Immune landscape in rejection of renal transplantation revealed by high-throughput single-cell RNA sequencing

Background: The role of the cellular level in kidney transplant rejection is unclear, and single-cell RNA sequencing (scRNA-seq) can reveal the single-cell landscape behind rejection of human kidney allografts at the single-cell level. Methods: High-quality transcriptomes were generated from scRNA-seq data from five human kidney transplantation biopsy cores. Cluster analysis was performed on the scRNA-seq data by known cell marker genes in order to identify different cell types. In addition, pathways, pseudotime developmental trajectories and transcriptional regulatory networks involved in different cell subpopulations were explored. Next, we systematically analyzed the scoring of gene sets regarding single-cell expression profiles based on biological processes associated with oxidative stress. Results: We obtained 81,139 single cells by scRNA-seq from kidney transplant tissue biopsies of three antibody-mediated rejection (ABMR) patients and two acute kidney injury (AKI) patients with non-rejection causes and identified 11 cell types, including immune cells, renal cells and several stromal cells. Immune cells such as macrophages showed inflammatory activation and antigen presentation and complement signaling, especially in rejection where some subpopulations of cells specifically expressed in rejection showed specific pro-inflammatory responses. In addition, patients with rejection are characterized by an increased number of fibroblasts, and further analysis of subpopulations of fibroblasts revealed their involvement in inflammatory and fibrosis-related pathways leading to increased renal rejection and fibrosis. Notably, the gene set score for response to oxidative stress was higher in patients with rejection. Conclusion: Insight into histological differences in kidney transplant patients with or without rejection was gained by assessing differences in cellular levels at single-cell resolution. In conclusion, we applied scRNA-seq to rejection after renal transplantation to deconstruct its heterogeneity and identify new targets for personalized therapeutic approaches.

[1]  J. Westra,et al.  Changes in T and B cell subsets in end stage renal disease patients before and after kidney transplantation , 2021, Immunity & ageing : I & A.

[2]  A. Keshtkar,et al.  Transitional immature regulatory B cells and regulatory cytokines can discriminate chronic antibody-mediated rejection from stable graft function. , 2020, International immunopharmacology.

[3]  Yvan Saeys,et al.  A scalable SCENIC workflow for single-cell gene regulatory network analysis , 2020, Nature Protocols.

[4]  R. Fulton,et al.  Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant , 2020, bioRxiv.

[5]  J. Cooper.  Evaluation and Treatment of Acute Rejection in Kidney Allografts. , 2020, Clinical journal of the American Society of Nephrology : CJASN.

[6]  Hongfu Zhang,et al.  Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis , 2020, Theranostics.

[7]  Z. Mo,et al.  Single-cell RNA sequencing of human kidney , 2020, Scientific Data.

[8]  Kathy O. Lui,et al.  Regulatory T-cells regulate neonatal heart regeneration by potentiating cardiomyocyte proliferation in a paracrine manner , 2019, Theranostics.

[9]  Y. Caliskan,et al.  Urinary CXCL9 and CXCL10 Levels and Acute Renal Graft Rejection. , 2019, International journal of organ transplantation medicine.

[10]  A. McMahon,et al.  A late B lymphocyte action in dysfunctional tissue repair following kidney injury and transplantation , 2019, Nature Communications.

[11]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[12]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[13]  T. Hirano,et al.  Ficolin-1 is a promising therapeutic target for autoimmune diseases , 2018, International immunology.

[14]  Haojia Wu,et al.  Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response. , 2018, Journal of the American Society of Nephrology : JASN.

[15]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[16]  J. Augustine.  Kidney transplant: New opportunities and challenges , 2018, Cleveland Clinic Journal of Medicine.

[17]  M. Posch,et al.  A Randomized Trial of Bortezomib in Late Antibody-Mediated Kidney Transplant Rejection. , 2017, Journal of the American Society of Nephrology : JASN.

[18]  Hong Jiang,et al.  Macrophage-to-Myofibroblast Transition Contributes to Interstitial Fibrosis in Chronic Renal Allograft Injury. , 2017, Journal of the American Society of Nephrology : JASN.

[19]  E. Reed,et al.  Antibody-mediated rejection across solid organ transplants: manifestations, mechanisms, and therapies , 2017, The Journal of clinical investigation.

[20]  R. Lechler,et al.  Strategies for long-term preservation of kidney graft function , 2017, The Lancet.

[21]  T. Tuschl,et al.  Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis. , 2017, JCI insight.

