory, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mariya Mardamshina
- Science for Life Laboratory, Solna, Sweden
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Martinez Casals
- Science for Life Laboratory, Solna, Sweden
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Frederic Ballllosera Navarro
- Science for Life Laboratory, Solna, Sweden
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Zaneta Andrusivova
- Science for Life Laboratory, Solna, Sweden
- Department of Gene Technology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiaofei Li
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, Solna, Sweden
- Department of Gene Technology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Solna, Sweden
- Department of Gene Technology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Christos Samakovlis
- Science for Life Laboratory, Solna, Sweden
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Molecular Pneumology, Cardiopulmonary Institute, Justus Liebig University, Giessen, Germany
| | - Emma Lundberg
- Science for Life Laboratory, Solna, Sweden.
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Burcu Ayoglu
- Science for Life Laboratory, Solna, Sweden.
- Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden.
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27
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Luo Y, Liang H. Developmental-status-aware transcriptional decomposition establishes a cell state panorama of human cancers. Genome Med 2024; 16:124. [PMID: 39468667 PMCID: PMC11514945 DOI: 10.1186/s13073-024-01393-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/03/2024] [Indexed: 10/30/2024] Open
Abstract
BACKGROUND Cancer cells evolve under unique functional adaptations that unlock transcriptional programs embedded in adult stem and progenitor-like cells for progression, metastasis, and therapeutic resistance. However, it remains challenging to quantify the stemness-aware cell state of a tumor based on its gene expression profile. METHODS We develop a developmental-status-aware transcriptional decomposition strategy using single-cell RNA-sequencing-derived tissue-specific fetal and adult cell signatures as anchors. We apply our method to various biological contexts, including developing human organs, adult human tissues, experimentally induced differentiation cultures, and bulk human tumors, to benchmark its performance and to reveal novel biology of entangled developmental signaling in oncogenic processes. RESULTS Our strategy successfully captures complex dynamics in developmental tissue bulks, reveals remarkable cellular heterogeneity in adult tissues, and resolves the ambiguity of cell identities in in vitro transformations. Applying it to large patient cohorts of bulk RNA-seq, we identify clinically relevant cell-of-origin patterns and observe that decomposed fetal cell signals significantly increase in tumors versus normal tissues and metastases versus primary tumors. Across cancer types, the inferred fetal-state strength outperforms published stemness indices in predicting patient survival and confers substantially improved predictive power for therapeutic responses. CONCLUSIONS Our study not only provides a general approach to quantifying developmental-status-aware cell states of bulk samples but also constructs an information-rich, biologically interpretable, cell-state panorama of human cancers, enabling diverse translational applications.
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Affiliation(s)
- Yikai Luo
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Spurgin S, Nguimtsop AM, Chaudhry FN, Michki SN, Salvador J, Iruela-Arispe ML, Zepp JA, Mukhopadhyay S, Cleaver O. Spatiotemporal dynamics of primary and motile cilia throughout lung development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.25.620342. [PMID: 39484464 PMCID: PMC11527191 DOI: 10.1101/2024.10.25.620342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Cilia are specialized structures found on a variety of mammalian cells, with variable roles in the transduction of mechanical and biological signals (by primary cilia, PC), as well as the generation of fluid flow (by motile cilia). Their critical role in the establishment of a left-right axis in early development is well described, as is the innate immune function of multiciliated upper airway epithelium. By contrast, the dynamics of ciliary status during organogenesis and postnatal development is largely unknown. In this study, we define the progression of ciliary status within the endothelium, epithelium, and mesenchyme of the lung. Remarkably, we find that endothelial cells (ECs) lack PC at all stages of development, except in low numbers in the most proximal portions of the pulmonary arteries. In the lung epithelium, a proximodistal ciliary gradient is established over time, as the uniformly mono-ciliated epithelium transitions into proximal, multiciliated cells, and the distal alveolar epithelium loses its cilia. Mesenchymal cells, interestingly, are uniformly ciliated in early development, but with restriction to PDGFRα+ fibroblasts in the adult alveoli. This dynamic process in multiple cellular populations both challenges prior assertions that PC are found on all cells, and highlights a need to understand their spatiotemporal functions.
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Affiliation(s)
- Stephen Spurgin
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA 75390
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA 75390
| | - Ange Michelle Nguimtsop
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA 75390
| | - Fatima N. Chaudhry
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania USA 19104
| | - Sylvia N. Michki
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania USA 19104
| | - Jocelynda Salvador
- Department of Cell and Developmental Biology, Northwestern Feinberg School of Medicine, Chicago, Illinois, USA 60611
| | - M. Luisa Iruela-Arispe
- Department of Cell and Developmental Biology, Northwestern Feinberg School of Medicine, Chicago, Illinois, USA 60611
| | - Jarod A. Zepp
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania USA 19104
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, USA 75390
| | - Ondine Cleaver
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA 75390
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Nájera-Martínez M, Lara-Vega I, Avilez-Alvarado J, Pagadala NS, Dzul-Caamal R, Domínguez-López ML, Tuszynski J, Vega-López A. The Generation of ROS by Exposure to Trihalomethanes Promotes the IκBα/NF-κB/p65 Complex Dissociation in Human Lung Fibroblast. Biomedicines 2024; 12:2399. [PMID: 39457711 PMCID: PMC11505202 DOI: 10.3390/biomedicines12102399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 10/13/2024] [Accepted: 10/16/2024] [Indexed: 10/28/2024] Open
Abstract
Background: Disinfection by-products used to obtain drinking water, including halomethanes (HMs) such as CH2Cl2, CHCl3, and BrCHCl2, induce cytotoxicity and hyperproliferation in human lung fibroblasts (MRC-5). Enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) modulate these damages through their biotransformation processes, potentially generating toxic metabolites. However, the role of the oxidative stress response in cellular hyperproliferation, modulated by nuclear factor-kappa B (NF-κB), remains unclear. Methods: In this study, MRC-5 cells were treated with these compounds to evaluate reactive oxygen species (ROS) production, lipid peroxidation, phospho-NF-κB/p65 (Ser536) levels, and the activities of SOD, CAT, and GPx. Additionally, the interactions between HMs and ROS with the IκBα/NF-κB/p65 complex were analyzed using molecular docking. Results: Correlation analysis among biomarkers revealed positive relationships between pro-oxidant damage and antioxidant responses, particularly in cells treated with CH2Cl2 and BrCHCl2. Conversely, negative relationships were observed between ROS levels and NF-κB/p65 levels in cells treated with CH2Cl2 and CHCl3. The estimated relative free energy of binding using thermodynamic integration with the p65 subunit of NF-κB was -3.3 kcal/mol for BrCHCl2, -3.5 kcal/mol for both CHCl3 and O2•, and -3.6 kcal/mol for H2O2. Conclusions: Chloride and bromide atoms were found in close contact with IPT domain residues, particularly in the RHD region involved in DNA binding. Ser281 is located within this domain, facilitating the phosphorylation of this protein. Similarly, both ROS interacted with the IPT domain in the RHD region, with H2O2 forming a side-chain oxygen interaction with Leu280 adjacent to the phosphorylation site of p65. However, the negative correlation between ROS and phospho-NF-κB/p65 suggests that steric hindrance by ROS on the C-terminal domain of NF-κB/p65 may play a role in the antioxidant response.
