Multiomics Analyses Reveal Sex Differences in Mouse Renal Proximal Subsegments

Abstract

Significance Statement Sex-dependent differences in kidney function are recognized but the underlying molecular mechanisms are largely unexplored. Advances in genomics and proteomic technologies now allow extensive characterization of differences between the same cell types of males and females. Multiomics integrating RNA-seq, ATAC-seq, and proteomics data to investigate differences in gene expression, chromatin accessibility, and protein expression in proximal tubules of male and female mice identified many sex-biased genes and proteins associated with kidney functions, including metabolic and transport processes. Sex differences may also arise from variations of the interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to advance understanding of sex differences in cells of the proximal tubule. Background Sex differences have been increasingly recognized as important in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. Methods RNA-seq and ATAC-seq of microdissected mouse proximal tubules and protein mass spectrometry of homogenized perfused mouse kidneys reveal differences in proximal tubule cells of males and females. Results The transcriptomic data indicated that the major differences in the proximal tubules between the sexes were in the S2/S3 segments, and most of the sex-biased transcripts mapped to autosomes rather than to the sex chromosomes. Many of the transcripts exhibiting sex-biased expression are involved in monocarboxylic acid metabolic processes, organic anion transport, and organic acid transport. The ATAC-seq method on microdissected tubules captured chromatin accessibility. Many of the more than 7000 differentially accessible DNA regions identified were in distal regions. Motif analyses revealed a lack of direct involvement of estrogen receptors or the androgen receptor (absence of canonical hormone response elements), suggesting an indirect regulatory role of sex hormones. Instead, analyses identified several transcription factors (TFs) (Tead1, Nfia/b, and Pou3f3) whose interplay with proximal tubule-specific TFs (e.g., Hnf1b, Hnf4a) may contribute to sex differences. Finally, the whole-kidney proteome was correlated with the transcriptome, and many sex-biased proteins (e.g., Cyp2e1, Acsm2/3) were identified. Conclusions Sex-dependent cis-regulatory elements interact with TFs in ways that lead to sex-biased gene expression in proximal tubule cells. These data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/MRECA/PT/.