Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma

// Caroline V.M. Verhagen 1, 2, * , David M. Vossen 1, 2, * , Kerstin Borgmann 3 , Floor Hageman 1 , Reidar Grenman 4 , Manon Verwijs-Janssen 1 , Lisanne Mout 1 , Roel J.C. Kluin 5 , Marja Nieuwland 5 , Tesa M. Severson 6 , Arno Velds 5 , Ron Kerkhoven 5 , Mark J. O’Connor 7 , Martijn van der Heijden 1, 2 , Marie-Louise van Velthuysen 8 , Marcel Verheij 1, 9 , Volkert B. Wreesmann 2 , Lodewyk F.A. Wessels 10 , Michiel W.M. van den Brekel 2, 11 and Conchita Vens 1, 9 1 Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands 2 Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands 3 Laboratory of Radiobiology and Experimental Radiation Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany 4 Department of Otorhinolaryngology, Turku University Hospital, University of Turku, Turku, Finland 5 Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands 6 Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands 7 Oncology Innovative Medicines, AstraZeneca, Saffron Walden, UK 8 Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands 9 Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands 10 Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands 11 Department of Oral and Maxillofacial Surgery, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands * Shared first authorship Correspondence to: Conchita Vens, email: c.vens@nki.nl Keywords: HNSCC; gene variants; homologous recombination; Fanconi anemia; DNA repair Received: November 16, 2017      Accepted: February 25, 2018      Published: April 06, 2018 ABSTRACT Mutations in Fanconi Anemia or Homologous Recombination (FA/HR) genes can cause DNA repair defects and could therefore impact cancer treatment response and patient outcome. Their functional impact and clinical relevance in head and neck squamous cell carcinoma (HNSCC) is unknown. We therefore questioned whether functional FA/HR defects occurred in HNSCC and whether they are associated with FA/HR variants. We assayed a panel of 29 patient-derived HNSCC cell lines and found that a considerable fraction is hypersensitive to the crosslinker Mitomycin C and PARP inhibitors, a functional measure of FA/HR defects. DNA sequencing showed that these hypersensitivities are associated with the presence of bi-allelic rare germline and somatic FA/HR gene variants. We next questioned whether such variants are associated with prognosis and treatment response in HNSCC patients. DNA sequencing of 77 advanced stage HNSCC tumors revealed a 19% incidence of such variants. Importantly, these variants were associated with a poor prognosis ( p = 0.027; HR = 2.6, 1.1–6.0) but favorable response to high cumulative cisplatin dose. We show how an integrated in vitro functional repair and genomic analysis can improve the prognostic value of genetic biomarkers. We conclude that repair defects are marked and frequent in HNSCC and are associated with clinical outcome.