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Affiliation(s)
- Minerva Nájera-Martínez
- Laboratorio de Toxicología Ambiental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n, Unidad Profesional Zacatenco, Mexico City 07738, Mexico; (M.N.-M.); (I.L.-V.)
| | - Israel Lara-Vega
- Laboratorio de Toxicología Ambiental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n, Unidad Profesional Zacatenco, Mexico City 07738, Mexico; (M.N.-M.); (I.L.-V.)
| | - Jhonatan Avilez-Alvarado
- Laboratorio de Visión Artificial, Unidad Culhuacán, Escuela Superior de Ingeniería Mecánica y Eléctrica, Instituto Politécnico Nacional, Av. Santa Ana 1000, San Francisco Culhuacán CTM V, Mexico City 04440, Mexico;
| | | | - Ricardo Dzul-Caamal
- Instituto EPOMEX, Universidad Autónoma de Campeche, Av. Héroe de Nacozari No. 480, Campeche 24070, Mexico;
| | - María Lilia Domínguez-López
- Laboratorio de Inmunoquímica I, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala s/n, Casco de Santo Tomás, Mexico City 11340, Mexico;
| | - Jack Tuszynski
- Li Ka Shing Applied Virology Institute, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Armando Vega-López
- Laboratorio de Toxicología Ambiental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu s/n, Unidad Profesional Zacatenco, Mexico City 07738, Mexico; (M.N.-M.); (I.L.-V.)
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Wang Z, Elbanna Y, Godet I, Peters L, Lampe G, Chen Y, Xavier J, Huse M, Massagué J. TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.15.618357. [PMID: 39463937 PMCID: PMC11507679 DOI: 10.1101/2024.10.15.618357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
The heterogeneity of epithelial-to-mesenchymal transition (EMT) programs is manifest in the diverse EMT-like phenotypes occurring during tumor progression. However, little is known about the mechanistic basis and functional role of specific forms of EMT in cancer. Here we address this question in lung adenocarcinoma (LUAD) cells that enter a dormancy period in response to TGF-β upon disseminating to distant sites. LUAD cells with the capacity to enter dormancy are characterized by expression of SOX2 and NKX2-1 primitive progenitor markers. In these cells, TGF-β induces growth inhibition accompanied by a full EMT response that subsequently transitions into an atypical mesenchymal state of round morphology and lacking actin stress fibers. TGF-β induces this transition by driving the expression of the actin-depolymerizing factor gelsolin, which changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the biomechanical stiffness of metastatic progenitors, protecting them from killing by mechanosensitive cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Inhibiting this actin depolymerization process clears tissues of dormant metastatic cells. Thus, LUAD primitive progenitors undergo an atypical EMT as part of a strategy to evade immune-mediated elimination during dormancy. Our results provide a mechanistic basis and functional role of this atypical EMT response of LUAD metastatic progenitors and further illuminate the role of TGF-β as a crucial driver of immune evasive metastatic dormancy.
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Affiliation(s)
- Zhenghan Wang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yassmin Elbanna
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gerstner Sloan Kettering Graduate School, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Inês Godet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lila Peters
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gerstner Sloan Kettering Graduate School, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - George Lampe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Current affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yanyan Chen
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Current affiliation: Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, 10032, USA
| | - Joao Xavier
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Morgan Huse
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Li X, Liu Y, Tang Y, Xia Z. Transformation of macrophages into myofibroblasts in fibrosis-related diseases: emerging biological concepts and potential mechanism. Front Immunol 2024; 15:1474688. [PMID: 39386212 PMCID: PMC11461261 DOI: 10.3389/fimmu.2024.1474688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/06/2024] [Indexed: 10/12/2024] Open
Abstract
Macrophage-myofibroblast transformation (MMT) transforms macrophages into myofibroblasts in a specific inflammation or injury microenvironment. MMT is an essential biological process in fibrosis-related diseases involving the lung, heart, kidney, liver, skeletal muscle, and other organs and tissues. This process consists of interacting with various cells and molecules and activating different signal transduction pathways. This review deeply discussed the molecular mechanism of MMT, clarified crucial signal pathways, multiple cytokines, and growth factors, and formed a complex regulatory network. Significantly, the critical role of transforming growth factor-β (TGF-β) and its downstream signaling pathways in this process were clarified. Furthermore, we discussed the significance of MMT in physiological and pathological conditions, such as pulmonary fibrosis and cardiac fibrosis. This review provides a new perspective for understanding the interaction between macrophages and myofibroblasts and new strategies and targets for the prevention and treatment of MMT in fibrotic diseases.
