TNFRSF13B genotypes control immune-mediated pathology by regulating the functions of innate B cells

Host genes define the severity of inflammation and immunity but specific loci doing so are unknown. Here we show that TNF receptor superfamily member 13B (TNFRSF13B) variants, which enhance defense against certain pathogens, also control immune-mediated injury of transplants, by regulating innate B cells’ functions. Analysis of TNFRSF13B in human kidney transplant recipients revealed that 33% of those with antibody-mediated rejection (AMR) but fewer than 6% of those with stable graft function had TNFRSF13B missense mutations. To explore mechanisms underlying aggressive immune responses, we investigated alloimmunity and rejection in mice. Cardiac allografts in Tnfrsf13b-mutant mice underwent early and severe AMR. The dominance and precocity of AMR in Tnfrsf13b-deficient mice were not caused by increased alloantibodies. Rather, Tnfrsf13b mutations decreased “natural” IgM and compromised complement regulation, leading to complement deposition in allografted hearts and autogenous kidneys. Thus, WT TNFRSF13B and Tnfrsf13b support innate B cell functions that limit complement-associated inflammation; in contrast, common variants of these genes intensify inflammatory responses that help clear microbial infections but allow inadvertent tissue injury to ensue. The wide variation in inflammatory reactions associated with TNFRSF13B diversity suggests polymorphisms could underlie variation in host defense and explosive inflammatory responses that sometimes enhance morbidity associated with immune responses.

[1]  Peter L. Freddolino,et al.  TNFRSF13B polymorphisms counter microbial adaptation to enteric IgA , 2021, JCI insight.

[2]  J. Platt,et al.  TNFRSF13B Diversification Fueled by B Cell Responses to Environmental Challenges—A Hypothesis , 2021, Frontiers in Immunology.

[3]  Xavier Duval,et al.  Clinical and virological data of the first cases of COVID-19 in Europe: a case series , 2020, The Lancet Infectious Diseases.

[4]  Olivier Aubert,et al.  Prediction system for risk of allograft loss in patients receiving kidney transplants: international derivation and validation study , 2019, BMJ.

[5]  L. Quintana-Murci Human Immunology through the Lens of Evolutionary Genetics , 2019, Cell.

[6]  C. Yau,et al.  Association of HLA-dependent islet autoimmunity with systemic antibody responses to intestinal commensal bacteria in children , 2019, Science Immunology.

[7]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[8]  Graham M Lord,et al.  The genetic determinants of renal allograft rejection , 2018, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[9]  D. Abramowicz,et al.  Reply to Hernandez et al. ‐ GWAS of acute renal graft rejection , 2018, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[10]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[11]  S. Serrano,et al.  mTOR intersects antibody-inducing signals from TACI in marginal zone B cells , 2017, Nature Communications.

[12]  Katherine M. Siewert,et al.  Detecting Long-Term Balancing Selection Using Allele Frequency Correlation , 2017, bioRxiv.

[13]  R. Geha,et al.  Heterozygosity for transmembrane activator and calcium modulator ligand interactor A144E causes haploinsufficiency and pneumococcal susceptibility in mice , 2017, The Journal of allergy and clinical immunology.

[14]  Trevor Hastie,et al.  REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. , 2016, American journal of human genetics.

[15]  P. Lobo Role of Natural Autoantibodies and Natural IgM Anti-Leucocyte Autoantibodies in Health and Disease , 2016, Front. Immunol..

[16]  E. Boerwinkle,et al.  dbNSFP v3.0: A One‐Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice‐Site SNVs , 2016, Human mutation.

[17]  James Y. Zou Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[18]  D. Kaufman,et al.  C1q Binding Activity of De Novo Donor-specific HLA Antibodies in Renal Transplant Recipients With and Without Antibody-mediated Rejection , 2015, Transplantation.

[19]  M. Haas,et al.  Isolated endarteritis and kidney transplant survival: a multicenter collaborative study. , 2015, Journal of the American Society of Nephrology : JASN.

[20]  A. E. Sousa,et al.  TACI deficiency enhances antibody avidity and clearance of an intestinal pathogen. , 2014, The Journal of clinical investigation.

[21]  L. Abel,et al.  Combined Linkage and Association Studies Show that HLA Class II Variants Control Levels of Antibodies against Epstein-Barr Virus Antigens , 2014, PloS one.

[22]  R. Geha,et al.  CVID-associated TACI mutations affect autoreactive B cell selection and activation. , 2013, The Journal of clinical investigation.

[23]  I. Adzhubei,et al.  Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.

[24]  Liping Huang,et al.  Natural IgM Anti-Leukocyte Autoantibodies Attenuate Excess Inflammation Mediated by Innate and Adaptive Immune Mechanisms Involving Th-17 , 2012, The Journal of Immunology.

