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Simon Garinet Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France

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Juliette Nectoux Laboratory of Genetics and Molecular Biology, Hôpital Cochin, Assistance Publique – Hôpitaux de Paris, Paris, France

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Mario Neou Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France

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Eric Pasmant Laboratory of Genetics and Molecular Biology, Hôpital Cochin, Assistance Publique – Hôpitaux de Paris, Paris, France
INSERM UMR745, Biological and Pharmaceutical Sciences University, Université Paris Descartes, Sorbonne Paris Cité, Paris, France

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Anne Jouinot Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France
Department of Medical Oncology, Hôpital Cochin, Assistance Publique – Hôpitaux de Paris, Paris, France

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Mathilde Sibony Department of Pathology, Hôpital Cochin, Assistance Publique – Hôpitaux de Paris, Paris, France

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Lucie Orhant Laboratory of Genetics and Molecular Biology, Hôpital Cochin, Assistance Publique – Hôpitaux de Paris, Paris, France

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Juliana Pipoli da Fonseca Institut Cochin GENOMI’C Platform, Paris, France

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Karine Perlemoine Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France

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Léopoldine Bricaire Department of Endocrinology, Cochin Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France

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Lionel Groussin Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France
Department of Endocrinology, Cochin Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France

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Olivier Soubrane Department of Hepato-Pancreato-Biliary Surgery, Hôpital Beaujon, Assistance Publique – Hôpitaux de Paris, Paris, France

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Bertrand Dousset Department of Digestive and Endocrine Surgery, Assistance Publique – Hôpitaux de Paris, Paris, France

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Rossella Libe Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France
Department of Endocrinology, Cochin Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France

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Franck Letourneur Institut Cochin GENOMI’C Platform, Paris, France

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Jérome Bertherat Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France
Department of Endocrinology, Cochin Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France
Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Hôpital Cochin, AssistancePublique – Hôpitaux de Paris, Paris, France

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Guillaume Assié Institut Cochin INSERM U1016/UMR8104 and CNRS UMR-S8104, Paris, France
Department of Endocrinology, Cochin Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France
Reference Center for Rare Adrenal Diseases, Reference Center for Rare Adrenal Cancer Network COMETE, Hôpital Cochin, AssistancePublique – Hôpitaux de Paris, Paris, France

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Laura C Hernández-Ramírez Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Ryhem Gam Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada

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Nuria Valdés Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
Service of Endocrinology and Nutrition, Hospital Universitario Central de Asturias, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain

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Maya B Lodish Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Nathan Pankratz Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, USA

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Aurelio Balsalobre Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada

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Yves Gauthier Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada

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Fabio R Faucz Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Giampaolo Trivellin Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Prashant Chittiboina Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland, USA

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John Lane Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, USA

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Denise M Kay Newborn Screening Program, Wadsworth Center, New York State Department of Health, Albany, New York, USA

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Aggeliki Dimopoulos Division of Intramural Population Health Research, Epidemiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Stephan Gaillard Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
Department of Neurosurgery, Hôpital Foch, Suresnes, France

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Mario Neou Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France

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Jérôme Bertherat Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
Service d’Endocrinologie, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France

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Guillaume Assié Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
Service d’Endocrinologie, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France

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Chiara Villa Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
Department of Pathological Cytology and Anatomy, Hôpital Foch, Suresnes, France
Department of Endocrinology, CHU de Liège, University of Liège, Liège, Belgium

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James L Mills Division of Intramural Population Health Research, Epidemiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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Jacques Drouin Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada

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Constantine A Stratakis Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA

