Long Read sequencing in Kidney Disease

About This Grant

Project Summary Chronic kidney disease (CKD) poses a major global health burden, yet therapeutic options remain limited and largely repurposed from other diseases. A key barrier to therapeutic progress is the incomplete understanding of CKD’s molecular and genetic mechanisms. Genetic factors explain 30–50% of CKD risk, but genome-wide association studies primarily identify non-coding variants, complicating functional interpretation. Most gene expression studies in CKD have focused on total gene expression, overlooking alternative splicing. Short-read RNA sequencing of 404 human kidney samples showed alternative splicing explains an additional 5% of CKD heritability. However, short-read sequencing fragments RNA, limiting full isoform characterization. Long-read sequencing of 8 kidney samples identified 67% novel isoforms and revealed significant isoform differences between CKD and control samples. Given the limitations of short read sequencing, I will employ long read sequencing to comprehensively characterize the role splicing in kidney disease. I will first employ this in bulk kidney tissue to identify novel isoforms, compare the isoform expression between CKD and controls and to compare the identified isoforms with mass spectrometry data to clarify the relationship between the spliced isoforms and protein levels. I will then perform single cell long read sequencing to generate the first isoform-resolved atlas of kidney cell populations, enabling identification of cellular states associated with disease. Differential isoform usage at single-cell resolution will clarify which kidney cell types and isoforms drive disease pathology. This project will comprehensively characterize the splicing events in the kidney and the role in kidney disease.