1
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Cloutier JM, Wang M, Vemula SS, Mirza S, Weier J, Aquino JD, McCalmont TH, LeBoit PE, Bastian BC, Yeh I. Amplification of mutant NRAS in melanocytic tumors with features of Spitz tumors. Mod Pathol 2024:100469. [PMID: 38467248 DOI: 10.1016/j.modpat.2024.100469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/13/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
NRAS activating mutations are prevalent in melanocytic neoplasia, occurring in a subset of common acquired melanocytic nevi and approximately 30% of cutaneous melanomas. In this study, we describe a cohort of seven distinctive melanocytic tumors characterized by activating point mutations in codon 61 of NRAS with amplification of the mutant NRAS allele and shared clinicopathologic features. These tumors occurred predominantly in younger patients, with a median age of 20 years (ranging from 6 to 56). They presented as papules on the helix of the ear (four cases) or extremities (three cases). Microscopically, the tumors were cellular, relatively well-circumscribed, compound or intradermal proliferations. The tumor cells often extended into the deep reticular dermis, and involved the superficial subcutaneous fat in some cases. The melanocytes were epithelioid to spindled with moderate amounts of cytoplasm and conspicuous nucleoli. They were arranged in short plexiform fascicles, nests, and cords. Some cases had occasional pleomorphic and multinucleated melanocytes. Rare dermal mitotic figures were present in all cases. The dermis contained thick collagen bundles and minimal solar elastosis. Follow-up data were available for five patients, with a median period of 4.2 years (ranging from 1 to 9 years), during which no recurrences or metastases were reported. Our series highlights a clinicopathologically and molecularly distinctive subset of NRAS-mutated tumors with amplification of the mutant NRAS allele.
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Affiliation(s)
- Jeffrey M Cloutier
- Department of Pathology, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH.
| | - Meng Wang
- Department of Dermatology, University of California, San Francisco, CA
| | - Swapna S Vemula
- Department of Dermatology, University of California, San Francisco, CA
| | - Sonia Mirza
- Department of Dermatology, University of California, San Francisco, CA
| | - Jingly Weier
- Department of Dermatology, University of California, San Francisco, CA
| | - Jamie D Aquino
- Department of Pathology, University of California, San Francisco, CA
| | - Timothy H McCalmont
- Department of Dermatology, University of California, San Francisco, CA; Department of Pathology, University of California, San Francisco, CA; Golden State Dermatology Associates, Walnut Creek, CA
| | - Philip E LeBoit
- Department of Dermatology, University of California, San Francisco, CA; Department of Pathology, University of California, San Francisco, CA; Helen Diller Family Cancer Center, University of California, San Francisco, CA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, CA; Department of Pathology, University of California, San Francisco, CA; Helen Diller Family Cancer Center, University of California, San Francisco, CA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, CA; Department of Pathology, University of California, San Francisco, CA; Helen Diller Family Cancer Center, University of California, San Francisco, CA.
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2
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Lorbeer FK, Rieser G, Goel A, Wang M, Oh A, Yeh I, Bastian BC, Hockemeyer D. Distinct senescence mechanisms restrain progression of dysplastic nevi. PNAS Nexus 2024; 3:pgae041. [PMID: 38371417 PMCID: PMC10873501 DOI: 10.1093/pnasnexus/pgae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
Telomerase reverse transcriptase (TERT) promoter mutations (TPMs) are frequently found in different cancer types, including ∼70% of sun-exposed skin melanomas. In melanoma, TPMs are among the earliest mutations and can be present during the transition from nevus to melanoma. However, the specific factors that contribute to the selection of TPMs in certain nevi subsets are not well understood. To investigate this, we analyzed a group of dysplastic nevi (DN) by sequencing genes commonly mutated in melanocytic neoplasms. We examined the relationship between the identified mutations, patient age, telomere length, histological features, and the expression of p16. Our findings reveal that TPMs are more prevalent in DN from older patients and are associated with shorter telomeres. Importantly, these TPMs were not found in nevi with BRAF V600E mutations. Conversely, DN with BRAF V600E mutations were observed in younger patients, had longer telomeres and a higher proportion of p16-positive cells. This suggests that these nevi arrest growth independently of telomere shortening through a mechanism known as oncogene-induced senescence (OIS). These characteristics extend to melanoma-sequencing datasets, where melanomas with BRAF V600E mutations were more likely to have a CDKN2A inactivation, overriding OIS. In contrast, melanomas without BRAF V600E mutations showed a higher frequency of TPMs. Our data imply that TPMs are selected to bypass replicative senescence (RS) in cells that were not arrested by OIS. Overall, our results indicate that a subset of melanocytic neoplasms face constraints from RS, while others encounter OIS and RS. The order in which these barriers are overcome during progression to melanoma depends on the mutational context.
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Affiliation(s)
- Franziska K Lorbeer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabrielle Rieser
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aditya Goel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Meng Wang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Areum Oh
- Rebus Biosystems, Santa Clara, CA 95050, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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3
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Perkins IU, Tan SY, McCalmont TH, Chou PM, Mully TW, Gerami P, Pomerantz JH, Reyes-Múgica M, Balkin DM, Kruse LL, Huang B, Reichek JL, Gangopadhyay N, Chiosea S, Green JR, Chamlin SL, Frieden IJ, Bastian BC, Yeh I. Melanoma in infants, caused by a gene fusion involving the anaplastic lymphoma kinase (ALK). Pigment Cell Melanoma Res 2024; 37:6-14. [PMID: 37475109 DOI: 10.1111/pcmr.13115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
We describe the first cases of pediatric melanoma with ALK fusion gene arising within giant congenital melanocytic nevi. Two newborn boys presented with large pigmented nodular plaques and numerous smaller satellite nevi. Additional expansile nodules developed within both nevi and invasive melanomas were diagnosed before 10 months of age in both boys. Oncogenic driver mutations in NRAS and BRAF were absent in both cases. Instead, oncogenic ZEB2::ALK fusion genes were identified in both the nevus and melanoma developing within the nevus. In both cases, tumors were noted by ultrasound in utero, demonstrated significant nodularity at birth, and progressed to melanoma in the first year of life suggesting that congenital nevi with ALK fusion genes may behave more aggressively than those with other mutations. As ALK kinase inhibitors are effective against a range of tumors with similar ALK fusion kinases, identifying ALK fusion genes in congenital melanocytic nevi may provide an opportunity for targeted therapy.
