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Chen Y, Gilliland A, Liang Q, Han X, Yang H, Chan J, Lévesque D, Moon KM, Daneshgar P, Boisvert FM, Foster L, Zandberg WF, Bergstrom K, Yu HB, Vallance BA. Defining enteric bacterial pathogenesis using organoids: Citrobacter rodentium uses EspC, an atypical mucinolytic protease, to penetrate mouse colonic mucus. Gut Microbes 2025; 17:2494717. [PMID: 40323239 PMCID: PMC12054374 DOI: 10.1080/19490976.2025.2494717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 04/07/2025] [Accepted: 04/09/2025] [Indexed: 05/08/2025] Open
Abstract
Enteric bacterial pathogens pose significant threats to human health; however, the mechanisms by which they infect the mammalian gut in the face of daunting host defenses remain to be fully defined. For the attaching and effacing (A/E) bacterial family member and murine pathogen Citrobacter rodentium, its virulence strategy appears to involve penetration of the colonic mucus barrier to reach the underlying epithelium. To better define these interactions, we grew colonoids under air-liquid interface (ALI) conditions, producing a thick mucus layer that mimicked in vivo mucus composition and glycosylation. C. rodentium's penetration of ALI-derived mucus was dramatically enhanced upon exposure to sialic acid, in concert with the secretion of two serine protease autotransporter of Enterobacteriaceae (SPATE) proteins, Pic and EspC. Despite Pic being a class II SPATE, and already recognized as a mucinase, it was EspC, a class I SPATE family member, that degraded ALI-derived mucus, despite class I SPATEs not previously shown to possess mucinase activity. Confirming this finding, E. coli DH5α carrying a plasmid that expresses C. rodentium-derived EspC was able to degrade the mucus. Moreover, recombinant EspC alone also displayed mucinolytic activity in a dose-dependent manner. Collectively, our results reveal the utility of ALI-derived mucus in modeling microbe-host interactions at the intestinal mucosal surface, as well as identify EspC as an atypical class I SPATE that shows significant mucinolytic activity toward ALI-derived mucus.
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Affiliation(s)
- Yan Chen
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Ashley Gilliland
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Qiaochu Liang
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Xiao Han
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Hyungjun Yang
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Jocelyn Chan
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Parandis Daneshgar
- Department of Chemistry, University of British Columbia, Kelowna, BC, Canada
| | | | - Leonard Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Wesley F. Zandberg
- Department of Chemistry, University of British Columbia, Kelowna, BC, Canada
| | - Kirk Bergstrom
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Hong B. Yu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas, USA
| | - Bruce A. Vallance
- Division of Gastroenterology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
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2
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De Cock L, Palubeckaitė I, Bersani F, Faehling T, Pasquali S, Umbaugh S, Meister MT, Danks MR, Manasterski P, Miallot R, Krumbholz M, Roohani S, Heymann D, Cidre-Aranaz F, Wozniak A, Schöffski P, Bovée JVMG, Merlini A, Venneker S. Establishment of patient-derived 3D in vitro models of sarcomas: literature review and guidelines on behalf of the FORTRESS working group. Neoplasia 2025; 65:101171. [PMID: 40324303 DOI: 10.1016/j.neo.2025.101171] [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: 03/21/2025] [Accepted: 04/24/2025] [Indexed: 05/07/2025]
Abstract
Sarcomas are a large family of rare and heterogeneous mesenchymal tumors, which respond poorly to available systemic treatments. Translation of preclinical findings into clinical applications has been slow, limiting improvements in patients' outcomes and ultimately highlighting the need for a better understanding of sarcoma biology to develop more effective, subtype-specific therapies. To this end, reliable preclinical models are crucial, but the development of 3D in vitro sarcoma models has been lagging behind that of epithelial cancers. This is primarily due to the rarity and heterogeneity of sarcomas, and lack of widespread knowledge regarding the optimal growth conditions of these in vitro models. In this review, we provide an overview of currently available sarcoma tumoroid models, together with guidelines and suggestions for model development and characterization, on behalf of the FORTRESS (Forum For Translational Research in Sarcomas) international research working group on 3D sarcoma models.
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Affiliation(s)
- Lore De Cock
- Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium; Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Ieva Palubeckaitė
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Francesca Bersani
- Department of Oncology, Translational Oncology Laboratory "Paola Gilardi", University of Turin, Turin, Italy
| | - Tobias Faehling
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Sandro Pasquali
- Molecular Pharmacology, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sam Umbaugh
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany; Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Torsten Meister
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Molly R Danks
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Piotr Manasterski
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard Miallot
- Department of Surgical and Interventional Sciences, McGill University, Montreal, QC, Canada; Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Manuela Krumbholz
- University Hospital Erlangen, Department of Pediatrics Erlangen, Germany
| | - Siyer Roohani
- Charité - Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) Clinician Scientist Program, Berlin, Germany
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Institut de Cancérologie de l'Ouest, Saint-Herblain, France; Université of Sheffield, School of Medicine and Population Health, Sheffield, United Kingdom
| | - Florencia Cidre-Aranaz
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Agnieszka Wozniak
- Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Patrick Schöffski
- Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium; Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alessandra Merlini
- Department of Oncology, Translational Oncology Laboratory "Paola Gilardi", University of Turin, Turin, Italy; Division of Medical Oncology, San Luigi Gonzaga University Hospital, Orbassano, Turin, Italy
| | - Sanne Venneker
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
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3
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Rezaei Z, Wang N, Yang Y, Govindaraj K, Velasco JJ, Martinez Blanco AD, Bae NH, Lee H, Shin SR. Enhancing organoid technology with carbon-based nanomaterial biosensors: Advancements, challenges, and future directions. Adv Drug Deliv Rev 2025; 222:115592. [PMID: 40324529 DOI: 10.1016/j.addr.2025.115592] [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: 01/03/2025] [Revised: 03/26/2025] [Accepted: 04/24/2025] [Indexed: 05/07/2025]
Abstract
Various carbon-based nanomaterials (CBNs) have been utilized to develop nano- and microscale biosensors that enable real-time and continuous monitoring of biochemical and biophysical changes in living biological systems. The integration of CBN-based biosensors into organoids has recently provided valuable insights into organoid development, disease modeling, and drug responses, enhancing their functionality and expanding their applications in diverse biomedical fields. These biosensors have been particularly transformative in studying neurological disorders, cardiovascular diseases, cancer progression, and liver toxicity, where precise, non-invasive monitoring is crucial for understanding pathophysiological mechanisms and assessing therapeutic efficacy. This review introduces intra- and extracellular biosensors incorporating CBNs such as graphene, carbon nanotubes (CNTs), graphene oxide (GO), reduced graphene oxide (rGO), carbon dots (CDs), and fullerenes. Additionally, it discusses strategies for improving the biocompatibility of CBN-based biosensors and minimizing their potential toxicity to ensure long-term organoid viability. Key challenges such as biosensor integration, data accuracy, and functional compatibility with specific organoid models are also addressed. Furthermore, this review highlights how CBN-based biosensors enhance the precision and relevance of organoid models in biomedical research, particularly in organ-specific applications such as brain-on-a-chip systems for neurodegenerative disease studies, liver-on-a-chip platforms for hepatotoxicity screening, and cardiac organoids for assessing cardiotoxicity in drug development. Finally, it explores how biosensing technologies could revolutionize personalized medicine by enabling high throughput drug screening, patient-specific disease modeling, and integrated sensing platforms for early diagnostics. By capturing current advancements and future directions, this review underscores the transformative potential of carbon-based nanotechnology in organoid research and its broader impact on medical science.
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Affiliation(s)
- Zahra Rezaei
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Niyou Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Yipei Yang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Department of Orthopedic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen 518000, China
| | - Kannan Govindaraj
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Department of Developmental Bioengineering, TechMed Centre, University of Twente, Drienerlolaan 5, Enschede 7522NB, the Netherlands
| | - Jose Joaquin Velasco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Monterrey Institute of Technology, School of Science and Engineering, Eugenio Garza Sada Avenue 2501 South, Monterrey, Nuevo Leon 64849, Mexico
| | - Alvaro Dario Martinez Blanco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Monterrey Institute of Technology, School of Science and Engineering, Epigmenio González 500, Fraccionamiento San Pablo, Santiago de Querétaro, Querétaro 76130, Mexico
| | - Nam Ho Bae
- Center for Nano-Bio Developement, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - HeaYeon Lee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; MARA Nanotech, INC. 4th floor, Hanmir Hall, Yongdang Campus, Pukyung National University, 365 Sinseon-ro, Nam-gu, Busan 48547, Republic of Korea; MARA Nanotech New York, INC. 1 Pennsylvania Plaza, Suite 1423, New York, NY 10119, USA
| | - Su Ryon Shin
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA.
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Qi GX, Zhao RX, Gao C, Ma ZY, Wang S, Xu J. Recent advances and challenges in colorectal cancer: From molecular research to treatment. World J Gastroenterol 2025; 31:106964. [DOI: 10.3748/wjg.v31.i21.106964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Revised: 04/22/2025] [Accepted: 05/26/2025] [Indexed: 06/06/2025] Open
Abstract
Colorectal cancer (CRC) ranks among the top causes of cancer-related fatalities globally. Recent progress in genomics, proteomics, and bioinformatics has greatly improved our comprehension of the molecular underpinnings of CRC, paving the way for targeted therapies and immunotherapies. Nonetheless, obstacles such as tumor heterogeneity and drug resistance persist, hindering advancements in treatment efficacy. In this context, the integration of artificial intelligence (AI) and organoid technology presents promising new avenues. AI can analyze genetic and clinical data to forecast disease risk, prognosis, and treatment responses, thereby expediting drug development and tailoring treatment plans. Organoids replicate the genetic traits and biological behaviors of tumors, acting as platforms for drug testing and the formulation of personalized treatment approaches. Despite notable strides in CRC research and treatment - from genetic insights to therapeutic innovations - numerous challenges endure, including the intricate tumor microenvironment, tumor heterogeneity, adverse effects of immunotherapies, issues related to AI data quality and privacy, and the need for standardization in organoid culture. Future initiatives should concentrate on clarifying the pathogenesis of CRC, refining AI algorithms and organoid models, and creating more effective therapeutic strategies to alleviate the global impact of CRC.
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Affiliation(s)
- Gao-Xiu Qi
- Department of Pathology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Medical Group), Qingdao 266042, Shandong Province, China
| | - Rui-Xia Zhao
- Department of Pathology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Medical Group), Qingdao 266042, Shandong Province, China
| | - Chen Gao
- Department of Pathology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Medical Group), Qingdao 266042, Shandong Province, China
| | - Zeng-Yan Ma
- Department of Pathology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Medical Group), Qingdao 266042, Shandong Province, China
| | - Shang Wang
- Department of Pathology, School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Jing Xu
- Department of Pathology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Medical Group), Qingdao 266042, Shandong Province, China
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5
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Winsor NJ, Tsang DK, Ranger A, Singh O, Goyal S, Philpott DJ, Girardin SE. The IL-18 receptor is expressed on murine small-intestinal enterochromaffin cells and executes a recovery program upon injury. Proc Natl Acad Sci U S A 2025; 122:e2417149122. [PMID: 40424129 DOI: 10.1073/pnas.2417149122] [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: 08/22/2024] [Accepted: 04/21/2025] [Indexed: 05/29/2025] Open
Abstract
Upon injury, epithelial-derived IL-18 is released and induces an inflammatory response in underlying IL18R1+ lamina propria cells. Notably, Il18r1 is also predicted to be expressed and functional in intestinal epithelial cells (IECs), since epithelial IL18R1 deficiency contributes to worsened outcomes upon inflammatory challenge. However, the nature of Il18r1+ IECs, and their subsequent role in epithelial-intrinsic IL-18 signaling is poorly characterized. Here, we show that, in the murine small intestine, the IL-18 receptor is expressed by rare IECs that we identified to be a subset of enterochromaffin cells (ECC). While these cells are the major producers of serotonin in the intestine, we found no evidence that IL-18 regulated serotonin metabolism or release. Rather, upon radiation-induced injury, Il18r1+ cells appeared in the crypt base and took on a revival stem cell (revSC) program, marked by mixed expression of YAP/TAZ and enteroendocrine genes signatures. Functionally, irradiated Il18-/- mice display reduced epithelial proliferation and altered differentiation in the small intestine, characterized by increased Paneth cells (PC) and elevated Wnt3 levels, which was partially recapitulated in Il18-/- ileal organoids. In sum, we identified an Il18r1+ population in the epithelium and revealed a role for IEC-intrinsic IL-18 signaling during injury.
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Affiliation(s)
- Nathaniel J Winsor
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Derek K Tsang
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
| | - Adrienne Ranger
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Ojas Singh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Shawn Goyal
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
| | - Stephen E Girardin
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
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6
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Wu Y, Zhang F, Du F, Huang J, Wei S. Combination of tumor organoids with advanced technologies: A powerful platform for tumor evolution and treatment response (Review). Mol Med Rep 2025; 31:140. [PMID: 40183402 PMCID: PMC11976518 DOI: 10.3892/mmr.2025.13505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 02/26/2025] [Indexed: 04/05/2025] Open
Abstract
Malignant tumors notably decrease life expectancy. Despite advances in cancer diagnosis and treatment, the mechanisms underlying tumorigenesis, progression and drug resistance have not been fully elucidated. An emerging method to study tumors is tumor organoids, which are a three‑dimensional miniature structure. These retain the patient‑specific tumor heterogeneity while demonstrating the histological, genetic and molecular features of original tumors. Compared with conventional cancer cell lines and animal models, patient‑derived tumor organoids are more advanced at physiological and clinical levels. Their synergistic combination with other technologies, such as organ‑on‑a‑chip, 3D‑bioprinting, tissue‑engineered cell scaffolds and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‑associated protein 9, may overcome limitations of the conventional 3D organoid culture and result in the development of more appropriate model systems that preserve the complex tumor stroma, inter‑organ and intra‑organ communications. The present review summarizes the evolution of tumor organoids and their combination with advanced technologies, as well as the application of tumor organoids in basic and clinical research.