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Affiliation(s)
- Xiujun Li
- Health Science Center, Chifeng University, Chifeng, China
| | - Yuyan Liu
- Rehabilitation Medicine College, Shandong Second Medical University, Jinan, China
| | - Yongjun Tang
- Department of Emergency, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Zhaoyi Xia
- Department of Library, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Library, Jinan Children’s Hospital, Jinan, China
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32
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Sang Y, Qiao L. Lung epithelial-endothelial-mesenchymal signaling network with hepatocyte growth factor as a hub is involved in bronchopulmonary dysplasia. Front Cell Dev Biol 2024; 12:1462841. [PMID: 39291265 PMCID: PMC11405311 DOI: 10.3389/fcell.2024.1462841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
Bronchopulmonary dysplasia (BPD) is fundamentally characterized by the arrest of lung development and abnormal repair mechanisms, which result in impaired development of the alveoli and microvasculature. Hepatocyte growth factor (HGF), secreted by pulmonary mesenchymal and endothelial cells, plays a pivotal role in the promotion of epithelial and endothelial cell proliferation, branching morphogenesis, angiogenesis, and alveolarization. HGF exerts its beneficial effects on pulmonary vascular development and alveolar simplification primarily through two pivotal pathways: the stimulation of neovascularization, thereby enriching the pulmonary microvascular network, and the inhibition of the epithelial-mesenchymal transition (EMT), which is crucial for maintaining the integrity of the alveolar structure. We discuss HGF and its receptor c-Met, interact with various growth factors throughout the process of lung development and BPD, and form a signaling network with HGF as a hub, which plays the pivotal role in orchestrating and integrating epithelial, endothelial and mesenchymal.
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Affiliation(s)
- Yating Sang
- Pediatric Intensive Care Unit, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lina Qiao
- Pediatric Intensive Care Unit, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
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Goltsis O, Bilodeau C, Wang J, Luo D, Asgari M, Bozec L, Pettersson A, Leibel SL, Post M. Influence of mesenchymal and biophysical components on distal lung organoid differentiation. Stem Cell Res Ther 2024; 15:273. [PMID: 39218985 PMCID: PMC11367854 DOI: 10.1186/s13287-024-03890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Chronic lung disease of prematurity, called bronchopulmonary dysplasia (BPD), lacks effective therapies, stressing the need for preclinical testing systems that reflect human pathology for identifying causal pathways and testing novel compounds. Alveolar organoids derived from human pluripotent stem cells (hPSC) are promising test platforms for studying distal airway diseases like BPD, but current protocols do not accurately replicate the distal niche environment of the native lung. Herein, we investigated the contributions of cellular constituents of the alveolus and fetal respiratory movements on hPSC-derived alveolar organoid formation. METHODS Human PSCs were differentiated in 2D culture into lung progenitor cells (LPC) which were then further differentiated into alveolar organoids before and after removal of co-developing mesodermal cells. LPCs were also differentiated in Transwell® co-cultures with and without human fetal lung fibroblast. Forming organoids were subjected to phasic mechanical strain using a Flexcell® system. Differentiation within organoids and Transwell® cultures was assessed by flow cytometry, immunofluorescence, and qPCR for lung epithelial and alveolar markers of differentiation including GATA binding protein 6 (GATA 6), E-cadherin (CDH1), NK2 Homeobox 1 (NKX2-1), HT2-280, surfactant proteins B (SFTPB) and C (SFTPC). RESULTS We observed that co-developing mesenchymal progenitors promote alveolar epithelial type 2 cell (AEC2) differentiation within hPSC-derived lung organoids. This mesenchymal effect on AEC2 differentiation was corroborated by co-culturing hPSC-NKX2-1+ lung progenitors with human embryonic lung fibroblasts. The stimulatory effect did not require direct contact between fibroblasts and NKX2-1+ lung progenitors. Additionally, we demonstrate that episodic mechanical deformation of hPSC-derived lung organoids, mimicking in situ fetal respiratory movements, increased AEC2 differentiation without affecting proximal epithelial differentiation. CONCLUSION Our data suggest that biophysical and mesenchymal components promote AEC2 differentiation within hPSC-derived distal organoids in vitro.
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Affiliation(s)
- Olivia Goltsis
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Claudia Bilodeau
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jinxia Wang
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Daochun Luo
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Meisam Asgari
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - Laurent Bozec
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - Ante Pettersson
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Sandra L Leibel
- Department of Pediatrics, Rady Children's Hospital, San Diego, University of California, San Diego, La Jolla, CA, USA
| | - Martin Post
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.
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Liu X, Zhang X, Liang J, Noble PW, Jiang D. Aging-Associated Molecular Changes in Human Alveolar Type I Cells. JOURNAL OF RESPIRATORY BIOLOGY AND TRANSLATIONAL MEDICINE 2024; 1:10012. [PMID: 39220636 PMCID: PMC11361087 DOI: 10.35534/jrbtm.2024.10012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Human alveolar type I (AT1) cells are specialized epithelial cells that line the alveoli in the lungs where gas exchange occurs. The primary function of AT1 cells is not only to facilitate efficient gas exchange between the air and the blood in the lungs, but also to contribute to the structural integrity of the alveoli to maintain lung function and homeostasis. Aging has notable effects on the structure, function, and regenerative capacity of human AT1 cells. However, our understanding of the molecular mechanisms driving these age-related changes in AT1 cells remains limited. Leveraging a recent single-cell transcriptomics dataset we generated on healthy human lungs, we identified a series of significant molecular alterations in AT1 cells from aged lungs. Notably, the aged AT1 cells exhibited increased cellular senescence and chemokine gene expression, alongside diminished epithelial features such as decreases in cell junctions, endocytosis, and pulmonary matrisome gene expression. Gene set analyses also indicated that aged AT1 cells were resistant to apoptosis, a crucial mechanism for turnover and renewal of AT1 cells, thereby ensuring alveolar integrity and function. Further research on these alterations is imperative to fully elucidate the impact on AT1 cells and is indispensable for developing effective therapies to preserve lung function and promote healthy aging.
