The Impact of APOL1 Copy Number Variation on Kidney Disjavascript:autoSave('https://apps.era.nih.gov:443/gmii/home.era?menu_itemPath=59%27)ease Susceptibility in African Americans

Project Summary African Americans are three to four times more likely to develop kidney failure than other populations. Coding variants in Apolipoprotein L1 (APOL1), termed G1 and G2, drive nondiabetic kidney disease risk in this population. Previous functional studies demonstrated that the APOL1 risk variants promote lysosomal dysfunction, cell death, and numerous kidney injury phenotypes in mouse models. While disease risk typically occurs in a recessive fashion, heterozygous risk variant carriers can develop kidney disease, and not all individuals carrying the risk variants develop disease, highlighting our incomplete understanding of the APOL1 genetic susceptibility to kidney disease in African Americans. The Pollak Lab identified a 101kb duplication encompassing APOL1 and postulated that APOL1 copy number variations (CNVs) contribute to the phenotypic heterogeneity of APOL1-associated kidney diseases. Inheriting additional alleles of APOL1 increases the risk of kidney disease. More recent data suggest there have been additional duplication events, and the structure and consequences of the CNVs remain unexplored. APOL1 CNVs harboring various non-risk or risk variant copies illustrates an additional complexity to APOL1- mediated disease susceptibility. We hypothesize there are APOL1 CNVs with duplicated risk variant combinations that mediate disease risk through increased risk allele expression, thereby driving cell death. This proposal will explore the importance of CNVs for kidney disease by: 1) developing a computational approach to characterize the risk variant architecture of APOL1 CNVs (how many non-risk and risk variants present in an APOL1 CNV carrier) and identify risk variant combinations in patients with nondiabetic kidney diseases, and 2) determining the in vitro functional consequences of harboring APOL1 CNVs through investigations of allelic dosage mechanisms and cell death upon interferon treatment. Preliminary examination of whole genome sequencing data from 1000Genomes APOL1 CNV carriers shows that utilizing CNV region and allelic read depths will facilitate duplicated risk variant determination. This proposed work will advance our knowledge of the APOL1 genetic susceptibility to nondiabetic kidney diseases and aid in kidney disease risk assessment for individuals carrying APOL1 risk alleles and CNVs. Beth Israel Deaconess Medical Center (BIDMC), a Harvard Medical School affiliated institution, provides an exceptional learning environment for conducting this proposed research. Fellowship training will include obtaining computational skills for studying structural variations, genomic allelic discrimination of the APOL1 risk variants in CNVs, transcriptomic analyses for analyzing allelic dosage, and wet-lab techniques for functional investigation of APOL1 CNVs. Mentorship from investigators at BIDMC who are leaders in APOL1 genetics and nondiabetic kidney diseases, in addition to collaborations from members at the Broad Institute, will create a foundation for achieving academic career goals of becoming a principal investigator.