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Affiliation(s)
- Ifeoma U Perkins
- Department of Pathology, University of Colorado School of Medicine, Denver, Colorado, USA
| | - Serena Y Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Timothy H McCalmont
- Department of Dermatology, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
- GS Dermatology Associates, Walnut Creek, California, USA
| | - Pauline M Chou
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thaddeus W Mully
- Department of Dermatology, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
| | - Pedram Gerami
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jason H Pomerantz
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of California, San Francisco, California, USA
- Department of Orofacial Sciences, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, California, USA
| | - Miguel Reyes-Múgica
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel M Balkin
- Department of Plastic & Oral Surgery, Boston's Children's Hospital, Boston, Massachusetts, USA
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Lacey L Kruse
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Benjamin Huang
- Department of Pediatrics, University of California, San Francisco, California, USA
| | - Jennifer L Reichek
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Noopur Gangopadhyay
- Division of Plastic Surgery, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Simon Chiosea
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jared R Green
- Envision Radiology Associates of Hollywood, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Sarah L Chamlin
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ilona J Frieden
- Department of Dermatology, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
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4
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Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biol 2023; 24:273. [PMID: 38037084 PMCID: PMC10688493 DOI: 10.1186/s13059-023-03121-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.
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Affiliation(s)
- Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Darwin Chang
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Chris Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Andrew L Ji
- Department of Dermatology, Department of Oncological Sciences, Black Family Stem Cell Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA.
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Erdmann-Pham DD, Batra SS, Turkalo TK, Durbin J, Blanchette M, Yeh I, Shain H, Bastian BC, Song YS, Rokhsar DS, Hockemeyer D. Tracing cancer evolution and heterogeneity using Hi-C. Nat Commun 2023; 14:7111. [PMID: 37932252 PMCID: PMC10628133 DOI: 10.1038/s41467-023-42651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Chromosomal rearrangements can initiate and drive cancer progression, yet it has been challenging to evaluate their impact, especially in genetically heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new computational framework for analyzing chromatin conformation capture in heterogeneous samples that can infer somatic copy number alterations, characterize large-scale chromosomal rearrangements, and estimate cancer cell fractions. After validating HiDENSEC with in silico and in vitro controls, we used it to characterize chromosome-scale evolution during melanoma progression in formalin-fixed tumor samples from three patients. The resulting comprehensive annotation of the genomic events includes copy number neutral translocations that disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity involving PTEN. These findings show that large-scale chromosomal rearrangements occur throughout cancer evolution and that characterizing these events yields insights into drivers of melanoma progression.
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Affiliation(s)
- Dan Daniel Erdmann-Pham
- Department of Mathematics, University of California, Berkeley, CA, 94720, USA
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Sanjit Singh Batra
- Computer Science Division, University of California, Berkeley, CA, 94720, USA
| | - Timothy K Turkalo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - James Durbin
- Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Marco Blanchette
- Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Iwei Yeh
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Hunter Shain
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Boris C Bastian
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Department of Statistics, University of California, Berkeley, CA, 94720, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Okinawa Institute for Science and Technology, Tancha, Okinawa, Japan.
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
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de la Fouchardière A, Pissaloux D, Houlier A, Paindavoine S, Tirode F, LeBoit PE, Bastian BC, Yeh I. Histologic and Genetic Features of 51 Melanocytic Neoplasms With Protein Kinase C Fusion Genes. Mod Pathol 2023; 36:100286. [PMID: 37474004 DOI: 10.1016/j.modpat.2023.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/18/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
Fusion genes involving homologs of protein kinase C (PKC) have been identified in a variety of tumors. We report the clinical and histologic presentation of 51 cutaneous melanocytic neoplasms with a PKC fusion gene (involving PRKCA in 35 cases, PRKCB in 15 cases, and PRKCG in a single case). Most tumors were in young adults (median age, 29.5 years; range, 1-73 years) but some presented in newborns. Histologically, 42 tumors were classified as benign, presenting predominantly as biphasic dermal proliferation (88%) with nests of small melanocytes surrounded by fibrosis with haphazardly arranged spindled and dendritic melanocytes, resembling those reported as "combined blue nevi." Most tumors (60%) were heavily pigmented and in 15%, hyperpigmented epithelioid melanocytes were present at the dermoepidermal junction. Two lesions were paucicellular and showed marked sclerosis. Three tumors, including 2 proliferating nodules, were considered intermediate grade. Six tumors had sheets of atypical melanocytes infiltrating the dermis and were classified as melanomas. Two of the melanomas displayed loss of BAP1 nuclear expression. The median follow-up time was 12 months, with 1 patient alive with metastatic disease and 1 dying of their melanoma. These results suggest that melanocytic tumors with PKC fusion genes have characteristic histopathologic features, which are more similar to blue nevi than to pigmented epithelioid melanocytomas. As is the case with GNA-mutated blue nevi, they can progress to melanomas via BAP1 inactivation and metastasize.