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Affiliation(s)
- Xue Liu
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xuexi Zhang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jiurong Liang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W. Noble
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dianhua Jiang
- Department of Medicine and Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Ma J, Zhang L, Zhang X, Zhang L, Zhang H, Zhu Y, Huang X, Zhang T, Tang X, Wang Y, Chen L, Pu Q, Yang L, Cao Z, Ding BS. Inhibiting endothelial Rhoj blocks profibrotic vascular intussusception and angiocrine factors to sustain lung regeneration. Sci Transl Med 2024; 16:eado5266. [PMID: 39196961 DOI: 10.1126/scitranslmed.ado5266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/07/2024] [Indexed: 08/30/2024]
Abstract
Lung regeneration after fibrosis requires formation of functional new vasculature, which is essential for gas exchange and cellular cross-talk with other lung cells. It remains unknown how the lung vasculature can be regenerated without fibrosis. Here, we tested the role of N6-methyladenosine (m6A) modification of forkhead box protein O1 (Foxo1) mRNA in lung regeneration after pneumonectomy (PNX) in mice, a model for lung regrowth after surgical resection. Endothelial cell (EC)-specific knockout of methyltransferase-like 3 (Mettl3) and Foxo1 caused nonproductive intussusceptive angiogenesis (IA), which impaired regeneration and enhanced fibrosis. This nonproductive IA was characterized by enhanced endothelial proliferation and increased vascular splitting with increased numbers of pillar ECs. Endothelial-selective knockout of Mettl3 in mice stimulated nonproductive IA and up-regulation of profibrotic factors after PNX, promoting regeneration to fibrotic transition. EC-specific mutation of m6A modification sites in the Foxo1 gene in mice revealed that endothelial Mettl3 modified A504 and A2035 sites in the Foxo1 mRNA to maintain pro-regenerative endothelial glycolysis, ensuring productive IA and lung regeneration without fibrosis. Suppression of Mettl3-Foxo1 signaling stimulated a subset of hyperglycolytic and hyperproliferative 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (Pfkfb3)+, Ras homolog family member J (Rhoj)+, and platelet-derived growth factor subunit B (Pdgfb)+ ECs in both human and mouse lungs with fibrosis. Inhibiting this Pfkfb3+Rhoj+Pdgfb+ EC subset normalized IA, alleviated fibrosis, and restored regeneration in bleomycin (BLM)-injured mouse lungs. We found that m6A modification of Foxo1 in the mouse vasculature promoted lung regeneration over fibrosis after PNX and BLM injury.
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Affiliation(s)
- Jie Ma
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Liyin Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Xu Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150081, China
| | - Lanlan Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Hua Zhang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Yulei Zhu
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Xingming Huang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Ting Zhang
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Xiangdong Tang
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Yuan Wang
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Lu Chen
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Qiang Pu
- Department of Respiratory and Critical Care Medicine, Department of Thoracic Surgery and Institute of Thoracic Oncology, and Laboratory of Liver Transplantation, West China Hospital, Chengdu 610041, China
| | - Liming Yang
- Department of Pathophysiology, Harbin Medical University, Harbin 150081, China
| | - Zhongwei Cao
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Bi-Sen Ding
- Key Lab of Birth Defects and Related Diseases of Women and Children of MOE; State Key Lab of Biotherapy; State Key Laboratory of Respiratory Health and Multimorbidity; NHC Key Laboratory of Chronobiology; Sichuan-Chongqing Key Lab of Bio-Resource Research and Utilization; Development and Related Diseases of Women and Children Key Lab of Sichuan Province; West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu 610041, China
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Peak KE, Rajaguru P, Khan A, Gleghorn JP, Obaid G, Ferruzzi J, Varner VD. Photo-induced changes in tissue stiffness alter epithelial budding morphogenesis in the embryonic lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609268. [PMID: 39229009 PMCID: PMC11370601 DOI: 10.1101/2024.08.22.609268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Extracellular matrix (ECM) stiffness has been shown to influence the differentiation of progenitor cells in culture, but a lack of tools to perturb the mechanical properties within intact embryonic organs has made it difficult to determine how changes in tissue stiffness influence organ patterning and morphogenesis. Photocrosslinking of the ECM has been successfully used to stiffen soft tissues, such as the cornea and skin, which are optically accessible, but this technique has not yet been applied to developing embryos. Here, we use photocrosslinking with Rose Bengal (RB) to locally and ectopically stiffen the pulmonary mesenchyme of explanted embryonic lungs cultured ex vivo . This change in mechanical properties was sufficient to suppress FGF-10-mediated budding morphogenesis along the embryonic airway, without negatively impacting patterns of cell proliferation or apoptosis. A computational model of airway branching was used to determine that FGF-10-induced buds form via a growth-induced buckling mechanism and that increased mesenchymal stiffness is sufficient to inhibit epithelial buckling. Taken together, our data demonstrate that photocrosslinking can be used to create regional differences in mechanical properties within intact embryonic organs and that these differences influence epithelial morphogenesis and patterning. Further, this photocrosslinking assay can be readily adapted to other developing tissues and model systems.