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Affiliation(s)
- Ying Wu
- Department of Obstetrics and Gynecology, The 920th Hospital of Joint Logistics Support Force, Kunming, Yunnan 650032, P.R. China
| | - Fan Zhang
- Department of Comprehensive Medicine, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Furong Du
- Department of Medicine, Kingbio Medical Co., Ltd., Chongqing 401123, P.R. China
| | - Juan Huang
- Department of Breast Surgery and Multidisciplinary Breast Cancer Center, Clinical Research Center of Breast Cancer in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Shuqing Wei
- Department of Comprehensive Medicine, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
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7
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Klima S, Hurrell T, Goolam M, Gouws C, Engelbrecht AM, Kaur M, van den Bout I. A new dawn: Vitalising translational oncology research in Africa with the help of advanced cell culture models. Transl Oncol 2025; 56:102391. [PMID: 40228390 PMCID: PMC12017847 DOI: 10.1016/j.tranon.2025.102391] [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: 11/27/2024] [Revised: 03/12/2025] [Accepted: 04/07/2025] [Indexed: 04/16/2025] Open
Abstract
The advent of in vitro models such as induced pluripotent stem cells (iPSC) and patient derived (disease) organoids is supporting the development of population and patient specific model systems reflecting human physiology and disease. However, there remains a significant underrepresentation of non-European, especially African model systems. The development of such models should be enthusiastically embraced by Sub-Saharan African countries (SSAC) and middle-income countries (LIMC) to direct their own research focused on the improvement of health of their own populations at a sustainable cost within their respective funding environments. Great care needs to be taken to develop national frameworks to direct, sustainably fund and support such efforts in a way that maximises the output of such models for the investment required. Here, we highlight how advanced culture models can play a role in vitalising local healthcare research by focusing on locally relevant health care questions using appropriate cell culture models. We also provide a potential national platform example that could maximise such output at the lowest cost. This framework presents an opportunity for SSAC and LMIC to base their healthcare research on locally relevant models to ensure that developed health care initiatives and interventions are best suited for the populations they serve and thus represent a reset in global health care research at large.
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Affiliation(s)
- Stefanie Klima
- Centre for Neuroendocrinology and Department of Immunology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Tracey Hurrell
- Bioengineering and Integrated Genomics Group, Council for Scientific and Industrial Research, Pretoria, South Africa; Department of Pharmacology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Mubeen Goolam
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, South Africa; UCT Neuroscience Institute, Cape Town, South Africa
| | - Chrisna Gouws
- Centre of Excellence for Pharmaceutical Sciences (Pharmacen™), Faculty of Health Sciences, North-West University, South Africa; Desmond Tutu School of Medicine, Faculty of Health Sciences, North-West University, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, WITS, South Africa
| | - Iman van den Bout
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, South Africa.
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8
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Bacon J, Kitchel H, Stutz J, Chen JH, Smith A, Van Horn RD, Moreland C, Abraham T, Baker T, Aihara E, Hillgren K. Porcine intestinal organoids cultured in an organ-on-a-chip microphysiological system. Biochem Biophys Rep 2025; 42:102036. [PMID: 40421277 PMCID: PMC12104630 DOI: 10.1016/j.bbrep.2025.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 04/16/2025] [Accepted: 04/25/2025] [Indexed: 05/28/2025] Open
Abstract
Preclinical studies are a vital component of pharmaceutical development and improvements in the predictive value of in vitro studies are essential. Organ-on-a-chip in vitro models are a recent advancement in the pursuit of improved reproduction of in vivo tissue complexity. Here, we report the development and characterization of porcine intestinal cells from organoids on chips with microfluid dynamics and peristaltic-like strain in a microphysiological system. Intestinal epithelial cells were grown on a porous membrane as a co-culture with human intestinal microvascular endothelial cells for up to 12 days. These cultures formed villi-like structures and established a tight barrier replete with F-actin and tight junctions. A demarcated region of the epithelial cells was in an actively proliferative stage, reminiscent of intestinal crypts. The intestinal epithelial cell growth was characterized for the presence of enterocytes, goblet cells and enteroendocrine cells. Notable drug transporters and CYP450 metabolic activity were present in these cultures. The organoid chip maintained barrier function as the paracellular permeability was low. In contrast, the permeability enhancer, sodium caprate (C10), increased the apparent permeability of molecular weight marker compounds by 2- to 3-fold, and upon removal of C10, the barrier was shown to be recovered. The porcine intestinal chip represents a new in vitro model with potential application in multiple aspects of pharmaceutical testing including drug metabolism, drug transporters and safety.
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Affiliation(s)
- James Bacon
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Halie Kitchel
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - John Stutz
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Jack Hua Chen
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Aaron Smith
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Robert D. Van Horn
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | | | - Trent Abraham
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | | | - Eitaro Aihara
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Kathleen Hillgren
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
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9
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Moskal K, Khurana N, Siegert L, Lee YS, Clevers H, Elinav E, Puschhof J. Modeling cancer-microbiome interactions in vitro: A guide to co-culture platforms. Int J Cancer 2025; 156:2053-2067. [PMID: 39716471 PMCID: PMC11970552 DOI: 10.1002/ijc.35298] [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: 07/15/2024] [Revised: 10/10/2024] [Accepted: 10/29/2024] [Indexed: 12/25/2024]
Abstract
The biology of cancer is characterized by an intricate interplay of cells originating not only from the tumor mass, but also its surrounding environment. Different microbial species have been suggested to be enriched in tumors and the impacts of these on tumor phenotypes is subject to intensive investigation. For these efforts, model systems that accurately reflect human-microbe interactions are rapidly gaining importance. Here we present a guide for selecting a suitable in vitro co-culture platform used to model different cancer-microbiome interactions. Our discussion spans a variety of in vitro models, including 2D cultures, tumor spheroids, organoids, and organ-on-a-chip platforms, where we delineate their respective advantages, limitations, and applicability in cancer microbiome research. Particular focus is placed on methodologies that facilitate the exposure of cancer cells to microbes, such as organoid microinjections and co-culture on microfluidic devices. We highlight studies offering critical insights into possible cancer-microbe interactions and underscore the importance of in vitro models in those discoveries. We anticipate the integration of more complex microbial communities and the inclusion of immune cells into co-culture systems to more accurately simulate the tumor microenvironment. The advent of ever more sophisticated co-culture models will aid in unraveling the mechanisms of cancer-microbiome interplay and contribute to exploiting their potential in novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Kamil Moskal
- Junior Research Group Epithelium Microbiome Interactions (EMIL), German Cancer Research CenterHeidelbergGermany
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- DKFZ Hector Cancer Institute at the University Medical CenterMannheimGermany
| | - Nimisha Khurana
- Junior Research Group Epithelium Microbiome Interactions (EMIL), German Cancer Research CenterHeidelbergGermany
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Luisa Siegert
- Junior Research Group Epithelium Microbiome Interactions (EMIL), German Cancer Research CenterHeidelbergGermany
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
| | - Ye Seul Lee
- Junior Research Group Epithelium Microbiome Interactions (EMIL), German Cancer Research CenterHeidelbergGermany
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Hans Clevers
- Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtHubrecht InstituteUtrechtThe Netherlands
- Present address:
Roche Pharmaceutical Research and Early DevelopmentBaselSwitzerland
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Jens Puschhof
- Junior Research Group Epithelium Microbiome Interactions (EMIL), German Cancer Research CenterHeidelbergGermany
- Microbiome and Cancer Division, German Cancer Research CenterHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- DKFZ Hector Cancer Institute at the University Medical CenterMannheimGermany
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10
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Chaudhary JK, Danga AK, Kumari A, Bhardwaj A, Rath PC. Role of stem cells in ageing and age-related diseases. Mech Ageing Dev 2025; 225:112069. [PMID: 40324541 DOI: 10.1016/j.mad.2025.112069] [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: 01/17/2025] [Revised: 04/30/2025] [Accepted: 05/01/2025] [Indexed: 05/07/2025]
Abstract
Stem cell functions and ageing are deeply interconnected, continually influencing each other in multiple ways. Stem cells play a vital role in organ maintenance, regeneration, and homeostasis, all of which decline over time due to gradual reduction in their self-renewal, differentiation, and growth factor secretion potential. The functional decline is attributed to damaging extrinsic environmental factors and progressively worsening intrinsic genetic and biochemical processes. These ageing-associated deteriorative changes have been extensively documented, paving the way for the discovery of novel biomarkers of ageing for detection, diagnosis, and treatment of age-related diseases. Age-dependent changes in adult stem cells include numerical decline, loss of heterogeneity, and reduced self-renewal and differentiation, leading to a drastic reduction in regenerative potential and thereby driving the ageing process. Conversely, ageing also adversely alters the stem cell niche, disrupting the molecular pathways underlying stem cell homing, self-renewal, differentiation, and growth factor secretion, all of which are critical for tissue repair and regeneration. A holistic understanding of these molecular mechanisms, through empirical research and clinical trials, is essential for designing targeted therapies to modulate ageing and improve health parameters in older individuals.
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Affiliation(s)
- Jitendra Kumar Chaudhary
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Zoology, Shivaji College, University of Delhi, New Delhi 110027, India.
| | - Ajay Kumar Danga
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Anita Kumari
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Akshay Bhardwaj
- Global Research Alliances, Ashoka University, Rajiv Gandhi Education City, Sonepat, Haryana 131029, India.
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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11
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Pike CM, Levi JA, Boone LA, Peddibhotla S, Johnson J, Zwarycz B, Bunger MK, Thelin W, Boazak EM. High-throughput assay for predicting diarrhea risk using a 2D human intestinal stem cell-derived model. Toxicol In Vitro 2025; 106:106040. [PMID: 40086646 DOI: 10.1016/j.tiv.2025.106040] [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: 10/09/2024] [Revised: 01/29/2025] [Accepted: 03/05/2025] [Indexed: 03/16/2025]
Abstract
Gastrointestinal toxicities (GITs) in clinical trials often lead to dose-limitations that reduce drug efficacy and delay treatment optimization. Preclinical animal models do not accurately replicate human physiology, leaving few options for early detection of GITs, such as diarrhea, before human studies. Chemotherapeutic agents, known to cause clinical diarrhea, frequently target mitotic cells. Therefore, we hypothesized a model utilizing proliferative cell populations derived from human intestinal crypts would predict clinical diarrhea occurrence with high accuracy. Here, we describe the development of a diarrhea prediction assay utilizing RepliGut® Planar, a primary intestinal stem cell-derived platform. To evaluate the ability of this model to predict clinical diarrhea risk, we assessed toxicity of 30 marketed drugs by measuring cell proliferation (EdU incorporation), cell abundance (nuclei quantification), and barrier formation (TEER) in cells derived from three human donors. Dose response curves were generated for each drug, and the IC15 to Cmax ratio was used to identify a threshold for assay positivity. This model accurately predicted diarrhea potential, achieving an accuracy of 91 % for proliferation, 90 % for abundance, and 88 % for barrier formation. In vitro toxicity screening using primary proliferative cells may reduce clinical diarrhea and ultimately lead to safer and more effective treatments for patients.
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12
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Shao F, Huang X, Ma Z, Li L, Qi C. Differences in chemotherapeutic drug sensitivity before and after patient-derived tumor organoid construction. Toxicol Appl Pharmacol 2025; 499:117340. [PMID: 40228674 DOI: 10.1016/j.taap.2025.117340] [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: 11/04/2024] [Revised: 03/19/2025] [Accepted: 04/08/2025] [Indexed: 04/16/2025]
Abstract
BACKGROUND Patient-derived organoids (PDOs) have emerged as promising preclinical models for various tumor types. This study aimed to optimize the process of constructing 3D organoid models and facilitate the development of personalized therapies for gastric and colon cancers. METHODS Tumor tissues were divided into two parts: one part was dissociated into a single-cell suspension, and the other part was used to culture tumor organoids. RNA sequencing (RNA-seq) was performed on both tumor cells and cultured organoids. Four chemotherapeutic agents-Oxaliplatin (L-OHP), Gemcitabine (GEM), 5-Fluorouracil (5-FU), and Paclitaxel (PTX)-were utilized to assess cytotoxicity and proliferation in both organoids and freshly isolated tumor cells, then the effects of these agents were evaluated. RESULTS Organoids were successfully established from both surgically resected and biopsy-derived tumor tissues. Phenotypic analysis indicated that the organoids retained the histological features and expression profiles of the original tumors. Notably, the morphological characteristics of the organoids remained stable across passages, demonstrating robust growth over time. Differentially expressed genes were identified in both gastric and colon cancer PDOs. GO and KEGG pathway analyses revealed similar gene enrichment in gastric and colon PDOs. Both gastric and colon cancer PDOs exhibited increased significant sensitivity to PTX and 5-FU compared to freshly isolated cancer cells. Furthermore, the expression of most stemness-related genes was reduced after organoid culture. CONCLUSIONS We successfully established organoid models that demonstrated robust growth and heightened drug sensitivity compared to freshly isolated tumor cells. These findings suggest that caution should be exercised when interpreting drug sensitivity results from organoid-based assays.
