Genetic polymorphisms of Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3) gene in African American kidney transplant recipients are associated with post-transplant graft failure

Abstract

Background: African American (AA) kidney transplant recipients exhibit a higher rate of graft loss compared to other racial and ethnic populations, highlighting the need to identify causative factors underlying this disparity. Method: We analyzed RNA sequences of pretransplant whole blood from subjects followed in three kidney transplant cohorts to identify single nucleotide polymorphisms (SNPs) associated with death censored graft loss (DCGL). We employed a meta-analysis to uncover key transcriptional signatures and pathways associated with the identified SNPs and used single cell RNA to define cellular specificity. We characterized SNP functions using in vitro immunological and survival assays and tested for associations between the identified SNPs and other immune-related diseases using a ~30,100 subject, electronic health record (EHR)-linked database. Results: We uncovered a cluster of four consecutive missense SNPs in the Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3, a negative immune response regulator) gene that strongly associated with DCGL. This LILRB3-4SNPs cluster encodes missense mutations at amino acids 617-618 proximal to a SHP-1/2 phosphatase-binding ITIM motif. LILRB3-4SNPs is specifically enriched within subjects of AA ancestry (8.6% prevalence vs 2.3% in Hispanic and 0.1% in European populations), is not linked to APOL1 G1/G2 alleles, and exhibited a strong association with DCGL. Analysis of PBMC and transplant biopsies from recipients with LILRB3-4SNPs showed evidence of enhanced adaptive immune responsiveness and ferroptosis-associated death in monocytes. Overexpression of the variant allele in THP-1 cells (macrophage line) induced augmented inflammation and ferroptosis, which were attenuated by a ferroptosis inhibitor, verifying a causal link. The LILRB3-4SNPs also associated with multiple systemic and organ-specific immune-related diseases in AAs, consistent with conferring a broadly relevant immune function. Conclusion: the LILRB3-4SNPs represent a functionally important, distinct genetic risk factor for kidney transplant outcome and development/severity of other immune-related diseases in patients of AA ancestry. Pharmacological targeting of ferroptosis should be tested to prevent or treat these disease processes in AA recipients carrying LILRB3-4SNPs.

Competing Interest Statement

Dr. Zhang reports personal fees from VericiDx and reports the patents (1. Patents US Provisional Patent Application F&R ref 27527-0134P01, Serial No. 61/951,651, filled March 2014. Method for identifying kidney allograft recipients at risk for chronic injury; 2. US Provisional Patent Application: Methods for Diagnosing Risk of Renal Allograft Fibrosis and Rejection (miRNA); 3. US Provisional Patent Application: Method for Diagnosing Subclinical Acute Rejection by RNA sequencing Analysis of a Predictive Gene Set; 4. US Provisional Patent Application: Pretransplant prediction of post- transplant acute rejection.); Dr Menon receives research support from Natera. Dr. Cravedi is a consultant for Chinook therapeutics. Dr. Lorenzo Gallon is the non-executive Director and Chair of the science advisory board for Verici. Other investigators have no financial interest to declare.