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Affiliation(s)
- Arnaud de la Fouchardière
- Department of Biopathology, Centre Léon Bérard, Lyon, France; Department of Research, University of Lyon, Université Claude Bernard Lyon 1, Cancer Research Centre of Lyon, Lyon, France.
| | - Daniel Pissaloux
- Department of Biopathology, Centre Léon Bérard, Lyon, France; Department of Research, University of Lyon, Université Claude Bernard Lyon 1, Cancer Research Centre of Lyon, Lyon, France
| | - Aurélie Houlier
- Department of Biopathology, Centre Léon Bérard, Lyon, France
| | | | - Franck Tirode
- Department of Research, University of Lyon, Université Claude Bernard Lyon 1, Cancer Research Centre of Lyon, Lyon, France
| | - Philip E LeBoit
- Department of Dermatology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California
| | - Boris C Bastian
- Department of Dermatology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California
| | - Iwei Yeh
- Department of Dermatology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco, California
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Wang M, Fukushima S, Sheen YS, Ramelyte E, Pacheco NC, Shi C, Liu S, Banik I, Aquino JD, Acosta MS, Levesque M, Dummer R, Liau JY, Chu CY, Shain AH, Yeh I, Bastian BC. The genetic evolution of acral melanoma. bioRxiv 2023:2023.10.18.562802. [PMID: 37904969 PMCID: PMC10614839 DOI: 10.1101/2023.10.18.562802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Acral melanoma is an aggressive type of melanoma with unknown origins, arising on the sole, palm, or nail apparatus. It is the most common type of melanoma in individuals with dark skin and is notoriously challenging to treat. Our study examined exome sequencing data from 139 tissue samples, spanning different progression stages, collected from 37 patients. We found that 78.4% of the melanomas displayed one or more clustered copy number transitions with focal amplifications, recurring predominantly on chromosomes 5, 11, 12, and 22. These genomic "hailstorms" were typically shared across all progression stages within individual patients. Genetic alterations known to activate TERT also arose early. By contrast, mutations in the MAP-kinase pathway appeared later during progression, often leading to different tumor areas harboring non-overlapping driver mutations. We conclude that the evolutionary trajectories of acral melanomas substantially diverge from those of melanomas on sun-exposed skin, where MAP-kinase pathway activation initiates the neoplastic cascade followed by immortalization later. The punctuated formation of hailstorms, paired with early TERT activation, suggests a unique mutational mechanism underlying the origins of acral melanoma. Our findings highlight an essential role for telomerase, likely in re-stabilizing tumor genomes after hailstorms have initiated the tumors. The marked genetic heterogeneity, in particular of MAP-kinase pathway drivers, may partly explain the limited success of targeted and other therapies in treating this melanoma subtype.
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Affiliation(s)
- Meng Wang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yi-Shuan Sheen
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Egle Ramelyte
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Noel Cruz Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Chenxu Shi
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Shanshan Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ishani Banik
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jamie D. Aquino
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Mitchell Levesque
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Jau-Yu Liau
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Yu Chu
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - A. Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- These authors jointly supervised this project
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- These authors jointly supervised this project
| | - Boris C. Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- These authors jointly supervised this project
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8
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Lorbeer FK, Rieser G, Goel A, Wang M, Oh A, Yeh I, Bastian BC, Hockemeyer D. Distinct senescence mechanisms restrain progression of dysplastic nevi. bioRxiv 2023:2023.07.14.548818. [PMID: 37503286 PMCID: PMC10369942 DOI: 10.1101/2023.07.14.548818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
TERT promoter mutations (TPMs) are frequently found in different cancer types, including approximately 70% of sun-exposed skin melanomas. In melanoma, TPMs are among the earliest mutations and can be present during the transition from nevus to melanoma. However, the specific factors that contribute to the selection of TPMs in certain nevi subsets are not well understood. To investigate this, we analyzed a group of dysplastic nevi (DN) by sequencing genes commonly mutated in melanocytic neoplasms. We examined the relationship between the identified mutations, patient age, telomere length, histological features, and the expression of p16. Our findings reveal that TPMs are more prevalent in DN from older patients and are associated with shorter telomeres. Importantly, these TPMs were not found in nevi with BRAF V600E mutations. Conversely, DN with BRAF V600E mutations were observed in younger patients, had longer telomeres, and a higher proportion of p16-positive cells. This suggests that these nevi arrest growth independently of telomere shortening through a mechanism known as oncogene-induced senescence (OIS). These characteristics extend to melanoma sequencing data sets, where melanomas with BRAF V600E mutations were more likely to have CDKN2A inactivation, overriding OIS. In contrast, melanomas without BRAF V600E mutations showed a higher frequency of TPMs. Our data imply that TPMs are selected to bypass replicative senescence (RS) in cells that were not arrested by OIS. Overall, our results indicate that a subset of melanocytic neoplasms face constraints from RS, while others encounter OIS and RS. The order in which these barriers are overcome during progression to melanoma depends on the mutational context.
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9
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Roy SF, Milante R, Pissaloux D, Tirode F, Bastian BC, Fouchardière ADL, Yeh I. Spectrum of Melanocytic Tumors Harboring BRAF Gene Fusions: 58 Cases With Histomorphologic and Genetic Correlations. Mod Pathol 2023; 36:100149. [PMID: 36841436 DOI: 10.1016/j.modpat.2023.100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/27/2023]
Abstract
We report a series of 58 melanocytic tumors that harbor an activating fusion of BRAF, a component of the mitogen-activated protein kinase (MAPK) signaling cascade. Cases were diagnosed as melanocytic nevus (n = 12, 21%), diagnostically ambiguous favor benign (n = 22, 38%), and diagnostically ambiguous concerning for melanoma (n = 12, 21%) or melanoma (n = 12, 21%). Three main histopathologic patterns were observed. The first pattern (buckshot fibrosis) was characterized by large, epithelioid melanocytes arrayed as single cells or "buckshot" within marked stromal desmoplasia. The second pattern (cords in whorled fibrosis) demonstrated polypoid growth with a whorled arrangement of cords and single melanocytes within desmoplasia. The third pattern (spindle-cell fascicles) showed fascicular growth of spindled melanocytes. Cytomorphologic features characteristic of Spitz nevi were observed in most cases (n = 50, 86%). Most of the cases (n = 54, or 93%) showed stromal desmoplasia. Histomorphology alone was not sufficient in distinguishing benign from malignant melanocytic tumors with BRAF fusion gene because the only histopathologic features more commonly associated with a diagnosis of malignancy included dermal mitoses (P = .046) and transepidermal elimination of melanocytes (P = .013). BRAF fusion kinases are targetable by kinase inhibitors and, thus, should be considered as relevant genetic alterations in the molecular workup of melanomas. Recognizing the 3 main histopathologic patterns of melanocytic tumors with BRAF fusion gene will aid in directing ancillary testing.
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Affiliation(s)
- Simon F Roy
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Riza Milante
- Department of Dermatology, University of California in San Francisco, San Francisco, California
| | - Daniel Pissaloux
- Department of Biopathology, Centre Léon Bérard, Lyon, France; University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Franck Tirode
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Boris C Bastian
- Department of Dermatology, University of California in San Francisco, San Francisco, California; Department of Pathology, University of California in San Francisco, San Francisco, California
| | - Arnaud de la Fouchardière
- Department of Biopathology, Centre Léon Bérard, Lyon, France; University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Iwei Yeh
- Department of Dermatology, University of California in San Francisco, San Francisco, California; Department of Pathology, University of California in San Francisco, San Francisco, California.
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10
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Ma J, Wang M, Manglik A, Bastian BC, Chen X. Abstract 3885: A secondary Gαq mutation confers resistance to Gαq inhibitors in uveal melanoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Uveal melanoma (UM) is a rare subtype of melanoma that originates from melanocytes of the choroidal plexus, ciliary body and iris. Despite successful treatment of the primary by radiation or surgery, 50% of UM patients develop metastases, mostly in the liver, as an invariably lethal complication. Over 90% of UM harbor activating mutations in the closely related GNAQ or GNA11 genes, mainly at codons Q209, compromising the GTPase activity. Mutant GNAQ and GNA11 can be successfully targeted by the cyclic depsipeptide YM-254890. To anticipate mechanisms of resistance that might arise under treatment with this novel class of Gαq inhibitors, we generated UM cell lines resistant to YM-254890 using an in-vitro cell culture system. Upon chronic growth suppression of a GNA11Q209L mutant UM cell line, we established 12 YM-254890 resistance clones. We identified a secondary GNA11F75Y mutation in one clone and GNA11Y192H mutations in the other 11 clones. The secondary mutations were present in cis with the original GNA11 Q209L mutations. To validate the functional role of these secondary mutations in conveying resistance, we engineered two double mutants, GNA11Q209L/F75Y and GNA11Q209L/Y192H, and introduced them into 293FT cells respectively and confirmed that both F75Y and Y192H convey resistance to YM-254890 treatment. The proliferation of YM-254890-resistant cell lines was still dependent on GNA11 and downstream PKC/MAPK signaling. Combined inhibition of PKC and MEK synergistically reduced cell viability in YM-254890 resistant UM cells. Analysis of the crystal structure of YM-2548890 in complex with GNAQ predicts both F75Y and Y192H mutations directly affect the binding of YM-254890 to Gαq. Our data suggest that direct targeting mutant GNAQ/11 is promising but will select for secondary mutations within GNAQ/11 that will result in resistance. Combinatorial targeting of other components in the Gαq signaling pathway will increase clinical efficacy.
Citation Format: Jiafang Ma, Meng Wang, Aashish Manglik, Boris C. Bastian, Xu Chen. A secondary Gαq mutation confers resistance to Gαq inhibitors in uveal melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3885.
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Affiliation(s)
- Jiafang Ma
- 1UCSF Helen Diller Family Comprehensive Cancer Ctr., San Francisco, CA
| | - Meng Wang
- 1UCSF Helen Diller Family Comprehensive Cancer Ctr., San Francisco, CA
| | | | - Boris C. Bastian
- 1UCSF Helen Diller Family Comprehensive Cancer Ctr., San Francisco, CA
| | - Xu Chen
- 1UCSF Helen Diller Family Comprehensive Cancer Ctr., San Francisco, CA
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11
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Barnhill RL, Elder DE, Piepkorn MW, Knezevich SR, Reisch LM, Eguchi MM, Bastian BC, Blokx W, Bosenberg M, Busam KJ, Carr R, Cochran A, Cook MG, Duncan LM, Elenitsas R, de la Fouchardière A, Gerami P, Johansson I, Ko J, Landman G, Lazar AJ, Lowe L, Massi D, Messina J, Mihic-Probst D, Parker DC, Schmidt B, Shea CR, Scolyer RA, Tetzlaff M, Xu X, Yeh I, Zembowicz A, Elmore JG. Revision of the Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis Classification Schema for Melanocytic Lesions: A Consensus Statement. JAMA Netw Open 2023; 6:e2250613. [PMID: 36630138 PMCID: PMC10375511 DOI: 10.1001/jamanetworkopen.2022.50613] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
IMPORTANCE A standardized pathology classification system for melanocytic lesions is needed to aid both pathologists and clinicians in cataloging currently existing diverse terminologies and in the diagnosis and treatment of patients. The Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis (MPATH-Dx) has been developed for this purpose. OBJECTIVE To revise the MPATH-Dx version 1.0 classification tool, using feedback from dermatopathologists participating in the National Institutes of Health-funded Reducing Errors in Melanocytic Interpretations (REMI) Study and from members of the International Melanoma Pathology Study Group (IMPSG). EVIDENCE REVIEW Practicing dermatopathologists recruited from 40 US states participated in the 2-year REMI study and provided feedback on the MPATH-Dx version 1.0 tool. Independently, member dermatopathologists participating in an IMPSG workshop dedicated to the MPATH-Dx schema provided additional input for refining the MPATH-Dx tool. A reference panel of 3 dermatopathologists, the original authors of the MPATH-Dx version 1.0 tool, integrated all feedback into an updated and refined MPATH-Dx version 2.0. FINDINGS The new MPATH-Dx version 2.0 schema simplifies the original 5-class hierarchy into 4 classes to improve diagnostic concordance and to provide more explicit guidance in the treatment of patients. This new version also has clearly defined histopathological criteria for classification of classes I and II lesions; has specific provisions for the most frequently encountered low-cumulative sun damage pathway of melanoma progression, as well as other, less common World Health Organization pathways to melanoma; provides guidance for classifying intermediate class II tumors vs melanoma; and recognizes a subset of pT1a melanomas with very low risk and possible eventual reclassification as neoplasms lacking criteria for melanoma. CONCLUSIONS AND RELEVANCE The implementation of the newly revised MPATH-Dx version 2.0 schema into clinical practice is anticipated to provide a robust tool and adjunct for standardized diagnostic reporting of melanocytic lesions and management of patients to the benefit of both health care practitioners and patients.
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Affiliation(s)
- Raymond L Barnhill
- Department of Translational Research, Institut Curie, Unit of Formation and Research of Medicine University of Paris, Paris, France
| | - David E Elder
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Michael W Piepkorn
- Division of Dermatology, Department of Medicine, University of Washington School of Medicine, Seattle
- Dermatopathology Northwest, Bellevue, Washington
| | | | - Lisa M Reisch
- Department of Biostatistics, University of Washington School of Medicine, Seattle
| | - Megan M Eguchi
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles
| | - Boris C Bastian
- Departments of Pathology and Dermatology, University of California, San Francisco
| | - Willeke Blokx
- Department of Pathology, Division Laboratories, Pharmacy and Biomedical Genetics University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology, and Immunobiology, Yale School of Medicine, New Haven, Connecticut
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Carr
- Cellular Pathology, South Warwickshire NHS Trust, Warwick, United Kingdom
| | - Alistair Cochran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles
| | - Martin G Cook
- Department of Histopathology, Royal Surrey NHS Foundation Trust, Guildford, United Kingdom
| | - Lyn M Duncan
- Pathology Service, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Rosalie Elenitsas
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia
| | - Arnaud de la Fouchardière
- Department of Biopathology, Centre Léon Bérard, Lyon, France
- University of Lyon, Université Claude Bernard Lyon 1, National Center for Scientific Research, Mixed Research Unit 5286, National Institute of Health and Medical Research U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Pedram Gerami
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Iva Johansson
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jennifer Ko
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, Ohio
| | - Gilles Landman
- Department of Pathology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Alexander J Lazar
- Departments of Pathology, Dermatology, and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Lori Lowe
- Departments of Pathology and Dermatology, University of Michigan, Ann Arbor
| | - Daniela Massi
- Section of Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Jane Messina
- Departments of Pathology and Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Daniela Mihic-Probst
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Douglas C Parker
- Departments of Pathology and Dermatology, Emory University School of Medicine, Atlanta, Georgia
| | - Birgitta Schmidt
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher R Shea
- Department of Dermatology, University of Chicago Medicine, Chicago, Illinois
| | - Richard A Scolyer
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, Australia
| | - Michael Tetzlaff
- Departments of Pathology and Dermatology, University of California, San Francisco
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Iwei Yeh
- Departments of Pathology and Dermatology, University of California, San Francisco
| | - Artur Zembowicz
- Tufts University, Boston, Massachusetts
- Lahey Clinic, Burlington, Massachusetts
- Dermatopathology Consultations, Needham, Massachusetts
| | - Joann G Elmore
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles
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12
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Solomon DA, Ramani B, Eiger-Moscovich M, Milman T, Uludag G, Crawford JB, Phan I, Char DH, Shields CL, Eagle RC, Bastian BC, Bloomer MM, Pekmezci M. Iris and Ciliary Body Melanocytomas Are Defined by Solitary GNAQ Mutation Without Additional Oncogenic Alterations. Ophthalmology 2022; 129:1429-1439. [PMID: 35835335 DOI: 10.1016/j.ophtha.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE To analyze the genetic features of melanocytomas and melanomas of the anterior uvea and assess the value of molecular testing for diagnosis and prognostication. DESIGN Retrospective case-control study. SUBJECTS Patients with melanocytoma (n = 16) and melanoma (n = 19) of the anterior uvea. METHODS Targeted next-generation sequencing was performed on formalin-fixed, paraffin-embedded tumor tissue from anterior uveal melanocytic tumors and correlated with clinicopathologic features. MAIN OUTCOME MEASURES Presence or absence of accompanying oncogenic alterations beyond GNAQ/GNA11 and their association with histologic features and local recurrence. RESULTS Hotspot missense mutations in GNAQ/GNA11 were identified in 91% (32/35) of all cases. None of the melanocytomas with or without atypia demonstrated chromosomal imbalances or additional oncogenic variants beyond GNAQ mutation, and none recurred over a median follow-up of 36 months. Additional alterations identified in a subset of melanomas include mutations in BAP1 (n = 3), EIF1AX (n = 4), SRSF2 (n = 1), PTEN (n = 1), and EP300 (n = 1); monosomy 3p (n = 6); trisomy 6p (n = 3); trisomy 8q (n = 2); and an ultraviolet mutational signature (n = 5). Local recurrences were limited to melanomas, all of which demonstrated oncogenic alterations in addition to GNAQ/GNA11 (n = 5). A single melanoma harboring GNAQ and BAP1 mutations and monosomy 3 was the only tumor that metastasized. CONCLUSIONS In this study, anterior segment uveal melanocytomas did not display oncogenic alterations beyond GNAQ/GNA11. Therefore, they are genetically similar to uveal nevi rather than uveal melanoma based on their molecular features known from the literature. Molecular testing can be performed on borderline cases to aid risk stratification and clinical management decisions.
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Affiliation(s)
- David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Biswarathan Ramani
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Maya Eiger-Moscovich
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Tatyana Milman
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gunay Uludag
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - J Brooks Crawford
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Isabella Phan
- Department of Ophthalmology, Kaiser Permanente San Francisco, San Francisco, California
| | - Devron H Char
- Department of Ophthalmology, California Pacific Medical Center, San Francisco, California
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ralph C Eagle
- Department of Pathology, Wills Eye Hospital, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Boris C Bastian
- Department of Pathology, University of California, San Francisco, San Francisco, California; Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - Michele M Bloomer
- Department of Pathology, University of California, San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, San Francisco, California.