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Affiliation(s)
- Fang Shao
- Laboratory of Oncology, The Second People's Hospital of Changzhou, The Third Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China; Largescale Equipment Platform, Changzhou Medical Center, The Second People's Hospital of Changzhou, The Third Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Xin Huang
- Laboratory of Oncology, The Second People's Hospital of Changzhou, The Third Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Zhihong Ma
- TCM Key Laboratory Cultivation Base of Zhejiang Province for the Development and Clinical Transformation of Immunomodulatory Drugs, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Liqin Li
- TCM Key Laboratory Cultivation Base of Zhejiang Province for the Development and Clinical Transformation of Immunomodulatory Drugs, Huzhou Central Hospital, Huzhou, Zhejiang, China.
| | - Chunjian Qi
- Laboratory of Oncology, The Second People's Hospital of Changzhou, The Third Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China.
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13
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Wong FC, Kim CE, Garcia-Alonso L, Vento-Tormo R. The human endometrium: atlases, models, and prospects. Curr Opin Genet Dev 2025; 92:102341. [PMID: 40154154 DOI: 10.1016/j.gde.2025.102341] [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: 01/31/2025] [Accepted: 02/26/2025] [Indexed: 04/01/2025]
Abstract
Approximately every month, the human endometrium undergoes a cycle of proliferation, differentiation, and, in the absence of pregnancy, shedding and repair. Each cycle relies on intricate interorgan coordination of hormonal secretions. Endometrial dysfunction causes significant health complications, including abnormal menstrual bleeding and endometriosis. However, effective diagnosis and treatments are hampered by understudied aetiology. Recent single-cell profiling has disentangled the diverse and dynamic nature of the endometrium, revealing regulatory roles of WNT, NOTCH, and TGFβ signalling. These insights have informed mechanistic studies enabled by advanced in vitro models that capture endometrial cellular heterogeneity and structure. In this review, we outline key single-cell transcriptomics atlases and models that provided new avenues for studying endometrial biology, discuss their limitations, and propose future directions.
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Affiliation(s)
- Frederick Ck Wong
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| | | | - Luz Garcia-Alonso
- Wellcome Sanger Institute, Cambridge, UK. https://twitter.com/@LuzGarAl
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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14
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Golshan M, Dortaj H, Omidi Z, Golshan M, Pourentezari M, Rajabi M, Rajabi A. Cartilage repair: unleashing PRP's potential in organoid models. Cytotechnology 2025; 77:86. [PMID: 40190423 PMCID: PMC11968630 DOI: 10.1007/s10616-025-00739-1] [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: 10/09/2024] [Accepted: 02/27/2025] [Indexed: 04/09/2025] Open
Abstract
Platelet-rich plasma (PRP) has emerged as a promising biological therapy in regenerative medicine due to its high concentration of growth factors and cytokines, which promote tissue healing and regeneration. In recent years, its application in cartilage tissue engineering has garnered significant attention. This study explores the synergistic interaction between PRP and cartilage organoids, a novel three-dimensional in vitro culture system that closely mimics the structural and functional properties of native cartilage. Cartilage organoids serve as a physiologically relevant model for studying cartilage development, disease progression, and regeneration. By integrating PRP with cartilage organoids, this review aims to enhance chondrogenesis, extracellular matrix synthesis, and cellular proliferation within the organoids. Emerging evidence suggests that PRP supplementation significantly improves chondrocyte viability, growth, and differentiation in cartilage organoids, thereby accelerating their maturation. This combination holds great potential for advancing cartilage repair strategies, providing a robust platform for preclinical studies, and paving the way for innovative therapeutic approaches for cartilage-related injuries and degenerative diseases. These key aspects-chondrogenesis, matrix synthesis, and cellular proliferation-were specifically selected due to their fundamental roles in cartilage tissue engineering and regeneration. Chondrogenesis is crucial for chondrocyte differentiation and maintenance, matrix synthesis ensures the structural integrity and functional properties of regenerated cartilage, and cellular proliferation supports tissue viability and repair. Addressing these factors is essential, as current cartilage regeneration strategies often suffer from limited long-term efficacy and inadequate extracellular matrix production. By elucidating the synergistic effects of PRP and cartilage organoids in these areas, this study seeks to bridge existing knowledge gaps and provide valuable insights for improving regenerative approaches in clinical applications, particularly for osteoarthritis and cartilage defects.
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Affiliation(s)
- Mahsa Golshan
- Department of Tissue Engineering and Applied Cell Science, Shiraz University of Medical Science, P.O.Box: 7154614111, Shiraz, Iran
| | - Hengameh Dortaj
- Tissue Engineering Research Group (TERG), Department of Anatomy and Cell Biology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeinab Omidi
- Department of Cardiovascular Disease, Alzahra Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Golshan
- Shiraz Transplant Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Majid Pourentezari
- Department of Anatomical Sciences, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Yazd Neuroendocrine Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mehrdad Rajabi
- Postgraduate Student or Periodontist, Department of Periodontics, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rajabi
- Department of Tissue Engineering and Applied Cell Science, Shiraz University of Medical Science, P.O.Box: 7154614111, Shiraz, Iran
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15
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Canhão PGM, Snoeys J, Geerinckx S, van Heerden M, Van den Bergh A, Holm C, Markus J, Ayehunie S, Monshouwer M, Evers R, Augustijns P, Kourula S. Human organotypic colon in vitro microtissue: unveiling a new window into colonic drug disposition. Eur J Pharm Sci 2025; 209:107025. [PMID: 39864598 DOI: 10.1016/j.ejps.2025.107025] [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: 12/06/2024] [Revised: 01/22/2025] [Accepted: 01/23/2025] [Indexed: 01/28/2025]
Abstract
The purpose of this study was to evaluate EpiColon, a novel human organotypic 3D colon microtissue prototype, developed to assess colonic drug disposition, with a particular focus on permeability ranking, and compare its performance to Caco-2 monolayers. EpiColon was characterized for barrier function using transepithelial electrical resistance (TEER), morphology via histology and immunohistochemistry, and functionality through drug transport studies measuring apparent permeability (Papp). Cutoff thresholds for the permeability of FITC-dextran 4 kDa (FD4), FITC-dextran 10 kDa (FD10S), and [14C]mannitol were established to monitor microtissue integrity. Permeability of EpiColon for 20 benchmark drugs was compared with Caco-2 data, and the activity of pivotal efflux transporters, including multidrug resistance protein 1/P-glycoprotein (MDR1/P-gp), along with multidrug resistance protein 2 (MRP2) and breast cancer resistance protein (BCRP), was evaluated using selective substrates. EpiColon exhibited a physiological barrier function (272.0 ± 53.05 Ω x cm2) and effectively discriminated between high (e.g., budesonide and [3H]metoprolol) and low permeable compounds (e.g., [3H]atenolol and [14C]mannitol). The model demonstrated functional activity for key efflux transporters, with efflux ratios of 2.32 for [3H]digoxin (MDR1/P-gp) and 3.34 for sulfasalazine (MRP2 and BCRP). Notably, EpiColon showed an enhanced dynamic range in the low permeability range, differentiating Papp between FD4 and FD10S, in contrast to Caco-2 monolayers. Significant positive correlations were observed between human fraction absorbed (fabs) and logarithmically transformed Papp [AP-BL] values for both EpiColon (rs = 0.68) and Caco-2 (rs = 0.68). Furthermore, EpiColon recapitulates some essential phenotypic and cellular features of the human colon, including the expression of critical marker genes (Pan-Cytokeratin+: epithelial/colonocytes, Vimentin+: mesenchymal/fibroblast, and Alcian Blue+: goblet cell/mucus). In conclusion, EpiColon is a promising platform that offers a valuable complement to conventional Caco-2 monolayers for studying colonic drug disposition. However, the presence of flat and some cuboidal cells, along with low throughput, must be addressed to improve its applicability in both academic research and pharmaceutical industry.
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Affiliation(s)
- Pedro G M Canhão
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium; Drug Delivery and Disposition, KU Leuven, Gasthuisberg O&N II, Herestraat 49 - box 921, 3000 Leuven, Belgium
| | - Jan Snoeys
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Suzy Geerinckx
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Marjolein van Heerden
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - An Van den Bergh
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Camden Holm
- MatTek Corporation, 200 Homer Avenue, Ashland, MA, USA
| | - Jan Markus
- MatTek In Vitro Life Science Laboratories, Bratislava, Slovak Republic
| | | | - Mario Monshouwer
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Raymond Evers
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Spring House, PA, USA
| | - Patrick Augustijns
- Drug Delivery and Disposition, KU Leuven, Gasthuisberg O&N II, Herestraat 49 - box 921, 3000 Leuven, Belgium
| | - Stephanie Kourula
- Preclinical Sciences & Translational Safety, Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium.
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16
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Yue T, Dong Y, Huo Q, Li W, Wang X, Zhang S, Fan H, Wu X, He X, Zhao Y, Li D. Nicotinamide riboside alleviates ionizing radiation-induced intestinal senescence by alleviating oxidative damage and regulating intestinal metabolism. J Adv Res 2025; 72:421-432. [PMID: 39029900 DOI: 10.1016/j.jare.2024.07.010] [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: 03/15/2024] [Revised: 04/11/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024] Open
Abstract
INTRODUCTION The intestine, frequently subjected to pelvic or abdominal radiotherapy, is particularly vulnerable to delayed effects of acute radiation exposure (DEARE) owing to its high radiation sensitivity. Radiation-induced intestinal senescence, a result of DEARE, profoundly affects the well-being and quality of life of radiotherapy patients. However, targeted pharmaceutical interventions for radiation-induced senescence are currently scarce. Our findings showcase that nicotinamide riboside(NR) effectively alleviates radiation-induced intestinal senescence, offering crucial implications for utilizing NR as a pharmacological agent to combat intestinal DEARE. OBJECTIVES The aim of this study was to investigate the ability of NR to reduce radiation induced intestinal senescence and explore its related mechanisms. METHODS Male C57BL/6J mice were randomly divided into CON, IR, and IR + NR groups. The mice in the IR and IR + NR groups were subjected to a 6.0 Gy γ-ray total body exposure. After 8 weeks, the mice in the IR + NR group received NR via gavage at a dose of 400 mg/kg/d for 21 days. Then the mice were used for sample collection. RESULTS Our results demonstrate that NR can significantly mitigate radiation-induced intestinal senescence. Furthermore, our findings indicate that NR can mitigate oxidative damage, restore the normal function of intestinal stem cells, regulate the disruption of the intestinal symbiotic ecosystem and address metabolic abnormalities. In addition, the underlying mechanisms involve the activation of SIRT6, SIRT7 and the inhibition of the mTORC1 pathway by NR. CONCLUSION In conclusion, our results reveal the substantial inhibitory effects of NR on radiation-induced intestinal senescence. These findings offer valuable insights into the potential therapeutic use of NR as a pharmacological agent for alleviating intestinal DEARE.
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Affiliation(s)
- Tongpeng Yue
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Yinping Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Qidong Huo
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Wenxuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Xinyue Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Shiyi Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Huirong Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Xin Wu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Xin He
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China
| | - Yu Zhao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China.
| | - Deguan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin 300192, China.
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17
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Hu JW, Pan YZ, Zhang XX, Li JT, Jin Y. Applications and challenges of patient-derived organoids in hepatobiliary and pancreatic cancers. World J Gastroenterol 2025; 31:106747. [DOI: 10.3748/wjg.v31.i20.106747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 04/12/2025] [Accepted: 05/12/2025] [Indexed: 05/28/2025] Open
Abstract
Hepatobiliary and pancreatic (HBP) cancers are among the most aggressive malignancies, with recurrence and metastasis driven by tumor heterogeneity and drug resistance, presenting considerable challenges to effective treatment. Currently, personalized and accurate treatment prediction models for these cancers are lacking. Patient-derived organoids (PDOs) tumor are three-dimensional in vitro models created from the tumor tissues of individual patients. Recent reports and our cultivation data indicate that the success rate of cultivating organoids for HBP cancers consistently exceeds 70%. The predictive accuracy of these tumor organoids has been shown to surpass 90%. However, PDOs still face notable limitations, especially in simulating the tumor microenvironment, including tumor angiogenesis and the surrounding cellular context, which require further refinement. While co-culture techniques and microfluidic platforms have been developed to mimic multi-cellular environments and functional vascular perfusion, they remain insufficient in accurately recapitulating the complexities of the in vivo environment. Additionally, PDOs are needed to fully assess their potential in predicting the efficacy of multi-drug combination therapies. This review provides an overview of the applications, challenges, and prospects for organoid models in the study of HBP cancer.
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Affiliation(s)
- Jia-Wei Hu
- Department of Hepatic-Biliary-Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Yan-Zhi Pan
- Department of Hepatic-Biliary-Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Xiao-Xiao Zhang
- Department of Hepatic-Biliary-Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Jiang-Tao Li
- Department of Hepatic-Biliary-Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Yun Jin
- Department of Hepatic-Biliary-Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
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Xie X, Chen X, Zhou J, Wang T, Yang G, Han F, Wei Z. Dynamic Hydrogels with Tunable Mechanics for 3D Organoid Derivation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2501862. [PMID: 40434214 DOI: 10.1002/smll.202501862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 05/04/2025] [Indexed: 05/29/2025]
Abstract
The mechanical properties of the hydrogel play a pivotal role in governing the formation and development of 3D organoids in vitro. However, commonly employed natural hydrogels, such as Matrigel and other extracellular matrix (ECM)-derived products, are characterized by ill-defined and complex compositions, resulting in non-tunable mechanical properties. This limitation poses challenges in controlling organoids' developmental trajectory and 3D morphology. Although numerous synthetic hydrogels with well-defined chemical structures have recently been adopted to study organoids by modulating stiffness, advanced research emphasizes the importance of dynamic mechanical cues, such as dynamic stiffness softening and dynamic viscoelasticity, for optimal organoid derivation. These cues are essential for mimicking the dynamic physiological states of organoids during their growth. Despite their potential, the concept of dynamic hydrogels is often used interchangeably, and a systematic review is lacking to clarify this ambiguity. Furthermore, the mechanisms through which dynamic mechanical cues regulate organoid formation have not been thoroughly reported. This review endeavors to summarize and categorize dynamic hydrogels and reveal the effects of dynamic mechanics on organoid derivation. Additionally, the prospects of dynamic hydrogels in organoid derivation are deliberated to promote a more rational design of synthetic hydrogels, guiding organoid derivation and propelling organoid technology in biomedicine.
