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Hernandez-Suarez L, Diez-Martin E, Egiguren-Ortiz J, Fernandez R, Etxebarria A, Astigarraga E, Miguelez C, Ramirez-Garcia A, Barreda-Gómez G. Serological Antibodies against Kidney, Liver, and Spleen Membrane Antigens as Potential Biomarkers in Patients with Immune Disorders. Int J Mol Sci 2024; 25:2025. [PMID: 38396703 PMCID: PMC10888476 DOI: 10.3390/ijms25042025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Immune disorders arise from complex genetic and environmental factors, which lead to dysregulation at the cellular and inflammatory levels and cause tissue damage. Recent research highlights the crucial role of reactive antibodies in autoimmune diseases and graft rejection, but their complex determination poses challenges for clinical use. Therefore, our study aimed to ascertain whether the presence of reactive antibodies against membrane antigens in tissues from both animal models and humans could serve as biomarkers in patients with autoimmune disorders. To address this issue, we examined the binding profile of serological antibodies against a diverse panel of cell membranes from the spleen, liver, and kidney tissues of monkeys, rats, and humans. After developing the cell membrane microarrays, human sera were immunologically assayed. The study was first conducted on sera from two groups, healthy subjects and patients with inflammatory and autoimmune disorders, and then optimized for kidney transplant patient sera. A significant increase in antibody reactivity against specific monkey kidney and spleen membranes was observed in the serum of patients with lupus nephritis, while kidney transplant patients showed a significant enhancement against human tissues and human embryonic kidney 293 cells. These results show the potential importance for clinical and basic research purposes of studying the presence of specific IgG against membrane antigens in patients' serum as potential biomarkers of immune disorders. However, it is important to note that these results need to be verified in further studies with a larger sample size to confirm their relevance.
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Affiliation(s)
- Leidi Hernandez-Suarez
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Eguzkiñe Diez-Martin
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - June Egiguren-Ortiz
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
- Department of Pharmacology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Roberto Fernandez
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
| | - Aitor Etxebarria
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
| | - Egoitz Astigarraga
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
| | - Cristina Miguelez
- Department of Pharmacology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Neurodegenerative Diseases Group, BioBizkaia Health Research Institute, 48940 Barakaldo, Spain
| | - Andoni Ramirez-Garcia
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Gabriel Barreda-Gómez
- Department of Research and Development, IMG Pharma Biotech S.L., 48170 Zamudio, Spain; (L.H.-S.); (E.D.-M.); (J.E.-O.); (R.F.); (A.E.); (E.A.)
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Zhang D, Zhang H, Lu J, Hu X. Multiomics Data Reveal the Important Role of ANXA2R in T Cell-mediated Rejection After Renal Transplantation. Transplantation 2024; 108:430-444. [PMID: 37677931 PMCID: PMC10798590 DOI: 10.1097/tp.0000000000004754] [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: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND T cell-mediated rejection (TCMR) is a severe issue after renal transplantation, but research on its T cell-receptor (TCR) repertoire is lacking. This study intended to elucidate the TCR repertoire landscape in TCMR and hence identify novel potential targets. METHODS A total of 12 multiomics data sets were collected. The TRUST4 algorithm was used to construct and analyze the TCR repertoire in renal allografts with TCMR and stable renal function. Then, novel TCR-related key genes were identified through various criteria and literature research. In bulk transcriptome, cell line, single-cell transcriptome data sets, multiple immune cell infiltration algorithms, and gene set enrichment analysis were used to analyze potential mechanisms of the identified key gene. Twenty-three pathological sections were collected for immunofluorescence staining in the clinical cohort. Finally, the diagnostic and prognostic values of ANXA2R were evaluated in multiple renal transplant data sets. RESULTS Allografts with TCMR showed significantly increased clonotype and specific clonal expansion. ANXA2R was found to be a novel key gene for TCMR and showed strong positive connections with the TCR complex and lymphocyte cells, especially CD8 + T cells. Immunofluorescence staining confirmed the existence of ANXA2R + CD8 + T cells, with their percentage significantly elevated in TCMR compared with stable renal function. Finally, both mRNA and protein levels of ANXA2R showed promising diagnostic and prognostic value for renal transplant recipients. CONCLUSIONS ANXA2R , identified as a novel TCR-related gene, had critical roles in clinicopathology, diagnosis, and prognosis in renal transplantation, which offered promising potential therapeutic targets.
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Affiliation(s)
- Di Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - He Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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Novacescu D, Latcu SC, Bardan R, Daminescu L, Cumpanas AA. Contemporary Biomarkers for Renal Transplantation: A Narrative Overview. J Pers Med 2023; 13:1216. [PMID: 37623466 PMCID: PMC10456039 DOI: 10.3390/jpm13081216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Renal transplantation (RT) is the preferred treatment for end-stage renal disease. However, clinical challenges persist, i.e., early detection of graft dysfunction, timely identification of rejection episodes, personalization of immunosuppressive therapy, and prediction of long-term graft survival. Biomarkers have emerged as valuable tools to address these challenges and revolutionize RT patient care. Our review synthesizes the existing scientific literature to highlight promising biomarkers, their biological characteristics, and their potential roles in enhancing clinical decision-making and patient outcomes. Emerging non-invasive biomarkers seemingly provide valuable insights into the immunopathology of nephron injury and allograft rejection. Moreover, we analyzed biomarkers with intra-nephron specificities, i.e., glomerular vs. tubular (proximal vs. distal), which can localize an injury in different nephron areas. Additionally, this paper provides a comprehensive analysis of the potential clinical applications of biomarkers in the prediction, detection, differential diagnosis and assessment of post-RT non-surgical allograft complications. Lastly, we focus on the pursuit of immune tolerance biomarkers, which aims to reclassify transplant recipients based on immune risk thresholds, guide personalized immunosuppression strategies, and ultimately identify patients for whom immunosuppression may safely be reduced. Further research, validation, standardization, and prospective studies are necessary to fully harness the clinical utility of RT biomarkers and guide the development of targeted therapies.
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Affiliation(s)
- Dorin Novacescu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Silviu Constantin Latcu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Razvan Bardan
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Liviu Daminescu
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
| | - Alin Adrian Cumpanas
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
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McDaniels JM, Shetty AC, Kuscu C, Kuscu C, Bardhi E, Rousselle T, Drachenberg C, Talwar M, Eason JD, Muthukumar T, Maluf DG, Mas VR. Single nuclei transcriptomics delineates complex immune and kidney cell interactions contributing to kidney allograft fibrosis. Kidney Int 2023; 103:1077-1092. [PMID: 36863444 PMCID: PMC10200746 DOI: 10.1016/j.kint.2023.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023]
Abstract
Chronic allograft dysfunction (CAD), characterized histologically by interstitial fibrosis and tubular atrophy, is the major cause of kidney allograft loss. Here, using single nuclei RNA sequencing and transcriptome analysis, we identified the origin, functional heterogeneity, and regulation of fibrosis-forming cells in kidney allografts with CAD. A robust technique was used to isolate individual nuclei from kidney allograft biopsies and successfully profiled 23,980 nuclei from five kidney transplant recipients with CAD and 17,913 nuclei from three patients with normal allograft function. Our analysis revealed two distinct states of fibrosis in CAD; low and high extracellular matrix (ECM) with distinct kidney cell subclusters, immune cell types, and transcriptional profiles. Imaging mass cytometry analysis confirmed increased ECM deposition at the protein level. Proximal tubular cells transitioned to an injured mixed tubular (MT1) phenotype comprised of activated fibroblasts and myofibroblast markers, generated provisional ECM which recruited inflammatory cells, and served as the main driver of fibrosis. MT1 cells in the high ECM state achieved replicative repair evidenced by dedifferentiation and nephrogenic transcriptional signatures. MT1 in the low ECM state showed decreased apoptosis, decreased cycling tubular cells, and severe metabolic dysfunction, limiting the potential for repair. Activated B, T and plasma cells were increased in the high ECM state, while macrophage subtypes were increased in the low ECM state. Intercellular communication between kidney parenchymal cells and donor-derived macrophages, detected several years post-transplantation, played a key role in injury propagation. Thus, our study identified novel molecular targets for interventions aimed to ameliorate or prevent allograft fibrogenesis in kidney transplant recipients.
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Affiliation(s)
- Jennifer M McDaniels
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Elissa Bardhi
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Thomas Rousselle
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cinthia Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Manish Talwar
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - James D Eason
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Daniel G Maluf
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA; Program in Transplantation, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Valeria R Mas
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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Virmani S, Rao A, Menon MC. Allograft tissue under the microscope: only the beginning. Curr Opin Organ Transplant 2023; 28:126-132. [PMID: 36787238 PMCID: PMC10214011 DOI: 10.1097/mot.0000000000001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
PURPOSE OF REVIEW To review novel modalities for interrogating a kidney allograft biopsy to complement the current Banff schema. RECENT FINDINGS Newer approaches of Artificial Intelligence (AI), Machine Learning (ML), digital pathology including Ex Vivo Microscopy, evaluation of the biopsy gene expression using bulk, single cell, and spatial transcriptomics and spatial proteomics are now available for tissue interrogation. SUMMARY Banff Schema of classification of allograft histology has standardized reporting of tissue pathology internationally greatly impacting clinical care and research. Inherent sampling error of biopsies, and lack of automated morphometric analysis with ordinal outputs limit its performance in prognostication of allograft health. Over the last decade, there has been an explosion of newer methods of evaluation of allograft tissue under the microscope. Digital pathology along with the application of AI and ML algorithms could revolutionize histopathological analyses. Novel molecular diagnostics such as spatially resolved single cell transcriptomics are identifying newer mechanisms underlying the pathologic diagnosis to delineate pathways of immunological activation, tissue injury, repair, and regeneration in allograft tissues. While these techniques are the future of tissue analysis, costs and complex logistics currently limit their clinical use.
