Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells.

Iris E Glykofridis ,Franziska Böttger,Puck Veen,Sepide Derakhshan,Denise Westland,Jarno Drost,Irma Van De Beek,Martin A Rooimans ,Arjan C Houweling ,Renée X De Menezes ,Connie R Jiménez ,Sander R Piersma ,Saskia E Van Mil ,Sinéad M Lougheed ,Pino J Poddighe ,Thang V Pham ,Hanne Meijers-Heijboer ,Jaco C Knol ,Jesper A Balk ,Fried Zwartkruis ,Rob M F Wolthuis

doi:10.7554/elife.61630

Abstract

Germline mutations in the Folliculin (FLCN) tumor suppressor gene cause Birt-Hogg-Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing carriers to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanism by which FLCN prevents kidney cancer remains unknown. Here, we show that disrupting FLCN in human renal tubular epithelial cells (RPTEC/TERT1) activates TFE3, upregulating expression of its E-box targets, including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, the absence of FLCN or its binding partners FNIP1/FNIP2 induces interferon response genes independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence immune responses. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.

Highlights

Renal cell carcinoma (RCC) is the most common form of kidney cancer representing up to 5% of newly identified cancer cases (Ferlay et al, 2019; Lopez-Beltran et al, 2006; Siegel et al, 2018)
We propose that TFE3 and STAT1/2 are the two main, independent transcriptional effectors of FLCN-FNIP1/2 loss in human renal epithelial cells
Because a TP53dependent DNA damage response prohibits effective gene editing in some cell types (Haapaniemi et al, 2018; Ihry et al, 2018), we simultaneously knocked-out TP53 and FLCN to improve targeting efficiency

Summary

Introduction

Renal cell carcinoma (RCC) is the most common form of kidney cancer representing up to 5% of newly identified cancer cases (Ferlay et al, 2019; Lopez-Beltran et al, 2006; Siegel et al, 2018). Birt-Hogg-Dubesyndrome (BHD) is a dominantly inherited kidney cancer syndrome caused by mono-allelic germline loss-of-function mutations of the essential and conserved Folliculin (FLCN) gene (Nahorski et al, 2011; Nickerson et al, 2002). The lifetime risk for BHD patients to develop RCC is ~10 times higher than for the unaffected population

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