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Affiliation(s)
- Xueyong Xie
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Xuewen Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Jian Zhou
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, P. R. China
| | - Tiansong Wang
- Department of Industrial and Systems Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gen Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, P. R. China
- School of Physics, Peking University, Beijing, 100871, P. R. China
| | - Fei Han
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Zhao Wei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P. R. China
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Sharma P, Kim CY, Keys HR, Imada S, Joseph AB, Ferro L, Kunchok T, Anderson R, Sun Y, Yilmaz ÖH, Weng JK, Jain A. Genetically encoded fluorescent reporter for polyamines. Nat Commun 2025; 16:4921. [PMID: 40425580 PMCID: PMC12117157 DOI: 10.1038/s41467-025-60147-z] [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: 11/05/2024] [Accepted: 05/16/2025] [Indexed: 05/29/2025] Open
Abstract
Polyamines are abundant and evolutionarily conserved metabolites that are essential for life. Dietary polyamine supplementation extends life-span and health-span. Dysregulation of polyamine homeostasis is linked to Parkinson's disease and cancer, driving interest in therapeutically targeting this pathway. However, measuring cellular polyamine levels, which vary across cell types and states, remains challenging. We introduce a genetically encoded polyamine reporter for real-time measurement of polyamine concentrations in single living cells. This reporter utilizes the polyamine-responsive ribosomal frameshift motif from the OAZ1 gene. We demonstrate broad applicability of this approach and reveal dynamic changes in polyamine levels in response to genetic and pharmacological perturbations. Using this reporter, we conduct a genome-wide CRISPR screen and uncover an unexpected link between mitochondrial respiration and polyamine import, which are both risk factors for Parkinson's disease. By offering a lens to examine polyamine biology, this reporter may advance our understanding of these ubiquitous metabolites and accelerate therapy development.
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Affiliation(s)
- Pushkal Sharma
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Shinya Imada
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Alex B Joseph
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Luke Ferro
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rachel Anderson
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yulin Sun
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Zhang J, Guo H, Xu Y, Xiong Z, Du Y, Zhu P, Fan Z. Snora54 negatively regulates self-renewal of intestinal stem cells and gut regeneration via suppression of Notch2 signaling. SCIENCE ADVANCES 2025; 11:eadv4725. [PMID: 40408479 PMCID: PMC12101510 DOI: 10.1126/sciadv.adv4725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 04/17/2025] [Indexed: 05/25/2025]
Abstract
The self-renewal of intestinal stem cells (ISCs) is essential for maintaining intestinal homeostasis and ensuring regeneration of the intestinal epithelium. However, whether small nucleolar RNAs participate in the regulation of ISC self-renewal remains unclear. Here, we identified a small nucleolar RNA (Snora54) that was highly expressed in the nucleolus of ISCs. Snora54 knockout enhanced the self-renewal capacity of ISCs and intestinal regeneration. Mechanistically, in a steady state, highly expressed Snora54 anchored the nucleolar protein Lyar in the nucleolus of ISCs, preventing Lyar from translocation into the nucleoplasm. Thereby, Lyar failed to recruit on the Notch2 promoter region in the nucleoplasm to promote Notch2 transcription, leading to suppression of ISC self-renewal. By contrast, with deletion of Snora54, Lyar translocated to the nucleoplasm of ISCs where it enriched on the Notch2 promoter to initiate its transcription resulting in the activation of Notch2 signaling pathway. Therefore, Snora54 negatively regulates self-renewal of ISCs and gut regeneration via suppression of Notch2 signaling.
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Affiliation(s)
- Jiahang Zhang
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Guo
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Xu
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhen Xiong
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Du
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zusen Fan
- State Key Laboratory of RNA Science and Engineering, State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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21
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Cavalloro V, Malacrida A, Miloso M, Ronchi D, Porta A, Fossati A, Gheza G, De Siervi S, Mantovani S, Oliviero B, Mondelli MU, Pugliese L, Turato C, Martino E, Collina S. From lichen to organoids: Usnic acid enantiomers show promise against Cholangiocarcinoma via MNK2 targeting and MAPK pathway modulation. Biomed Pharmacother 2025; 188:118208. [PMID: 40412357 DOI: 10.1016/j.biopha.2025.118208] [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: 04/04/2025] [Revised: 05/12/2025] [Accepted: 05/21/2025] [Indexed: 05/27/2025] Open
Abstract
Cholangiocarcinoma (CC) remains one of the most challenging biliary tract malignancies, with limited therapeutic options and poor survival rates. We report the discovery and mechanistic investigation of usnic acid (UA) enantiomers as novel anti-CC agents. We identified the lichen Cladonia foliacea as a potential source of anticancer agents and developed a sustainable protocol to isolate (S)-UA as the most abundant metabolite. Our comprehensive comparative study of both enantiomers revealed time-dependent enantio-preference in their anti-cancer activity. While (S)-UA demonstrated twice the potency at 24 h, (R)-UA exhibited nearly ten-fold greater activity at 48 h and 72 h, particularly at lower concentrations (2.9 and 29 mM). Overall, both enantiomers inhibited EGI-1 cell proliferation in the micromolar range in a dose- and time-dependent manner. In silico studies and kinase profiling identified MNK2 as a primary target, with subsequent validation confirming direct binding and inhibition. Mechanistic studies demonstrated that UA enantiomers modulate the MAPK pathway, leading to decreased phosphorylation of eIF4E and suppression of cancer-promoting proteins. The successful translation of activity from 2D cell cultures to patient-derived 3D organoid models further validates their therapeutic potential. Our findings establish usnic acid as a promising natural product scaffold for CC treatment and provide detailed insights into its mechanism of action through MNK2 targeting and MAPK pathway modulation, with important considerations for enantiomer-specific temporal efficacy.
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Affiliation(s)
- Valeria Cavalloro
- Department of Earth and Environmental Sciences, University of Pavia Via Ferrata 1, Pavia 27100, Italy; NBFC-National Biodiversity Future Center, Piazza Marina 61, Palermo 90133, Italy
| | - Alessio Malacrida
- School of Medicine and Surgery, University of Milan-Bicocca, Monza 20900, Italy
| | - Mariarosaria Miloso
- School of Medicine and Surgery, University of Milan-Bicocca, Monza 20900, Italy
| | - Davide Ronchi
- Department of Electrical, Computer and Biomedical Engineering, Via A. Ferrata, 5, Pavia 27100, Italy
| | - Alessio Porta
- Department of Chemistry, University of Pavia, Via Taramelli, 12, Pavia 27100, Italy
| | - Alice Fossati
- Department of Earth and Environmental Sciences, University of Pavia Via Ferrata 1, Pavia 27100, Italy; NBFC-National Biodiversity Future Center, Piazza Marina 61, Palermo 90133, Italy
| | - Gabriele Gheza
- BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy
| | - Silvia De Siervi
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, Pavia 27100, Italy
| | - Stefania Mantovani
- Research Department, Laboratory of Clinical Immunology, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Barbara Oliviero
- Research Department, Laboratory of Clinical Immunology, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Mario Umberto Mondelli
- Research Department, Laboratory of Clinical Immunology, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Luisa Pugliese
- S.A.F.AN. BIOINFORMATICS s.a.s., via Don Giovanni Grioli 4, Torino 10137, Italy
| | - Cristian Turato
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, Pavia 27100, Italy.
| | - Emanuela Martino
- Department of Earth and Environmental Sciences, University of Pavia Via Ferrata 1, Pavia 27100, Italy; NBFC-National Biodiversity Future Center, Piazza Marina 61, Palermo 90133, Italy.
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Via Taramelli, 12, Pavia 27100, Italy
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22
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Dash P, Yadav V, Das B, Satapathy SR. Experimental toolkit to study the oncogenic role of WNT signaling in colorectal cancer. Biochim Biophys Acta Rev Cancer 2025; 1880:189354. [PMID: 40414319 DOI: 10.1016/j.bbcan.2025.189354] [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: 10/28/2024] [Revised: 05/19/2025] [Accepted: 05/19/2025] [Indexed: 05/27/2025]
Abstract
Colorectal cancer (CRC) is linked to the WNT/β-catenin signaling as its primary driver. Aberrant activation of WNT/β-catenin signaling is closely correlated with increased incidence, malignancy, poorer prognosis, and even higher cancer-related death. Research over the years has postulated various experimental models that have facilitated an understanding of the complex mechanisms underlying WNT signaling in CRC. In the present review, we have comprehensively summarized the in vitro, in vivo, patient-derived, and computational models used to study the role of WNT signaling in CRC. We discuss the use of CRC cell lines and organoids in capturing the molecular intricacies of WNT signaling and implementing xenograft and genetically engineered mouse models to mimic the tumor microenvironment. Patient-derived models, including xenografts and organoids, provide valuable insights into personalized medicine approaches. Additionally, we elaborated on the role of computational models in simulating WNT signaling dynamics and predicting therapeutic outcomes. By evaluating the advantages and limitations of each model, this review highlights the critical contributions of these systems to our understanding of WNT signaling in CRC. We emphasize the need to integrate diverse model systems to enhance translational research and clinical applications, which is the primary goal of this review.
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Affiliation(s)
- Pujarini Dash
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Vikas Yadav
- Cell and Experimental Pathology, Department of Translational Medicine, Clinical Research Centre, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Biswajit Das
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, USA
| | - Shakti Ranjan Satapathy
- Cell and Experimental Pathology, Department of Translational Medicine, Clinical Research Centre, Skåne University Hospital, Lund University, Malmö, Sweden
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23
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Feng Y, He D, An X. Hydrogel innovations for 3D organoid culture. Biomed Mater 2025; 20:042001. [PMID: 40359965 DOI: 10.1088/1748-605x/add82d] [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: 12/11/2024] [Accepted: 05/13/2025] [Indexed: 05/15/2025]
Abstract
Organoids are functional cell-tissue complexes that mimic structural and functional characteristics of organsin vitroin three dimensions (3D). Mimicking the natural extracellular matrix (ECM) environment is critical for guiding stem cell fate within organoid cultures. Current organoid cultures predominantly utilize animal- or tumor-derived ECMs such as dECMs and Matrigel. However, these materials introduce batch variability and uncertainty in composition, which hinders reproducibility. In contrast, naturally derived and synthetic hydrogels with excellent biocompatibility offer precise and adjustable compositions, along with tunable mechanical properties, thereby providing robust support for organoid development and maturation. We explore innovative hydrogel designs tailored specifically for organoid cultures, emphasizing the influence and meticulous control of functional hydrogels on organoid formation, differentiation, and maturation processes. Furthermore, the review highlights the potential of functionalized hydrogel scaffolds to advance both research and industrial applications in tissue and organ engineering. As research progresses, investigations will further concentrate on improving the adjustable properties, expanding their scope of application, and more biologically compatible gelation strategies of hydrogels.
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Affiliation(s)
- Yicheng Feng
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, People's Republic of China
| | - Dongyang He
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, People's Republic of China
| | - Xiao An
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, People's Republic of China
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24
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Marei HE. Stem cell therapy: a revolutionary cure or a pandora's box. Stem Cell Res Ther 2025; 16:255. [PMID: 40405306 PMCID: PMC12096755 DOI: 10.1186/s13287-025-04334-1] [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: 02/18/2025] [Accepted: 04/10/2025] [Indexed: 05/24/2025] Open
Abstract
This review article examines how stem cell therapies can cure various diseases and injuries while also discussing the difficulties and moral conundrums that come with their application. The article focuses on the revolutionary developments in stem cell research, especially the introduction of gene editing tools like CRISPR-Cas9, which can potentially improve the safety and effectiveness of stem cell-based treatments. To guarantee the responsible use of stem cells in clinical applications, it is also argued that standardizing clinical procedures and fortifying ethical and regulatory frameworks are essential first steps. The assessment also highlights the substantial obstacles that still need to be addressed, such as the moral dilemmas raised by the use of embryonic stem cells, the dangers of unlicensed stem cell clinics, and the difficulties in obtaining and paying for care for patients. The study emphasizes how critical it is to address these problems to stop exploitation, guarantee patient safety, and increase the accessibility of stem cell therapy. The review also addresses the significance of thorough clinical trials, public education, and policy development to guarantee that stem cell research may fulfill its full potential. The review concludes by describing stem cell research as a promising but complicated topic that necessitates a thorough evaluation of both the hazards and the benefits. To overcome the ethical, legal, and accessibility obstacles and eventually guarantee that stem cell treatments may be safely and fairly included in conventional healthcare, it urges cooperation between the scientific community, legislators, and the general public.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35116, Egypt.