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Li F, Tan Z, Chen H, Gao Y, Xia J, Huang T, Liang L, Zhang J, Zhang X, Shi X, Chen Q, Shu Q, Yu L. Integrative analysis of bulk and single-cell RNA sequencing reveals the gene expression profile and the critical signaling pathways of type II CPAM. Cell Biosci 2024; 14:94. [PMID: 39026356 PMCID: PMC11264590 DOI: 10.1186/s13578-024-01276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUD Type II congenital pulmonary airway malformation (CPAM) is a rare pulmonary microcystic developmental malformation. Surgical excision is the primary treatment for CPAM, although maternal steroids and betamethasone have proven effective in reducing microcystic CPAM. Disturbed intercellular communication may contribute to the development of CPAM. This study aims to investigate the expression profile and analyze intercellular communication networks to identify genes potentially associated with type II CPAM pathogenesis and therapeutic targets. METHODS RNA sequencing (RNA-seq) was performed on samples extracted from both the cystic area and the adjacent normal tissue post-surgery in CPAM patients. Iterative weighted gene correlation network analysis (iWGCNA) was used to identify genes specifically expressed in type II CPAM. Single-cell RNA-seq (scRNA-seq) was integrated to unveil the heterogeneity in cell populations and analyze the communication and interaction within epithelial cell sub-populations. RESULTS A total of 2,618 differentially expressed genes were identified, primarily enriched in cilium-related biological process and inflammatory response process. Key genes such as EDN1, GPR17, FPR2, and CHRM1, involved in the G protein-coupled receptor (GPCR) signaling pathway and playing roles in cell differentiation, apoptosis, calcium homeostasis, and the immune response, were highlighted based on the protein-protein interaction network. Type II CPAM-associated modules, including ciliary function-related genes, were identified using iWGCNA. By integrating scRNA-seq data, AGR3 (related to calcium homeostasis) and SLC11A1 (immune related) were identified as the only two differently expressed genes in epithelial cells of CPAM. Cell communication analysis revealed that alveolar type 1 (AT1) and alveolar type 2 (AT2) cells were the predominant communication cells for outgoing and incoming signals in epithelial cells. The ligands and receptors between epithelial cell subtypes included COLLAGEN genes enriched in PI3K-AKT singaling and involved in epithelial to mesenchymal transition. CONCLUSIONS In summary, by integrating bulk RNA-seq data of type II CPAM with scRNA-seq data, the gene expression profile and critical signaling pathways such as GPCR signaling and PI3K-AKT signaling pathways were revealed. Abnormally expressed genes in these pathways may disrupt epithelial-mesenchymal transition and contribute to the development of CPAM. Given the effectiveness of prenatal treatments of microcystic CPAM using maternal steroids and maternal betamethasone administration, targeting the genes and signaling pathways involved in the development of CPAM presents a promising therapeutic strategy.
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Affiliation(s)
- Fengxia Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Zheng Tan
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Hongyu Chen
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yue Gao
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jie Xia
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ting Huang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Liang Liang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jian Zhang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xucong Shi
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Chen
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Jiangxi, China.
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Lan Yu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
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Wen B, Li E, Wang G, Kalin TR, Gao D, Lu P, Kalin TV, Kalinichenko VV. CRISPR-Cas9 Genome Editing Allows Generation of the Mouse Lung in a Rat. Am J Respir Crit Care Med 2024; 210:167-177. [PMID: 38507610 PMCID: PMC11273307 DOI: 10.1164/rccm.202306-0964oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/20/2024] [Indexed: 03/22/2024] Open
Abstract
Rationale: Recent efforts in bioengineering and embryonic stem cell (ESC) technology allowed the generation of ESC-derived mouse lung tissues in transgenic mice that were missing critical morphogenetic genes. Epithelial cell lineages were efficiently generated from ESC, but other cell types were mosaic. A complete contribution of donor ESCs to lung tissue has never been achieved. The mouse lung has never been generated in a rat. Objective: We sought to generate the mouse lung in a rat. Methods: Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing was used to disrupt the Nkx2-1 gene in rat one-cell zygotes. Interspecies mouse-rat chimeras were produced by injection of wild-type mouse ESCs into Nkx2-1-deficient rat embryos with lung agenesis. The contribution of mouse ESCs to the lung tissue was examined by immunostaining, flow cytometry, and single-cell RNA sequencing. Measurements and Main Results: Peripheral pulmonary and thyroid tissues were absent in rat embryos after CRISPR-Cas9-mediated disruption of the Nkx2-1 gene. Complementation of rat Nkx2-1-/- blastocysts with mouse ESCs restored pulmonary and thyroid structures in mouse-rat chimeras, leading to a near-99% contribution of ESCs to all respiratory cell lineages. Epithelial, endothelial, hematopoietic, and stromal cells in ESC-derived lungs were highly differentiated and exhibited lineage-specific gene signatures similar to those of respiratory cells from the normal mouse lung. Analysis of receptor-ligand interactions revealed normal signaling networks between mouse ESC-derived respiratory cells differentiated in a rat. Conclusions: A combination of CRISPR-Cas9 genome editing and blastocyst complementation was used to produce mouse lungs in rats, making an important step toward future generations of human lungs using large animals as "bioreactors."
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Affiliation(s)
- Bingqiang Wen
- Phoenix Children’s Research Institute, Department of Child Health, College of Medicine Phoenix, University of Arizona, Phoenix, Arizona
| | - Enhong Li
- Phoenix Children’s Research Institute, Department of Child Health, College of Medicine Phoenix, University of Arizona, Phoenix, Arizona
| | | | - Timothy R. Kalin
- College of Arts and Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China; and
| | - Peixin Lu
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Tanya V. Kalin
- Phoenix Children’s Research Institute, Department of Child Health, College of Medicine Phoenix, University of Arizona, Phoenix, Arizona
- Division of Pulmonary Biology and
| | - Vladimir V. Kalinichenko
- Phoenix Children’s Research Institute, Department of Child Health, College of Medicine Phoenix, University of Arizona, Phoenix, Arizona
- Division of Neonatology, Phoenix Children’s Hospital, Phoenix, Arizona
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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40
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Luo Y, Cao K, Chiu J, Chen H, Wang HJ, Thornton ME, Grubbs BH, Kolb M, Parmacek MS, Mishina Y, Shi W. Defective mesenchymal Bmpr1a-mediated BMP signaling causes congenital pulmonary cysts. eLife 2024; 12:RP91876. [PMID: 38856718 PMCID: PMC11164533 DOI: 10.7554/elife.91876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
Abnormal lung development can cause congenital pulmonary cysts, the mechanisms of which remain largely unknown. Although the cystic lesions are believed to result directly from disrupted airway epithelial cell growth, the extent to which developmental defects in lung mesenchymal cells contribute to abnormal airway epithelial cell growth and subsequent cystic lesions has not been thoroughly examined. In the present study using genetic mouse models, we dissected the roles of bone morphogenetic protein (BMP) receptor 1a (Bmpr1a)-mediated BMP signaling in lung mesenchyme during prenatal lung development and discovered that abrogation of mesenchymal Bmpr1a disrupted normal lung branching morphogenesis, leading to the formation of prenatal pulmonary cystic lesions. Severe deficiency of airway smooth muscle cells and subepithelial elastin fibers were found in the cystic airways of the mesenchymal Bmpr1a knockout lungs. In addition, ectopic mesenchymal expression of BMP ligands and airway epithelial perturbation of the Sox2-Sox9 proximal-distal axis were detected in the mesenchymal Bmpr1a knockout lungs. However, deletion of Smad1/5, two major BMP signaling downstream effectors, from the lung mesenchyme did not phenocopy the cystic abnormalities observed in the mesenchymal Bmpr1a knockout lungs, suggesting that a Smad-independent mechanism contributes to prenatal pulmonary cystic lesions. These findings reveal for the first time the role of mesenchymal BMP signaling in lung development and a potential pathogenic mechanism underlying congenital pulmonary cysts.