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Affiliation(s)
- Sarthak Virmani
- Section of Nephrology, Division of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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Halawi A, El Kurdi AB, Vernon KA, Solhjou Z, Choi JY, Saad AJ, Younis NK, Elfekih R, Mohammed MT, Deban CA, Weins A, Abdi R, Riella LV, De Serres SA, Cravedi P, Greka A, Khoueiry P, Azzi JR. Uncovering a novel role of focal adhesion and interferon-gamma in cellular rejection of kidney allografts at single cell resolution. Front Immunol 2023; 14:1139358. [PMID: 37063857 PMCID: PMC10102512 DOI: 10.3389/fimmu.2023.1139358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 04/03/2023] Open
Abstract
BackgroundKidney transplant recipients are currently treated with nonspecific immunosuppressants that cause severe systemic side effects. Current immunosuppressants were developed based on their effect on T-cell activation rather than the underlying mechanisms driving alloimmune responses. Thus, understanding the role of the intragraft microenvironment will help us identify more directed therapies with lower side effects.MethodsTo understand the role of the alloimmune response and the intragraft microenvironment in cellular rejection progression, we conducted a Single nucleus RNA sequencing (snRNA-seq) on one human non-rejecting kidney allograft sample, one borderline sample, and T-cell mediated rejection (TCMR) sample (Banff IIa). We studied the differential gene expression and enriched pathways in different conditions, in addition to ligand-receptor (L-R) interactions.ResultsPathway analysis of T-cells in borderline sample showed enrichment for allograft rejection pathway, suggesting that the borderline sample reflects an early rejection. Hence, this allows for studying the early stages of cellular rejection. Moreover, we showed that focal adhesion (FA), IFNg pathways, and endomucin (EMCN) were significantly upregulated in endothelial cell clusters (ECs) of borderline compared to ECs TCMR. Furthermore, we found that pericytes in TCMR seem to favor endothelial permeability compared to borderline. Similarly, T-cells interaction with ECs in borderline differs from TCMR by involving DAMPS-TLRs interactions.ConclusionOur data revealed novel roles of T-cells, ECs, and pericytes in cellular rejection progression, providing new clues on the pathophysiology of allograft rejection.
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Affiliation(s)
- Ahmad Halawi
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Abdullah B. El Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Zhabiz Solhjou
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Scripps Clinic Medical Group, San Diego, CA, United States
| | - John Y. Choi
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Anis J. Saad
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Nour K. Younis
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Rania Elfekih
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Mostafa Tawfeek Mohammed
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Clinical Pathology Department, Faculty of Medicine, Minia University, Minia, Egypt
| | - Christa A. Deban
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Astrid Weins
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Reza Abdi
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Leonardo V. Riella
- Department of Medicine, Division of Nephrology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Boston, MA, United States
| | - Sasha A. De Serres
- Transplantation Unit, Renal Division, Department of Medicine, University Health Center of Quebec, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Paolo Cravedi
- Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anna Greka
- The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jamil R. Azzi
- Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Jamil R. Azzi,
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Salvadori M. Role of Biomarkers in Detecting Acute Rejection in Kidney Transplantation. TRANSPLANTOLOGY 2023; 4:18-21. [DOI: 10.3390/transplantology4010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025] Open
Abstract
Medicine has evolved from the so-called experience-based medicine to evidence-based medicine, which is now evolving into precision-based medicine [...]
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Affiliation(s)
- Maurizio Salvadori
- Department of Renal Transplantation, Careggi University Hospital, Viale Pieraccini 18, 50139 Florence, Italy
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McDaniels JM, Shetty AC, Rousselle TV, Bardhi E, Maluf DG, Mas VR. The cellular landscape of the normal kidney allograft: Main players balancing the alloimmune response. FRONTIERS IN TRANSPLANTATION 2022; 1:988238. [PMID: 38994377 PMCID: PMC11235379 DOI: 10.3389/frtra.2022.988238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/22/2022] [Indexed: 07/13/2024]
Abstract
Despite recent advances made in short-term outcomes; minimal improvements have been observed in long-term kidney transplantation outcomes. Due to an imbalance between organ transplant availability and patient waiting list, expanding kidney allograft longevity is a critical need in the field. Prior studies have either focused on early ischemic and immunological conditions affecting kidney allografts (e.g., delayed graft function, acute rejection) or late stage chronic injury when interventions are no longer feasible. However, studies characterizing kidney allografts with normal function by its cellular distribution, cell-cell interactions, and associated molecular pathways are lacking. Herein, we used single nuclei RNA-sequencing to uncover the cellular landscape and transcriptome of the normal kidney allograft. We profiled 40,950 nuclei from seven human kidney biopsies (normal native, N = 3; normal allograft, N = 4); normal allograft protocol biopsies were collected ≥15-months post-transplant. A total of 17 distinct cell clusters were identified with proximal tubules (25.70 and 21.01%), distal tubules (15.22 and 18.20%), and endothelial cells (EC) (4.26 and 9.94%) constituting the major cell populations of normal native and normal allograft kidneys, respectively. A large proportion of cycling cells from normal native kidneys were in G1-phase (43.96%) whereas cells from normal allograft were predominantly in S-phase (32.69%). This result suggests that transcriptional differences between normal native and normal allograft biopsies are dependent on the new host environment, immunosuppression, and injury-affliction. In the normal allograft, EC-specific genes upregulated metabolism, the immune response, and cellular growth, emphasizing their role in maintaining homeostasis during the ongoing alloreactive stress response. Immune cells, including B (2.81%), macrophages (24.96%), monocytes (15.29%), natural killer (NK) (12.83%), neutrophils (8.44%), and T cells (14.41%, were increased in normal allografts despite lack of histological or clinical evidence of acute rejection. Phenotypic characterization of immune cell markers supported lymphocyte activation and proinflammatory cytokines signaling pathways (i.e., IL-15, IL-32). The activation of B, NK, and T cells reveals potential immune cells underlying subclinical inflammation and repair. These single nuclei analyses provide novel insights into kidney and immune cell associated signaling pathways that portray kidney grafts with normal allograft function beyond 2-years post-transplant, revealing a novel perspective in understanding long-term allograft graft survival.
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Affiliation(s)
- Jennifer M McDaniels
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Amol C Shetty
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Thomas V Rousselle
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Elissa Bardhi
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Daniel G Maluf
- Program in Transplantation, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Valeria R Mas
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
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Chen Y, Zhang B, Liu T, Chen X, Wang Y, Zhang H. T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation. Front Immunol 2022; 13:895762. [PMID: 35844542 PMCID: PMC9283858 DOI: 10.3389/fimmu.2022.895762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
In kidney transplantation, deteriorated progression of rejection is considered to be a leading course of postoperative mortality. However, the conventional histologic diagnosis is limited in reading the rejection status at the molecular level, thereby triggering mismatched pathogenesis with clinical phenotypes. Here, by applying uniform manifold approximation and projection and Leiden algorithms to 2,611 publicly available microarray datasets of renal transplantation, we uncovered six rejection states with corresponding signature genes and revealed a high-risk (HR) state that was essential in promoting allograft loss. By identifying cell populations from single-cell RNA sequencing data that were associated with the six rejection states, we identified a T-cell population to be the pathogenesis-triggering cells associated with the HR rejection state. Additionally, by constructing gene regulatory networks, we identified that activated STAT4, as a core transcription factor that was regulated by PTPN6 in T cells, was closely linked to poor allograft function and prognosis. Taken together, our study provides a novel strategy to help with the precise diagnosis of kidney allograft rejection progression, which is powerful in investigating the underlying molecular pathogenesis, and therefore, for further clinical intervention.
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Affiliation(s)
- Yihan Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bao Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yaning Wang, ; Hongbo Zhang,
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yaning Wang, ; Hongbo Zhang,
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Van Loon E, Lamarthée B, Barba T, Claes S, Coemans M, de Loor H, Emonds MP, Koshy P, Kuypers D, Proost P, Senev A, Sprangers B, Tinel C, Thaunat O, Van Craenenbroeck AH, Schols D, Naesens M. Circulating Donor-Specific Anti-HLA Antibodies Associate With Immune Activation Independent of Kidney Transplant Histopathological Findings. Front Immunol 2022; 13:818569. [PMID: 35281018 PMCID: PMC8904423 DOI: 10.3389/fimmu.2022.818569] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 12/17/2022] Open
Abstract
Despite the critical role of cytokines in allograft rejection, the relation of peripheral blood cytokine profiles to clinical kidney transplant rejection has not been fully elucidated. We assessed 28 cytokines through multiplex assay in 293 blood samples from kidney transplant recipients at time of graft dysfunction. Unsupervised hierarchical clustering identified a subset of patients with increased pro-inflammatory cytokine levels. This patient subset was hallmarked by a high prevalence (75%) of donor-specific anti-human leukocyte antigen antibodies (HLA-DSA) and histological rejection (70%) and had worse graft survival compared to the group with low cytokine levels (HLA-DSA in 1.7% and rejection in 33.7%). Thirty percent of patients with high pro-inflammatory cytokine levels and HLA-DSA did not have histological rejection. Exploring the cellular origin of these cytokines, we found a corresponding expression in endothelial cells, monocytes, and natural killer cells in single-cell RNASeq data from kidney transplant biopsies. Finally, we confirmed secretion of these cytokines in HLA-DSA-mediated cross talk between endothelial cells, NK cells, and monocytes. In conclusion, blood pro-inflammatory cytokines are increased in kidney transplant patients with HLA-DSA, even in the absence of histology of rejection. These observations challenge the concept that histology is the gold standard for identification of ongoing allo-immune activation after transplantation.
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Affiliation(s)
- Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Thomas Barba
- Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital Lyon, Hospices Civils de Lyon, Lyon, France
| | - Sandra Claes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Maarten Coemans
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Leuven Biostatistics and Statistical Bioinformatics Centre, Department of Public Health and Primary Care, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Henriette de Loor
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Marie-Paule Emonds
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, Mechelen, Belgium
| | - Priyanka Koshy
- Department of Imaging and Pathology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Aleksandar Senev
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, Mechelen, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium.,Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Claire Tinel
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Olivier Thaunat
- Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital Lyon, Hospices Civils de Lyon, Lyon, France
| | - Amaryllis H Van Craenenbroeck
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
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11
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Abstract
The current standard of serum creatinine and biopsy to monitor allograft health has many limitations. The most significant drawback of the current standard is the lack of sensitivity and specificity to allograft injuries, which are diagnosed only after significant damage to the allograft. Thus, it is of critical need to identify a biomarker that is sensitive and specific to the early detection of allograft injuries. Urine, as the direct renal ultrafiltrate that can be obtained noninvasively, directly reflects intrarenal processes in the allograft at greater accuracy than analysis of peripheral blood. We review transcriptomic, metabolomic, genomic, and proteomic discovery-based approaches to identifying urinary biomarkers for the noninvasive detection of allograft injuries, as well as the use of urine cell-free DNA in the QSant urine assay as a sensitive surrogate for the renal allograft biopsy for rejection diagnosis.
