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Flynn A, Dwight T, Harris J, Benn D, Zhou L, Hogg A, Catchpoole D, James P, Duncan EL, Trainer A, Gill AJ, Clifton-Bligh R, Hicks RJ, Tothill RW. Pheo-Type: A Diagnostic Gene-expression Assay for the Classification of Pheochromocytoma and Paraganglioma. J Clin Endocrinol Metab 2016; 101:1034-43. [PMID: 26796762 DOI: 10.1210/jc.2015-3889] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT Pheochromocytomas and paragangliomas (PPGLs) are heritable neoplasms that can be classified into gene-expression subtypes corresponding to their underlying specific genetic drivers. OBJECTIVE This study aimed to develop a diagnostic and research tool (Pheo-type) capable of classifying PPGL tumors into gene-expression subtypes that could be used to guide and interpret genetic testing, determine surveillance programs, and aid in elucidation of PPGL biology. DESIGN A compendium of published microarray data representing 205 PPGL tumors was used for the selection of subtype-specific genes that were then translated to the Nanostring gene-expression platform. A support vector machine was trained on the microarray dataset and then tested on an independent Nanostring dataset representing 38 familial and sporadic cases of PPGL of known genotype (RET, NF1, TMEM127, MAX, HRAS, VHL, and SDHx). Different classifier models involving between three and six subtypes were compared for their discrimination potential. RESULTS A gene set of 46 genes and six endogenous controls was selected representing six known PPGL subtypes; RTK1-3 (RET, NF1, TMEM127, and HRAS), MAX-like, VHL, and SDHx. Of 38 test cases, 34 (90%) were correctly predicted to six subtypes based on the known genotype to gene-expression subtype association. Removal of the RTK2 subtype from training, characterized by an admixture of tumor and normal adrenal cortex, improved the classification accuracy (35/38). Consolidation of RTK and pseudohypoxic PPGL subtypes to four- and then three-class architectures improved the classification accuracy for clinical application. CONCLUSIONS The Pheo-type gene-expression assay is a reliable method for predicting PPGL genotype using routine diagnostic tumor samples.
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Affiliation(s)
- Aidan Flynn
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Trisha Dwight
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Jessica Harris
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Diana Benn
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Li Zhou
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Annette Hogg
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Daniel Catchpoole
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Paul James
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Emma L Duncan
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Alison Trainer
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Anthony J Gill
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Roderick Clifton-Bligh
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer Centre (A.F., A.H., P.J., A.T., R.J.H., R.W.T.), East Melbourne, Victoria, 3002 Australia; The Department of Pathology (R.W.T., A.F.), University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Genetics (T.D., D.B., R.C.-B.), Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia; University of Sydney (T.D., D.B., A.J.G., R.C.-B.), Sydney, New South Wales 2006, Australia; The University of Queensland Diamantina Institute, Translational Research Institute (J.H., E.L.D.), Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia; The Tumor Bank (L.Z., D.C.), Children's Cancer Research Unit, The Children's Hospital at Westmead, St Westmead, New South Wales 2145, Australia; The Sir Peter MacCallum Department of Oncology (P.J., A.T., R.J.H.), University of Melbourne, Parkville, Victoria 3010, Australia; Department of Endocrinology (E.L.D.), Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Royal Melbourne Hospital and Department of Medicine (A.T.), University of Melbourne, Parkville, Victoria 3010, Australia; and Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research and the Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
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116
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Juhlin CC, Stenman A, Haglund F, Clark VE, Brown TC, Baranoski J, Bilguvar K, Goh G, Welander J, Svahn F, Rubinstein JC, Caramuta S, Yasuno K, Günel M, Bäckdahl M, Gimm O, Söderkvist P, Prasad ML, Korah R, Lifton RP, Carling T. Whole-exome sequencing defines the mutational landscape of pheochromocytoma and identifies KMT2D as a recurrently mutated gene. Genes Chromosomes Cancer 2015; 54:542-54. [PMID: 26032282 PMCID: PMC4755142 DOI: 10.1002/gcc.22267] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 12/13/2022] Open
Abstract
As subsets of pheochromocytomas (PCCs) lack a defined molecular etiology, we sought to characterize the mutational landscape of PCCs to identify novel gene candidates involved in disease development. A discovery cohort of 15 PCCs wild type for mutations in PCC susceptibility genes underwent whole‐exome sequencing, and an additional 83 PCCs served as a verification cohort for targeted sequencing of candidate mutations. A low rate of nonsilent single nucleotide variants (SNVs) was detected (6.1/sample). Somatic HRAS and EPAS1 mutations were observed in one case each, whereas the remaining 13 cases did not exhibit variants in established PCC genes. SNVs aggregated in apoptosis‐related pathways, and mutations in COSMIC genes not previously reported in PCCs included ZAN, MITF, WDTC1, and CAMTA1. Two somatic mutations and one constitutional variant in the well‐established cancer gene lysine (K)‐specific methyltransferase 2D (KMT2D, MLL2) were discovered in one sample each, prompting KMT2D screening using focused exome‐sequencing in the verification cohort. An additional 11 PCCs displayed KMT2D variants, of which two were recurrent. In total, missense KMT2D variants were found in 14 (11 somatic, two constitutional, one undetermined) of 99 PCCs (14%). Five cases displayed somatic mutations in the functional FYR/SET domains of KMT2D, constituting 36% of all KMT2D‐mutated PCCs. KMT2D expression was upregulated in PCCs compared to normal adrenals, and KMT2D overexpression positively affected cell migration in a PCC cell line. We conclude that KMT2D represents a recurrently mutated gene with potential implication for PCC development. © 2015 The Authors. Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.
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Affiliation(s)
- C Christofer Juhlin
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT, 06520.,Department of Surgery, Yale School of Medicine, New Haven, CT.,Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, CCK, Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, CCK, Stockholm, Sweden
| | - Felix Haglund
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, CCK, Stockholm, Sweden
| | - Victoria E Clark
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT
| | - Taylor C Brown
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT, 06520.,Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Jacob Baranoski
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT
| | - Kaya Bilguvar
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT
| | - Gerald Goh
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT
| | - Jenny Welander
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, SE-58185, Sweden
| | - Fredrika Svahn
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, CCK, Stockholm, Sweden
| | - Jill C Rubinstein
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT, 06520.,Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Stefano Caramuta
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, CCK, Stockholm, Sweden
| | - Katsuhito Yasuno
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT.,Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Murat Günel
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT
| | - Martin Bäckdahl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Oliver Gimm
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, SE-58185, Sweden.,Department of Surgery, County Council of Östergötland, Linköping, SE-58185, Sweden
| | - Peter Söderkvist
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, SE-58185, Sweden
| | - Manju L Prasad
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Reju Korah
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT, 06520.,Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT.,Yale Center for Mendelian Genomics, New Haven, CT
| | - Tobias Carling
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT, 06520.,Department of Surgery, Yale School of Medicine, New Haven, CT
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