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25
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Wang CM, Oberoi HS, Law D, Li Y, Kassis T, Griffith LG, Breault DT, Carrier RL. Human mesofluidic intestinal model for studying transport of drug carriers and bacteria through a live mucosal barrier. LAB ON A CHIP 2025. [PMID: 40392585 DOI: 10.1039/d4lc00774c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2025]
Abstract
The intestinal mucosal barrier forms a critical interface between lumen contents such as bacteria, drugs, and drug carriers and the underlying tissue. Current in vitro intestinal models, while recapitulating certain aspects of this barrier, generally present challenges with respect to imaging transport across mucus and uptake into enterocytes. A human mesofluidic small intestinal chip was designed to enable facile visualization of a mucosal interface created by growing primary human intestinal cells on a vertical hydrogel wall separating channels representing the intestinal lumen and circulatory flow. Type I collagen, fortified via cross-linking to prevent deformation and leaking during culture, was identified as a suitable gel wall material for supporting primary organoid-derived human duodenal epithelial cell attachment and monolayer formation. Addition of DAPT and PGE2 to culture medium paired with air-liquid interface culture increased the thickness of the mucus layer on epithelium grown within the device for 5 days from approximately 5 μm to 50 μm, making the model suitable for revealing intriguing features of interactions between luminal contents and the mucus barrier using live cell imaging. Time-lapse imaging of nanoparticle diffusion within mucus revealed a zone adjacent to the epithelium largely devoid of nanoparticles up to 4.5 h after introduction to the lumen channel, as well as pockets of dimly lectin-stained mucus within which particles freely diffused, and apparent clumping of particles by mucus components. Multiple particle tracking conducted on the intact mucus layer in the chip revealed significant size-dependent differences in measured diffusion coefficients. E. coli introduced to the lumen channel were freely mobile within the mucus layer and appeared to intermittently contact the epithelial surface over 30 minute periods of culture. Mucus shedding into the lumen and turnover of mucus components within cells were visualized. Taken together, this system represents a powerful tool for visualization of interactions between luminal contents and an intact live mucosal barrier.
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Affiliation(s)
- Chia-Ming Wang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA.
| | - Hardeep S Oberoi
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Devalina Law
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Yuan Li
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Timothy Kassis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Rebecca L Carrier
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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26
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O'Mahony ET, Arian CM, Aryeh KS, Wang K, Thummel KE, Kelly EJ. Human intestinal enteroids: Nonclinical applications for predicting oral drug disposition, toxicity, and efficacy. Pharmacol Ther 2025:108879. [PMID: 40398537 DOI: 10.1016/j.pharmthera.2025.108879] [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: 11/12/2024] [Revised: 02/19/2025] [Accepted: 05/15/2025] [Indexed: 05/23/2025]
Abstract
The application of human enteroid systems presents a significant opportunity within the drug development pipeline, highlighting considerable potential for advancements in the characterization and evaluation of new molecular entities. Derived from LGR5+ crypt-based columnar cells, enteroid systems more accurately recapitulate the microanatomy and physiological processes of the human intestinal mucosa compared to traditionally used systems. They contain the complement of major mucosal epithelial cell types, maintain the genetic identity of the donor and intestinal segment they were derived from, and exhibit biological functions and specific activities that are seen in vivo. In this review, we examine the applications of human enteroid systems in nonclinical drug development and compare findings to existing and emerging in vitro models of the small intestine. Specifically, we explore enteroid systems in the context of predicting oral drug disposition, focusing on apparent permeability, intestinal first-pass metabolism, and drug interactions, as well as their utility in assessing drug-induced gastrointestinal toxicity and screening therapeutic efficacy against enteric diseases. Additionally, we highlight aspects of enteroid systems that warrant further study.
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Affiliation(s)
- Eimear T O'Mahony
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America
| | - Christopher M Arian
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America
| | - Kayenat S Aryeh
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America
| | - Kai Wang
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America
| | - Kenneth E Thummel
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America; Center of Excellence for Natural Product Drug Interaction Research, Spokane, WA, United States of America
| | - Edward J Kelly
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, United States of America; Kidney Research Institute, University of Washington, Seattle, WA, United States of America.
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27
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Tonini L, Ahn C. Latest Advanced Techniques for Improving Intestinal Organoids Limitations. Stem Cell Rev Rep 2025:10.1007/s12015-025-10894-9. [PMID: 40388043 DOI: 10.1007/s12015-025-10894-9] [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] [Accepted: 05/06/2025] [Indexed: 05/20/2025]
Abstract
Intestinal organoids are valuable tools across different disciplines, from a clinical aspect to the biomedical research, providing a unique perspective on the complexity of the gastrointestinal system. They are alternatives to common cell lines as they can offer insights into architectural functionality and reduce the use of animal models. A deeper understanding of their organoid characteristics is required to harness their full potential. Despite their beneficial uses and multiple advantages, organoids have limitations that remain unaddressed. This review aims to elucidate the principal limitations of intestinal organoids, investigate structural defects such as the deficiency in a vascularized and lymphatic system, and absence of the microbiome, restrictions in mimicking the physiological gut model, including the lack of an acid-neutralizing system or a shortage of digestive enzymes, and the difficulties in their long-term maintenance and polarity accessibility. Development of innovative techniques to address these limitations will lead to improve in vivo recapitulation and pioneering further advancements in this field.
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Affiliation(s)
- Lisa Tonini
- Laboratory of Veterinary Physiology, College of Veterinary Medicine, Jeju National University, Jeju, 63243, Republic of Korea
| | - Changhwan Ahn
- Laboratory of Veterinary Physiology, College of Veterinary Medicine, Jeju National University, Jeju, 63243, Republic of Korea.
- Veterinary Medical Research Institute, Jeju National University, Jeju, 63243, Republic of Korea.
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28
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Zhou X, Yang L, Song S, Yin X. A modified system to promote stemness of mouse intestinal stem cells by activating Nrf2 and α2-adrenergic receptor signaling pathway. Acta Biochim Biophys Sin (Shanghai) 2025. [PMID: 40390578 DOI: 10.3724/abbs.2025078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2025] Open
Abstract
Intestinal stem cells (ISCs) maintain epithelial homeostasis through continuous self-renewal and differentiation, but their regulatory mechanisms remain incompletely understood. Using a simplified culture system, we identify two novel pathways that synergistically enhance stem cell characteristics: antioxidant signaling through 2-phospho-L-ascorbic acid (pVc) and α2-adrenergic receptor (α2-AR) activation by dexmedetomidine (Dex). Mechanistic studies reveal that pVc promotes stem cell maintenance through Nrf2-mediated antioxidant responses, while α2-AR activation functions through suppression of cAMP signaling. In vivo administration of these compounds enhances intestinal epithelial renewal while maintaining proper stem cell positioning and identity. Notably, α2-AR activation promotes regeneration after radiation injury by enhancing proliferation of stem cells produced by Bmi1 + cells in the post-injury process, demonstrating therapeutic potential. These findings advance our understanding of ISC regulation and suggest new strategies for protecting intestinal integrity during injury or disease.
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Affiliation(s)
- Xingyu Zhou
- Institute for Regenerative Medicine, State Key Laboratory of Cardiovascular Diseases, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Li Yang
- Institute for Regenerative Medicine, State Key Laboratory of Cardiovascular Diseases, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Sentao Song
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiaolei Yin
- Institute for Regenerative Medicine, State Key Laboratory of Cardiovascular Diseases, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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29
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Kumar D, Gupta S, Gupta V, Tanwar R, Chandel A. Engineering the Future of Regenerative Medicines in Gut Health with Stem Cell-Derived Intestinal Organoids. Stem Cell Rev Rep 2025:10.1007/s12015-025-10893-w. [PMID: 40380985 DOI: 10.1007/s12015-025-10893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2025] [Indexed: 05/19/2025]
Abstract
The advent of intestinal organoids, three-dimensional structures derived from stem cells, has significantly advanced the field of biology by providing robust in vitro models that closely mimic the architecture and functionality of the human intestine. These organoids, generated from induced pluripotent stem cells (iPSCs), embryonic stem cells (ESCs), or adult stem cells, possess remarkable capabilities for self-renewal, differentiation into diverse intestinal cell types, and functional recapitulation of physiological processes, including nutrient absorption, epithelial barrier integrity, and host-microbe interactions. The utility of intestinal organoids has been extensively demonstrated in disease modeling, drug screening, and personalized medicine. Notable examples include iPSC-derived organoids, which have been effectively employed to model enteric infections, and ESC-derived organoids, which have provided critical insights into fetal intestinal development. Patient-derived organoids have emerged as powerful tools for investigating personalized therapeutics and regenerative interventions for conditions such as inflammatory bowel disease (IBD), cystic fibrosis, and colorectal cancer. Preclinical studies involving transplantation of human intestinal organoids into murine models have shown promising outcomes, including functional integration, epithelial restoration, and immune system interactions. Despite these advancements, several challenges persist, particularly in achieving reproducibility, scalability, and maturation of organoids, which hinder their widespread clinical translation. Addressing these limitations requires the establishment of standardized protocols for organoid generation, culture, storage, and analysis to ensure reproducibility and comparability of findings across studies. Nevertheless, intestinal organoids hold immense promise for transforming our understanding of gastrointestinal pathophysiology, enhancing drug development pipelines, and advancing personalized medicine. By bridging the gap between preclinical research and clinical applications, these organoids represent a paradigm shift in the exploration of novel therapeutic strategies and the investigation of gut-associated diseases.
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Affiliation(s)
- Dinesh Kumar
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh, Punjab, India.
| | - Sonia Gupta
- Swami Devi Dyal Group of Professional Institute, Panchkula, India
| | - Vrinda Gupta
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh, Punjab, India
| | - Rajni Tanwar
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh, Punjab, India
| | - Anchal Chandel
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh, Punjab, India
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30
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Liu C, Ma R, Li H, Pan X, Qian H, Yang T, Tian Y. Akkermansia muciniphila ameliorates fatty liver through microbiota-derived α-ketoisovaleric acid metabolism and hepatic PI3K/Akt signaling. iScience 2025; 28:112458. [PMID: 40343268 PMCID: PMC12059670 DOI: 10.1016/j.isci.2025.112458] [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: 09/24/2024] [Revised: 12/10/2024] [Accepted: 04/11/2025] [Indexed: 05/11/2025] Open
Abstract
Akkermansia muciniphila (Akk) has been shown to improve obesity via gut microbiota, while its effects on modulating gut fungi remain underexplored. This study investigates the effects of Akk on obese mice, focusing on gut fungi, metabolites, and hepatic lipid metabolism. We found that Akk treatment significantly modulated gut fungal diversity, enhanced gut immune responses, and improved fatty liver. Specifically, the abundance of harmful fungi Fusarium decreased. Subsequently, Akk improved hepatic lipid metabolism via the PI3K/Akt pathway, as determined by proteomics analysis. Additionally, an in vitro colonic organoid and microbiota co-culture system confirmed these effects by validating changes in key fungi and metabolites. Crucially, α-ketoisovaleric acid was identified as a pivotal metabolite, as its supplementation significantly improved hepatic lipid metabolism via PI3K/Akt pathway in obese mice. This study highlights Akk's potential as a therapeutic agent for obesity by modulating gut fungi and identifying α-ketoisovaleric acid as a critical metabolite.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Rongrong Ma
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Han Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xiaohua Pan
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - He Qian
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Tianyi Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- Analysis and Testing Center, Jiangnan University, Wuxi 214122, China
| | - Yaoqi Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- Analysis and Testing Center, Jiangnan University, Wuxi 214122, China
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Xu H, Wang Y, Wang W, Fu YX, Qiu J, Shi Y, Yuan L, Dong C, Hu X, Chen YG, Guo X. ILC3s promote intestinal tuft cell hyperplasia and anthelmintic immunity through RANK signaling. Sci Immunol 2025; 10:eadn1491. [PMID: 40378237 DOI: 10.1126/sciimmunol.adn1491] [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: 11/30/2023] [Revised: 08/01/2024] [Accepted: 04/24/2025] [Indexed: 05/18/2025]
Abstract
Helminth infections, particularly in developing countries, remain a notable health burden worldwide. Group 3 innate lymphoid cells (ILC3s) are enriched in the intestine and play a critical role in immunity against extracellular bacteria and fungi. However, whether ILC3s are involved in intestinal helminth infection is still unclear. Here, we report that helminth infection reprograms ILC3s, which, in turn, promote anthelmintic immunity. ILC3-derived RANKL [receptor activator of NF-κB (nuclear factor κB) ligand] synergizes with interleukin-13 (IL-13) to facilitate intestinal tuft cell expansion after helminth infection, which further activates the tuft cell-group 2 innate lymphoid cell (ILC2) circuit to control helminth infection. Deletion of RANKL in ILC3s or deletion of RANK or its downstream adaptor RelB in intestinal epithelial cells substantially diminishes tuft cell hyperplasia and dampens anthelmintic immunity. Thus, ILC3s play an indispensable role in protecting against helminth infection through the regulation of intestinal tuft cell hyperplasia and type 2 immunity.
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Affiliation(s)
- Hongkai Xu
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Immunological Research of Allergy (LIRA), Tsinghua University, Beijing 100084, China
| | - Yibo Wang
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Immunological Research of Allergy (LIRA), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wenyan Wang
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yang-Xin Fu
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ju Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Shi
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Immunological Research of Allergy (LIRA), Tsinghua University, Beijing 100084, China
| | - Lei Yuan
- Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Chen Dong
- Westlake University, Hangzhou 310030, China
| | - Xiaoyu Hu
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Immunological Research of Allergy (LIRA), Tsinghua University, Beijing 100084, China
| | - Ye-Guang Chen
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaohuan Guo
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Immunological Research of Allergy (LIRA), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Molecular Oncology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
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32
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Dal Secco C, Tonon S, Trevisan C, Martinis E, Valeri V, Codrich M, Tell G, Frossi B, Pucillo CEM. Mast cells-intestinal cancer cells crosstalk is mediated by TNF-alpha and sustained by the IL-33/ST2 axis. Cancer Immunol Immunother 2025; 74:205. [PMID: 40372523 DOI: 10.1007/s00262-025-04054-8] [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: 07/16/2024] [Accepted: 04/11/2025] [Indexed: 05/16/2025]
Abstract
It is common knowledge that mast cells (MCs) exert different roles in the gastrointestinal tract, from the maintenance of homeostasis to the onset and propagation of different gut diseases such as food allergies, infections, inflammation, and cancer. However, the mechanisms through which MCs dialog and influence the intestinal tissue are not completely known. To get insight into the bidirectional crosstalk between MCs and the intestinal microenvironment, both in homeostatic and pathological settings, colon organoids from intestinal epithelium of healthy mice and adenomas from AOM/DSS-treated mice have been exploited and co-cultured with MCs. The influence of MCs on organoid architecture and the effect of healthy and tumoral organoids on the phenotype and responsiveness of MCs have been addressed. We observed that MCs interact with intestinal organoids and contribute to the differentiation of healthy organoids by upregulating the expression of mucin-2, chromogranin A, cadherin-1, and claudin 4. On the contrary, in co-culture with tumoral organoids a decrease in cell proliferation, chromogranin A, and lysozyme expression was observed. Tumoral organoids have been shown to activate MCs via the IL-33/ST2 axis leading to increased release of TNF-α which in turn was responsible for the observed effects on tumoral organoids. Our results indicate that MCs are important mediators of intestinal tissue homeostasis and that a different environment can shape and direct MCs toward the dampening or propagation of the inflammatory response. Ultimately, our MC-organoid co-cultures represent a valid in vitro tool to investigate the role of MCs in the gut.