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12
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Akalin E, Weir MR, Bunnapradist S, Brennan DC, Delos Santos R, Langone A, Djamali A, Xu H, Jin X, Dholakia S, Woodward RN, Bromberg JS. Clinical Validation of an Immune Quiescence Gene Expression Signature in Kidney Transplantation. KIDNEY360 2021; 2:1998-2009. [PMID: 35419538 PMCID: PMC8986041 DOI: 10.34067/kid.0005062021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023]
Abstract
Background Despite advances in immune suppression, kidney allograft rejection and other injuries remain a significant clinical concern, particularly with regards to long-term allograft survival. Evaluation of immune activity can provide information about rejection status and help guide interventions to extend allograft life. Here, we describe the validation of a blood gene expression classifier developed to differentiate immune quiescence from both T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR). Methods A five-gene classifier (DCAF12, MARCH8, FLT3, IL1R2, and PDCD1) was developed on 56 peripheral blood samples and validated on two sample sets independent of the training cohort. The primary validation set comprised 98 quiescence samples and 18 rejection samples: seven TCMR, ten ABMR, and one mixed rejection. The second validation set included eight quiescence and 11 rejection samples: seven TCMR, two ABMR, and two mixed rejection. AlloSure donor-derived cell-free DNA (dd-cfDNA) was also evaluated. Results AlloMap Kidney classifier scores in the primary validation set differed significantly between quiescence (median, 9.49; IQR, 7.68-11.53) and rejection (median, 13.09; IQR, 11.25-15.28), with P<0.001. In the second validation set, the cohorts were statistically different (P=0.03) and the medians were similar to the primary validation set. The AUC for discriminating rejection from quiescence was 0.786 for the primary validation and 0.800 for the second validation. AlloMap Kidney results were not significantly correlated with AlloSure, although both were elevated in rejection. The ability to discriminate rejection from quiescence was improved when AlloSure and AlloMap Kidney were used together (AUC, 0.894). Conclusion Validation of AlloMap Kidney demonstrated the ability to differentiate between rejection and immune quiescence using a range of scores. The diagnostic performance suggests that assessment of the mechanisms of immunologic activity is complementary to allograft injury information derived from AlloSure dd-cfDNA. Together, these biomarkers offer a more comprehensive assessment of allograft health and immune quiescence.
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Affiliation(s)
- Enver Akalin
- Division of Nephrology, Kidney Transplant Program, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Matthew R. Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Suphamai Bunnapradist
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California
| | - Daniel C. Brennan
- Comprehensive Transplant Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rowena Delos Santos
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Anthony Langone
- Vanderbilt University Medical Center, Medical Specialties Clinic, Veteran Affairs Hospital Renal Transplant Program, Nashville, Tennessee
| | - Arjang Djamali
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Hua Xu
- Research and Development, CareDx, Brisbane, California
| | - Xia Jin
- Research and Development, CareDx, Brisbane, California
| | - Sham Dholakia
- Medical Affairs, CareDx, South San Francisco, California
| | | | - Jonathan S. Bromberg
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
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13
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Bloom RD, Augustine JJ. Beyond the Biopsy: Monitoring Immune Status in Kidney Recipients. Clin J Am Soc Nephrol 2021; 16:1413-1422. [PMID: 34362810 PMCID: PMC8729582 DOI: 10.2215/cjn.14840920] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Improved long-term kidney allograft survival is largely related to better outcomes at 12 months, in association with declining acute rejection rates and more efficacious immunosuppression. Finding the right balance between under- and overimmunosuppression or rejection versus immunosuppression toxicity remains one of transplant's holy grails. In the absence of precise measures of immunosuppression burden, transplant clinicians rely on nonspecific, noninvasive tests and kidney allograft biopsy generally performed for cause. This review appraises recent advances of conventional monitoring strategies and critically examines the plethora of emerging tests utilizing tissue, urine, and blood samples to improve upon the diagnostic precision of allograft surveillance.
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Affiliation(s)
- Roy D Bloom
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joshua J Augustine
- Department of Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio
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14
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Molecular Analysis of Renal Allograft Biopsies: Where Do We Stand and Where Are We Going? Transplantation 2021; 104:2478-2486. [PMID: 32150035 DOI: 10.1097/tp.0000000000003220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A renal core biopsy for histological evaluation is the gold standard for diagnosing renal transplant pathology. However, renal biopsy interpretation is subjective and can render insufficient precision, making it difficult to apply a targeted therapeutic regimen for the individual patient. This warrants a need for additional methods assessing disease state in the renal transplant. Significant research activity has been focused on the role of molecular analysis in the diagnosis of renal allograft rejection. The identification of specific molecular expression patterns in allograft biopsies related to different types of allograft injury could provide valuable information about the processes underlying renal transplant dysfunction and can be used for the development of molecular classifier scores, which could improve our diagnostic and prognostic ability and could guide treatment. Molecular profiling has the potential to be more precise and objective than histological evaluation and may identify injury even before it becomes visible on histology, making it possible to start treatment at the earliest time possible. Combining conventional diagnostics (histology, serology, and clinical data) and molecular evaluation will most likely offer the best diagnostic approach. We believe that the use of state-of-the-art molecular analysis will have a significant impact in diagnostics after renal transplantation. In this review, we elaborate on the molecular phenotype of both acute and chronic T cell-mediated rejection and antibody-mediated rejection and discuss the additive value of molecular profiling in the setting of diagnosing renal allograft rejection and how this will improve transplant patient care.
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15
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Zarinsefat A, Guerra JMA, Sigdel T, Damm I, Sarwal R, Chan-on C, Szabo G, Aguilar-Frasco JL, Ixtlapale-Carmona X, Salinas-Ramos C, Ramirez-Martinez L, Ramirez C, Vilatoba M, Morales Buenrostro LE, Alberu JM, Sarwal MM. Use of the Tissue Common Rejection Module Score in Kidney Transplant as an Objective Measure of Allograft Inflammation. Front Immunol 2021; 11:614343. [PMID: 33613539 PMCID: PMC7886808 DOI: 10.3389/fimmu.2020.614343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/21/2020] [Indexed: 12/03/2022] Open
Abstract
Long-term kidney transplant (KT) allograft outcomes have not improved as expected despite a better understanding of rejection and improved immunosuppression. Previous work had validated a computed rejection score, the tissue common rejection module (tCRM), measured by amplification-based assessment of 11 genes from formalin-fixed paraffin-embedded (FFPE) biopsy specimens, which allows for quantitative, unbiased assessment of immune injury. We applied tCRM in a prospective trial of 124 KT recipients, and contrasted assessment by tCRM and histology reads from 2 independent pathologists on protocol and cause biopsies post-transplant. Four 10-μm shaves from FFPE biopsy specimens were used for RNA extraction and amplification by qPCR of the 11 tCRM genes, from which the tCRM score was calculated. Biopsy diagnoses of either acute rejection (AR) or borderline rejection (BL) were considered to have inflammation present, while stable biopsies had no inflammation. Of the 77 biopsies that were read by both pathologists, a total of 40 mismatches in the diagnosis were present. The median tCRM scores for AR, BL, and stable diagnoses were 4.87, 1.85, and 1.27, respectively, with an overall significant difference among all histologic groups (Kruskal-Wallis, p < 0.0001). There were significant differences in tCRM scores between pathologists both finding inflammation vs. disagreement (p = 0.003), and both finding inflammation vs. both finding no inflammation (p < 0.001), along with overall significance between all scores (Kruskal-Wallis, p < 0.001). A logistic regression model predicting graft inflammation using various clinical predictor variables and tCRM revealed the tCRM score as the only significant predictor of graft inflammation (OR: 1.90, 95% CI: 1.40-2.68, p < 0.0001). Accurate, quantitative, and unbiased assessment of rejection of the clinical sample is critical. Given the discrepant diagnoses between pathologists on the same samples, individuals could utilize the tCRM score as a tiebreaker in unclear situations. We propose that the tCRM quantitative score can provide unbiased quantification of graft inflammation, and its rapid evaluation by PCR on the FFPE shave can become a critical adjunct to help drive clinical decision making and immunosuppression delivery.
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Affiliation(s)
- Arya Zarinsefat
- Department of Surgery, University of California, San Francisco, CA, United States
| | - Jose M. Arreola Guerra
- Department of Internal Medicine, Centenario Hospital Miguel Hidalgo, Aguascalientes, Mexico
| | - Tara Sigdel
- Department of Surgery, University of California, San Francisco, CA, United States
| | - Izabella Damm
- Department of Surgery, University of California, San Francisco, CA, United States
| | - Reuben Sarwal
- Department of Surgery, University of California, San Francisco, CA, United States
| | - Chitranon Chan-on
- Department of Surgery, University of California, San Francisco, CA, United States
| | - Gyula Szabo
- Department of Pathology, University of California, San Francisco, CA, United States
| | | | | | - Carlos Salinas-Ramos
- Instituto Nacional de Ciencias Medicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Claudio Ramirez
- Instituto Nacional de Ciencias Medicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Mario Vilatoba
- Instituto Nacional de Ciencias Medicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Josefina M. Alberu
- Department of Medicine, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Minnie M. Sarwal
- Department of Surgery, University of California, San Francisco, CA, United States
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16
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Seifert S, Gundlach S, Junge O, Szymczak S. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. Bioinformatics 2021; 36:4301-4308. [PMID: 32399562 PMCID: PMC7520048 DOI: 10.1093/bioinformatics/btaa483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput technologies allow comprehensive characterization of individuals on many molecular levels. However, training computational models to predict disease status based on omics data is challenging. A promising solution is the integration of external knowledge about structural and functional relationships into the modeling process. We compared four published random forest-based approaches using two simulation studies and nine experimental datasets. RESULTS The self-sufficient prediction error approach should be applied when large numbers of relevant pathways are expected. The competing methods hunting and learner of functional enrichment should be used when low numbers of relevant pathways are expected or the most strongly associated pathways are of interest. The hybrid approach synthetic features is not recommended because of its high false discovery rate. AVAILABILITY AND IMPLEMENTATION An R package providing functions for data analysis and simulation is available at GitHub (https://github.com/szymczak-lab/PathwayGuidedRF). An accompanying R data package (https://github.com/szymczak-lab/DataPathwayGuidedRF) stores the processed and quality controlled experimental datasets downloaded from Gene Expression Omnibus (GEO). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stephan Seifert
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Sven Gundlach
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
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17
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Abstract
IMPORTANCE Clinical decision and immunosuppression dosing in kidney transplantation rely on transplant biopsy tissue histology even though histology has low specificity, sensitivity, and reproducibility for rejection diagnosis. The inclusion of stable allografts in mechanistic and clinical studies is vital to provide a normal, noninjured comparative group for all interrogative studies on understanding allograft injury. OBJECTIVE To refine the definition of a stable allograft as one that is clinically, histologically, and molecularly quiescent using publicly available transcriptomics data. DESIGN, SETTING, AND PARTICIPANTS In this prognostic study, the National Center for Biotechnology Information Gene Expression Omnibus was used to search for microarray gene expression data from kidney transplant tissues, resulting in 38 studies from January 1, 2017, to December 31, 2018. The diagnostic annotations included 510 acute rejection (AR) samples, 1154 histologically stable (hSTA) samples, and 609 normal samples. Raw fluorescence intensity data were downloaded and preprocessed followed by data set merging and batch correction. MAIN OUTCOMES AND MEASURES The primary measure was area under the receiver operating characteristics curve from a set of feature selected genes and cell types for distinguishing AR from normal kidney tissue. RESULTS Within the 28 data sets, the feature selection procedure identified a set of 6 genes (KLF4, CENPJ, KLF2, PPP1R15A, FOSB, TNFAIP3) (area under the curve [AUC], 0.98) and 5 immune cell types (CD4+ T-cell central memory [Tcm], CD4+ T-cell effector memory [Tem], CD8+ Tem, natural killer [NK] cells, and Type 1 T helper [TH1] cells) (AUC, 0.92) that were combined into 1 composite Instability Score (InstaScore) (AUC, 0.99). The InstaScore was applied to the hSTA samples: 626 of 1154 (54%) were found to be immune quiescent and redefined as histologically and molecularly stable (hSTA/mSTA); 528 of 1154 (46%) were found to have molecular evidence of rejection (hSTA/mAR) and should not have been classified as stable allografts. The validation on an independent cohort of 6 months of protocol biopsy samples in December 2019 showed that hSTA/mAR samples had a significant change in graft function (r = 0.52, P < .001) and graft loss at 5-year follow-up (r = 0.17). A drop by 10 mL/min/1.73m2 in estimated glomerular filtration rate was estimated as a threshold in allograft transitioning from hSTA/mSTA to hSTA/mAR. CONCLUSIONS AND RELEVANCE The results of this prognostic study suggest that the InstaScore could provide an important adjunct for comprehensive and highly quantitative phenotyping of protocol kidney transplant biopsy samples and could be integrated into clinical care for accurate estimation of subsequent patient clinical outcomes.
