Cellular and Molecular Drivers of Nephronophthisis

February 14, 2019

Nephronophthisis (NPHP) is a highly heterogeneous disease with genetic origins that mainly affects a pediatric population, but the condition can also manifest in older individuals during adolescence or even later in one’s 20s or 30s. A multigene disorder, there are currently more than 30 identified genes known to be causative of the condition, but an individual only needs a mutation in a single gene for disease to occur. Although NPHP has long been considered a “ciliopathy,” caused by a dysfunction in cilia, recent gene identification in humans has linked the pathogenesis of NPHP to defective DNA damage response signaling, resulting in genome instability and cell-cycle defects.

“This is for sure a disease that presents itself on a broad spectrum, and one in which the underlying pathomechanisms are not well understood,” says Rannar Airik, PhD, a research specialist in pediatric nephrology who is currently an assistant professor of pediatrics and developmental biology at UPMC Children’s and the University of Pittsburgh. Dr. Airik joined the Division in 2015 after previous appointments and fellowships at the University of Michigan and Boston Children’s Hospital.

Dr. Airik’s lab is currently focused on deciphering the mechanisms of chronic kidney disease resulting from NPHP using knockout murine models of SDCCAG8, CEP164, and FAN1 — genes known to cause NPHP in humans. Dr. Airik’s postdoctoral research was responsible for identifying for the first time the role of these three specific genes in NPHP, and specifically how DNA damage response and instability drives degenerative phenotypes of tubular atrophy and interstitial fibrosis that result from mutations in these target genes.

Pathomechanical Hallmarks of NPHP

While NPHP is highly heterogeneous, the clinical picture of the disease has certain commonalities, including tubular cysts and progressive interstitial scarring or fibrosis of the affected kidneys. Since the diseased kidneys display classic features of chronic kidney disease, NPHP represents an ideal genetic model to study the underlying mechanisms of this degenerative condition. “NPHP is an autosomal recessive disease, so it requires two alleles of a gene to be mutated in order to manifest. While the disease mechanisms remain largely enigmatic, it has been established, that the proteins encoded by NPHP genes localize to the primary cilium or centrosome. This shared subcellular localization is thought to unite the clinical phenotype of the condition,” says Dr. Airik.

Accordingly, the current thinking postulates that NPHP proteins function in the cilium or at the centrosome, which in ciliated cells forms the base of the cilium. The ciliary axoneme is essentially a microtubular extension of the centrosome, that forms at the apical side of the renal tubular epithelial cells and protrudes into the tubular lumen. Various chemical and mechanical signals in this space are perceived by the primary cilium, which interprets them and relays to the cytoplasm. Dysregulation of this signaling axis precipitates NPHP. Although, this model of NPHP pathogenesis is widely accepted, recent gene identification in humans has challenged it, and linked the pathogenesis of NPHP to defective DNA damage response signaling, resulting in genome instability and cell-cycle defects. These findings have provided new insights to NPHP proteins’ role in the primary cilium and cell cycle regulation.

“During my postdoctoral research, we discovered that, in addition to ciliary and centrosomal localization, some NPHP proteins localize to the nucleus where they participate in DNA replication and repair. Being normally components of the DNA replication machinery, their absence leads to destabilized replication forks, activation of DNA damage response, and ultimately to cellular senescence which underpins tubular atrophy and interstitial fibrosis in NPHP, and in chronic kidney disease in general.”

Chronic Kidney Disease and the FAN1 Gene

Dr. Airik’s past work with the FAN1 gene has led to his securing a new NIH RO1 grant to continue his research into interrogating the role of DNA damage response signaling in the development of chronic kidney disease. FAN1, a DNA structure-specific endonuclease, functions at DNA repair and replication fork stabilization. Individuals with mutations in FAN1 gene develop a form of chronic kidney disease, known as karyomegalic tubulointerstitial nephritis, in their thirties. The affected kidneys display features of aged kidneys, suggesting that FAN1 is required to protect kidneys from premature senescence.

“DNA damage repair is a very important component of the aging kidney required to avoid chronic kidney disease. Defective DNA repair via genetic mutation appears to be one of the culprits based on our FAN1 knockout model. We’re very interested in how the process of DNA repair through this pathway affords a protective function in the kidney, and are investigating how dysregulation of the process could be targeted therapeutically in order to slow or halt fibrotic progression and CKD,” says Dr. Airik. Dr. Airik’s new RO1 from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) seeks to better understand the damage response that occurs in FAN1 deficient models to better characterize the process and identify targets of possible intervention.

References and Further Reading

The Role of DNA Damage Response in Chronic Kidney Disease. NIH Project Number: 1R01DK115403-01A1. Principal Investigator: Rannar Airik, PhD. Sponsor: NIDDKD.

Chaki M, Airik R, et al. Exome Capture Reveals ZNF423 and CEP164 Mutations, Linking Renal Ciliopathies to DNA Damage Response Signaling. Cell. 2012; 150(3): 533-548.

Airik R, Schueler M, Airik M, Cho J, Porath JD, Mukerjee E, Sims-Lucas S, Hildebrand F. A FANCD2/FANCI-Associated Nuclease 1-Knockout Model Develops Karyomegalic Interstitial Nephritis. J Am Soc Nephrol. 2016; 27(12): 3552-3559.