[25]  W. Guan,et al.  Validation of single nucleotide polymorphisms associated with acute rejection in kidney transplant recipients using a large multi‐center cohort , 2011, Transplant international : official journal of the European Society for Organ Transplantation.

[26]  J. Platt,et al.  TACI deficiency impairs sustained Blimp-1 expression in B cells decreasing long-lived plasma cells in the bone marrow. , 2011, Blood.

[27]  Jamie K. Scott,et al.  Reactivity profiles of broadly neutralizing anti-HIV-1 antibodies are distinct from those of pathogenic autoantibodies , 2011, AIDS.

[28]  J. Platt Antibodies in transplantation. , 2010, Discovery medicine.

[29]  M. Suthanthiran,et al.  Identification of a B cell signature associated with renal transplant tolerance in humans. , 2010, The Journal of clinical investigation.

[30]  R. Geha,et al.  The murine equivalent of the A181E TACI mutation associated with common variable immunodeficiency severely impairs B-cell function. , 2009, Blood.

[31]  R. Geha,et al.  Transmembrane activator, calcium modulator, and cyclophilin ligand interactor drives plasma cell differentiation in LPS-activated B cells. , 2009, The Journal of allergy and clinical immunology.

[32]  W. Hörl,et al.  In Vitro Detection of C4d‐Fixing HLA Alloantibodies: Associations With Capillary C4d Deposition in Kidney Allografts , 2007, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[33]  R. Bram,et al.  TACI Is Required for Efficient Plasma Cell Differentiation in Response to T-Independent Type 2 Antigens1 , 2007, The Journal of Immunology.

[34]  Gordon K. Smyth,et al.  Empirical array quality weights in the analysis of microarray data , 2006, BMC Bioinformatics.

[35]  R. Geha,et al.  TACI is mutant in common variable immunodeficiency and IgA deficiency , 2005, Nature Genetics.

[36]  A. Schäffer,et al.  Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans , 2005, Nature Genetics.

[37]  A. Plebani,et al.  The loss of IgM memory B cells correlates with clinical disease in common variable immunodeficiency. , 2005, The Journal of allergy and clinical immunology.

[38]  R. Geha,et al.  TACI and BAFF-R mediate isotype switching in B cells , 2005, The Journal of experimental medicine.

[39]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[40]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[41]  M. Ballow,et al.  Primary immunodeficiency disorders: antibody deficiency. , 2002, The Journal of allergy and clinical immunology.

[42]  J. V. van Deursen,et al.  Regulation of the T-independent humoral response by TACI. , 2001, Immunity.

[43]  M. Wabl,et al.  VH gene replacement in hyperselected B cells of the quasimonoclonal mouse. , 1997, Journal of immunology.

[44]  R. Bram,et al.  NF-AT activation induced by a CAML-interacting member of the tumor necrosis factor receptor superfamily. , 1997, Science.

[45]  M. Wabl,et al.  A Quasi-Monoclonal Mouse , 1996, Science.

[46]  M. Frank,et al.  Regulation of complement activity by immunoglobulin. I. Effect of immunoglobulin isotype on C4 uptake on antibody-sensitized sheep erythrocytes and solid phase immune complexes. , 1996, Journal of immunology.

[47]  L. Glimcher,et al.  The role of "indirect" recognition in initiating rejection of skin grafts from major histocompatibility complex class II-deficient mice. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[48]  J. R. Batchelor,et al.  Immunology/Transplantation , 1992, Diabetes.

[49]  G. Snell,et al.  Studies on the Genetic and Antigenic Basis of Tumour Transplantation. Linkage between a Histocompatibility Gene and 'Fused' in Mice , 1948, Proceedings of the Royal Society of London. Series B - Biological Sciences.

[50]  P. Gorer The genetic and antigenic basis of tumour transplantation , 1937 .

[51]  L. Loeb Ueber Entstehung eines Sarkoms nach Transplantation eines Adenocarcinoms einer japanischen Maus , 1908, Zeitschrift für Krebsforschung.

[52]  Qin Ning,et al.  Clinical and immunological features of severe and moderate coronavirus disease 2019 , 2020 .

[53]  F. Luan,et al.  Incidences of preformed and de novo donor-specific HLA antibodies and their clinicohistological correlates in the early course of kidney transplantation. , 2012, Clinical transplants.

[54]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[55]  A. Novick,et al.  Antibody-Mediated Rejection of Cardiac Allografts in CCR5-Deficient Recipients , 2007 .

[56]  M. Frank,et al.  Immunoglobulin in the control of complement action , 2000, Immunologic research.

[57]  M. Daha,et al.  Immunoglobulin M-enriched human intravenous immunoglobulin prevents complement activation in vitro and in vivo in a rat model of acute inflammation. , 1999, Blood.

[58]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .