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Makris EA, Sharma AK, Bergstrom EN, Xu X, de la Torre J, Banerjee S, Nguyen V, Hosseini M, Burgoyne A, Harismendy O, Alexandrov LB, Sicklick JK. Synchronous, Yet Genomically Distinct, GIST Offer New Insights Into Precise Targeting of Tumor Driver Mutations. JCO Precis Oncol 2021; 5:PO.20.00384. [PMID: 34250403 PMCID: PMC8232556 DOI: 10.1200/po.20.00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/04/2021] [Accepted: 02/18/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Eleftherios A Makris
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA.,Moores Cancer Center, UC San Diego, La Jolla, CA
| | - Ashwyn K Sharma
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA.,Moores Cancer Center, UC San Diego, La Jolla, CA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, San Diego, CA.,Department of Bioengineering, UC San Diego Jacobs School of Engineering, San Diego, CA
| | - Xiaojun Xu
- Moores Cancer Center, UC San Diego, La Jolla, CA.,Department of Medicine, Division of Biomedical Informatics, UC San Diego School of Medicine, San Diego, CA
| | - Jorge de la Torre
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA.,Moores Cancer Center, UC San Diego, La Jolla, CA
| | - Sudeep Banerjee
- Moores Cancer Center, UC San Diego, La Jolla, CA.,Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Vi Nguyen
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA.,Moores Cancer Center, UC San Diego, La Jolla, CA
| | - Mojgan Hosseini
- Department of Pathology, UC San Diego School of Medicine, San Diego, CA
| | - Adam Burgoyne
- Moores Cancer Center, UC San Diego, La Jolla, CA.,Department of Medicine, Division of Hematology-Oncology, UC San Diego School of Medicine, San Diego, CA
| | - Olivier Harismendy
- Moores Cancer Center, UC San Diego, La Jolla, CA.,Department of Medicine, Division of Biomedical Informatics, UC San Diego School of Medicine, San Diego, CA
| | - Ludmil B Alexandrov
- Moores Cancer Center, UC San Diego, La Jolla, CA.,Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, San Diego, CA.,Department of Bioengineering, UC San Diego Jacobs School of Engineering, San Diego, CA
| | - Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA.,Moores Cancer Center, UC San Diego, La Jolla, CA
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Wu J, Zhou H, Yi X, He Q, Lei T, Tan F, Liu H, Li B. Targeted Deep Sequencing Reveals Unrecognized KIT Mutation Coexistent with NF1 Deficiency in GISTs. Cancer Manag Res 2021; 13:297-306. [PMID: 33469372 PMCID: PMC7811451 DOI: 10.2147/cmar.s280174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/10/2020] [Indexed: 01/16/2023] Open
Abstract
Purpose NF1-deficient GISTs account for about 1% of gastrointestinal stromal tumors (GISTs) and are usually considered as a subtype of KIT/PDGFRA wild-type GISTs that have no detectable KIT and PDGFRA mutations. Some KIT/PDGFRA wild-type GISTs actually have cryptic KIT mutations (mKIT). So we investigate whether concurrent mKIT existed in NF1-associated GISTs. Patients and Methods Three independent cohorts were retrospectively analyzed. KIT/PDGFRA wild-type GISTs in Xiangya Hospital between May 2017 and Oct 2019 were investigated by next-generation sequencing (NGS) approach targeted 1021 cancer-related genes regions. GISTs cases in Gene+ dataset from May 2017 to May 2020 were collected from the platform of this company. The genotypes of GISTs in MSKCC cohort were downloaded from cBioPortal. Results A total of 290 cases including 23 KIT/PDGFRA wild-type GISTs in Xiangya Hospital, 136 GISTs in Gene+ database, and 131 GISTs in MSKCC were enrolled. Twenty-six cases have NF1 mutations (mNF1), and 48% (12/26) of NF1-mutated GISTs have concurrent mKIT. Compared with MSKCC (2/10, 20%), a higher ratio of mKIT in NF1-associated GISTs was detected in Xiangya Hospital (3/5, 60%) and Gene+ (7/11, 64%) (p<0.05). No mutation hotspot existed in mNF1. Most of mKIT centered within exon 11 (7/12, 58%) and others including exon 17 (3/12, 25%), exon 9(1/12, 8%), exon 13 (1/12, 8%) and exon 21 (1/12, 8%). No differences in age, gender, and location were detected between NF1-related GISTs with mKIT and those without mKIT. Three GIST cases of type I neurofibromatosis, skin neurofibromas and micro-GISTs (≤1 cm) were devoid of mKIT, but all the mini-GISTs (1~2 cm) and clinic GIST lesions (>2 cm) in two cases harbored mKIT. Conclusion mKIT was not unusual in NF1-associated GISTs, especially in Chinese populations. The gain-of-function mKIT possibly facilitated the progression of NF1-deficient lesions to clinic GISTs, however, the underlying mechanism warrants further studies.
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Affiliation(s)
- Jinchun Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Haiyan Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xiaoping Yi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Qiongzhi He
- Geneplus-Beijing Institute, Beijing, People's Republic of China
| | - Tianxiang Lei
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Fengbo Tan
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Heli Liu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Bin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
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5
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Banerjee S, Corless CL, Miettinen MM, Noh S, Ustoy R, Davis JL, Tang CM, Yebra M, Burgoyne AM, Sicklick JK. Loss of the PTCH1 tumor suppressor defines a new subset of plexiform fibromyxoma. J Transl Med 2019; 17:246. [PMID: 31362756 PMCID: PMC6668176 DOI: 10.1186/s12967-019-1995-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Plexiform fibromyxoma (PF) is a rare gastric tumor often confused with gastrointestinal stromal tumor. These so-called "benign" tumors often present with upper GI bleeding and gastric outlet obstruction. It was recently demonstrated that approximately one-third of PF have activation of the GLI1 oncogene, a transcription factor in the hedgehog (Hh) pathway, via a MALAT1-GLI1 fusion protein or GLI1 up-regulation. Despite this discovery, the biology of most PFs remains unknown. METHODS Next generation sequencing (NGS) was performed on formalin-fixed paraffin-embedded (FFPE) samples of PF specimens collected from three institutions (UCSD, NCI and OHSU). Fresh frozen tissue from one tumor was utilized for in vitro assays, including quantitative RT-PCR and cell viability assays following drug treatment. RESULTS Eight patients with PF were identified and 5 patients' tumors were analyzed by NGS. An index case had a mono-allelic PTCH1 deletion of exons 15-24 and a second case, identified in a validation cohort, also had a PTCH1 gene loss associated with a suspected long-range chromosome 9 deletion. Building on the role of Hh signaling in PF, PTCH1, a tumor suppressor protein, functions upstream of GLI1. Loss of PTCH1 induces GLI1 activation and downstream gene transcription. Utilizing fresh tissue from the index PF case, RT-qPCR analysis demonstrated expression of Hh pathway components, SMO and GLI1, as well as GLI1 transcriptional targets, CCND1 and HHIP. In turn, short-term in vitro treatment with a Hh pathway inhibitor, sonidegib, resulted in dose-dependent cell killing. CONCLUSIONS For the first time, we report a novel association between PTCH1 inactivation and the development of plexiform fibromyxoma. Hh pathway inhibition with SMO antagonists may represent a target to study for treating a subset of plexiform fibromyxomas.
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Affiliation(s)
- Sudeep Banerjee
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Christopher L. Corless
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | | | - Sangkyu Noh
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
| | - Rowan Ustoy
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
| | - Jessica L. Davis
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Chih-Min Tang
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
| | - Mayra Yebra
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
| | - Adam M. Burgoyne
- Division of Hematology Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA USA
| | - Jason K. Sicklick
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California, San Diego, UC San Diego Health Sciences, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA 92093-0987 USA
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7
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Koczkowska M, Callens T, Gomes A, Sharp A, Chen Y, Hicks AD, Aylsworth AS, Azizi AA, Basel DG, Bellus G, Bird LM, Blazo MA, Burke LW, Cannon A, Collins F, DeFilippo C, Denayer E, Digilio MC, Dills SK, Dosa L, Greenwood RS, Griffis C, Gupta P, Hachen RK, Hernández-Chico C, Janssens S, Jones KJ, Jordan JT, Kannu P, Korf BR, Lewis AM, Listernick RH, Lonardo F, Mahoney MJ, Ojeda MM, McDonald MT, McDougall C, Mendelsohn N, Miller DT, Mori M, Oostenbrink R, Perreault S, Pierpont ME, Piscopo C, Pond DA, Randolph LM, Rauen KA, Rednam S, Rutledge SL, Saletti V, Schaefer GB, Schorry EK, Scott DA, Shugar A, Siqveland E, Starr LJ, Syed A, Trapane PL, Ullrich NJ, Wakefield EG, Walsh LE, Wangler MF, Zackai E, Claes KBM, Wimmer K, van Minkelen R, De Luca A, Martin Y, Legius E, Messiaen LM. Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype-phenotype correlation. Genet Med 2019; 21:867-876. [PMID: 30190611 PMCID: PMC6752285 DOI: 10.1038/s41436-018-0269-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. METHODS A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. RESULTS None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofibromas. We did not identify any complications, such as symptomatic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_2972del. CONCLUSION We demonstrate that individuals with the NF1 p.Met992del pathogenic variant have a mild NF1 phenotype lacking clinically suspected plexiform, cutaneous, or subcutaneous neurofibromas. However, learning difficulties are clearly part of the phenotypic presentation in these individuals and will require specialized care.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Angela Sharp
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alesha D Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amedeo A Azizi
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Donald G Basel
- Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gary Bellus
- Department of Clinical Genetics and Metabolism, Children's Hospital, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego; Division of Genetics/Dysmorphology, Rady Children's Hospital, San Diego, California, USA
| | | | - Leah W Burke
- Clinical Genetics Program, University of Vermont Medical Center, Burlington, Vermont, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Felicity Collins
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Colette DeFilippo
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, California, USA
| | - Ellen Denayer
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Maria C Digilio
- Medical Genetics Unit, Bambino Gesù Children's, IRCCS, Rome, Italy
| | | | - Laura Dosa
- SOC Genetica Medica, AOU Meyer, Florence, Italy
| | - Robert S Greenwood
- Department of Neurology, Division of Child Neurology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Punita Gupta
- Neurofibromatosis Diagnostic & Treatment Program, St. Joseph's Children's Hospital, Paterson, New Jersey, USA
| | - Rachel K Hachen
- Neurofibromatosis Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Concepción Hernández-Chico
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Madrid, Spain
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristi J Jones
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Justin T Jordan
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert H Listernick
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Maurice J Mahoney
- Department of Genetics, Yale University, New Haven, Connecticut, USA
| | - Mayra Martinez Ojeda
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nancy Mendelsohn
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Mari Mori
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Rianne Oostenbrink
- Department of General Pediatrics, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Sebastién Perreault
- CHU Sainte-Justine, Mother and Child University Hospital Center, Montréal, Québec, Canada
| | - Mary Ella Pierpont
- Department of Pediatrics and Ophthalmology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Carmelo Piscopo
- U.O.S.C. Medical Genetics, A.O.R.N. "A. Cardarelli", Naples, Italy
| | - Dinel A Pond
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Katherine A Rauen
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, California, USA
| | - Surya Rednam
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - G Bradley Schaefer
- Division of Medical Genetics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Elizabeth K Schorry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Andrea Shugar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth Siqveland
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - Lois J Starr
- Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ashraf Syed
- DCH Regional Medical Center and Northport Medical Center, Northport, Alabama, USA
| | - Pamela L Trapane
- Stead Family Department of Pediatrics, University of Iowa Hospitals & Clinics, Iowa City, Iowa, USA
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Emily G Wakefield
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Laurence E Walsh
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharina Wimmer
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alessandro De Luca
- IRCCS Casa Sollievo della Sofferenza, Molecular Genetics Unit, San Giovanni Rotondo, Foggia, Italy
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Madrid, Spain
| | - Eric Legius
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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