Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant

Abstract

Transplant rejection is the critical clinical end-point limiting indefinite survival after histocompatibility antigen (HLA) mismatched organ transplantation. The predominant cause of late graft loss is antibody-mediated rejection (AMR), a process whereby injury to the organ is caused by donor-specific antibodies, which bind to HLA and non-HLA (nHLA) antigens. AMR is incompletely diagnosed as donor/recipient (D/R) matching is only limited to the HLA locus and critical nHLA immunogenic antigens remain to be identified. We have developed an integrative computational approach leveraging D/R exome sequencing and gene expression to predict clinical post-transplant outcome. We performed a rigorous statistical analysis of 28 highly annotated D/R kidney transplant pairs with biopsy-confirmed clinical outcomes of rejection [either AMR or T-cell-mediated rejection (CMR)] and no-rejection (NoRej), identifying a significantly higher number of mismatched nHLA variants in AMR (ANOVA—p-value = 0.02). Using Fisher’s exact test, we identified 123 variants associated mainly with risk of AMR (p-value < 0.001). In addition, we applied a machine-learning technique to circumvent the issue of statistical power and we found a subset of 65 variants using random forest, that are predictive of post-tx AMR showing a very low error rate. These variants are functionally relevant to the rejection process in the kidney and AMR as they relate to genes and/or expression quantitative trait loci (eQTLs) that are enriched in genes expressed in kidney and vascular endothelium and underlie the immunobiology of graft rejection. In addition to current D/R HLA mismatch evaluation, additional mismatch nHLA D/R variants will enhance the stratification of post-tx AMR risk even before engraftment of the organ. This innovative study design is applicable in all solid organ transplants, where the impact of mitigating AMR on graft survival may be greater, with considerable benefits on improving human morbidity and mortality and opens the door to precision immunosuppression and extended tx survival.

Histological picture of antibody-mediated rejection without donor-specific anti-HLA antibodies: Clinical presentation and implications for outcome

“…[9][10][11][12][13][14][15] Uncertainty about the clinical significance of cases that are "suspicious for ABMR" has important implications for the management of patients, as it remains unclear whether they require additional treatment for ABMR. The latter category could be explained by the presence of injurious antibodies that remain undetected due to the limitation of the current testing methods and to the fact that these methods only focus on circulating anti-HLA antibodies, thereby missing non-HLA antibodies or by the presence of HLA-specific memory B cells.…”

“…The latter category could be explained by the presence of injurious antibodies that remain undetected due to the limitation of the current testing methods and to the fact that these methods only focus on circulating anti-HLA antibodies, thereby missing non-HLA antibodies or by the presence of HLA-specific memory B cells. [9][10][11][12][13][14][15] Uncertainty about the clinical significance of cases that are "suspicious for ABMR" has important implications for the management of patients, as it remains unclear whether they require additional treatment for ABMR. The Banff 2017 consensus proposed considering C4d-positivity as alternative for the DSA criterion in cases where DSA testing is not available or potentially false negative.…”

Precision Sub-phenotyping of Histologically Stable Kidney Transplants by a Composite Molecular and Cellular Instability Score

“…In this study we identified discrepancies in the current histological recognition of stable allografts and demonstrated a new Instability Score (or InstaScore), a linear combination of selected features based on the input from tissue gene expression and inferred cell type biopsy molecular data modeled on AR biology, that provides precise (sub-)phenotyping and early recognition of molecular and cellular rejection of otherwise functionally and histologically stable allografts on protocol biopsies. Unlike other published studies by others [61][62][63][64][65] and our group [2,54,66,67] that have only studied gene expression transcriptional perturbation in AR, this is the first development and application of a combined genes and cell types into Instability Score in tissue that can rapidly reclassify samples into molecularly and even more importantly, functionally relevant, diverse groups: those most similar to the normal kidneys (hSTA/mSTA) and those most similar to the rejected kidneys (hSTA/mAR).…”

Determining the Quantitative Principles of T Cell Response to Antigenic Disparity: The Case of Stem Cell Transplant Donor-Recipient Exome Wide Mismatching and HLA Bound Alloreactive Peptides

“…Two developments in the past decade have changed this situation. One, the emergence of next generation DNA sequencing techniques, such as single nucleotide polymorphism mapping 13,14 and whole exome sequencing (WES) to identify the potential antigenic differences 15,16 . The second is the development of machine learning algorithms which allow determination of the binding affinity that different antigens may have for specific HLA molecules 17,18,19 .…”

“…This knowledge of mHA in turn may allow simulation of alloreactive T cell responses in equivalently HLA matched SCT donor-recipient pairs (DRP) to identify donors with optimal alloreactivity. Studies reporting exome-wide or other genomic disparities in donors and recipients, have demonstrated a large body of DNA sequence differences between transplant donors and recipients, independent of relatedness and HLA matching 14,15,16 . These large genomic differences have been translated to peptides and HLA affinities for the resulting peptides determined 20 .…”