Bulk and single-cell nanopore transcriptomics to identify alternative splicing in renal tubule cells

Abstract These studies aim to understand how alternative splicing may be driving kidney disease progression. The serine/arginine-rich splicing factor 7 (SRSF7) was shown to be downregulated in the proximal tubule of human and mouse diabetic kidney disease. SRSF7 was knocked down in human proximal tubule cells in vitro and submitted for bulk nanopore RNA sequencing. Nanopore sequencing can more accurately detect and quantify full-length gene isoforms to better resolve alternative splicing events. Genes with alternative splicing between control and SRSF7 knockdown were enriched in pathways related to inflammation, mRNA splicing, cell cycle, and apoptosis. We examined differential transcript usage (DTU) between PT-S1 and TAL cells in mouse kidney using single-cell nanopore transcriptomics, identifying CLDN10 as having isoform switching between these cell types, resulting in functional consequences. Understanding the mechanisms of alternative splicing in the kidney could lead to new therapeutic targets to treat kidney diseases. Biography Megan Noonan is a post-doctoral researcher at Washington University School of Medicine in St. Louis, Division of Nephrology. She completed her PhD in Medical and Molecular Genetics at Indiana University, Indianapolis. Her research aims to uncover novel mechanisms of kidney disease progression via dysregulated alternative splicing. She uses nanopore sequencing to better resolve isoforms for more accurate alternative splicing analysis in bulk and single-cell RNA sequencing datasets.