Long noncoding RNA Hoxb3os is dysregulated in autosomal dominant polycystic kidney disease and regulates mTOR signaling

Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is a debilitating disease that is characterized by the accumulation of numerous fluid-filled cysts in the kidney. ADPKD is primarily caused by mutations in two genes, <i>PKD1</i> and <i>PKD2</i> Long noncoding RNAs (lncRNA), defined by a length >200 nucleotides and absence of a long ORF, have recently emerged as epigenetic regulators of development and disease; however, their involvement in PKD has not been explored previously. Here, we performed deep RNA-Seq to identify lncRNAs that are dysregulated in two orthologous mouse models of ADPKD (kidney-specific <i>Pkd1</i> and <i>Pkd2</i> mutant mice). We identified a kidney-specific, evolutionarily conserved lncRNA called <i>Hoxb3os</i> that was down-regulated in cystic kidneys from <i>Pkd1</i> and <i>Pkd2</i> mutant mice. The human ortholog <i>HOXB3-AS1</i> was down-regulated in cystic kidneys from ADPKD patients. <i>Hoxb3os</i> was highly expressed in renal tubules in adult WT mice, whereas its expression was lost in the cyst epithelium of mutant mice. To investigate the function of <i>Hoxb3os</i>, we utilized CRISPR/Cas9 to knock out its expression in mIMCD3 cells. Deletion of <i>Hoxb3os</i> resulted in increased phosphorylation of mTOR and its downstream targets, including p70 S6 kinase, ribosomal protein S6, and the translation repressor 4E-BP1. Consistent with activation of mTORC1 signaling, <i>Hoxb3os</i> mutant cells displayed increased mitochondrial respiration. The <i>Hoxb3os</i> mutant phenotype was partially rescued upon re-expression of <i>Hoxb3os</i> in knockout cells. These findings identify <i>Hoxb3os</i> as a novel lncRNA that is down-regulated in ADPKD and regulates mTOR signaling and mitochondrial respiration.