The HOPS complex subunit VPS39 controls ciliogenesis through autophagy

Abstract

Primary cilia are microtubule-based organelles that assemble and protrude from the surface of most mammalian cells during quiescence. The biomedical relevance of cilia is indicated by disorders ascribed to cilia dysfunction, known as ciliopathies, that display distinctive features including renal cystic disease. In this report, we demonstrate that vacuolar protein sorting 39 (VPS39), a component of the homotypic fusion and vacuole protein sorting (HOPS) complex, acts as a negative regulator of ciliogenesis in human renal cells, by controlling the localization of the intraflagellar transport 20 protein at the base of cilia through autophagy. Moreover, we show that VPS39 controls ciliogenesis through autophagy also in vivo in renal tubules of medaka fish. These observations suggest a direct involvement of the HOPS complex in the regulation of autophagy-mediated ciliogenesis and eventually in target selection. Interestingly, we show that the impact of autophagy modulation on ciliogenesis is cell-type dependent and strictly related to environmental stimuli. This report adds a further tile to the cilia-autophagy connection and suggests that VPS39 could represent a new biological target for the recovery of the cilia-related phenotypes observed in the kidneys of patients affected by ciliopathies.

RAB19 Directs Cortical Remodeling and Membrane Growth for Primary Ciliogenesis

“…In support of our data, VPS41 and other HOPS subunits were identified as positive regulators of ciliary signaling in a genome-wide CRISPR screen (Breslow et al, 2018). Moreover, while this manuscript was in preparation, work implicating VPS39, the other HOPSspecific subunit, in ciliogenesis was published (Iaconis et al, 2020).…”

Pathophysiology of Primary Cilia: Signaling and Proteostasis Regulation

“…Genetic silencing of VPS39, by reducing OFD1 levels at pericentriolar satellites and promoting recruitment of IFT20 at ciliary structures, induces cilia overgrowth. This effect was reversed by concomitant activation of the autophagy machinery, supporting the notion that in renal cells autophagy prevents cilia elongation by controlling OFD1 and IFT20 localization at pericentriolar satellites ( Iaconis et al, 2020 ). A similar role for autophagy in ciliogenesis has been described in epithelial cells of the respiratory tract.…”

A ZFYVE19 gene mutation associated with neonatal cholestasis and cilia dysfunction: case report with a novel pathogenic variant

“…Cells were grown on glass coverslips pretreated with poly-lysine (Sigma-Aldrich) to facilitate attachment of cells in 24-well plates and cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 20% FBS, 1 mM l-glutamine, and 1% antibiotics (penicillin/streptomycin). When cells attained 90% confluence, they were cultured in serum-free media for another 48 h to induce ciliogenesis as described [ 10 , 11 ]. Cells were fixed with ice-cold methanol for 5 min, then permeabilized and immunostained with antibodies against the ciliary component ADP-ribosylation factor-like GTPase 13B (ARL13B; rabbit polyclonal antibody, 17711-1-AP, 1:1000 dilution; Proteintech) and the centriole marker γ-tubulin (T6557, 1:2000 dilution; Sigma-Aldrich).…”