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13
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Wang M, Banik I, Shain AH, Yeh I, Bastian BC. Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes. Genome Med 2022; 14:65. [PMID: 35706047 PMCID: PMC9202124 DOI: 10.1186/s13073-022-01068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/03/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Acral and mucosal melanomas are aggressive subtypes of melanoma, which have a significantly lower burden of somatic mutations than cutaneous melanomas, but more frequent copy number variations, focused gene amplifications, and structural alterations. The landscapes of their genomic alterations remain to be fully characterized. METHODS We compiled sequencing data of 240 human acral and mucosal melanoma samples from 11 previously published studies and applied a uniform pipeline to call tumor cell content, ploidy, somatic and germline mutations, as well as CNVs, LOH, and SVs. We identified genes that are significantly mutated or recurrently affected by CNVs and implicated in oncogenesis. We further examined the difference in the frequency of recurrent pathogenic alterations between the two melanoma subtypes, correlation between pathogenic alterations, and their association with clinical features. RESULTS We nominated PTPRJ, mutated and homozygously deleted in 3.8% (9/240) and 0.8% (2/240) of samples, respectively, as a probable tumor suppressor gene, and FER and SKP2, amplified in 3.8% and 11.7% of samples, respectively, as probable oncogenes. We further identified a long tail of infrequent pathogenic alterations, involving genes such as CIC and LZTR1. Pathogenic germline mutations were observed on MITF, PTEN, ATM, and PRKN. We found BRAF V600E mutations in acral melanomas with fewer structural variations, suggesting that they are distinct and related to cutaneous melanomas. Amplifications of PAK1 and GAB2 were more commonly observed in acral melanomas, whereas SF3B1 R625 codon mutations were unique to mucosal melanomas (12.9%). Amplifications at 11q13-14 were frequently accompanied by fusion to a region on chromosome 6q12, revealing a recurrent novel structural rearrangement whose role remains to be elucidated. CONCLUSIONS Our meta-analysis expands the catalog of driver mutations in acral and mucosal melanomas, sheds new light on their pathogenesis and broadens the catalog of therapeutic targets for these difficult-to-treat cancers.
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Affiliation(s)
- Meng Wang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ishani Banik
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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14
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Griffin L, Ho L, Akhurst RJ, Arron ST, Boggs JME, Conlon P, O'Kelly P, Toland AE, Epstein EH, Balmain A, Bastian BC, Moloney FJ, Murphy GM, Laing ME. Genetic polymorphism in Methylenetetrahydrofolate Reductase chloride transport protein 6 ( MTHFR CLCN6) gene is associated with keratinocyte skin cancer in a cohort of renal transplant recipients. Skin Health Dis 2022; 2:e95. [PMID: 35677930 PMCID: PMC9168012 DOI: 10.1002/ski2.95] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 12/18/2022]
Abstract
Background Renal transplant recipients (RTRs) are at increased risk of keratinocyte cancer (KC), especially cutaneous squamous cell carcinoma (cSCC). Previous studies identified a genetic variant of the Methylenetetrahydrofolate Reductase (MTHFR) gene, C677T, which conferred a risk for diagnosis of cSCC in Irish RTRs. Objective We sought to find further genetic variation in MTHFR and overlap genes that may be associated with a diagnosis of KC in RTRs. Methods Genotyping of a combined RTR population (n = 821) from two centres, Ireland (n = 546) and the USA (n = 275), was performed. This included 290 RTRs with KC and 444 without. Eleven single nucleotide polymorphisms (SNPs) in the MTHFR gene and seven in the overlap gene MTHFR Chloride transport protein 6 (CLCN6) were evaluated and association explored by time to event analysis (from transplant to first KC) using Cox proportional hazards model. Results Polymorphism at MTHFR CLCN6 (rs9651118) was significantly associated with KC in RTRs (HR 1.50, 95% CI 1.17–1.91, p < 0.00061) and cSCC (HR 1.63, 95% CI 1.14–2.34, p = 0.007). A separate SNP, MTHFR C677T, was also significantly associated with KC in the Irish population (HR 1.31, 95% CI 1.05–1.63, p = 0.016), but not American RTRs. Conclusions We report the association of a SNP in the MTHFR overlap gene, CLCN6 and KC in a combined RTR population. While the exact function of CLCN6 is not known, it is proposed to be involved in folate availability. Future applications could include incorporation in a polygenic risk score for KC in RTRs to help identify those at increased risk beyond traditional risk factor assessment.
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Affiliation(s)
- L Griffin
- Department of Dermatology University Hospital Galway Galway Ireland
| | - L Ho
- Department of Dermatology Beaumont Hospital Dublin 9 Ireland
| | - R J Akhurst
- Helen Diller Family Comprehensive Cancer Center University of California San Francisco California USA
| | - S T Arron
- Helen Diller Family Comprehensive Cancer Center University of California San Francisco California USA
| | - J M E Boggs
- Department of Dermatology University Hospital Galway Galway Ireland
| | - P Conlon
- Department of Nephrology Beaumont Hospital Dublin 9 Ireland
| | - P O'Kelly
- Department of Nephrology Beaumont Hospital Dublin 9 Ireland
| | - A E Toland
- Department of Molecular Virology, Immunology and Medical Genetics Comprehensive Cancer Centre Ohio State University Columbus Ohio USA
| | - E H Epstein
- Helen Diller Family Comprehensive Cancer Center University of California San Francisco California USA
| | - A Balmain
- Helen Diller Family Comprehensive Cancer Center University of California San Francisco California USA
| | - B C Bastian
- Helen Diller Family Comprehensive Cancer Center University of California San Francisco California USA
| | - F J Moloney
- Department of Dermatology Beaumont Hospital Dublin 9 Ireland
| | - G M Murphy
- Department of Dermatology Beaumont Hospital Dublin 9 Ireland
| | - M E Laing
- Department of Dermatology University Hospital Galway Galway Ireland.,Department of Dermatology Beaumont Hospital Dublin 9 Ireland.,Department of Medicine National University of Ireland Galway Ireland
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Abstract
Cancer is caused by the accumulation of pathogenic alterations of the genome and epigenome that result in permanent changes that disrupt cellular homeostasis. The genes that become corrupted in this process vary among different tumour types, reflecting specific vulnerabilities and dependencies of the cell from which the cancer originated. This also applies to 'melanoma', a cancer that constitutes not one, but multiple diseases that can be separated based on their cell of origin, aetiology, clinical appearance and course, and response to treatment. In this article, we review the current classification of melanoma within distinct evolutionary pathways and the associated genetic alterations. In addition, we review the application of molecular diagnostics to the diagnosis of melanocytic tumours in the context of histopathological assessment.