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Affiliation(s)
- Dmitry Rychkov
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - Swastika Sur
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco
- Department of Pediatrics, University of California, San Francisco
| | - Minnie M. Sarwal
- Division of Multi-Organ Transplantation, Department of Surgery, University of California, San Francisco
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18
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Bhargava R, Maeda K, Tsokos MG, Pavlakis M, Stillman IE, Tsokos GC. N-glycosylated IgG in patients with kidney transplants increases calcium/calmodulin kinase IV in podocytes and causes injury. Am J Transplant 2021; 21:148-160. [PMID: 32531122 PMCID: PMC8188503 DOI: 10.1111/ajt.16140] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/29/2020] [Accepted: 06/06/2020] [Indexed: 01/25/2023]
Abstract
Transplant glomerulopathy (TG) is a major cause of late allograft loss. Increased urine podocin/creatinine ratio in TG signifies accelerated podocyte loss. The mechanisms that lead to podocyte injury in TG remain unclear. We report that IgG from kidney transplant recipients with TG, but not from those without TG, cause a reduction in the expression of nephrin, significant podocyte actin cytoskeleton, and motility changes. These changes are preceded by increased expression of calcium/calmodulin kinase IV (CAMK4). Mechanistically, we found that CAMK4 phosphorylates GSK3β (glycogen synthase kinase 3 beta), activates the Wnt pathway and stabilizes the nephrin transcriptional repressor SNAIL. Silencing neonatal Fc Receptor (FcRn) or CAMK4 prevented the podocyte-damaging effects of IgG from patients with TG. Furthermore, we show that removal of N-linked glycosyl residues from these IgG did not interfere with its entry into the podocytes but eliminated its ability to upregulate CAMK4 and cause podocyte injury. The translational value of these findings is signified by the fact that CAMK4 is increased in podocytes of patients with TG but not in those without TG despite other forms of renal dysfunction. Our results offer novel considerations to limit podocyte injury in patients with kidney transplants, which may lead to eventual glomerular destabilization and transplant glomerulopathy.
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Affiliation(s)
- Rhea Bhargava
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kayaho Maeda
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Maria G. Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Martha Pavlakis
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Isaac E. Stillman
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - George C. Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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19
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Jackson AM, Glass C. Rejection in the setting of non-HLA antibody: New tools for navigating bench to bedside. Am J Transplant 2020; 20:2639-2641. [PMID: 32372531 DOI: 10.1111/ajt.15975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | - Carolyn Glass
- Department of Pathology, Duke University, Durham, North Carolina, USA
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20
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Yi Z, Keung KL, Li L, Hu M, Lu B, Nicholson L, Jimenez-Vera E, Menon MC, Wei C, Alexander S, Murphy B, O’Connell PJ, Zhang W. Key driver genes as potential therapeutic targets in renal allograft rejection. JCI Insight 2020; 5:136220. [PMID: 32634125 PMCID: PMC7455082 DOI: 10.1172/jci.insight.136220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Acute rejection (AR) in renal transplantation is an established risk factor for reduced allograft survival. Molecules with regulatory control among immune pathways of AR that are inadequately suppressed, despite standard-of-care immunosuppression, could serve as important targets for therapeutic manipulation to prevent rejection. Here, an integrative, network-based computational strategy incorporating gene expression and genotype data of human renal allograft biopsy tissue was applied, to identify the master regulators - the key driver genes (KDGs) - within dysregulated AR pathways. A 982-meta-gene signature with differential expression in AR versus non-AR was identified from a meta-analysis of microarray data from 735 human kidney allograft biopsy samples across 7 data sets. Fourteen KDGs were derived from this signature. Interrogation of 2 publicly available databases identified compounds with predicted efficacy against individual KDGs or a key driver-based gene set, respectively, which could be repurposed for AR prevention. Minocycline, a tetracycline antibiotic, was chosen for experimental validation in a murine cardiac allograft model of AR. Minocycline attenuated the inflammatory profile of AR compared with controls and when coadministered with immunosuppression prolonged graft survival. This study demonstrates that a network-based strategy, using expression and genotype data to predict KDGs, assists target prioritization for therapeutics in renal allograft rejection.
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Affiliation(s)
- Zhengzi Yi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karen L. Keung
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Department of Nephrology, Prince of Wales Hospital, Sydney, Australia
| | - Li Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, Connecticut, USA
| | - Min Hu
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Bo Lu
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Leigh Nicholson
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Elvira Jimenez-Vera
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Madhav C. Menon
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen Alexander
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Nephrology Department, The Children’s Hospital at Westmead, Sydney, Australia
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip J. O’Connell
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Department of Nephrology, Westmead Hospital, Sydney, Australia
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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21
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Shaw BI, Cheng DK, Acharya CR, Ettenger RB, Lyerly HK, Cheng Q, Kirk AD, Chambers ET. An age-independent gene signature for monitoring acute rejection in kidney transplantation. Theranostics 2020; 10:6977-6986. [PMID: 32550916 PMCID: PMC7295062 DOI: 10.7150/thno.42110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Acute rejection (AR) remains a significant problem that negatively impacts long-term renal allograft survival. Numerous therapies are used to prevent AR that differ by center and recipient age. This variability confounds diagnostic methods. Methods: To develop an age-independent gene signature for AR effective across a broad array of immunosuppressive regimens, we compiled kidney transplant biopsy (n=1091) and peripheral blood (n=392) gene expression profiles from 12 independent public datasets. After removing genes differentially expressed in pediatric and adult patients, we compared gene expression profiles from biopsy and peripheral blood samples of patients with AR to those who were stable (STA), using Mann-Whitney U Tests with validation in independent testing datasets. We confirmed this signature in pediatric and adult patients (42 AR and 47 STA) from our institutional biorepository. Results: We identified a novel age-independent gene network that identified AR from both kidney and blood samples. We developed a 90-probe set signature targeting 76 genes that differentiated AR from STA and found an 8 gene subset (DIP2C, ENOSF1, FBXO21, KCTD6, PDXDC1, REXO2, HLA-E, and RAB31) that was associated with AR. Conclusion: We used publicly available datasets to create a gene signature of AR that identified AR irrespective of immunosuppression regimen or recipient age. This study highlights a novel model to screen and validate biomarkers across multiple treatment regimens.
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Affiliation(s)
- Brian I Shaw
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Daniel K. Cheng
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | | | - Robert B Ettenger
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, United States
| | - Herbert Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Qing Cheng
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Allan D Kirk
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | - Eileen T Chambers
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
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22
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Abstract
PURPOSE OF REVIEW A key aspect of posttransplant management is to identify and treat graft injury before it becomes irreversible. The gold-standard for detection is histology, but biopsy is uncomfortable for the patient and carries a risk of complications. Detection of changes at a molecular level may preempt histological injury, and thereby identify injury earlier. RECENT FINDINGS Indicators of immune system activation, such as candidate chemokines CXCL9 and CXCL10, and by-products of neutrophil activity, have been related to acute rejection and early allograft function. Transcriptomic studies of multiple-gene panels have identified candidate combinations that have proven very promising in risk-stratification and prediction of acute rejection, as well as diagnosis of both T-cell-mediated and antibody-mediated rejection. Serum and urine cell-free DNA is also a promising area of investigation, particularly in antibody-mediated rejection. SUMMARY Noninvasive, rapid, and accurate tests for risk-prediction and diagnosis in renal transplant allografts are urgently required. The ideal candidate is one that can be measured in either urine or blood, is cheap, and is both sensitive and specific for the condition of interest. Numerous strategies have been proposed, with varying degrees of clinical and preclinical success. A few that meet the essential criteria have been evaluated; a few have made it as far as clinical testing.
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23
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Moreso F, Sellarès J, Soler MJ, Serón D. Transcriptome Analysis in Renal Transplant Biopsies Not Fulfilling Rejection Criteria. Int J Mol Sci 2020; 21:ijms21062245. [PMID: 32213927 PMCID: PMC7139324 DOI: 10.3390/ijms21062245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/11/2020] [Accepted: 03/20/2020] [Indexed: 01/02/2023] Open
Abstract
The clinical significance of renal transplant biopsies displaying borderline changes suspicious for T-cell mediated rejection (TCMR) or interstitial fibrosis and tubular atrophy (IFTA) with interstitial inflammation has not been well defined. Molecular profiling to evaluate renal transplant biopsies using microarrays has been shown to be an objective measurement that adds precision to conventional histology. We review the contribution of transcriptomic analysis in surveillance and indication biopsies with borderline changes and IFTA associated with variable degrees of inflammation. Transcriptome analysis applied to biopsies with borderline changes allows to distinguish patients with rejection from those in whom mild inflammation mainly represents a response to injury. Biopsies with IFTA and inflammation occurring in unscarred tissue display a molecular pattern similar to TCMR while biopsies with IFTA and inflammation in scarred tissue, apart from T-cell activation, also express B cell, immunoglobulin and mast cell-related genes. Additionally, patients at risk for IFTA progression can be identified by genes mainly reflecting fibroblast dysregulation and immune activation. At present, it is not well established whether the expression of rejection gene transcripts in patients with fibrosis and inflammation is the consequence of an alloimmune response, tissue damage or a combination of both.
