Multi-omics Analyses Reveal Sex Differences in Mouse Renal Proximal Tubules

Sex differences have been increasingly recognized to play an important role in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. Here, we coupled renal tubule microdissection with RNA-seq and ATAC-seq with a focus on proximal tubules that exhibited the greatest sex differences and carried out whole-kidney proteomics to build a comprehensive sex difference landscape between male and female mouse kidneys. The transcriptomic data indicate that the major sex differences are in S2 and S3 of proximal tubule segments, where signaling pathways including monocarboxylic acid metabolic process, organic anion transport, and organic acid transport display the greatest differences. We develop an ATAC-seq method on microdissected tubules to capture chromatin accessibility differences between sexes. The analysis reveals that major sex differences are in autosomes instead of sex chromosomes, and many of them are in S2/S3 segments related to the signaling pathways identified by transcriptomic analysis. Motif analysis identifies several transcription factors (Tead1, Nfia/b, and Pou3f3) whose interplay with other transcription factors (e.g. Hnf1b, Hnf4a) may contribute to sex differences. Finally, whole-kidney quantitative proteomics analysis correlates with the transcriptome analysis and identifies a large number of proteins (Cyp2e1, Acsm2/3) that are sex-dependent. We develop a knowledge portal to promote our understanding of sex differences in kidneys in kidneys at https://esbl.nhlbi.nih.gov/MRECA/PT/. Here, we combined renal tubule microdissection with RNA-seq and ATAC-seq to characterize gene expression and chromatin accessibly in proximal tubule S1, S2, and S3. We provide insights into specific genes and pathways that differ between male and female mouse kidneys. We identify sex-dependent cis-regulatory elements and reveal the interplay between transcription factors, which may result in sex-biased gene expression. We report sex differences in protein expression in kidneys to complement our gene expression data. Finally, we develop a web-based portal that allows users to download and promote understanding of the sex differences in kidneys.