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Affiliation(s)
- I Yeh
- Department of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - B C Bastian
- Department of Dermatology and Pathology, University of California, San Francisco, CA, USA
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16
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de la Fouchardière A, Tee MK, Peternel S, Valdebran M, Pissaloux D, Tirode F, Busam KJ, LeBoit PE, McCalmont TH, Bastian BC, Yeh I. Fusion partners of NTRK3 affect subcellular localization of the fusion kinase and cytomorphology of melanocytes. Mod Pathol 2021; 34:735-747. [PMID: 32968185 PMCID: PMC7985048 DOI: 10.1038/s41379-020-00678-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 02/08/2023]
Abstract
A subset of Spitz tumors harbor fusions of NTRK3 with ETV6, MYO5A, and MYH9. We evaluated a series of 22 melanocytic tumors in which an NTRK3 fusion was identified as part of the diagnostic workup. Tumors in which NTRK3 was fused to ETV6 occurred in younger patients were predominantly composed of epithelioid melanocytes and were classified by their histopathologic features as Spitz tumors. In contrast, those in which NTRK3 was fused to MYO5A were predominantly composed of spindled melanocytes arrayed in fascicles with neuroid features such as pseudo-Verocay bodies. To further investigate the effects of the fusion kinases ETV6-NTRK3 and MYO5A-NTRK3 in melanocytes, we expressed them in immortalized melanocytes and determined their subcellular localization by immunofluorescence. ETV6-NTRK3 was localized to the nucleus and diffusely within the cytoplasm and caused melanocytes to adopt an epithelioid cytomorphology. In contrast, MYO5A-NTRK3, appeared excluded from the nucleus of melanocytes, was localized to dendrites, and resulted in a highly dendritic cytomorphology. Our findings indicate that ETV6-NTRK3 and MYO5A-NTRK3 have distinct subcellular localizations and effects on cellular morphology.
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Affiliation(s)
- Arnaud de la Fouchardière
- Department of Biopathology, Center Léon Bérard, Lyon, France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Meng Kian Tee
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Peternel
- Department of Dermatovenereology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Manuel Valdebran
- Department of Dermatology and Dermatologic Surgery, Medical College of South Carolina, Charleston, SC, USA
| | - Daniel Pissaloux
- Department of Biopathology, Center Léon Bérard, Lyon, France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Franck Tirode
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip E LeBoit
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Departments of Dermatology and Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Timothy H McCalmont
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Departments of Dermatology and Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Departments of Dermatology and Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Departments of Dermatology and Pathology, University of California San Francisco, San Francisco, CA, USA.
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17
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Roy SF, Bastian BC, Maguiness S, Giubellino A, Vemula SS, McCalmont TH, Yeh I. Multiple desmoplastic Spitz nevi with BRAF fusions in a patient with ring chromosome 7 syndrome. Pigment Cell Melanoma Res 2021; 34:987-993. [PMID: 33522711 DOI: 10.1111/pcmr.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/04/2021] [Accepted: 01/25/2021] [Indexed: 11/29/2022]
Abstract
Patients with non-supernumerary ring chromosome 7 syndrome have an increased incidence of hemangiomas, café-au-lait spots, and melanocytic nevi. The mechanism for the increased incidence of these benign neoplasms is unknown. We present the case of a 22-year-old man with ring chromosome 7 and multiple melanocytic nevi. Two nevi, one on the right ear and the other on the right knee, were biopsied and diagnosed as desmoplastic Spitz nevi. Upon targeted next-generation DNA sequencing, both harbored BRAF fusions. Copy number alterations and fluorescence in situ hybridization (FISH) for BRAF suggested that the fusions arose on the ring chromosome 7. Hence, one reason for increased numbers of nevi in patients with non-supernumerary ring chromosome 7 syndrome may be increased likelihood of BRAF fusions, due to the instability of the ring chromosome.
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Affiliation(s)
- Simon F Roy
- Department of Pathology, University of Montréal, Montréal, OC, Canada
| | - Boris C Bastian
- Department of Dermatology, University of California in San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California in San Francisco, San Francisco, CA, USA
| | - Sheilagh Maguiness
- Department of Dermatology, University of Minnesota, Minneapolis, MN, USA
| | - Alessio Giubellino
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Swapna S Vemula
- Department of Pathology, University of California in San Francisco, San Francisco, CA, USA
| | - Timothy H McCalmont
- Department of Dermatology, University of California in San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California in San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California in San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California in San Francisco, San Francisco, CA, USA
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18
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Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IPM, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020; 587:126-132. [PMID: 32879494 PMCID: PMC7611706 DOI: 10.1038/s41586-020-2698-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.