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24
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Trailin A, Hruba P, Viklicky O. Molecular Assessment of Kidney Allografts: Are We Closer to a Daily Routine? Physiol Res 2020; 69:215-226. [PMID: 32199018 DOI: 10.33549/physiolres.934278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Kidney allograft pathology assessment has been traditionally based on clinical and histological criteria. Despite improvements in Banff histological classification, the diagnostics in particular cases is problematic reflecting a complex pathogenesis of graft injuries. With the advent of molecular techniques, polymerase-chain reaction, oligo- and microarray technologies allowed to study molecular phenotypes of graft injuries, especially acute and chronic rejections. Moreover, development of the molecular microscope diagnostic system (MMDx) to assess kidney graft biopsies, represents the first clinical application of a microarray-based method in transplantation. Whether MMDx may replace conventional pathology is the subject of ongoing research, however this platform is particularly useful in complex histological findings and may help clinicians to guide the therapy.
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Affiliation(s)
- A Trailin
- Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
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25
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Yang JYC, Sarwal RD, Sigdel TK, Damm I, Rosenbaum B, Liberto JM, Chan-On C, Arreola-Guerra JM, Alberu J, Vincenti F, Sarwal MM. A urine score for noninvasive accurate diagnosis and prediction of kidney transplant rejection. Sci Transl Med 2020; 12:eaba2501. [PMID: 32188722 PMCID: PMC8289390 DOI: 10.1126/scitranslmed.aba2501] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022]
Abstract
Accurate and noninvasive monitoring of renal allograft posttransplant is essential for early detection of acute rejection (AR) and to affect the long-term survival of the transplant. We present the development and validation of a noninvasive, spot urine-based diagnostic assay based on measurements of six urinary DNA, protein, and metabolic biomarkers. The performance of this assay for detecting kidney injury in both native kidneys and renal allografts is presented on a cohort of 601 distinct urine samples. The urinary composite score enables diagnosis of AR, with a receiver-operator characteristic curve area under the curve of 0.99 and an accuracy of 96%. In addition, we demonstrate the clinical utility of this assay for predicting AR before a rise in the serum creatinine, enabling earlier detection of rejection than currently possible by standard of care tests. This noninvasive, sensitive, and quantitative approach is a robust and informative method for the rapid and routine monitoring of renal allografts.
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Affiliation(s)
- Joshua Y C Yang
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Reuben D Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tara K Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Izabella Damm
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ben Rosenbaum
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Juliane M Liberto
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chitranon Chan-On
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - José M Arreola-Guerra
- Department of Surgery, University of Mexico, Instituto Nacional de Ciencias Medicas y Nutricion, Ciudad de México, CDMX 14080, Mexico
| | - Josefina Alberu
- Department of Surgery, University of Mexico, Instituto Nacional de Ciencias Medicas y Nutricion, Ciudad de México, CDMX 14080, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L. 64710, Mexico
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
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26
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Song L, Fang F, Liu P, Zeng G, Liu H, Zhao Y, Xie X, Tseng G, Randhawa P, Xiao K. Quantitative Proteomics for Monitoring Renal Transplant Injury. Proteomics Clin Appl 2020; 14:e1900036. [PMID: 31999393 DOI: 10.1002/prca.201900036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 12/25/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE This study is aimed at developing a molecular diagnostics platform to enhance the interpretation of renal allograft biopsies using quantitative proteomic profiling of formalin-fixed and paraffin-embedded (FFPE) specimens. EXPERIMENTAL DESIGN A quantitative proteomics platform composed of 1) an optimized FFPE protein sample preparation method, 2) a tandem mass tag TMT10-plex-based proteomic workflow, and 3) a systematic statistical analysis pipeline to reveal differentially expressed proteins has been developed. This platform is then tested on a small sample set (five samples per phenotype) to reveal proteomic signatures that can differentiate T-cell mediated rejection (TCMR) and polyomavirus BK nephropathy (BKPyVN) from healthy functionally stable kidney tissue (STA). RESULTS Among 2798 quantified proteins, the expression levels of 740 BKPyVN and 638 TCMR associated proteins are significantly changed compared to STA specimens. Principal component analysis demonstrated good segregation of all three phenotypes investigated. Protein detection and quantitation are highly reproducible: replicate comparative analyses demonstrated 71-84% overlap of detected proteins, and the coefficient of variation for protein measurements is <15% in triplicate liquid chromatography-tandem mass spectrometry runs. CONCLUSIONS AND CLINICAL RELEVANCE Quantitative proteomics can be applied to archived FFPE specimens to differentiate different causes of renal allograft injury.
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Affiliation(s)
- Lei Song
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Department of Urological Organ Transplantation, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Fei Fang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Gang Zeng
- Department of Pathology, The Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Xubiao Xie
- Department of Urological Organ Transplantation, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Parmjeet Randhawa
- Department of Pathology, The Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kunhong Xiao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
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27
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Bioinformatics analyses on the immune status of renal transplant patients, a systemic research of renal transplantation. BMC Med Genomics 2020; 13:24. [PMID: 32046717 PMCID: PMC7014750 DOI: 10.1186/s12920-020-0673-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Kidney transplantation is the most effective treatment for end-stage renal disease. Allograft rejections severely affect survivals of allograft kidneys and recipients. METHODS Using bioinformatics approaches, the present study was designed to investigate immune status in renal transplant recipients. Fifteen datasets from Gene Expression Omnibus (GEO) were collected and analysed. Analysis of gene enrichment and protein-protein interactions were also used. RESULTS There were 40 differentially expressed genes (DEGs) identified in chronic rejection group when compared with stable recipients, which were enriched in allograft rejection module. There were 135 DEGs identified in acute rejection patients, compared with stable recipients, in which most genes were enriched in allograft rejection and immune deficiency. There were 288 DEGs identified in stable recipients when compared to healthy subjects. Most genes were related to chemokine signalling pathway. In integrated comparisons, expressions of MHC molecules and immunoglobulins were increased in both acute and chronic rejection; expressions of LILRB and MAP 4 K1 were increased in acute rejection patients, but not in stable recipients. There were no overlapping DEGs in blood samples of transplant recipients. CONCLUSION By performing bioinformatics analysis on the immune status of kidney transplant patients, the present study reports several DEGs in the renal biopsy of transplant recipients, which are requested to be validated in clinical practice.
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28
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Sigdel T, Nguyen M, Liberto J, Dobi D, Junger H, Vincenti F, Laszik Z, Sarwal MM. Assessment of 19 Genes and Validation of CRM Gene Panel for Quantitative Transcriptional Analysis of Molecular Rejection and Inflammation in Archival Kidney Transplant Biopsies. Front Med (Lausanne) 2019; 6:213. [PMID: 31632976 PMCID: PMC6781675 DOI: 10.3389/fmed.2019.00213] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background: There is an urgent need to develop and implement low cost, high-throughput standardized methods for routine molecular assessment of transplant biopsies. Given the vast archive of formalin-fixed and paraffin-embedded (FFPE) tissue blocks in transplant centers, a reliable protocol for utilizing this tissue bank for clinical validation of target molecules as predictors of graft outcome over time, would be of great value. Methods: We designed and optimized assays to quantify 19 target genes, including previously reported set of tissue common rejection module (tCRM) genes. We interrogated their performance for their clinical utility for detection of graft rejection and inflammation by analyzing gene expression microarrays analysis of 163 renal allograft biopsies, and subsequently validated in 40 independent FFPE archived kidney transplant biopsies at a single center. Results: A QPCR (Fluidigm) and a barcoded oligo-based (NanoString) gene expression platform were compared for evaluation of amplification of gene expression signal for 19 genes from degraded RNA extracted from FFPE biopsy sections by a set protocol. Increased expression of the selected 19 genes, that reflect a combination of specific cellular infiltrates (8/19 genes) and a graft inflammation score (11/19 genes which computes the tCRM score allowed for segregation of kidney transplant biopsies with stable allograft function and normal histology from those with histologically confirmed acute rejection (AR; p = 0.0022, QPCR; p = 0.0036, barcoded assay) and many cases of histological borderline inflammation (BL). Serial biopsy shaves used for gene expression were also processed for in-situ hybridization (ISH) for a subset of genes. ISH confirmed a high degree of correlation of signal amplification and tissue localization. Conclusions: Target gene expression amplification across a custom set of genes can identify AR independent of histology, and quantify inflammation from archival kidney transplant biopsy tissue, providing a new tool for clinical correlation and outcome analysis of kidney allografts, without the need for prospective kidney biopsy biobanking efforts.
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Affiliation(s)
- Tara Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Mark Nguyen
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Dejan Dobi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Henrik Junger
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Zoltan Laszik
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
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29
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Xu J, Hu J, Xu H, Zhou H, Liu Z, Zhou Y, Liu R, Zhang W. Long Non-coding RNA Expression Profiling in Biopsy to Identify Renal Allograft at Risk of Chronic Damage and Future Graft Loss. Appl Biochem Biotechnol 2019; 190:660-673. [PMID: 31422559 DOI: 10.1007/s12010-019-03082-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/05/2019] [Indexed: 02/05/2023]
Abstract
The loss of allograft from chronic damage is still the major risk that renal transplant recipients face today. Biomarkers for early detection of chronic damage are needed to improve the long-term graft survival. This study aimed to identify long non-coding RNA (lncRNA) biomarkers associated with chronic damage and graft loss after renal transplantation. Gene Expression Omnibus (GEO) datasets including GSE57387 (n = 101), GSE21374 (n = 282), and GSE25902 (n = 24) from three high-quality studies were analyzed. By repurposing the publicly available array-based data coupled with Affymetrix Human Exon 1.0 ST and Human U133 Plus 2.0 arrays, we obtained expression profiles of 11323 and 3383 lncRNAs in biopsies after renal transplantation, respectively. The logistic regression model and Cox regression model were applied to identify lncRNAs associated with chronic damage and graft survival. High AC093673.5 expression was identified as significantly associated with the three endpoints including chronic damage, progressive chronic histological damage, and graft failure across these three datasets. A six-lncRNA signature was created to predict renal allograft at risk of chronic damage with a high predictive ability (AUC = 0.94). Gene set enrichment analysis (GSEA) indicated that our lncRNA signature was related with allograft rejection and immunity. Our study highlights the importance of lncRNAs in chronic graft damage and allograft loss, supporting their potential role as prognosis biomarkers.
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Affiliation(s)
- Jing Xu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jinglei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Heng Xu
- Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Yong Zhou
- Department of Orthopaedics, The Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan, People's Republic of China.
