Deep Phenotyping of the Renal Allograft to Prognosticate Clinical Outcomes

This study is exploratory in nature and aims to elucidate the phenotypic, transcriptional, and epigenetic underpinnings of renal transplant rejection. The study is designed to provide improved understanding of the regulation of intra-graft alloimmune response in the renal transplant recipients.

In this single center, prospective, longitudinal, observational cohort study, sequential assessment of renal biopsies will be performed at baseline (pre-implantation), 3 months and at one-year post-transplantation in addition to any for-cause biopsies within the first five years post-transplantation. Blood samples will be also collected at the time of renal biopsies for comparison analyses.

HYPOTHESIS It is proposed that unique phenotypic, transcriptional, and epigenetic changes within the parenchymal and the infiltrating nonparenchymal inflammatory cells dictate the evolution of renal allograft inflammation and rejection.

The following research specimens will be obtained from each study participant:

1. The day of transplantation (by the UPMC operating surgeon): Pre-implantation core renal biopsy and post-perfusion core renal biopsy: Two research cores for each biopsy will be taken from the transplanted kidney. The pre-implantation biopsy specimens are obtained on the back table, and the post-perfusion cores are taken prior to closure of the surgical incision. The 1st research core will be used for routine histopathological examination and left over tissue from this core will be used for deep phenotyping using multiparameter immunophenotyping, and digital spatial profiling. The second research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq. Blood samples will be processed to obtain plasma (for cytokine, chemokine and DSA measurements) and PBMC (for deep phenotyping and molecular analyses). For each collection timepoint, up to 75 mL (about 5 tablespoons) will be collected.
2. Protocol biopsies at 3 months and 12 months (by the transplant nephrologist): Renal transplant recipients at UPMC routinely undergo clinical post-transplant biopsies at 3 months and at 12 months. An additional research core will be collected along with the clinically indicated biopsy cores at both these time points (3 total passes of the biopsy needle for each collection). Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping, and digital spatial profiling. The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq. Blood samples will be processed to obtain plasma (for cytokine, chemokine and DSA measurements) and PBMC (for deep phenotyping and molecular analyses).
3. For-cause biopsies from time-0 to 1-yr post-transplantation (by the transplant nephrologist): Along with the protocol biopsies, UPMC renal transplant patients also undergo biopsies for clinical indication (for-cause biopsies). Again, an additional research core will be collected along with the clinically indicated biopsy cores whenever a patient undergoes any for-cause biopsy between time-0 and 1-year post-transplantation (3 total passes of the biopsy needle for each collection). Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping, and digital spatial profiling. The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq. Blood samples will be processed to obtain plasma (for cytokine, chemokine and DSA measurements) and PBMC (for deep phenotyping and molecular analyses).