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Affiliation(s)
- Chiara Dal Secco
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Silvia Tonon
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Caterina Trevisan
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Eleonora Martinis
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Viviana Valeri
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Marta Codrich
- Molecular Biology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Gianluca Tell
- Molecular Biology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Barbara Frossi
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy
| | - Carlo E M Pucillo
- Immunology Section, Department of Medicine, University of Udine, Udine, Italy.
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Shi R, Lu W, Zhao Z, Wang B. Low-density Lipoprotein Regulates Intestinal Stem Cell Homeostasis via PPAR Pathway. J Lipid Res 2025:100826. [PMID: 40379213 DOI: 10.1016/j.jlr.2025.100826] [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: 01/31/2025] [Revised: 04/15/2025] [Accepted: 05/10/2025] [Indexed: 05/19/2025] Open
Abstract
Epidemiological studies have highlighted a strong association between hyperlipidemia and an increased risk of cancer in the gut. Intestinal stem cells (ISCs) have been demonstrated as the cells of origin for tumorigenesis in the gut. However, the impact of hyperlipidemia on ISC homeostasis remains unclear. Here, we show that hyperlipidemia induced by low-density lipoprotein receptor (Ldlr) deficiency enhances ISC proliferation in vivo. Additionally, LDL treatment impairs organoid survival but increases ISC stemness ex vivo, as evidenced by the formation of poorly differentiated spheroid and higher ISC self-renewal capacity. Mechanistically, LDL treatment activates PPAR pathways, and pharmacological inhibition of PPAR and its downstream targets, including CPT1A and PDK4, mitigates the effect of LDL on ISCs. These findings demonstrate that hyperlipidemia modulates ISC homeostasis, providing new insights into the mechanism linking hyperlipidemia with tumorigenesis in the gut.
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Affiliation(s)
- Ruicheng Shi
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wei Lu
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhiming Zhao
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bo Wang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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34
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Patil S, Yu S, Jobby R, Ravichandran V, Sarkar S. A critical review on In Vivo and Ex Vivo models for the investigation of Helicobacter pylori infection. Front Cell Infect Microbiol 2025; 15:1516237. [PMID: 40438238 PMCID: PMC12116454 DOI: 10.3389/fcimb.2025.1516237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 04/21/2025] [Indexed: 06/01/2025] Open
Abstract
Helicobacter pylori is a stomach-dwelling bacterium with a crude global prevalence of nearly 45% in adults and 35% in children and adolescents. Chronic H. pylori infection and the resulting inflammation are major causes of gastritis, peptic ulcer disease and gastric cancer. Since its discovery in 1982, various animal models have been proposed to recreate the specific pathophysiological interactions between H. pylori and the human host. These infection models have been instrumental in dissecting the key drivers of H. pylori colonization, persistence and mediators of host immune responses. However, a comprehensive understanding of the molecular triggers for malignant transformation of the gastric mucosa is still lacking. Vaccine development in this area has stalled, as promising candidates identified through animal studies have failed in advanced human clinical trials. Currently, H. pylori eradication is heavily reliant on different antimicrobial agents. As with other bacterial pathogens, the growing antimicrobial resistance in H. pylori remains a major challenge, making eradication therapy increasingly complex and prolonged, over time. Recent drug approvals have mostly been for newer combinations of conventional antibiotics and proton pump inhibitors. Thus, the development of novel treatments and innovative models are crucial for advancing the drug development pipeline. This review encompasses the development and recent advances in animal and non-animal models of H. pylori gastric infection and its applications in investigating novel therapeutics and vaccine candidates.
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Affiliation(s)
- Shwetlaxmi Patil
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai, India
| | - Songmin Yu
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Renitta Jobby
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai, India
- Amity Centre of Excellence in Astrobiology, Amity University Maharashtra, Mumbai, India
| | - Vinothkannan Ravichandran
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai, India
- Center for Drug Discovery and Development (CD3), Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai, India
| | - Sohinee Sarkar
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia
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35
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Rossen ND, Touhara KK, Castro J, Harrington AM, Caraballo SG, Deng F, Li Y, Brierley SM, Julius D. Population imaging of enterochromaffin cell activity reveals regulation by somatostatin. Proc Natl Acad Sci U S A 2025; 122:e2501525122. [PMID: 40327690 DOI: 10.1073/pnas.2501525122] [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: 01/21/2025] [Accepted: 04/07/2025] [Indexed: 05/08/2025] Open
Abstract
Sensory enteroendocrine cells in the intestinal epithelium detect and relay information about the luminal environment to other cells within and outside the gut. Serotonergic enterochromaffin (EC) cells are a subset of enteroendocrine cells that detect noxious stimuli within the gut lumen, such as chemical irritants and microbial byproducts, and transduce this information to sensory nerve fibers to elicit defensive responses such as nausea and visceral pain. While much has recently been learned about the pharmacological and biophysical characteristics of EC cells, a more broadscale investigation of their properties has been hindered by their relatively low prevalence and sparse anatomical distribution within the gut epithelium. Here, we introduce a method for large-scale parallel analysis of individual EC cell activity within a physiologically relevant epithelial context. Using this approach, we identify somatostatin-28 as a potent inhibitor of both basal and stimulus-evoked serotonin release from EC cells and delineate the signaling pathway that underlies this modulatory response. Our analysis suggests that targeting this inhibitory signaling pathway may offer therapeutic avenues for treating gastrointestinal disorders associated with EC cell function and dysregulated serotonin signaling. Together with the ongoing development of specific biosensors, this platform provides a template for the efficient characterization of other rare sensory cell types and their pharmacological modulators.
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Affiliation(s)
- Nathan D Rossen
- Department of Physiology, University of California, San Francisco, CA 94158
- Tetrad Graduate Program, Graduate Division, University of California, San Francisco, CA 94158
| | - Kouki K Touhara
- Department of Physiology, University of California, San Francisco, CA 94158
| | - Joel Castro
- Visceral Pain Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Andrea M Harrington
- Visceral Pain Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Sonia Garcia Caraballo
- Visceral Pain Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Fei Deng
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, School of Life Sciences, Peking University, Beijing 100871, China
- International Data Group / McGovern Institute for Brain Research at Peking University, Beijing 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, School of Life Sciences, Peking University, Beijing 100871, China
- International Data Group / McGovern Institute for Brain Research at Peking University, Beijing 100871, China
| | - Stuart M Brierley
- Visceral Pain Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - David Julius
- Department of Physiology, University of California, San Francisco, CA 94158
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Sheng X, Jin L, Yao Z, Gu J, Zhu L, Huang A, Peng J, Xu X, Ge X, Zhou W, Sheng J, Xu Z, Bai R. Psychological stress-induced systemic corticosterone directly sabotages intestinal stem cells and exacerbates colitis. Cell Discov 2025; 11:46. [PMID: 40360481 PMCID: PMC12075755 DOI: 10.1038/s41421-025-00796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 03/15/2025] [Indexed: 05/15/2025] Open
Abstract
Psychological stress has profound impacts on the gastrointestinal tract via the brain‒gut axis. However, its effects on intestinal stem cells (ISCs) and the resulting implication for intestinal homeostasis remain poorly understood. Here, we observed a notable reduction in both the quantity and proliferative capacity of ISCs under chronic stress conditions, driven by elevated levels of corticosterone resulting from activation of the hypothalamic‒pituitary‒adrenal (HPA) axis. Mechanistically, corticosterone directly interacts with its receptor, nuclear receptor subfamily 3 group c member 1 (NR3C1), leading to increased expression of FKBP prolyl isomerase 5 (FKBP5) in ISCs. Subsequently, FKBP5 negatively regulates AKT activation by facilitating its dephosphorylation at Ser473, ultimately enhancing nuclear translocation of forkhead box O (FoxO) and inhibiting ISC proliferative activity. Consequently, ISC dysfunction contributes to the stress-driven exacerbation of DSS-induced colitis. Collectively, these findings reveal an intrinsic brain-to-gut regulatory pathway whereby psychological stress impairs ISC activity via corticosterone elevation, providing a mechanistic explanation for stress-enhanced susceptibility to colitis.
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Affiliation(s)
- Xiaole Sheng
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lanfei Jin
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengrong Yao
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiaji Gu
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Longtao Zhu
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Andi Huang
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Junxuan Peng
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin Xu
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaolong Ge
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinghao Sheng
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhengping Xu
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Rongpan Bai
- Department of General Surgery, Sir Run Run Shaw Hospital and Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
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37
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Yang R, Wang S, Li Z, Yin C, Huang W, Huang W. Patient-derived organoid co-culture systems as next-generation models for bladder cancer stem cell research. Cancer Lett 2025; 625:217793. [PMID: 40368172 DOI: 10.1016/j.canlet.2025.217793] [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: 03/30/2024] [Revised: 04/10/2025] [Accepted: 05/11/2025] [Indexed: 05/16/2025]
Abstract
Three-dimensional patient-derived organoids (PDOs) have emerged as a powerful model for investigating the molecular and cellular mechanisms underlying bladder cancer, particularly in the context of cancer stem cells (CSCs) and drug screening. However, a significant limitation of conventional PDOs is the absence of tumor microenvironment (TME), which includes critical stromal, immune and microbial components that influence tumor behavior and treatment response. In this review, we provide a comprehensive overview of the recent advancements in PDO co-culture systems designed to integrate TME elements. Additionally, we emphasize the role of biomedical engineering technologies, such as 3D bioprinting and organoids-on-a-chip, in enhancing the physiological relevance of these models. Furthermore, we explore how bladder PDO co-culture systems are applied in research on bladder CSC characterization, evolution and treatment responses. Finally, we discuss future directions for improving PDO systems to achieve more accurate preclinical modeling and drug discovery.
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Affiliation(s)
- Ruici Yang
- Medical Innovation Technology Transformation Center, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Institute for Advanced Study, Synthetic Biology Research Center, International Cancer Center, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shanzhao Wang
- Medical Innovation Technology Transformation Center, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Institute for Advanced Study, Synthetic Biology Research Center, International Cancer Center, Shenzhen University, Shenzhen 518060, China
| | - Zhichao Li
- Medical Innovation Technology Transformation Center, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Institute for Advanced Study, Synthetic Biology Research Center, International Cancer Center, Shenzhen University, Shenzhen 518060, China
| | - Cong Yin
- Medical Innovation Technology Transformation Center, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Institute for Advanced Study, Synthetic Biology Research Center, International Cancer Center, Shenzhen University, Shenzhen 518060, China
| | - Wei Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Weiren Huang
- Medical Innovation Technology Transformation Center, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Institute for Advanced Study, Synthetic Biology Research Center, International Cancer Center, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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38
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Ren J, Huang S. Intestinal organoids in inflammatory bowel disease: advances, applications, and future directions. Front Cell Dev Biol 2025; 13:1517121. [PMID: 40421006 PMCID: PMC12104276 DOI: 10.3389/fcell.2025.1517121] [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: 10/28/2024] [Accepted: 04/21/2025] [Indexed: 05/28/2025] Open
Abstract
Inflammatory bowel disease (IBD), characterized by chronic gastrointestinal inflammation, is a significant global health challenge. Traditional models often fail to accurately reflect human pathophysiology, leading to suboptimal treatments. This review provides an overview of recent advancements in intestinal organoid technology and its role in IBD research. Organoids, derived from patient-specific or pluripotent stem cells, retain the genetic, epigenetic, and structural characteristics of the native gut, allowing for precise modeling of key aspects of IBD. Innovations in CRISPR editing, organoid-microbe co-cultures, and organ-on-a-chip systems have enhanced the physiological relevance of these models, facilitating drug discovery and personalized therapy screening. However, challenges such as vascularization deficits and the need for standardized protocols remain. This review underscores the need for interdisciplinary efforts to bridge the gap between models and the complex reality of IBD. Future directions include the development of scalable vascularized models and robust regulatory frameworks to accelerate therapeutic translation. Organoids hold promise for unraveling IBD heterogeneity and transforming disease management.
