Proximal Tubule Translational Profiling during Kidney Fibrosis Reveals Proinflammatory and Long Noncoding RNA Expression Patterns with Sexual Dimorphism

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Significance Statement Having a comprehensive transcriptional profile of the proximal tubule in health and fibrosis would likely enhance understanding of fibrosis and perhaps help explain why CKD progresses more quickly in males versus females. To obtain a more complete picture of gene expression in the proximal tubule, the authors performed deep translational profiling of this segment in a mouse model of kidney fibrosis. Their findings demonstrate substantial sex differences in transcripts expressed in proximal tubule cells of males versus females, and indicate that the proximal tubule drives fibrosis through inflammatory and profibrotic paracrine signaling. The study also identified 439 long noncoding RNAs expressed in the proximal tubule, 143 of which undergo differential regulation in fibrosis, suggesting that this type of RNA has unanticipated regulatory roles kidney fibrosis. Background Proximal tubule injury can initiate CKD, with progression rates that are approximately 50% faster in males versus females. The precise transcriptional changes in this nephron segment during fibrosis and potential differences between sexes remain undefined. Methods We generated mice with proximal tubule–specific expression of an L10a ribosomal subunit protein fused with enhanced green fluorescent protein. We performed unilateral ureteral obstruction surgery on four male and three female mice to induce inflammation and fibrosis, collected proximal tubule–specific and bulk cortex mRNA at day 5 or 10, and sequenced samples to a depth of 30 million reads. We applied computational methods to identify sex-biased and shared molecular responses to fibrotic injury, including up- and downregulated long noncoding RNAs (lncRNAs) and transcriptional regulators, and used in situ hybridization to validate critical genes and pathways. Results We identified >17,000 genes in each proximal tubule group, including 145 G-protein–coupled receptors. More than 700 transcripts were differentially expressed in the proximal tubule of males versus females. The >4000 genes displaying altered expression during fibrosis were enriched for proinflammatory and profibrotic pathways. Our identification of nearly 150 differentially expressed proximal tubule lncRNAs during fibrosis suggests they may have unanticipated regulatory roles. Network analysis prioritized proinflammatory and profibrotic transcription factors such as Irf1 , Nfkb1 , and Stat3 as drivers of fibrosis progression. Conclusions This comprehensive transcriptomic map of the proximal tubule revealed sexually dimorphic gene expression that may reflect sex-related disparities in CKD, proinflammatory gene modules, and previously unappreciated proximal tubule–specific bidirectional lncRNA regulation.