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
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30
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Comparative transcriptome analysis of peripheral blood mononuclear cells in renal transplant recipients in everolimus- and tacrolimus-based immunosuppressive therapy. Eur J Pharmacol 2019; 859:172494. [PMID: 31238062 DOI: 10.1016/j.ejphar.2019.172494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/19/2022]
Abstract
To better define the biological impact of immunosuppression on peripheral blood mononuclear cells (PBMC), we employed RNASeq analysis to compare the whole transcriptomic profile of a group of renal transplant recipients undergoing maintenance treatment with Everolimus (EVE) with those treated with Tacrolimus (TAC). Then, obtained results were validated by classical biomolecular methodologies. The statistical analysis allowed the identification of four genes discriminating the 2 study groups: Sushi Domain Containing 4 (SUSD4, P = 0.02), T Cell Leukemia/Lymphoma 1A (TCL1A, P = 0.02), adhesion G protein-coupled receptor E3 (ADGRE3, P = 0.01), Immunoglobulin Heavy Constant Gamma 3 (IGHG3, P = 0.03). All of them were significantly down-regulated in patients treated with EVE compared to TAC. The Area under Receiver Operating Characteristic (AUROC) of the final model based on these 4 genes was 73.1% demonstrating its good discriminative power. RT-PCR and ELISA validated transcriptomic results. Additionally, an in vitro model confirmed that EVE significantly down-regulates (P<0.001) TCL1A, SUSD4, ADGRE3 and IgHG3 in PBMCs as well as in T cells and monocytes isolated from healthy subjects. Taken together, our data, revealed, for the first time, a new four gene-based transcriptomic fingerprint down-regulated by EVE in PBMCs of renal transplant patients that could improve the available knowledge regarding some of the biological/cellular effects of the mTOR-Is (including their antineoplastic and immune-regulatory properties).
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31
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Sensitization to endothelial cell antigens: Unraveling the cause or effect paradox. Hum Immunol 2019; 80:614-620. [PMID: 31054781 DOI: 10.1016/j.humimm.2019.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/02/2019] [Accepted: 04/23/2019] [Indexed: 01/03/2023]
Abstract
Anti-endothelial cell antibodies (AECAs) have been correlated with increased acute and chronic rejection across all organ types and early graft dysfunction in kidney and heart transplantation. Nevertheless, the lack of appropriate tools and clear criteria for defining injurious versus non-injurious AECAs prohibits their routine inclusion in clinical risk assessments and diagnostic algorithms for antibody mediated injury. Clinical characterization of AECAs is complicated due to the wide range of polymorphic and non-polymorphic antigens expressed across different vascular tissues and the diverse array of specificities observed between individuals. This complexity is also reflected in the broad spectrum of reported injury phenotypes. AECAs detected at time of allograft dysfunction may represent biomarkers of past vascular injury or active contributors to a current rejection process. New tools within the fields of proteomics, genomics, bioinformatics, and imaging are currently being validated and hold great promise for unraveling the AECA paradox.
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32
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Watson D, Yang JYC, Sarwal RD, Sigdel TK, Liberto JM, Damm I, Louie V, Sigdel S, Livingstone D, Soh K, Chakraborty A, Liang M, Lin PC, Sarwal MM. A Novel Multi-Biomarker Assay for Non-Invasive Quantitative Monitoring of Kidney Injury. J Clin Med 2019; 8:E499. [PMID: 31013714 PMCID: PMC6517941 DOI: 10.3390/jcm8040499] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
The current standard of care measures for kidney function, proteinuria, and serum creatinine (SCr) are poor predictors of early-stage kidney disease. Measures that can detect chronic kidney disease in its earlier stages are needed to enable therapeutic intervention and reduce adverse outcomes of chronic kidney disease. We have developed the Kidney Injury Test (KIT) and a novel KIT Score based on the composite measurement and validation of multiple biomarkers across a unique set of 397 urine samples. The test is performed on urine samples that require no processing at the site of collection and without target sequencing or amplification. We sought to verify that the pre-defined KIT test, KIT Score, and clinical thresholds correlate with established chronic kidney disease (CKD) and may provide predictive information on early kidney injury status above and beyond proteinuria and renal function measurements alone. Statistical analyses across six DNA, protein, and metabolite markers were performed on a subset of residual spot urine samples with CKD that met assay performance quality controls from patients attending the clinical labs at the University of California, San Francisco (UCSF) as part of an ongoing IRB-approved prospective study. Inclusion criteria included selection of patients with confirmed CKD and normal healthy controls; exclusion criteria included incomplete or missing information for sample classification, logistical delays in transport/processing of urine samples or low sample volume, and acute kidney injury. Multivariate logistic regression of kidney injury status and likelihood ratio statistics were used to assess the contribution of the KIT Score for prediction of kidney injury status and stage of CKD as well as assess the potential contribution of the KIT Score for detection of early-stage CKD above and beyond traditional measures of renal function. Urine samples were processed by a proprietary immunoprobe for measuring cell-free DNA (cfDNA), methylated cfDNA, clusterin, CXCL10, total protein, and creatinine. The KIT Score and stratified KIT Score Risk Group (high versus low) had a sensitivity and specificity for detection of kidney injury status (healthy or CKD) of 97.3% (95% CI: 94.6-99.3%) and 94.1% (95% CI: 82.3-100%). In addition, in patients with normal renal function (estimated glomerular filtration rate (eGFR) ≥ 90), the KIT Score clearly identifies those with predisposing risk factors for CKD, which could not be detected by eGFR or proteinuria (p < 0.001). The KIT Score uncovers a burden of kidney injury that may yet be incompletely recognized, opening the door for earlier detection, intervention and preservation of renal function.
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Affiliation(s)
- Drew Watson
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
| | - Joshua Y C Yang
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Reuben D Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Juliane M Liberto
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Izabella Damm
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Victoria Louie
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Shristi Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Devon Livingstone
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Katherine Soh
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Arjun Chakraborty
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Michael Liang
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Pei-Chen Lin
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Minnie M Sarwal
- KIT Bio, 665 3rd Street, San Francisco, CA 94107, USA.
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- Masters in Translational Medicine Program, University of California Berkeley, Berkeley, CA 94720, USA.
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Sigdel TK, Yang JYC, Bestard O, Schroeder A, Hsieh SC, Liberto JM, Damm I, Geraedts ACM, Sarwal MM. A urinary Common Rejection Module (uCRM) score for non-invasive kidney transplant monitoring. PLoS One 2019; 14:e0220052. [PMID: 31365568 PMCID: PMC6668802 DOI: 10.1371/journal.pone.0220052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
A Common Rejection Module (CRM) consisting of 11 genes expressed in allograft biopsies was previously reported to serve as a biomarker for acute rejection (AR), correlate with the extent of graft injury, and predict future allograft damage. We investigated the use of this gene panel on the urine cell pellet of kidney transplant patients. Urinary cell sediments collected from patients with biopsy-confirmed acute rejection, borderline AR (bAR), BK virus nephropathy (BKVN), and stable kidney grafts with normal protocol biopsies (STA) were analyzed for expression of these 11 genes using quantitative polymerase chain reaction (qPCR). We assessed these 11 CRM genes for their abundance, autocorrelation, and individual expression levels. Expression of 10/11 genes were elevated in AR when compared to STA. Psmb9 and Cxcl10could classify AR versus STA as accurately as the 11-gene model (sensitivity = 93.6%, specificity = 97.6%). A uCRM score, based on the geometric mean of the expression levels, could distinguish AR from STA with high accuracy (AUC = 0.9886) and correlated specifically with histologic measures of tubulitis and interstitial inflammation rather than tubular atrophy, glomerulosclerosis, intimal proliferation, tubular vacuolization or acute glomerulitis. This urine gene expression-based score may enable the non-invasive and quantitative monitoring of AR.
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Affiliation(s)
- Tara K. Sigdel
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Joshua Y. C. Yang
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Oriol Bestard
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Kidney Transplant Unit, Bellvitge University Hospital, UB, Barcelona, Spain
| | - Andrew Schroeder
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Szu-Chuan Hsieh
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Juliane M. Liberto
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Izabella Damm
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Anna C. M. Geraedts
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Minnie M. Sarwal
- Division of Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Wee YM, Lee HW, Choi MY, Jung HR, Choi JY, Kwon HW, Jung JH, Kim YH, Han DJ, Shin S. A composite of urinary biomarkers for differentiating between tubulointerstitial inflammation and interstitial fibrosis/tubular atrophy in kidney allografts. Ann Hepatobiliary Pancreat Surg 2018; 22:310-320. [PMID: 30588521 PMCID: PMC6295379 DOI: 10.14701/ahbps.2018.22.4.310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/20/2018] [Accepted: 10/20/2018] [Indexed: 01/28/2023] Open
Abstract
Backgrounds/Aims Compared with a single urinary biomarker, a composite of multiple urinary biomarkers may be more helpful for differentiating tubulointerstitial inflammation from interstitial fibrosis/tubular atrophy (IFTA) in kidney allografts. Methods In this cross-sectional cohort study, we collected urine samples from 115 patients with for-cause biopsy, 53 patients with stable allografts, and 50 living kidney donors. We measured the urinary levels of transglutaminase 2 (TG2), syndecan-4 (SDC4), alpha 1 microglobulin (A1M), interferon-inducible protein 10 (IP-10), interleukin 6 (IL-6), and monocyte chemoattractant protein-1 (MCP-1). Results The for-cause biopsy group showed significantly higher levels of logeTG2/Cr, logeA1M/Cr, logeIL-6/Cr, and logeMCP-1/Cr compared with other groups. In the for-cause biopsy group, logeTG2/Cr level was positively correlated with the severity of IFTA. After adjusting for age, sex, body mass index, diabetes, hypertension, cardiovascular disease, and the interval between kidney transplant and biopsy, TG2 and the interval between transplant and biopsy were significantly correlated variables for the severity of IFTA. Regarding tubulointerstitial inflammation, Body mass index, TG2, SDC4, and IP-10 were positively-correlated variables, and MCP-1 and the interval between transplant and biopsy were negatively-correlated variables. Conclusions Our results show that post-transplant urinary levels of TG2, SDC4, MCP-1 and IP-10 may be a useful biomarker for tubulointerstitial inflammation and IFTA.
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Affiliation(s)
- Yu-Mee Wee
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hae-Won Lee
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Monica Young Choi
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hey Rim Jung
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji Yoon Choi
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyun Wook Kwon
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Joo Hee Jung
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young Hoon Kim
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Duck Jong Han
- Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung Shin
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Division of Kidney and Pancreas Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Meng H, Liang Y, Hao J, Lu J. Comparison of Rejection-Specific Genes in Peripheral Blood and Allograft Biopsy From Kidney Transplant. Transplant Proc 2018; 50:115-123. [PMID: 29407293 DOI: 10.1016/j.transproceed.2017.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Although improved understanding and assessment of organ rejection significantly contribute to long-term allograft survival after kidney transplantation, reliable and predictive biomarkers that enable diagnoses of rejection state are lacking. Patient rejection of a kidney graft displays a specific blood and biopsy transcriptional pattern, raising the question of whether transcript biomarkers in blood could reflect events within the allograft. METHODS Differential expression genes were screened on large-scale transcriptomic data from blood and allograft biopsies, which included recipients undergoing rejection and recipients with stable renal function. RESULTS We found that the number of rejection-related genes in biopsy samples was much greater than in blood. We observed only one overlapping gene, HIST1H4A, consistently expressed in biopsy samples and blood. Functional association of the identified genes in biopsies implicated a strong involvement of inflammatory-immune pathways. Rejection-related genes in the mammalian target of rapamycin-signaling pathway were down-regulated, and genes related to allograft rejection and graft-versus-host disease were up-regulated in allograft biopsy samples. We also recognized the core signaling elements (PIK3R2 and EGFR) in inflammatory-immune pathways based on biopsy samples. CONCLUSIONS We have expanded our understanding of rejection-specific gene expression pattern in allograft biopsy and peripheral blood, and provided a candidate set of overlapping genes for screening of rejection in kidney transplant recipients.