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Affiliation(s)
- Yongfeng Luo
- Department of Surgery, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Ke Cao
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Joanne Chiu
- Department of Surgery, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Hui Chen
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Hong-Jun Wang
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Matthew E Thornton
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Brendan H Grubbs
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Martin Kolb
- Department of Medicine, McMaster UniversityHamiltonCanada
| | - Michael S Parmacek
- Department of Medicine, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Yuji Mishina
- Department of Biologic and Material Sciences, University of Michigan-Ann ArborAnn ArborUnited States
| | - Wei Shi
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Internal Medicine, University of Cincinnati College of MedicineCincinnatiUnited States
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41
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Banavar SP, Fowler EW, Nelson CM. Biophysics of morphogenesis in the vertebrate lung. Curr Top Dev Biol 2024; 160:65-86. [PMID: 38937031 DOI: 10.1016/bs.ctdb.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Morphogenesis is a physical process that sculpts the final functional forms of tissues and organs. Remarkably, the lungs of terrestrial vertebrates vary dramatically in form across species, despite providing the same function of transporting oxygen and carbon dioxide. These divergent forms arise from distinct physical processes through which the epithelium of the embryonic lung responds to the mechanical properties of its surrounding mesenchymal microenvironment. Here we compare the physical processes that guide folding of the lung epithelium in mammals, birds, and reptiles, and suggest a conceptual framework that reconciles how conserved molecular signaling generates divergent mechanical forces across these species.
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Affiliation(s)
- Samhita P Banavar
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Eric W Fowler
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Celeste M Nelson
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States; Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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42
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Yang X, Chen Y, Yang Y, Li S, Mi P, Jing N. The molecular and cellular choreography of early mammalian lung development. MEDICAL REVIEW (2021) 2024; 4:192-206. [PMID: 38919401 PMCID: PMC11195428 DOI: 10.1515/mr-2023-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/08/2024] [Indexed: 06/27/2024]
Abstract
Mammalian lung development starts from a specific cluster of endodermal cells situated within the ventral foregut region. With the orchestrating of delicate choreography of transcription factors, signaling pathways, and cell-cell communications, the endodermal diverticulum extends into the surrounding mesenchyme, and builds the cellular and structural basis of the complex respiratory system. This review provides a comprehensive overview of the current molecular insights of mammalian lung development, with a particular focus on the early stage of lung cell fate differentiation and spatial patterning. Furthermore, we explore the implications of several congenital respiratory diseases and the relevance to early organogenesis. Finally, we summarize the unprecedented knowledge concerning lung cell compositions, regulatory networks as well as the promising prospect for gaining an unbiased understanding of lung development and lung malformations through state-of-the-art single-cell omics.
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Affiliation(s)
- Xianfa Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yingying Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yun Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Shiting Li
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan Province, China
| | - Panpan Mi
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Naihe Jing
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
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43
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Parslow VR, Elmore SA, Cochran RZ, Bolon B, Mahler B, Sabio D, Lubeck BA. Histology Atlas of the Developing Mouse Respiratory System From Prenatal Day 9.0 Through Postnatal Day 30. Toxicol Pathol 2024; 52:153-227. [PMID: 39096105 DOI: 10.1177/01926233241252114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Respiratory diseases are one of the leading causes of death and disability around the world. Mice are commonly used as models of human respiratory disease. Phenotypic analysis of mice with spontaneous, congenital, inherited, or treatment-related respiratory tract abnormalities requires investigators to discriminate normal anatomic features of the respiratory system from those that have been altered by disease. Many publications describe individual aspects of normal respiratory tract development, primarily focusing on morphogenesis of the trachea and lung. However, a single reference providing detailed low- and high-magnification, high-resolution images of routine hematoxylin and eosin (H&E)-stained sections depicting all major structures of the entire developing murine respiratory system does not exist. The purpose of this atlas is to correct this deficiency by establishing one concise reference of high-resolution color photomicrographs from whole-slide scans of H&E-stained tissue sections. The atlas has detailed descriptions and well-annotated images of the developing mouse upper and lower respiratory tracts emphasizing embryonic days (E) 9.0 to 18.5 and major early postnatal events. The selected images illustrate the main structures and events at key developmental stages and thus should help investigators both confirm the chronological age of mouse embryos and distinguish normal morphology as well as structural (cellular and organ) abnormalities.