[22]  N. Rogers,et al.  CD47 regulates renal tubular epithelial cell self-renewal and proliferation following renal ischemia reperfusion. , 2016, Kidney international.

[23]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[24]  K. Famulski,et al.  Relationships among injury, fibrosis, and time in human kidney transplants. , 2016, JCI insight.

[25]  E. Reed,et al.  The divergent roles of macrophages in solid organ transplantation , 2015, Current opinion in organ transplantation.

[26]  Toshiaki Suzuki,et al.  Alternatively activated macrophages in the pathogenesis of chronic kidney allograft injury , 2015, Pediatric Nephrology.

[27]  H. Lan,et al.  Macrophages promote renal fibrosis through direct and indirect mechanisms , 2014, Kidney international supplements.

[28]  Xiao-ming Meng,et al.  Inflammatory processes in renal fibrosis , 2014, Nature Reviews Nephrology.

[29]  J. Chapman,et al.  The Role of Macrophages in the Development of Human Renal Allograft Fibrosis in the First Year After Transplantation , 2014, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[30]  A. Saliba,et al.  Single-cell RNA-seq: advances and future challenges , 2014, Nucleic acids research.

[31]  Cole Trapnell,et al.  Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions , 2014, Nature Biotechnology.

[32]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[33]  A. Matas,et al.  Understanding the Causes of Kidney Transplant Failure: The Dominant Role of Antibody‐Mediated Rejection and Nonadherence , 2012, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[34]  M. Nafar,et al.  Oxidative stress in kidney transplantation: causes, consequences, and potential treatment. , 2011, Iranian journal of kidney diseases.

[35]  K. Lai,et al.  Mechanism of chronic aristolochic acid nephropathy: role of Smad3. , 2010, American journal of physiology. Renal physiology.

[36]  K. Mills,et al.  Interleukin-1 and IL-23 induce innate IL-17 production from gammadelta T cells, amplifying Th17 responses and autoimmunity. , 2009, Immunity.

[37]  C. Sasakawa,et al.  Differential roles of interleukin-17A and -17F in host defense against mucoepithelial bacterial infection and allergic responses. , 2009, Immunity.

[38]  T. Kipari,et al.  Depletion of Cells of Monocyte Lineage Prevents Loss of Renal Microvasculature in Murine Kidney Transplantation , 2008, Transplantation.

[39]  M. Hattori,et al.  Glomerular Expression of Plasmalemmal Vesicle‐Associated Protein‐1 in Patients with Transplant Glomerulopathy , 2007, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[40]  M. Merrilees,et al.  The Macrophage Is the Predominant Inflammatory Cell in Renal Allograft Intimal Arteritis , 2005, Transplantation.

[41]  T. Hovig,et al.  Glomerular monocyte/macrophage influx correlates strongly with complement activation in 1-week protocol kidney allograft biopsies. , 2004, Clinical nephrology.

[42]  A. Roberts,et al.  Targeted disruption of TGF-beta1/Smad3 signaling protects against renal tubulointerstitial fibrosis induced by unilateral ureteral obstruction. , 2003, The Journal of clinical investigation.

[43]  A. Magil,et al.  Monocytes and peritubular capillary C4d deposition in acute renal allograft rejection. , 2003, Kidney international.

[44]  P. Nickerson,et al.  Neointimal and tubulointerstitial infiltration by recipient mesenchymal cells in chronic renal-allograft rejection. , 2001, The New England journal of medicine.

[45]  F. Oppenheimer,et al.  Role of transforming growth factor‐ β1 in the progression of chronic allograft nephropathy , 2001 .

[46]  R. Bloom,et al.  Immunosuppression for kidney transplantation: Where are we now and where are we going? , 2017, Transplantation reviews.

[47]  J. Sellarésa,et al.  Understanding the Causes of Kidney Transplant Failure : The Dominant Role of Antibody-Mediated Rejection and Nonadherence , 2011 .

[48]  Transforming Growth Factor- (cid:2) 1 Induces Smad3-Dependent (cid:2) 1 Integrin Gene Expression in Epithelial-to-Mesenchymal Transition during Chronic Tubulointerstitial Fibrosis , 2022 .

[49]  A. Woltman,et al.  J Am Soc Nephrol 11: 2044–2055, 2000 Interleukin-17 and CD40-Ligand Synergistically Enhance Cytokine and Chemokine Production by Renal Epithelial Cells , 2022 .