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Comprehensive Genomic Profiling of Patient-Matched Head and Neck Cancer Cells: a Preclinical Pipeline for Metastatic and Recurrent Disease

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Comprehensive Genomic Profiling of Patient-Matched Head and Neck Cancer Cells: a Preclinical Pipeline for Metastatic and Recurrent Disease Published OnlineFirst August 14, 2018; DOI: 10.1158/1541-7786.MCR-18-0056 Genomics Molecular Cancer Research Comprehensive Genomic Profiling of Patient- matched Head and Neck Cancer Cells: A Preclinical Pipeline for Metastatic and Recurrent Disease Lluís Nisa1,2,3, David Barras4, Michaela Medova1,2, Daniel M. Aebersold1,2, Matus Medo1,2, Michaela Poliakova1,2, Jonas Koch1,2, Beat Bojaxhiu1, Olgun Elicin¸ 1, Matthias S. Dettmer5, Paolo Angelino4, Roland Giger3, Urs Borner3, Marco D. Caversaccio3, Thomas E. Carey6,7,LizaHo8, Thomas A. McKee8, Mauro Delorenzi4,9,10, and Yitzhak Zimmer1,2 Abstract Metastases and tumor recurrence have a major prognostic confirmedcommonSPRR2Adownregulationinprimary impact in head and neck squamous cell carcinoma tumors (61.9% of cases) and lymph node metastases (HNSCC); however, cellular models that comprehensively (31.3%), but not in normal tissue. High expression of characterize metastatic and recurrent HNSCC are lacking. To SPRR2A in lymph node metastases was, along with non- this end, we obtained genomic, transcriptomic, and copy oropharyngeal location of the primary tumor, an indepen- number profiles of the UM-SCC cell line panel, encompass- dent prognostic factor for regional disease recurrence after ing patient-matched metastatic and recurrent cells. UM-SCC surgery and radiotherapy (HR 2.81; 95% CI, 1.16–6.79; P ¼ cells recapitulate the most prevalent genomic alterations 0.02). These results suggest that SPRR2A plays a dual role in described in HNSCC, featuring common TP53, PI3K, invasion and therapeutic resistance in HNSCC, respectively NOTCH, and Hippo pathway mutations. This analysis through its downregulation and overexpression. identified a novel F977Y kinase domain PIK3CA mutation exclusively present in a recurrent cell line (UM-SCC14B), Implications: The current study reveals translationally rele- potentially conferring resistance to PI3K inhibitors. Small vant mechanisms underlying metastasis and recurrence in proline-rich protein 2A (SPRR2A), a protein involved in HNSCC and represents an adjuvant tool for preclinical epithelial homeostasis and invasion, was one of the most research in this disease setting. Underlining its discovery consistently downregulated transcripts in metastatic and potential this approach identified a PIK3CA-resistant muta- recurrent UM-SCC cells. Assessment of SPRR2A protein tion as well as SPRR2A as possible theragnostic markers. expression in a clinical cohort of patients with HNSCC Mol Cancer Res; 1–15. Ó2018 AACR. 1Department of Radiation Oncology, Inselspital, Bern University Hospital, Introduction 2 University of Bern, Bern, Switzerland. Department for BioMedical Research, Development of regional or distant metastases and recurrence Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland. fi 3Department of Otorhinolaryngology – Head and Neck Surgery, Inselspital, after de nitive therapy are arguably the most outstanding issues in Bern University Hospital, University of Bern, Bern, Switzerland. 4SIB Swiss the management of patients with head and neck squamous cell Institute of Bioinformatics, Lausanne, Switzerland. 5Institute of Pathology, carcinoma (HNSCC). Presence of lymph node metastases has a University of Bern, Bern, Switzerland. 6Department of Otolaryngology - Head major prognostic impact, as it reduces survival of HNSCC patients and Neck Surgery, University of Michigan School of Medicine, Ann Arbor, roughly by half (1). Moreover, lymph node metastases do not 7 Michigan. Comprehensive Cancer Center, University of Michigan School of necessarily respond to given therapeutic approaches in the same Medicine, Ann Arbor, Michigan. 8Division of Clinical Pathology, Geneva University Hospitals, Geneva, Switzerland. 9Ludwig Center for Cancer Research, way as their matched primaries do, an observation likely under- University of Lausanne, Lausanne, Switzerland. 10Department of Oncology, lying different intrinsic biological mechanisms (2). Such a het- University of Lausanne, Lausanne, Switzerland. erogeneous behavior poses an obvious challenge to achieve Note: Supplementary data for this article are available at Molecular Cancer simultaneous local (primary tumor) and regional (lymph node Research Online (http://mcr.aacrjournals.org/). metastases) disease control. Indeed, while most early-stage (with L. Nisa and D. Barras are co-first authors of this article. the exception of oral squamous cell carcinoma) and some advanced-stage primaries can be usually managed by radiother- M. Delorenzi and Y. Zimmer are co-senior authors of this article. apy (with or without chemotherapy/cetuximab), presence of Corresponding Author: Yitzhak Zimmer, Department for BioMedical Research, lymph node metastases often requires combined approaches, € Maurice E. Muller-Haus, E-807, Murtenstrasse 35, Bern 3008, Switzerland. encompassing neck dissection and irradiation (3). Distant metas- Phone: 413-1632-2642; Fax: 413-1632-3297; E-mail: [email protected]. tases develop in approximately 10%–30% of HNSCC patients doi: 10.1158/1541-7786.MCR-18-0056 after definitive therapy and carries a meager prognosis (approx- Ó2018 American Association for Cancer Research. imately 5% overall 5-year survival; ref. 4). www.aacrjournals.org OF1 Downloaded from mcr.