DCLK1 and regulation of the DNA damage response in proximal tubule injury

Project Summary Proximal tubule injury is an important mediator of chronic kidney disease (CKD) and single-cell sequencing has shown that human and animal models of CKD result in an increased proportion of proximal tubule cells with a pro-inflammatory phenotype. Subsequent rounds of proximal tubule injury and repair can result in the accumulation of DNA damage, leading to persistent activation of the DNA damage response pathway and injury of neighboring cells via secretion of cytokines. We have developed novel methods to estimate DNA damage burden in proximal tubule cells by characterizing somatic copy number alterations (CNA). Somatic CNA occur when a cell gains or loses a portion of its genome and cells with high proliferative rate, like the proximal tubule, may be particularly susceptible to somatic CNA. These alterations are more common than was previously thought and can be as large as an entire chromosome, which likely affects the ability of proximal tubule cells to repair themselves. We identified increased expression of DCLK1 in injured proximal tubule cells that was further increased in cells with somatic CNA and we hypothesize that targeting these cells may help to slow progression of CKD. DCLK1 is a microtubule-associated protein kinase that is important for cell division, DNA damage response, and epithelial-mesenchymal transition (EMT). DCLK1 may act as a pro- survival signal that helps injured proximal tubule cells to evade apoptosis while they attempt to repair DNA damage. However, a subset of injured proximal tubule cells may have DNA damage that is too severe to repair, resulting in persistent activation of the DNA damage response pathway. DCLK1 is of particular interest because increased DCLK1 expression correlates with fibrosis, it is conserved in animal models of kidney disease, and it has been associated with CKD in a genome-wide meta-analysis. Much of what is known about DCLK1 comes from the study of cancer, which has led to the development of DCLK1 inhibitors that selectively limit the kinase activity of DCLK1 to attenuate downstream inflammatory pathways. These advances present an opportunity to repurpose DCLK1 inhibitors for CKD, but relatively little is known about how DCLK1 regulates inflammation and the DNA damage response in injured proximal tubule cells. DCLK1 has at least two isoforms that play variable roles in cell survival and inflammatory signaling. We hypothesize that proximal tubule injury and DNA damage result in biased expression of the short isoform and activation of pro-inflammatory signaling. We propose to quantify the ratio of DCLK1 long and short isoforms in human kidney. We will selectively target DCLK1 signaling in an animal model of CKD and further validate our predicted signaling mechanisms in cell culture models of the proximal tubule.