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The CABLES1 cell cycle regulator participates in the adrenal–pituitary negative feedback, and its expression is reduced in corticotropinomas, pituitary tumors with a largely unexplained genetic basis. We investigated the presence of CABLES1 mutations/copy number variations (CNVs) and their associated clinical, histopathological and molecular features in patients with Cushing’s disease (CD). Samples from 146 pediatric (118 germline DNA only/28 germline and tumor DNA) and 35 adult (tumor DNA) CD patients were screened for CABLES1 mutations. CNVs were assessed in 116 pediatric CD patients (87 germline DNA only/29 germline and tumor DNA). Four potentially pathogenic missense variants in CABLES1 were identified, two in young adults (c.532G > A, p.E178K and c.718C > T, p.L240F) and two in children (c.935G > A, p.G312D and c.1388A > G, and p.D463G) with CD; no CNVs were found. The four variants affected residues within or close to the predicted cyclin-dependent kinase-3 (CDK3)-binding region of the CABLES1 protein and impaired its ability to block cell growth in a mouse corticotropinoma cell line (AtT20/D16v-F2). The four patients had macroadenomas. We provide evidence for a role of CABLES1 as a novel pituitary tumor-predisposing gene. Its function might link two of the main molecular mechanisms altered in corticotropinomas: the cyclin-dependent kinase/cyclin group of cell cycle regulators and the epidermal growth factor receptor signaling pathway. Further studies are needed to assess the prevalence of CABLES1 mutations among patients with other types of pituitary adenomas and to elucidate the pituitary-specific functions of this gene.

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Simon Faillot Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Thomas Foulonneau Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Mario Néou Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Stéphanie Espiard Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Simon Garinet Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Anna Vaczlavik Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Anne Jouinot Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Windy Rondof Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Amandine Septier Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Ludivine Drougat Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Karine Hécale-Perlemoine Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Bruno Ragazzon Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Marthe Rizk-Rabin Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France

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Mathilde Sibony Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Pathology, AP-HP, Hôpital Pitié-Salpétrière, Pierre et Marie Curie Université, Paris, France

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Fidéline Bonnet-Serrano Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Endocrinology, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, Paris, France
Department of Hormonology, AP-HP, Hôpital Cochin, Paris, France

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Jean Guibourdenche Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Hormonology, AP-HP, Hôpital Cochin, Paris, France

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Rosella Libé Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Endocrinology, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, Paris, France

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Lionel Groussin Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Endocrinology, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, Paris, France

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Bertrand Dousset Department of Endocrine Surgery, AP-HP, Hôpital Cochin, Paris, France

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Aurélien de Reyniès Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France

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Jérôme Bertherat Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Endocrinology, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, Paris, France

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Guillaume Assié Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
Department of Endocrinology, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, Paris, France

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Benign adrenal tumors cover a spectrum of lesions with distinct morphology and steroid secretion. Current classification is empirical. Beyond a few driver mutations, pathophysiology is not well understood. Here, a pangenomic characterization of benign adrenocortical tumors is proposed, aiming at unbiased classification and new pathophysiological insights. Benign adrenocortical tumors (n = 146) were analyzed by transcriptome, methylome, miRNome, chromosomal alterations and mutational status, using expression arrays, methylation arrays, miRNA sequencing, SNP arrays, and exome or targeted next-generation sequencing respectively. Pathological and hormonal data were collected for all tumors. Pangenomic analysis identifies four distinct molecular categories: (1) tumors responsible for overt Cushing, gathering distinct tumor types, sharing a common cAMP/PKA pathway activation by distinct mechanisms; (2) adenomas with mild autonomous cortisol excess and non-functioning adenomas, associated with beta-catenin mutations; (3) primary macronodular hyperplasia with ARMC5 mutations, showing an ovarian expression signature; (4) aldosterone-producing adrenocortical adenomas, apart from other benign tumors. Epigenetic alterations and steroidogenesis seem associated, including CpG island hypomethylation in tumors with no or mild cortisol secretion, miRNA patterns defining specific molecular groups, and direct regulation of steroidogenic enzyme expression by methylation. Chromosomal alterations and somatic mutations are subclonal, found in less than 2/3 of cells. New pathophysiological insights, including distinct molecular signatures supporting the difference between mild autonomous cortisol excess and overt Cushing, ARMC5 implication into the adreno-gonadal differentiation faith, and the subclonal nature of driver alterations in benign tumors, will orient future research. This first genomic classification provides a large amount of data as a starting point.

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