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst August 14, 2018; DOI: 10.1158/1541-7786.MCR-18-0056 Nisa et al. With respect to therapeutic resistance, recurrences after defin- the most common aberrations found in HNSCC are recapitulated itive therapy in HNSCC occur in 30%–50% of the cases, depend- in the cell lines. Moreover, the current datasets underline the ing on primary tumor anatomic location, stage at presentation, discovery potential of the UM-SCC panel and represent a unique and human papillomavirus (HPV) status among other factors (5). toolset for the preclinical study of invasion and treatment resis- Management options for treatment failures after multimodal tance mechanisms in HNSCC. therapy, including extensive salvage surgery, reirradiation, or fi palliation, are limited and often of limited ef cacy. Moreover, Materials and Methods such approaches carry almost systematically high rates of severe toxicity and/or functional impairment of breathing, swallowing, Ethical statement airway protection, and speech production (6, 7). Patients' tissue and clinical data were collected after approval by The inescapable corollary of these clinical considerations is the the Bernese Cantonal Ethical Committee (Protocol 050/14). The pressing need to develop and implement more effective thera- UM-SCC cell lines were obtained from surgically excised tissues peutic strategies for metastatic and recurrent HNSCC. from patients treated at the University of Michigan (Ann Arbor, The ability to tailor individual management approaches and to MI) who gave written informed consent for the use of their tissues implement them requires thorough characterization of the molec- for research studies, including the development of permanent cell ular alterations in HNSCC and extensive preclinical validation. lines. In this sense, concerted next-generation sequencing (NGS) approaches in HNSCC have been published over the last few Cell lines and reagents years, providing an unprecedented amount of information on the UM-SCC cell lines were provided by Professor T. Carey most frequent alterations and mechanisms underlying tumori- (University of Michigan, Ann Arbor, MI). Culture, mainte- genesis (8–12). With respect to preclinical validation, cancer cell nance, and cell line identity confirmation were performed as lines and their related in vivo models represent major research described previously (18). For group analysis, cell lines were tools in preclinical oncology when it comes to addressing issues divided in invasive/metastatic (UM-SCC-10B, -14C, -17B and related to tumor biology and target discovery. Comprehensive -22B) and recurrent (UM-SCC-11B, -14B, -74B and -81B), and genomic characterization is often unavailable for commonly used compared with their matched primaries ("A" series). cell lines, a limitation that hinders the generalization of results PI3K was inhibited with pictilisib (GDC-0941, AbMole Bio- and accounts at least to a certain extent for the discordant Science). This drug was dissolved in DMSO and stored at À20 C. responses to novel therapies seen in preclinical versus clinical settings (13). Karyotypes Recognizing the crucial nature of this issue, Barretina and For chromosome analysis, cells were grown as monolayers on colleagues (14) established genomic profiles of a large number coverslips (35 mm dish, 22 Â 22 mm Glass, MatTek corporation) of human cancer cell lines. In their study, the authors explored and harvested in situ. Cultures in exponential growth were correlations between genomic background and responses arrested at metaphase by adding 10 mg/mL colcemid (KaryoMax to particular therapeutic agents, emphasizing the relevance of Colcemid, Gibco) for 20 minutes at 37 C. Cells were then genetically driven management approaches. Several other stud- harvested with hypotonic saline solution (60 mmol/L KCl), fixed ies provide similar datasets for cell lines from different tumor with fresh fixative (3:1 methanol: acetic acid, Scharlau), dried in a entities, and databases such as the catalogue of somatic muta- drying chamber (25 C and 40% humidity, CDS-5, Thermotron), tions in cancer (COSMIC) systematically gather results from aged for 1 hour at 93 C on a hot plate
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