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Affiliation(s)
| | - Silin Huang
- Department of Gastroenterology, South China Hospital, Medical School, Shenzhen University, Shenzhen, China
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Surakhy M, Matheson J, Barnes DJ, Carter EJ, Hughes J, Bühnemann C, Sanegre S, Morreau H, Metz P, Imianowski CJ, Hassan AB. Smad4 and TGFβ1 dependent gene expression signatures in conditional intestinal adenoma, organoids and colorectal cancer. Sci Rep 2025; 15:16330. [PMID: 40348815 PMCID: PMC12065906 DOI: 10.1038/s41598-025-00908-4] [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: 12/09/2024] [Accepted: 05/02/2025] [Indexed: 05/14/2025] Open
Abstract
TGF-β ligands suppress growth yet can paradoxically and potently promote cancer invasion and metastasis depending on downstream pathway mutational context, such as loss of Mothers against decapentaplegic homolog 4 (Smad4). Here, we characterised phenotypes and associated gene expression signatures in conditional murine intestinal adenoma with and without Smad4. Conditional Lgr5-CreERT2 activation in Apcfl/flSmad4fl/fl mice resulted in homozygote floxed alleles (ApcΔ/ΔSmad4Δ/Δ) and adenoma formation. The adenoma phenotype was discordant, with reduced small intestinal adenoma burden yet development of large non-metastatic caecal adenoma with nuclear localisation of phospho-Smad2/3. Derived ApcΔ/ΔSmad4Δ/Δ adenoma organoids resisted TGF-β1 dose dependent growth arrest and cell death (IC50 534 pM) compared to ApcΔ/ΔSmad4+/+ (IC50 24 pM). TGF-β1 (390 pM) altered adenoma bulk mRNA expression most significantly for Id1low and Spp1high in ApcΔ/ΔSmad4Δ/Δ. Single cell RNAseq of caecal adenoma identified expansion of Lgr5low, Pak3high and Id1low progenitor populations in ApcΔ/ΔSmad4Δ/Δ. Of the 76 Smad4 and TGF-β1 dependent genes identified in Apcfl/flSmad4fl/fl adenoma organoids, only 7 human equivalent genes were differentially expressed in SMAD4 mutated colorectal cancer (TCGA cohorts), including ID1low. SMAD4low, ID1low SPP1high and PAK3high all correlated with poorer survival. Murine adenoma identified Smad4 dependent gene expression signatures that require further evaluation as functional biomarker classifiers of SMAD4 mutated cancer subtypes.
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Affiliation(s)
- Mirvat Surakhy
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Julia Matheson
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - David J Barnes
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Emma J Carter
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Jennifer Hughes
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Claudia Bühnemann
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sabina Sanegre
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Paul Metz
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Charlotte J Imianowski
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Andrew Bassim Hassan
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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Aubert O, Dinwoodie OM, Wagner R, Ai X. Epithelial Dysfunction in Congenital Diaphragmatic Hernia: Mechanisms, Models and Emerging Therapies. Cells 2025; 14:687. [PMID: 40422190 PMCID: PMC12109814 DOI: 10.3390/cells14100687] [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: 04/18/2025] [Revised: 05/06/2025] [Accepted: 05/07/2025] [Indexed: 05/28/2025] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a complex disorder whereby improper formation of the diaphragm allows herniation of the internal organs into the thoracic cavity, resulting in pulmonary hypoplasia among other complications. Although epithelial dysfunction is central to CDH pathology, relatively little attention has been paid to the underlying mechanisms orchestrating epithelial malfunction. Proinflammatory signaling downstream of impaired mechanotransduction due to in utero lung compression has been elucidated to drive epithelial cell phenotypes. This has been illustrated by a reduction in nuclear YAP and the upregulation of NF-kB in CDH models. In this review, we draw from recent findings using emerging technologies to examine epithelial cell mechanisms in CDH and discuss the role of compression as a central and, crucially, sufficient driver of CDH phenotypes. In recognition of the limitations of using genetic knockout models to recapitulate such a heterogenic and etiologically complicated disease, we discuss alternative models such as the established nitrofen rat model, air-liquid interface (ALI) cultures, organoids and ex vivo lung explants. Throughout, we acknowledge the importance of involving mechanical compression in the modeling of CDH in order to faithfully recapitulate the disease. Finally, we explore novel therapeutic strategies from stem cell and regenerative therapies to precision medicine and the importance of defining CDH endotypes in order to guide treatments.
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Affiliation(s)
- Ophelia Aubert
- Department of Pediatric Surgery, University Medical Center Mannheim, 68165 Mannheim, Germany
| | - Olivia M. Dinwoodie
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Richard Wagner
- Department of Pediatric Surgery, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Xingbin Ai
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
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Verduijn K, de Rooster H, Meyer E, Steenbrugge J. Canine organoids: state-of-the-art, translation potential for human medicine and plea for standardization. Front Vet Sci 2025; 12:1562004. [PMID: 40417361 PMCID: PMC12098350 DOI: 10.3389/fvets.2025.1562004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 04/14/2025] [Indexed: 05/27/2025] Open
Abstract
Organoids have already shown great promise as research tools in human medicine. However, in veterinary medicine, such applications are limited and largely confined to canine organoids. In the Cross Health context, the potential of canine organoids lies in the translation to human diseases, such as cancer. This review provides a state-of-the-art, highlights the current challenges, and at first compares the reported culture conditions of canine organoids derived from both non-neoplastic and neoplastic tissue (i.e., tumoroids), identifying substantial gaps and discrepancies in used culture methods. We make a plea for the standardization of canine organoid culture characteristics and increased rigor in parameter reporting, which will ultimately enhance the reproducibility and applicability of canine organoids in both veterinary and human medicine, especially in the oncology field.
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Affiliation(s)
- Kim Verduijn
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Cancer Research Institute Ghent (CRIG)-Veterinary Oncology Network (VON), Ghent, Belgium
| | - Hilde de Rooster
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Cancer Research Institute Ghent (CRIG)-Veterinary Oncology Network (VON), Ghent, Belgium
| | - Evelyne Meyer
- Cancer Research Institute Ghent (CRIG)-Veterinary Oncology Network (VON), Ghent, Belgium
- Laboratory of Biochemistry, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jonas Steenbrugge
- Cancer Research Institute Ghent (CRIG)-Veterinary Oncology Network (VON), Ghent, Belgium
- Laboratory of Biochemistry, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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42
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Melnik BC, Weiskirchen R, John SM, Stremmel W, Leitzmann C, Weiskirchen S, Schmitz G. White Adipocyte Stem Cell Expansion Through Infant Formula Feeding: New Insights into Epigenetic Programming Explaining the Early Protein Hypothesis of Obesity. Int J Mol Sci 2025; 26:4493. [PMID: 40429638 PMCID: PMC12110815 DOI: 10.3390/ijms26104493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 05/03/2025] [Accepted: 05/06/2025] [Indexed: 05/29/2025] Open
Abstract
Prolonged breastfeeding (BF), as opposed to artificial infant formula feeding (FF), has been shown to prevent the development of obesity later in life. The aim of our narrative review is to investigate the missing molecular link between postnatal protein overfeeding-often referred to as the "early protein hypothesis"-and the subsequent transcriptional and epigenetic changes that accelerate the expansion of adipocyte stem cells (ASCs) in the adipose vascular niche during postnatal white adipose tissue (WAT) development. To achieve this, we conducted a search on the Web of Science, Google Scholar, and PubMed databases from 2000 to 2025 and reviewed 750 papers. Our findings revealed that the overactivation of mechanistic target of rapamycin complex 1 (mTORC1) and S6 kinase 1 (S6K1), which inhibits wingless (Wnt) signaling due to protein overfeeding, serves as the primary pathway promoting ASC commitment and increasing preadipocyte numbers. Moreover, excessive protein intake, combined with the upregulation of the fat mass and obesity-associated gene (FTO) and a deficiency of breast milk-derived microRNAs from lactation, disrupts the proper regulation of FTO and Wnt pathway components. This disruption enhances ASC expansion in WAT while inhibiting brown adipose tissue development. While BF has been shown to have protective effects against obesity, the postnatal transcriptional and epigenetic changes induced by excessive protein intake from FF may predispose infants to early and excessive ASC commitment in WAT, thereby increasing the risk of obesity later in life.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Swen Malte John
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm), University of Osnabrück, D-49076 Osnabrück, Germany
| | | | - Claus Leitzmann
- Institut für Ernährungswissenschaft, Universität Gießen, D-35392 Gießen, Germany;
| | - Sabine Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Gerd Schmitz
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, D-93053 Regensburg, Germany;
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Plenge M, Schnepel N, Müsken M, Rohde J, Goethe R, Breves G, Mazzuoli-Weber G, Benz P. Development and characterization of a 2D porcine colonic organoid model for studying intestinal physiology and barrier function. PLoS One 2025; 20:e0312989. [PMID: 40333830 PMCID: PMC12057940 DOI: 10.1371/journal.pone.0312989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 04/03/2025] [Indexed: 05/09/2025] Open
Abstract
The porcine colon epithelium plays a crucial role in nutrient absorption, ion transport, and barrier function. However ethical concerns necessitate the development of alternatives to animal models for its study. The objective of this study was to develop and characterize a two-dimensional (2D) in vitro model of porcine colonic organoids that closely mimics native colon tissue, thereby supporting in vitro research in gastrointestinal physiology, pathology, and pharmacology. Porcine colonic crypts were isolated and cultured in three-dimensional (3D) organoid systems, which were subsequently disaggregated to form 2D monolayers on transwell inserts. The integrity of the monolayers was evaluated through the measurement of transepithelial electrical resistance (TEER) and electron microscopy. The functional prerequisites of the model were evaluated through the measurement of the mRNA expression of key ion channels and transporters, using quantitative RT-PCR. Ussing chamber experiments were performed to verify physiological activity. The 2D monolayer displayed robust TEER values and retained structural characteristics, including microvilli and mucus-secreting goblet cells, comparable to those observed in native colon tissue. Gene expression analysis revealed no significant differences between the 2D organoid model and native tissue with regard to critical transporters. Ussing chamber experiments demonstrated physiological responses that were consistent with those observed in native colonic tissue. In conclusion, 2D porcine colonic organoid model can be recommended as an accurate representation of the physiological and functional attributes of the native colon epithelium. This model offers a valuable tool for investigating intestinal barrier properties, ion transport, and the pathophysiology of gastrointestinal diseases, while adhering to the 3R principles.
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Affiliation(s)
- Masina Plenge
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Nadine Schnepel
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Judith Rohde
- Institute of Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ralph Goethe
- Institute of Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gerhard Breves
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gemma Mazzuoli-Weber
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Pascal Benz
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hannover, Germany
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Wang Q, Yuan F, Zuo X, Li M. Breakthroughs and challenges of organoid models for assessing cancer immunotherapy: a cutting-edge tool for advancing personalised treatments. Cell Death Discov 2025; 11:222. [PMID: 40335487 PMCID: PMC12059183 DOI: 10.1038/s41420-025-02505-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 04/16/2025] [Accepted: 04/23/2025] [Indexed: 05/09/2025] Open
Abstract
Organoid models are powerful tools for evaluating cancer immunotherapy that provide a more accurate representation of the tumour microenvironment (TME) and immune responses than traditional models. This review focuses on the latest advancements in organoid technologies, including immune cell co-culture, 3D bioprinting, and microfluidic systems, which enhance the modelling of TME and facilitate the assessment of immune therapies such as immune checkpoint inhibitors (ICIs), CAR-T therapies, and oncolytic viruses. Although these models have great potential in personalised cancer treatment, challenges persist in immune cell diversity, long-term culture stability, and reproducibility. Future developments integrating artificial intelligence (AI), multi-omics, and high-throughput platforms are expected to improve the predictive power of organoid models and accelerate the clinical translation of immunotherapy.
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Affiliation(s)
- Qian Wang
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, 210009, Jiangsu, PR China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, 210009, Jiangsu, PR China
| | - Fangwei Yuan
- Department of Thoracic Surgery, Lian Shui County People's Hospital, Huaian, 223400, Jiangsu, PR China
| | - Xianglin Zuo
- Biobank of Jiangsu Cancer Hospital (Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University), Nanjing, 210000, Jiangsu, PR China.
| | - Ming Li
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, 210009, Jiangsu, PR China.
- The Fourth Clinical College of Nanjing Medical University, Nanjing, 210009, Jiangsu, PR China.
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45
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Dykstra GD, Kawasaki M, Burbick CR, McConnel CS, Ambrosini YM. From in vitro development to accessible luminal interface of neonatal bovine-derived intestinal organoids. BMC Vet Res 2025; 21:319. [PMID: 40325425 PMCID: PMC12054211 DOI: 10.1186/s12917-025-04773-1] [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: 01/29/2025] [Accepted: 04/21/2025] [Indexed: 05/07/2025] Open
Abstract
BACKGROUND Intestinal organoids provide physiologically relevant in vitro models that bridge the gap between conventional cell culture and animal studies. Although these systems have been developed for adult cattle, their use in neonatal calves-who are particularly vulnerable to enteric disease-has not been well established. Neonatal diarrhea remains a major health concern in modern agriculture, yet age-appropriate models for studying its pathogenesis are lacking. Given that host-pathogen interactions vary with developmental stage, there is a need for culture systems that reflect the distinct biology of the neonatal gut. In this study, we developed intestinal organoids and organoid-derived monolayers from 14-day-old dairy calves to enable research on early-life intestinal function and disease. RESULTS Organoids were successfully established from five intestinal sections of 14-day-old dairy calves using customized growth media and characterized by immunofluorescence and gene expression analyses. They remained viable for over 300 days of cryopreservation and were serially passaged at least 15 times. Rectal organoid-derived monolayers were further assessed by electron microscopy and barrier function assays, demonstrating stable transepithelial electrical resistance and controlled paracellular permeability. CONCLUSIONS Optimized methods for adult bovine intestinal organoids and rectal organoid-derived monolayers are applicable to neonatal intestinal epithelial stem cells. Organoids cultured from 14-day-old calves captured key aspects of the multicellularity and functionality of the native epithelium. Future work should focus on adapting monolayer culture methods for additional gut regions, particularly the proximal gastrointestinal tract. Neonatal rectal monolayers represent a promising platform for advancing veterinary research, agricultural innovation, and studies of zoonotic disease.