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Affiliation(s)
- H Meng
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Y Liang
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - J Hao
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - J Lu
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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Abstract
Detecting acute rejection in kidney transplantation has been traditionally done using histological analysis of invasive allograft biopsies, but this method carries a risk and is not perfect. Transplant professionals have been working to develop more accurate or less invasive biomarkers that can predict acute rejection or subsequent worse allograft survival. These biomarkers can use tissue, blood or urine as a source. They can comprise individual molecules or panels, singly or in combination, across different components or pathways of the immune system. This review highlights the most recent evidence for biomarker efficacy, especially from multicenter trials.
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Affiliation(s)
- Vikas R Dharnidharka
- Division of Pediatric Nephrology, Hypertension and Pheresis, Washington University in St Louis & St. Louis Children's Hospital, St Louis, MO, USA.
| | - Andrew Malone
- Division of Nephrology, Washington University School of Medicine, St Louis, MO, USA
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Nankivell BJ, Shingde M, Keung KL, Fung CLS, Borrows RJ, O'Connell PJ, Chapman JR. The causes, significance and consequences of inflammatory fibrosis in kidney transplantation: The Banff i-IFTA lesion. Am J Transplant 2018; 18:364-376. [PMID: 29194971 DOI: 10.1111/ajt.14609] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/25/2017] [Accepted: 10/28/2017] [Indexed: 01/25/2023]
Abstract
Inflammation within areas of interstitial fibrosis and tubular atrophy (i-IFTA) is associated with adverse outcomes in kidney transplantation. We evaluated i-IFTA in 429 indication- and 2052 protocol-driven biopsy samples from a longitudinal cohort of 362 kidney-pancreas recipients to determine its prevalence, time course, and relationships with T cell-mediated rejection (TCMR), immunosuppression, and outcome. Sequential histology demonstrated that i-IFTA was preceded by cellular interstitial inflammation and followed by IF/TA. The prevalence and intensity of i-IFTA increased with developing chronic fibrosis and correlated with inflammation, tubulitis, and immunosuppression era (P < .001). Tacrolimus era-based immunosuppression was associated with reduced histologic inflammation in unscarred and scarred i-IFTA compartments, ameliorated progression of IF, and increased conversion to inactive IF/TA (compared with cyclosporine era, P < .001). Prior acute (including borderline) TCMR and subclinical TCMR were followed by greater 1-year i-IFTA, remaining predictive by multivariate analysis and independent of humoral markers. One-year i-IFTA was associated with accelerated IF/TA, arterial fibrointimal hyperplasia, and chronic glomerulopathy and with reduced renal function (P < .001 versus no i-IFTA). In summary, i-IFTA is the histologic consequence of active T cell-mediated alloimmunity, representing the interface between inflammation and tubular injury with fibrotic healing. Uncontrolled i-IFTA is associated with adverse structural and functional outcomes.
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Affiliation(s)
| | - Meena Shingde
- Tissue Pathology and Diagnostic Oncology, Westmead Hospital, Sydney, Australia
| | - Karen L Keung
- Department of Renal Medicine, Westmead Hospital, Sydney, Australia
| | - Caroline L-S Fung
- Tissue Pathology and Diagnostic Oncology, Westmead Hospital, Sydney, Australia
| | | | | | - Jeremy R Chapman
- Department of Renal Medicine, Westmead Hospital, Sydney, Australia
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Azad TD, Donato M, Heylen L, Liu AB, Shen-Orr SS, Sweeney TE, Maltzman JS, Naesens M, Khatri P. Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival. JCI Insight 2018; 3:95659. [PMID: 29367465 PMCID: PMC5821209 DOI: 10.1172/jci.insight.95659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022] Open
Abstract
Late allograft failure is characterized by cumulative subclinical insults manifesting over many years. Although immunomodulatory therapies targeting host T cells have improved short-term survival rates, rates of chronic allograft loss remain high. We hypothesized that other immune cell types may drive subclinical injury, ultimately leading to graft failure. We collected whole-genome transcriptome profiles from 15 independent cohorts composed of 1,697 biopsy samples to assess the association of an inflammatory macrophage polarization-specific gene signature with subclinical injury. We applied penalized regression to a subset of the data sets and identified a 3-gene inflammatory macrophage-derived signature. We validated discriminatory power of the 3-gene signature in 3 independent renal transplant data sets with mean AUC of 0.91. In a longitudinal cohort, the 3-gene signature strongly correlated with extent of injury and accurately predicted progression of subclinical injury 18 months before clinical manifestation. The 3-gene signature also stratified patients at high risk of graft failure as soon as 15 days after biopsy. We found that the 3-gene signature also distinguished acute rejection (AR) accurately in 3 heart transplant data sets but not in lung transplant. Overall, we identified a parsimonious signature capable of diagnosing AR, recognizing subclinical injury, and risk-stratifying renal transplant patients. Our results strongly suggest that inflammatory macrophages may be a viable therapeutic target to improve long-term outcomes for organ transplantation patients.
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Affiliation(s)
- Tej D. Azad
- Stanford Institute for Immunity, Transplantation and Infection and
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Michele Donato
- Stanford Institute for Immunity, Transplantation and Infection and
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Line Heylen
- Department of Microbiology and Immunology, KU Leuven – University of Leuven, Leuven, Belgium
| | - Andrew B. Liu
- Stanford Institute for Immunity, Transplantation and Infection and
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Shai S. Shen-Orr
- Department of Immunology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Timothy E. Sweeney
- Stanford Institute for Immunity, Transplantation and Infection and
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Jonathan Scott Maltzman
- Division of Nephrology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Maarten Naesens
- Department of Microbiology and Immunology, KU Leuven – University of Leuven, Leuven, Belgium
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection and
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
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Foretelling Graft Outcome by Molecular Evaluation of Renal Allograft Biopsies: The GoCAR Study. Transplantation 2018; 101:5-7. [PMID: 28005695 DOI: 10.1097/tp.0000000000001512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Wang Z, Yang H, Guo M, Han Z, Tao J, Chen H, Ge Y, Wang K, Tan R, Wei JF, Gu M. Impact of complement component 3/4/5 single nucleotide polymorphisms on renal transplant recipients with antibody-mediated rejection. Oncotarget 2017; 8:94539-94553. [PMID: 29212248 PMCID: PMC5706894 DOI: 10.18632/oncotarget.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/24/2017] [Indexed: 01/29/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is an important risk of allograft dysfunction in kidney transplantation. The complement system is considered to be associated with the generation of alloreative antibodies and donor-specific antibodies. However, the association of complement single nucleotide polymorphisms (SNPs) with ABMR still remained unclear. Blood samples of 199 renal transplant recipients containing 68 with ABMR and 131 with stable graft function were collected, and analyzed by next-generation sequencing with an established gene panel. High quality readout was obtained in 18 C3 SNPs, 9 C4 SNPs and 22 C5 SNPs. Concerning C3 gene polymorphisms, after being adjusted with age, sex and immunosuppressive protocols, rs10411506 and rs2230205 were found to be statistically associated with ABMR in dominant model (rs10411506: OR=2.73, 95% CIs: 1.16, 6.68, P=0.028; rs2230205: OR=2.52, 95% CIs: 1.07, 5.92, P=0.034); rs10411506, rs2230205 and rs2230201 were found different in HET model (rs10411506: OR=3.05, 95% CIs: 1.22, 7.64, P=0.017; rs2230205: OR=2.90, 95% CIs: 1.20, 7.00, P=0.018; rs2230201: OR=2.41, 95% CIs: 1.03, 5.64, P=0.042). The linkage analysis showed relatively high linkage disequilibrium among these SNPs. In addition, no significant correlation was found between C4 SNPs, or C5 SNPs, and the development of ABMR. Our study firstly identified the two SNPs (rs10411506 and rs2230205) in C3 gene were statistically correlated with ABMR in kidney transplantation. These findings may have implications for the diagnosis and prevention of ABMR.
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Affiliation(s)
- Zijie Wang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Haiwei Yang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Miao Guo
- Research Division of Clinical Pharmacology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Zhijian Han
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Jun Tao
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Hao Chen
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Yuqiu Ge
- School of Public Health, Nanjing Medical University, Nanjing 211166, P.R. China
| | - Ke Wang
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Ruoyun Tan
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
| | - Min Gu
- Department of Urology, Nanjing Medical University First Affiliated Hospital, Nanjing 210029, P.R. China
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41
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Van Loon E, Lerut E, Naesens M. The time dependency of renal allograft histology. Transpl Int 2017; 30:1081-1091. [DOI: 10.1111/tri.13042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/05/2017] [Accepted: 08/21/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Elisabet Van Loon
- Laboratory of Nephrology; Department of Microbiology and Immunology; KU Leuven; Leuven Belgium
- Department of Nephrology and Renal Transplantation; University Hospitals Leuven; Leuven Belgium
| | - Evelyne Lerut
- Translational Cell and Tissue Research; Department of Imaging and Pathology; KU Leuven; Leuven Belgium
- Department of Morphology and Molecular Pathology; University Hospitals Leuven; Leuven Belgium
| | - Maarten Naesens
- Laboratory of Nephrology; Department of Microbiology and Immunology; KU Leuven; Leuven Belgium
- Department of Nephrology and Renal Transplantation; University Hospitals Leuven; Leuven Belgium
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Abstract
Precision medicine is an emerging integrative approach for disease prevention, early detection, and treatment which takes into account individual variability in genetic and other molecular measurements, medical history, environmental exposures, and lifestyle. The development and availability of genomic and other molecular profiling technologies provide an unprecedented opportunity to apply precision medicine strategies in transplantation research. Developing integrative computational methods to analyze these diverse types of data provides new opportunities to impact diagnostics and therapeutics. In this article, we discuss ways we can leverage molecular data sets to develop new hypotheses for disease mechanisms, identify new disease biomarkers, and reposition drugs for diseases with unmet needs. We specifically discuss computational methods that can be applied to achieve these goals in the context of organ transplant.
