Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

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Author summary

Birt-Hogg-Dube (BHD) syndrome is a dominantly inherited genetic disease characterized by predisposition to fibrofolliculomas, lung cysts, and renal cancer. The disease is linked to germline variants in the folliculin (FLCN) tumor suppressor gene. Here, we present a combined computational and experimental study, focusing on rare BHD-linked missense and single amino acid deletion variants. Our data show that many disease-causing FLCN variants lead to structural destabilization and rapid proteasomal degradation of the FLCN protein. The reduced level of FLCN, in turn, leads to degradation of the FLCN binding partners FNIP1 and FNIP2. Additional results show that the turnover of FLCN is regulated by the deubiquitylating enzyme Ubp15/USP7 and molecular chaperones. We propose that for some missense variants, stabilization and resulting restoration of function may hold therapeutic potential, and that our computational saturation scan encompassing both missense variants and single site deletions in FLCN may allow classification of rare FLCN variants of uncertain clinical significance.

Germline mutations in the folliculin (FLCN) tumor suppressor gene are linked to Birt-Hogg-Dube (BHD) syndrome, a dominantly inherited genetic disease characterized by predisposition to fibrofolliculomas, lung cysts, and renal cancer. Most BHD-linked FLCN variants include large deletions and splice site aberrations predicted to cause loss of function. The mechanisms by which missense variants and short in-frame deletions in FLCN trigger disease are unknown. Here, we present an integrated computational and experimental study that reveals that the majority of such disease-causing FLCN variants cause loss of function due to proteasomal degradation of the encoded FLCN protein, rather than directly ablating FLCN function. Accordingly, several different single-site FLCN variants are present at strongly reduced levels in cells. In line with our finding that FLCN variants are protein quality control targets, several are also highly insoluble and fail to associate with the FLCN-binding partners FNIP1 and FNIP2. The lack of FLCN binding leads to rapid proteasomal degradation of FNIP1 and FNIP2. Half of the tested FLCN variants are mislocalized in cells, and one variant (Delta E510) forms perinuclear protein aggregates. A yeast-based stability screen revealed that the deubiquitylating enzyme Ubp15/USP7 and molecular chaperones regulate the turnover of the FLCN variants. Lowering the temperature led to a stabilization of two FLCN missense proteins, and for one (R362C), function was re-established at low temperature. In conclusion, we propose that most BHD-linked FLCN missense variants and small in-frame deletions operate by causing misfolding and degradation of the FLCN protein, and that stabilization and resulting restoration of function may hold therapeutic potential of certain disease-linked variants. Our computational saturation scan encompassing both missense variants and single site deletions in FLCN may allow classification of rare FLCN variants of uncertain clinical significance.

Original languageEnglish
Article numbere1009187
JournalPLOS Genetics
Volume16
Issue number11
Number of pages28
ISSN1553-7404
DOIs
Publication statusPublished - 2020

    Research areas

  • PROTEIN-QUALITY CONTROL, AMINO-ACID DELETION, NIHON RAT MODEL, MOLECULAR CHAPERONES, BHD GENE, MISFOLDED PROTEINS, TUMOR-SUPPRESSOR, SPONTANEOUS PNEUMOTHORAX, CO-CHAPERONES, IN-SILICO

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