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Affiliation(s)
- Gerald D Dykstra
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Minae Kawasaki
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Claire R Burbick
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Craig S McConnel
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Yoko M Ambrosini
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America.
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Coppola F, Fratianni F, Bianco V, Wang Z, Pellegrini M, Coppola R, Nazzaro F. New Methodologies as Opportunities in the Study of Bacterial Biofilms, Including Food-Related Applications. Microorganisms 2025; 13:1062. [PMID: 40431235 PMCID: PMC12114119 DOI: 10.3390/microorganisms13051062] [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: 04/04/2025] [Revised: 04/19/2025] [Accepted: 04/30/2025] [Indexed: 05/29/2025] Open
Abstract
Traditional food technologies, while essential, often face limitations in sensitivity, real-time detection, and adaptability to complex biological systems such as microbial biofilms. These constraints have created a growing demand for more advanced, precise, and non-invasive tools to ensure food safety and quality. In response to these challenges, cross-disciplinary technological integration has opened new opportunities for the food industry and public health, leveraging methods originally developed in other scientific fields. Although their industrial-scale implementation is still evolving, their application in research and pilot settings has already significantly improved our ability to detect and control biofilms, thereby strengthening food safety protocols. Advanced analytical techniques, the identification of pathogenic species and their virulence markers, and the screening of "natural" antimicrobial compounds can now be conceptualized as interconnected elements within a virtual framework centered on "food" and "biofilm". In this short review, starting from the basic concepts of biofilm and associated microorganisms, we highlight a selection of emerging analytical approaches-from optical methods, microfluidics, Atomic Force Microscopy (AFM), and biospeckle techniques to molecular strategies like CRISPR, qPCR, and NGS, and the use of organoids. Initially conceived for biomedical and biotechnological applications, these tools have recently demonstrated their value in food science by enhancing our understanding of biofilm behavior and supporting the discovery of novel anti-biofilm strategies.
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Affiliation(s)
- Francesca Coppola
- Institute of Food Science, CNR-ISA, 83100 Avellino, Italy; (F.F.); (R.C.)
- Department of Agricultural Sciences, University of Naples “Federico II”, Piazza Carlo di Borbone 1, 80055 Portici, Italy
| | - Florinda Fratianni
- Institute of Food Science, CNR-ISA, 83100 Avellino, Italy; (F.F.); (R.C.)
| | - Vittorio Bianco
- Institute of Applied Sciences and Intelligent Systems “Eduardo Caianiello”, Via Campi Flegrei, 80078 Pozzuoli, Italy; (V.B.); (Z.W.)
| | - Zhe Wang
- Institute of Applied Sciences and Intelligent Systems “Eduardo Caianiello”, Via Campi Flegrei, 80078 Pozzuoli, Italy; (V.B.); (Z.W.)
- Dipartimento di Ingegneria Chimica, Dei Materiali e della Produzione Industriale, University of Napoli Federico II, Piazzale Vincenzo Tecchio 80, 80125 Napoli, Italy
| | - Michela Pellegrini
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Via Sondrio 2/a, 33100 Udine, Italy
| | - Raffaele Coppola
- Institute of Food Science, CNR-ISA, 83100 Avellino, Italy; (F.F.); (R.C.)
- DiAAA, University of Molise, Via De Sanctis s.n.c., 86100 Campobasso, Italy
| | - Filomena Nazzaro
- Institute of Food Science, CNR-ISA, 83100 Avellino, Italy; (F.F.); (R.C.)
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Lu D, Xia B, Feng T, Qi G, Ma Z. The Role of Cancer Organoids in Ferroptosis, Pyroptosis, and Necroptosis: Functions and Clinical Implications. Biomolecules 2025; 15:659. [PMID: 40427552 PMCID: PMC12108908 DOI: 10.3390/biom15050659] [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: 04/04/2025] [Revised: 04/28/2025] [Accepted: 05/01/2025] [Indexed: 05/29/2025] Open
Abstract
The enduring prevalence of cancer worldwide constitutes a significant public health challenge, thereby emphasizing the imperative for the development of therapeutic models capable of accounting for the heterogeneity inherent in tumors. In this context, cancer organoids have emerged as powerful tools for studying tumor biology, providing valuable insights into the complex interactions within the tumor microenvironment. Concurrently, research is increasingly focused on non-apoptotic forms of regulated cell death (RCD)-including ferroptosis, pyroptosis, and necroptosis-which exert pivotal influences on cancer development and progression. Cancer organoids not only recapitulate the genetic and phenotypic heterogeneity of the original tumors but also enable more precise investigations into the roles of non-apoptotic RCDs within oncology. This review explores the utility of cancer organoids in delineating the molecular mechanisms underlying RCDs and their implications for cancer biology and treatment responses. By synthesizing recent research findings, it highlights the essential role of organoid models in uncovering the intricate details of non-apoptotic RCDs. Furthermore, it emphasizes promising directions for future research that aim to deepen our understanding of these pathways and their therapeutic potential. The integration of organoid models into investigations of ferroptosis, pyroptosis, and necroptosis provides novel insights into oncogenic mechanisms and facilitates the development of targeted therapeutic strategies. By bridging cancer organoids with human pathophysiology, this approach not only provides a transformative framework for dissecting oncogenic pathways but also enables the design of precision therapeutics that selectively target the molecular machinery underlying non-apoptotic RCDs.
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Affiliation(s)
- Dingci Lu
- The First Affiliated Hospital of Yangtze University, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China; (D.L.); (B.X.); (T.F.)
- School of Basic Medicine, Health Science Center, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China
- Department of Clinical Laboratory, The Second Hospital of Jingzhou, Jingzhou 434000, China
| | - Bingqian Xia
- The First Affiliated Hospital of Yangtze University, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China; (D.L.); (B.X.); (T.F.)
- School of Basic Medicine, Health Science Center, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China
| | - Tianquan Feng
- The First Affiliated Hospital of Yangtze University, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China; (D.L.); (B.X.); (T.F.)
- School of Basic Medicine, Health Science Center, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China
| | - Gui Qi
- The First Affiliated Hospital of Yangtze University, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China; (D.L.); (B.X.); (T.F.)
- School of Basic Medicine, Health Science Center, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China
| | - Zhaowu Ma
- The First Affiliated Hospital of Yangtze University, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China; (D.L.); (B.X.); (T.F.)
- School of Basic Medicine, Health Science Center, Yangtze University, Nanhuan Road 1, Jingzhou 434023, China
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Domènech-Moreno E, Lim WW, Montrose MG, Sévigny M, Brandt A, Lemmetyinen TT, Viitala EW, Mäkelä TP, Cook SA, Ollila S. Interleukin-11 expressed in the polyp-enriched fibroblast subset is a potential therapeutic target in Peutz-Jeghers syndrome. J Pathol 2025; 266:66-80. [PMID: 40070038 DOI: 10.1002/path.6408] [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: 07/24/2024] [Revised: 12/12/2024] [Accepted: 01/17/2025] [Indexed: 04/12/2025]
Abstract
Peutz-Jeghers syndrome (PJS) is associated with early-onset gastrointestinal polyposis caused by hereditary inactivating pathogenic variants in the tumor suppressor gene STK11 (LKB1). Due to lack of prophylactic therapies, management of PJS polyps requires frequent surveillance. Interestingly, studies in mouse models have revealed that stromal cells drive the polyp formation, but detailed understanding of the cell types and interactions involved has been lacking. Using single-cell RNA sequencing of PJS mouse model polyps, we here identify a polyp-enriched crypt top fibroblast (pCTF) cluster characterized by a transcriptional signature also enriched in PJS patient polyps. The pCTF signature was also noted in primary fibroblasts in vitro following acute STK11 loss. Targeted deletion of Stk11 in crypt top fibroblasts using Foxl1-Cre led to upregulation of the pCTF signature genes and later to polyposis. pCTFs displayed similarity to inflammation-associated fibroblasts, and polyposis was exacerbated by inflammation. Cell-cell communication analysis identified interleukin 11 (IL-11) as a potential pCTF inducer, and consistent with this, IL-11 was required for fibroblast reprogramming toward pCTFs following STK11 loss. Importantly, a neutralizing IL-11 antibody efficiently reduced polyp formation in a PJS model indicating a key, targetable role for IL-11 in polyp development. Together the results characterize pCTFs as a PJS polyp-enriched fibroblast subset and identify IL-11 as a key mediator of fibroblast reprogramming and a potential therapeutic target in PJS. © 2025 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Eva Domènech-Moreno
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Wei-Wen Lim
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Melissa G Montrose
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Myriam Sévigny
- Translational Cancer Medicine Program, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Anders Brandt
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Toni T Lemmetyinen
- Translational Cancer Medicine Program, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Emma W Viitala
- Translational Cancer Medicine Program, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Tomi P Mäkelä
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Stuart A Cook
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, UK
| | - Saara Ollila
- Translational Cancer Medicine Program, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
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49
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Baruta G, Flannigan KL, Alston L, Thorne A, Zhang H, De Buck J, Colarusso P, Hirota SA. Mycobacterium avium subspecies paratuberculosis targets M cells in enteroid-derived monolayers through interactions with β1 integrins. Am J Physiol Gastrointest Liver Physiol 2025; 328:G482-G501. [PMID: 40112014 DOI: 10.1152/ajpgi.00250.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 10/09/2024] [Accepted: 02/16/2025] [Indexed: 03/22/2025]
Abstract
Paratuberculosis is an infectious disease caused by the bacterium, Mycobacterium avium subspecies paratuberculosis (MAP). MAP infection of ruminants triggers progressive wasting disease characterized by granulomatous lymphadenitis, enteritis, and severe intestinal pathology that often requires early culling of the animal. The resulting economic burden is significant, and MAP exposure in the workplace constitutes a significant zoonotic risk. Although it has been established that the MAP propagates within resident immune cells, less is known about how it traverses the epithelium. It is currently thought that MAP infects the small intestinal epithelium by targeting both enterocytes and M cells, with a potential tropism for the latter. In the current study, we developed and validated an enteroid-based in vitro assay containing functional M cells to identify the target cells for MAP's entry. Upon exposure to MAP, the bacteria were detected within both enterocytes and M cells; however, quantitative image analysis revealed significant tropism for the latter. Complementary studies using the Caco-2/Raji-B coculture system provided similar results. Since other mycobacteria have been shown to initiate cell attachment and entry by using a fibronectin-bridging process, we tested whether these interactions were involved in MAP's targeting of M cells. We found that MAP's M cell tropism was enhanced by fibronectin and that this effect was abolished when monolayers were pretreated with an integrin-blocking peptide. Our data demonstrate that MAP preferentially targets M cells and that this involves a fibronectin-bridging process. Furthermore, our study supports the utility of M cell-containing enteroids to study host-pathogen interaction at the intestinal epithelium.NEW & NOTEWORTHY We developed and validated a novel enteroid-based in vitro infection model with functional M cells and incorporated leading-edge imaging approaches to determine how MAP interacts with the intestinal epithelium. Using this model, we found that MAP preferentially enters M cells and that this process is enhanced by fibronectin opsonization and interactions with M cell-associated b1 integrins-the so-called fibronectin bridging mechanism that is used by other Mycobacterium to mediate cell attachment and entry.
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Affiliation(s)
- Grace Baruta
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Kyle L Flannigan
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Laurie Alston
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Thorne
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Hong Zhang
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Jeroen De Buck
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Pina Colarusso
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Simon A Hirota
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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50
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Metwaly A, Kriaa A, Hassani Z, Carraturo F, Druart C, Arnauts K, Wilmes P, Walter J, Rosshart S, Desai MS, Dore J, Fasano A, Blottiere HM, Maguin E, Haller D. A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research. Nat Rev Gastroenterol Hepatol 2025; 22:343-356. [PMID: 40033063 DOI: 10.1038/s41575-025-01041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/17/2025] [Indexed: 03/05/2025]
Abstract
The gut microbiome comprises trillions of microorganisms and profoundly influences human health by modulating metabolism, immune responses and neuronal functions. Disruption in gut microbiome composition is implicated in various inflammatory conditions, metabolic disorders and neurodegenerative diseases. However, determining the underlying mechanisms and establishing cause and effect is extremely difficult. Preclinical models offer crucial insights into the role of the gut microbiome in diseases and help identify potential therapeutic interventions. The Human Microbiome Action Consortium initiated a Delphi survey to assess the utility of preclinical models, including animal and cell-based models, in elucidating the causal role of the gut microbiome in these diseases. The Delphi survey aimed to address the complexity of selecting appropriate preclinical models to investigate disease causality and to study host-microbiome interactions effectively. We adopted a structured approach encompassing a literature review, expert workshops and the Delphi questionnaire to gather insights from a diverse range of stakeholders. Experts were requested to evaluate the strengths, limitations, and suitability of these models in addressing the causal relationship between the gut microbiome and disease pathogenesis. The resulting consensus statements and recommendations provide valuable insights for selecting preclinical models in future studies of gut microbiome-related diseases.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University Munich, Freising, Germany
- ZIEL Institute for Food & Health, Technical University Munich, Freising, Germany
| | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Federica Carraturo
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | | | - Kaline Arnauts
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Stephan Rosshart
- Department of Microbiome Research, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Department of Medicine II, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Joel Dore
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, France
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
- Department of Paediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center,Massachusetts General Hospital Brigham, Harvard Medical School, Boston, MA, USA
| | - Hervé M Blottiere
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, France
- Nantes Université, INRAE, UMR1280, PhAN, Nantes, France
| | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Dirk Haller
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University Munich, Freising, Germany.
- ZIEL Institute for Food & Health, Technical University Munich, Freising, Germany.
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