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Affiliation(s)
| | - Susan A Elmore
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Robert Z Cochran
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - Beth Mahler
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - David Sabio
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Beth A Lubeck
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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44
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Chang L, Chen Q, Wang B, Liu J, Zhang M, Zhu W, Jiang J. Single cell RNA analysis uncovers the cell differentiation and functionalization for air breathing of frog lung. Commun Biol 2024; 7:665. [PMID: 38816547 PMCID: PMC11139932 DOI: 10.1038/s42003-024-06369-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
The evolution and development of vertebrate lungs have been widely studied due to their significance in terrestrial adaptation. Amphibians possess the most primitive lungs among tetrapods, underscoring their evolutionary importance in bridging the transition from aquatic to terrestrial life. However, the intricate process of cell differentiation during amphibian lung development remains poorly understood. Using single-cell RNA sequencing, we identify 13 cell types in the developing lungs of a land-dwelling frog (Microhyla fissipes). We elucidate the differentiation trajectories and mechanisms of mesenchymal cells, identifying five cell fates and their respective driver genes. Using temporal dynamics analyses, we reveal the gene expression switches of epithelial cells, which facilitate air breathing during metamorphosis. Furthermore, by integrating the published data from another amphibian and two terrestrial mammals, we illuminate both conserved and divergent cellular repertoires during the evolution of tetrapod lungs. These findings uncover the frog lung cell differentiation trajectories and functionalization for breathing in air and provide valuable insights into the cell-type evolution of vertebrate lungs.
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Affiliation(s)
- Liming Chang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiheng Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Meihua Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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45
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Lim K, Lee MO, Choi J, Kim JH, Kim EM, Woo CG, Chung C, Cho YH, Hong SH, Cho YJ, Ahn SJ. Guidelines for Manufacturing and Application of Organoids: Lung. Int J Stem Cells 2024; 17:147-157. [PMID: 38777828 PMCID: PMC11170115 DOI: 10.15283/ijsc24041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The objective of standard guideline for utilization of human lung organoids is to provide the basic guidelines required for the manufacture, culture, and quality control of the lung organoids for use in non-clinical efficacy and inhalation toxicity assessments of the respiratory system. As a first step towards the utilization of human lung organoids, the current guideline provides basic, minimal standards that can promote development of alternative testing methods, and can be referenced not only for research, clinical, or commercial uses, but also by experts and researchers at regulatory institutions when assessing safety and efficacy.
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Affiliation(s)
- Kyungtae Lim
- Organoid Standards Initiative
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Mi-Ok Lee
- Organoid Standards Initiative
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- Department of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Jinwook Choi
- Organoid Standards Initiative
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Jung-Hyun Kim
- Organoid Standards Initiative
- Collage of Pharmacy, Ajou University, Suwon, Korea
- Department of Biohealth Regulatory Science, Graduate School of Ajou University, Suwon, Korea
| | - Eun-Mi Kim
- Organoid Standards Initiative
- Department of Bio and Environmental Technology, Seoul Women’s University, Seoul, Korea
| | - Chang Gyu Woo
- Organoid Standards Initiative
- School of Mechanical Engineering, Korea University of Technology and Education, Cheonan, Korea
| | - Chaeuk Chung
- Organoid Standards Initiative
- Department of Pulmonary and Critical Care Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Yong-Hee Cho
- Organoid Standards Initiative
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Korea
- Department of Medical Chemistry and Pharmacology, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Seok-Ho Hong
- Organoid Standards Initiative
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Korea
| | - Young-Jae Cho
- Organoid Standards Initiative
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sun-Ju Ahn
- Organoid Standards Initiative
- Department of Biophysics, Sungkyunkwan University, Suwon, Korea
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, Korea
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46
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Paramore SV, Trenado-Yuste C, Sharan R, Nelson CM, Devenport D. Vangl-dependent mesenchymal thinning shapes the distal lung during murine sacculation. Dev Cell 2024; 59:1302-1316.e5. [PMID: 38569553 PMCID: PMC11111357 DOI: 10.1016/j.devcel.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 10/18/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
The planar cell polarity (PCP) complex is speculated to function in murine lung development, where branching morphogenesis generates an epithelial tree whose distal tips expand dramatically during sacculation. Here, we show that PCP is dispensable in the airway epithelium for sacculation. Rather, we find a Celsr1-independent role for the PCP component Vangl in the pulmonary mesenchyme: loss of Vangl1/2 inhibits mesenchymal thinning and expansion of the saccular epithelium. Further, loss of mesenchymal Wnt5a mimics sacculation defects observed in Vangl2-mutant lungs, implicating mesenchymal Wnt5a/Vangl signaling as a key regulator of late lung morphogenesis. A computational model predicts that sacculation requires a fluid mesenchymal compartment. Lineage-tracing and cell-shape analyses are consistent with the mesenchyme acting as a fluid tissue, suggesting that loss of Vangl1/2 impacts the ability of mesenchymal cells to exchange neighbors. Our data thus identify an explicit function for Vangl and the pulmonary mesenchyme in actively shaping the saccular epithelium.
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Affiliation(s)
- Sarah V Paramore
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Carolina Trenado-Yuste
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rishabh Sharan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Celeste M Nelson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Fernandes-Silva H, Alves MG, Garcez MR, Correia-Pinto J, Oliveira PF, Homem CCF, Moura RS. Retinoic Acid-Mediated Control of Energy Metabolism Is Essential for Lung Branching Morphogenesis. Int J Mol Sci 2024; 25:5054. [PMID: 38732272 PMCID: PMC11084425 DOI: 10.3390/ijms25095054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Lung branching morphogenesis relies on intricate epithelial-mesenchymal interactions and signaling networks. Still, the interplay between signaling and energy metabolism in shaping embryonic lung development remains unexplored. Retinoic acid (RA) signaling influences lung proximal-distal patterning and branching morphogenesis, but its role as a metabolic modulator is unknown. Hence, this study investigates how RA signaling affects the metabolic profile of lung branching. We performed ex vivo lung explant culture of embryonic chicken lungs treated with DMSO, 1 µM RA, or 10 µM BMS493. Extracellular metabolite consumption/production was evaluated by using 1H-NMR spectroscopy. Mitochondrial respiration and biogenesis were also analyzed. Proliferation was assessed using an EdU-based assay. The expression of crucial metabolic/signaling components was examined through Western blot, qPCR, and in situ hybridization. RA signaling stimulation redirects glucose towards pyruvate and succinate production rather than to alanine or lactate. Inhibition of RA signaling reduces lung branching, resulting in a cystic-like phenotype while promoting mitochondrial function. Here, RA signaling emerges as a regulator of tissue proliferation and lactate dehydrogenase expression. Furthermore, RA governs fatty acid metabolism through an AMPK-dependent mechanism. These findings underscore RA's pivotal role in shaping lung metabolism during branching morphogenesis, contributing to our understanding of lung development and cystic-related lung disorders.