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Salvadori M, Tsalouchos A. Biomarkers in renal transplantation: An updated review. World J Transplant 2017; 7:161-178. [PMID: 28698834 PMCID: PMC5487307 DOI: 10.5500/wjt.v7.i3.161] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 02/05/2023] Open
Abstract
Genomics, proteomics and molecular biology lead to tremendous advances in all fields of medical sciences. Among these the finding of biomarkers as non invasive indicators of biologic processes represents a useful tool in the field of transplantation. In addition to define the principal characteristics of the biomarkers, this review will examine the biomarker usefulness in the different clinical phases following renal transplantation. Biomarkers of ischemia-reperfusion injury and of delayed graft function are extremely important for an early diagnosis of these complications and for optimizing the treatment. Biomarkers predicting or diagnosing acute rejection either cell-mediated or antibody-mediated allow a risk stratification of the recipient, a prompt diagnosis in an early phase when the histology is still unremarkable. The kidney solid organ response test detects renal transplant recipients at high risk for acute rejection with a very high sensitivity and is also able to make diagnosis of subclinical acute rejection. Other biomarkers are able to detect chronic allograft dysfunction in an early phase and to differentiate the true chronic rejection from other forms of chronic allograft nephropathies no immune related. Finally biomarkers recently discovered identify patients tolerant or almost tolerant. This fact allows to safely reduce or withdrawn the immunosuppressive therapy.
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Sigdel TK, Sarwal MM. Assessment of Circulating Protein Signatures for Kidney Transplantation in Pediatric Recipients. Front Med (Lausanne) 2017; 4:80. [PMID: 28670579 PMCID: PMC5472654 DOI: 10.3389/fmed.2017.00080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/31/2017] [Indexed: 11/17/2022] Open
Abstract
Identification and use of non-invasive biomarkers for kidney transplantation monitoring is an unmet need. A total of 121 biobanked sera collected from 111 unique kidney transplant (KT) patients (children and adolescent) and 10 age-matched healthy normal controls were used to profile serum proteins using semi-quantitative proteomics. The proteomics data were analyzed to identify panels of serum proteins that were specific to various transplant injuries, which included acute rejection (AR), BK virus nephropathy (BKVN), and chronic allograft nephropathy (CAN). Gene expression data from matching peripheral blood mononuclear cells were interrogated to investigate the association between soluble serum proteins and altered gene expression of corresponding genes in different injury phenotypes. Analysis of the proteomics data identified from different patient phenotypes, with criteria of false discovery rate <0.05 and at least twofold changes in either direction, resulted in a list of 10 proteins that distinguished KT injury from no injury. Similar analyses to identify proteins specific to chronic injury, acute injury, and AR after kidney transplantation identified 22, 6, and 10 proteins, respectively. Elastic-Net logistic regression method was applied on the 137 serum proteins to classify different transplant injuries. This algorithm has identified panels of 10 serum proteins specific for AR, BKVN, and CAN with classification rates 93, 93, and 95%, respectively. The identified proteins could prove to be potential surrogate biomarkers for routine monitoring of the injury status of pediatric KT patients.
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Affiliation(s)
- Tara K Sigdel
- University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- University of California, San Francisco, San Francisco, CA, United States
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45
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The Use of Genomics and Pathway Analysis in Our Understanding and Prediction of Clinical Renal Transplant Injury. Transplantation 2017; 100:1405-14. [PMID: 26447506 DOI: 10.1097/tp.0000000000000943] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development and application of high-throughput molecular profiling have transformed the study of human diseases. The problem of handling large, complex data sets has been facilitated by advances in complex computational analysis. In this review, the recent literature regarding the application of transcriptional genomic information to renal transplantation, with specific reference to acute rejection, acute kidney injury in allografts, chronic allograft injury, and tolerance is discussed, as is the current published data regarding other "omics" strategies-proteomics, metabolomics, and the microRNA transcriptome. These data have shed new light on our understanding of the pathogenesis of specific disease conditions after renal transplantation, but their utility as a biomarker of disease has been hampered by study design and sample size. This review aims to highlight the opportunities and obstacles that exist with genomics and other related technologies to better understand and predict renal allograft outcome.
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Rohan VS, Chavin KD. Knowing the allograft's destiny. Transl Androl Urol 2017; 6:313-314. [PMID: 28540243 PMCID: PMC5422678 DOI: 10.21037/tau.2017.03.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Vinayak S Rohan
- Division of Transplant Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - Kenneth D Chavin
- Division of Transplant Surgery, Medical University of South Carolina, Charleston, SC, USA
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Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy. Transplantation 2017; 100:2062-70. [PMID: 27140517 DOI: 10.1097/tp.0000000000001214] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Polyomavirus nephropathy (PVAN) is a common cause of kidney allograft dysfunction and loss. To identify PVAN-specific gene expression and underlying molecular mechanisms, we analyzed kidney biopsies with and without PVAN. METHODS The study included 168 posttransplant renal allograft biopsies (T cell-mediated rejection [TCMR] = 26, PVAN = 10, normal functioning graft = 73, and interstitial fibrosis/tubular atrophy = 59) from 168 unique kidney allograft recipients. We performed gene expression assays and bioinformatics analysis to identify a set of PVAN-specific genes. Validity and relevance of a subset of these genes are validated by quantitative polymerase chain reaction and immunohistochemistry. RESULTS Unsupervised hierarchical clustering analysis of all the biopsies revealed high similarity between PVAN and TCMR gene expression. Increased statistical stringency identified 158 and 252 unique PVAN and TCMR injury-specific gene transcripts respectively. Although TCMR-specific genes were overwhelmingly involved in immune response costimulation and TCR signaling, PVAN-specific genes were mainly related to DNA replication process, RNA polymerase assembly, and pathogen recognition receptors. A principal component analysis (PCA) using these genes further confirmed the most optimal separation between the 3 different clinical phenotypes. Validation of 4 PVAN-specific genes (RPS15, complement factor D, lactotransferrin, and nitric oxide synthase interacting protein) by quantitative polymerase chain reaction and confirmation by immunohistochemistry of 2 PVAN-specific proteins with antiviral function (lactotransferrin and IFN-inducible transmembrane 1) was done. CONCLUSIONS In conclusion, even though PVAN and TCMR kidney allografts share great similarities on gene perturbation, PVAN-specific genes were identified with well-known antiviral properties that provide tools for discerning PVAN and AR as well as attractive targets for rational drug design.
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Menon MC, Murphy B, Heeger PS. Moving Biomarkers toward Clinical Implementation in Kidney Transplantation. J Am Soc Nephrol 2017; 28:735-747. [PMID: 28062570 DOI: 10.1681/asn.2016080858] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Long-term kidney transplant outcomes remain suboptimal, delineating an unmet medical need. Although current immunosuppressive therapy in kidney transplant recipients is effective, dosing is conventionally adjusted empirically on the basis of time after transplant or altered in response to detection of kidney dysfunction, histologic evidence of allograft damage, or infection. Such strategies tend to detect allograft rejection after significant injury has already occurred, fail to detect chronic subclinical inflammation that can negatively affect graft survival, and ignore specific risks and immune mechanisms that differentially contribute to allograft damage among transplant recipients. Assays and biomarkers that reliably quantify and/or predict the risk of allograft injury have the potential to overcome these deficits and thereby, aid clinicians in optimizing immunosuppressive regimens. Herein, we review the data on candidate biomarkers that we contend have the highest potential to become clinically useful surrogates in kidney transplant recipients, including functional T cell assays, urinary gene and protein assays, peripheral blood cell gene expression profiles, and allograft gene expression profiles. We identify barriers to clinical biomarker adoption in the transplant field and suggest strategies for moving biomarker-based individualization of transplant care from a research hypothesis to clinical implementation.
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Affiliation(s)
- Madhav C Menon
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Barbara Murphy
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter S Heeger
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
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Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B. Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Sci Rep 2017; 7:39487. [PMID: 28051114 PMCID: PMC5209709 DOI: 10.1038/srep39487] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/21/2016] [Indexed: 12/12/2022] Open
Abstract
Chronic allograft damage, defined by interstitial fibrosis and tubular atrophy (IF/TA), is a leading cause of allograft failure. Few effective therapeutic options are available to prevent the progression of IF/TA. We applied a meta-analysis approach on IF/TA molecular datasets in Gene Expression Omnibus to identify a robust 85-gene signature, which was used for computational drug repurposing analysis. Among the top ranked compounds predicted to be therapeutic for IF/TA were azathioprine, a drug to prevent acute rejection in renal transplantation, and kaempferol and esculetin, two drugs not previously described to have efficacy for IF/TA. We experimentally validated the anti-fibrosis effects of kaempferol and esculetin using renal tubular cells in vitro and in vivo in a mouse Unilateral Ureteric Obstruction (UUO) model. Kaempferol significantly attenuated TGF-β1-mediated profibrotic pathways in vitro and in vivo, while esculetin significantly inhibited Wnt/β-catenin pathway in vitro and in vivo. Histology confirmed significantly abrogated fibrosis by kaempferol and esculetin in vivo. We developed an integrative computational framework to identify kaempferol and esculetin as putatively novel therapies for IF/TA and provided experimental evidence for their therapeutic activities in vitro and in vivo using preclinical models. The findings suggest that both drugs might serve as therapeutic options for IF/TA.
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Affiliation(s)
- Li Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 770 exington Ave., New York, NY 10065, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai
| | - Ilana Greene
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Benjamin Readhead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 770 exington Ave., New York, NY 10065, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai
| | - Madhav C Menon
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Brian A Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 770 exington Ave., New York, NY 10065, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai
| | - Andrew V Uzilov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1255 5th Avenue, New York, NY 10029, USA
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Nimrod Philippe
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Bernd Schroppel
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.,Section of Nephrology, University of Ulm, Albert-Einstein-Allee 23, Ulm, 89081 Germany
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1255 5th Avenue, New York, NY 10029, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 770 exington Ave., New York, NY 10065, USA.,Department of Health Policy and Research, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA.,Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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Liu Y, Kloc M, Li XC. Macrophages as Effectors of Acute and Chronic Allograft Injury. CURRENT TRANSPLANTATION REPORTS 2016; 3:303-312. [PMID: 28546901 PMCID: PMC5440082 DOI: 10.1007/s40472-016-0130-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Organ transplants give a second chance of life to patients with end-stage organ failure. However, the immuno-logical barriers prove to be very challenging to overcome and graft rejection remains a major hurdle to long-term transplant survival. For decades, adaptive immunity has been the focus of studies, primarily based on the belief that T cells are necessary and sufficient for rejection. With better-developed immunosuppressive drugs and protocols that effectively control adaptive cells, innate immune cells have emerged as key effector cells in triggering graft injury and have therefore attracted much recent attention. In this review, we discuss current understanding of macrophages and their role in transplant rejection, their dynamics, distinct phenotypes, locations, and functions. We also discuss novel therapeutic approaches under development to target macrophages in transplant recipients.
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Affiliation(s)
- Yianzhu Liu
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Texas Medical Center, 6670 Bertner Avenue, Houston, TX 77030, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Malgorzata Kloc
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Texas Medical Center, 6670 Bertner Avenue, Houston, TX 77030, USA
| | - Xian C. Li
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Texas Medical Center, 6670 Bertner Avenue, Houston, TX 77030, USA
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