Using transcriptomics and ex vivo organotypic models to discover mechanisms of APOL1-associated podocytopathies

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ABSTRACT Chronic Kidney Disease (CKD) is common among African American (AA) patients. The excess risk for CKD in this population is partially explained by genetic variations in the APOL1 gene (named G1 and G2) that are unique to African ancestral populations. Understanding the molecular basis for the association between genetic variants and the risk for kidney disease is an important goal in biomedical science. The APOL1 gene is unique to humans and a few primates creating limitations to research approaches using conventionally available experimental models. This career development research proposal is designed to train a promising early stage investigator to address these issues by using organotypic kidney models derived from human inducible stem cells (iPSC) in conjunction with state-of-the-art bioinformatics to interrogate human patient data and explore therapeutics. The current proposal is designed to test the hypothesis that APOL1 kidney disease risk variants drive transcriptional differences that can be identified by the integration of glomerular transcriptomes from people with APOL1-associated kidney disease and ex vivo models, to gain insight into APOL1 function in health and disease. Key preliminary data developed by the applicant demonstrates that a variant-dependent APOL1 transcriptional signatures identified in human glomeruli are conserved in mouse models expressing APOL1 variants. The applicant will acquire new skills in two general areas: 1) expertise in the use of novel ex vivo culture models for mechanistic studies, and 2) computational and bioinformatics analysis of large datasets. These skills will be acquired through mentorship, didactics and a pragmatic research program divided into three specific aims: 1) Define APOL1 risk genotype-associated transcriptional phenotypes in podocytes derived from isogenic cell lines homozygous for the G0, G1 and G2 alleles that are anchored to human glomerular gene expression; 2) Anchor APOL1 variants-associated podocyte transcriptional phenotypes to NEPTUNE glomerular gene co-expression modules and clinical outcomes, and identity compounds that could modulate such phenotypes and associated subcellular processes, and 3) Test the chemical perturbagens’ ability to reverse the APOL1 risk genotype transcriptional phenotype and identify kidney disease mechanisms. Completion of this proposal will provide insights into APOL1 biology and function that could be translated to clinical technology by providing early diagnosis and prognosis tools, identification of therapeutic targets and patient derived renal models. Additionally this proposal aims to establish the Principal Investigator (PI) as an independent translational scientist in nephrology. The plan includes mentored training in patient oriented research, extensive wet-lab training in the production of organotypic models from iPSC lines as well as comprehensive coursework in bioinformatics.