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Affiliation(s)
- Hugo Fernandes-Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (H.F.-S.); (J.C.-P.)
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
- PhDOC PhD Program, ICVS/3B’s, School of Medicine, University of Minho, 4710-057 Braga, Portugal
| | - Marco G. Alves
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Marcia R. Garcez
- iNOVA4Health, NOVA Medical School/Faculdade de Ciências Médicas (NMS/FCM), Universidade Nova de Lisboa, 1449-011 Lisbon, Portugal; (M.R.G.); (C.C.F.H.)
- Graduate Program in Areas of Basic and Applied Biology (GABBA), Universidade do Porto, 4050-313 Porto, Portugal
| | - Jorge Correia-Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (H.F.-S.); (J.C.-P.)
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
- Department of Pediatric Surgery, Hospital of Braga, 4710-243 Braga, Portugal
| | - Pedro F. Oliveira
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Catarina C. F. Homem
- iNOVA4Health, NOVA Medical School/Faculdade de Ciências Médicas (NMS/FCM), Universidade Nova de Lisboa, 1449-011 Lisbon, Portugal; (M.R.G.); (C.C.F.H.)
| | - Rute S. Moura
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (H.F.-S.); (J.C.-P.)
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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48
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Candeli N, Dayton T. Investigating pulmonary neuroendocrine cells in human respiratory diseases with airway models. Dis Model Mech 2024; 17:dmm050620. [PMID: 38813849 DOI: 10.1242/dmm.050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
Despite accounting for only ∼0.5% of the lung epithelium, pulmonary neuroendocrine cells (PNECs) appear to play an outsized role in respiratory health and disease. Increased PNEC numbers have been reported in a variety of respiratory diseases, including chronic obstructive pulmonary disease and asthma. Moreover, PNECs are the primary cell of origin for lung neuroendocrine cancers, which account for 25% of aggressive lung cancers. Recent research has highlighted the crucial roles of PNECs in lung physiology, including in chemosensing, regeneration and immune regulation. Yet, little is known about the direct impact of PNECs on respiratory diseases. In this Review, we summarise the current associations of PNECs with lung pathologies, focusing on how new experimental disease models, such as organoids derived from human pluripotent stem cells or tissue stem cells, can help us to better understand the contribution of PNECs to respiratory diseases.
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Affiliation(s)
- Noah Candeli
- European Molecular Biology Laboratory (EMBL) Barcelona, Tissue Biology and Disease Modelling, 08003, Barcelona, Spain
| | - Talya Dayton
- European Molecular Biology Laboratory (EMBL) Barcelona, Tissue Biology and Disease Modelling, 08003, Barcelona, Spain
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49
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Zhou Y, Li C, Chen Y, Yu Y, Diao X, Chiu R, Fang J, Shen Y, Wang J, Zhu L, Zhou J, Cai Z. Human Airway Organoids and Multimodal Imaging-Based Toxicity Evaluation of 1-Nitropyrene. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6083-6092. [PMID: 38547129 PMCID: PMC11008236 DOI: 10.1021/acs.est.3c07195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
Despite significant advances in understanding the general health impacts of air pollution, the toxic effects of air pollution on cells in the human respiratory tract are still elusive. A robust, biologically relevant in vitro model for recapitulating the physiological response of the human airway is needed to obtain a thorough understanding of the molecular mechanisms of air pollutants. In this study, by using 1-nitropyrene (1-NP) as a proof-of-concept, we demonstrate the effectiveness and reliability of evaluating environmental pollutants in physiologically active human airway organoids. Multimodal imaging tools, including live cell imaging, fluorescence microscopy, and MALDI-mass spectrometry imaging (MSI), were implemented to evaluate the cytotoxicity of 1-NP for airway organoids. In addition, lipidomic alterations upon 1-NP treatment were quantitatively analyzed by nontargeted lipidomics. 1-NP exposure was found to be associated with the overproduction of reactive oxygen species (ROS), and dysregulation of lipid pathways, including the SM-Cer conversion, as well as cardiolipin in our organoids. Compared with that of cell lines, a higher tolerance of 1-NP toxicity was observed in the human airway organoids, which might reflect a more physiologically relevant response in the native airway epithelium. Collectively, we have established a novel system for evaluating and investigating molecular mechanisms of environmental pollutants in the human airways via the combinatory use of human airway organoids, multimodal imaging analysis, and MS-based analyses.
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Affiliation(s)
- Yingyan Zhou
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Cun Li
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Yanyan Chen
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yifei Yu
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Xin Diao
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Raymond Chiu
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jiacheng Fang
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yuting Shen
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Jianing Wang
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Lin Zhu
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Jie Zhou
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Zongwei Cai
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
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50
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Basil MC, Alysandratos KD, Kotton DN, Morrisey EE. Lung repair and regeneration: Advanced models and insights into human disease. Cell Stem Cell 2024; 31:439-454. [PMID: 38492572 PMCID: PMC11070171 DOI: 10.1016/j.stem.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The respiratory system acts as both the primary site of gas exchange and an important sensor and barrier to the external environment. The increase in incidences of respiratory disease over the past decades has highlighted the importance of developing improved therapeutic approaches. This review will summarize recent research on the cellular complexity of the mammalian respiratory system with a focus on gas exchange and immunological defense functions of the lung. Different models of repair and regeneration will be discussed to help interpret human and animal data and spur the investigation of models and assays for future drug development.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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