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Affiliation(s)
- Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marina Petkovic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sergi Elizalde
- Department of Mathematics, Dartmouth College, Hanover, NH, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Lewis Au
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Mickael Escudero
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hang Xu
- Stanford Cancer Institute, Stanford, CA, USA
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Wei Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thanos P Mourikis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Lavinia Spain
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - George D Cresswell
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Philippe Lamy
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lucy R Yates
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Priscilla K Brastianos
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Fabrice Andre
- INSERM U981, PRISM Institute, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Medical School, Université Paris Saclay, Kremlin Bicetre, France
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute of Science & Technology, Okinawa, Japan
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, School of GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE-NAP Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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19
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Tang J, Fewings E, Chang D, Zeng H, Liu S, Jorapur A, Belote RL, McNeal AS, Tan TM, Yeh I, Arron ST, Judson-Torres RL, Bastian BC, Shain AH. The genomic landscapes of individual melanocytes from human skin. Nature 2020; 586:600-605. [PMID: 33029006 PMCID: PMC7581540 DOI: 10.1038/s41586-020-2785-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/03/2020] [Indexed: 01/13/2023]
Abstract
Every cell in the human body has a unique set of somatic mutations, yet it remains difficult to comprehensively genotype an individual cell1. Here, we developed solutions to overcome this obstacle in the context of normal human skin, thus offering the first glimpse into the genomic landscapes of individual melanocytes from human skin. As expected, sun-shielded melanocytes had fewer mutations than sun-exposed melanocytes. However, within sun-exposed sites, melanocytes on chronically sun-exposed skin (e.g. the face) displayed a lower mutation burden than melanocytes on intermittently sun-exposed skin (e.g. the back). Melanocytes located adjacent to a skin cancer had higher mutation burdens than melanocytes from donors without skin cancer, implying that the mutation burden of normal skin can be harnessed to measure cumulative sun damage and skin cancer risk. Moreover, melanocytes from healthy skin commonly harbor pathogenic mutations, though these mutations tended to be weakly oncogenic, likely explaining why they did not give rise to discernible lesions. Phylogenetic analyses identified groups of related melanocytes, suggesting that melanocytes spread throughout skin as fields of clonally related cells, invisible to the naked eye. Overall, our study offers an unprecedented view into the genomic landscapes of individual melanocytes, revealing key insights into the causes and origins of melanoma.
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Affiliation(s)
- Jessica Tang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Eleanor Fewings
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hanlin Zeng
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Shanshan Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aparna Jorapur
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rachel L Belote
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Andrew S McNeal
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tuyet M Tan
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sarah T Arron
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert L Judson-Torres
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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20
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Botton T, Talevich E, Mishra VK, Zhang T, Shain AH, Berquet C, Gagnon A, Judson RL, Ballotti R, Ribas A, Herlyn M, Rocchi S, Brown KM, Hayward NK, Yeh I, Bastian BC. Genetic Heterogeneity of BRAF Fusion Kinases in Melanoma Affects Drug Responses. Cell Rep 2020; 29:573-588.e7. [PMID: 31618628 DOI: 10.1016/j.celrep.2019.09.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 07/26/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022] Open
Abstract
BRAF fusions are detected in numerous neoplasms, but their clinical management remains unresolved. We identified six melanoma lines harboring BRAF fusions representative of the clinical cases reported in the literature. Their unexpected heterogeneous responses to RAF and MEK inhibitors could be categorized upon specific features of the fusion kinases. Higher expression level correlated with resistance, and fusion partners containing a dimerization domain promoted paradoxical activation of the mitogen-activated protein kinase (MAPK) pathway and hyperproliferation in response to first- and second-generation RAF inhibitors. By contrast, next-generation αC-IN/DFG-OUT RAF inhibitors blunted paradoxical activation across all lines and had their therapeutic efficacy further increased in vitro and in vivo by combination with MEK inhibitors, opening perspectives in the clinical management of tumors harboring BRAF fusions.
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Affiliation(s)
- Thomas Botton
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Eric Talevich
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Vivek Kumar Mishra
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MA 20892, USA
| | - A Hunter Shain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Céline Berquet
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Alexander Gagnon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Robert Ballotti
- U1065, Institut National de la Santé et de la Recherche Médicale, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, 06200 Nice, France
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Stéphane Rocchi
- U1065, Institut National de la Santé et de la Recherche Médicale, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, 06200 Nice, France
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MA 20892, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA.
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21
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Ma J, Bastian BC, Chen X. Abstract 1812: Adaptive and acquired resistance to GNAQ/11 inhibition in uveal melanoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Uveal Melanoma (UM) is a highly lethal cancer with 50% of patients developing lethal metastatic disease, primarily the liver, with currently no effective treatment options. UM is driven by mutations constitutively activating the Gαq pathway, about 90% affecting the heterotrimeric G-protein alpha subunits GNAQ or GNA11 and less commonly (<10%) CYSLTR2 (a GNAQ/11 coupled receptor) or PLCB4 (a direct effector of Gαq). Directly targeting GNAQ/11 therefore could be of therapeutic relevance for the majority of UMs. Here we found that YM-254890, a cyclic depsipeptide, inhibited downstream signaling induced by GNAQQ209L and GNA11Q209L, but not GNA14Q205L, GNA15Q212L and GNASQ227L in 293T cells, confirming that it is a GNAQ/11-specific inhibitor. We systematically examined its activity against other recurring mutations in the Gαq pathway (GNAQ: Q209P, G48V, T175R, R183Q, F228L; GNA11:E191G, R183C, E234K; CYSLTR2: L129Q; PLCB4: D630Y). In 293T cells GNAQQ209P, GNAQR183Q, CYSLTR2L129Q and PLCB4D630Y activated downstream signaling whereas other Gαq mutants did not. YM-254890 inhibited the downstream signaling induced by GNAQQ209P, GNAQR183Q and CYSLTR2L129Q whereas it remained expectedly ineffective against PLCB4D630Y. Furthermore, we found that YM-254890 selectively inhibited Gαq signaling and cell proliferation in a panel of UM cell lines with GNAQ/11 mutations but had no effect on Gαq wild type melanoma cells. In vivo, YM-254890 slowed the growth of liver metastases in a xenograft model of GNAQ mutant UM cells but did not induce tumor shrinkage. Analysis of the tumor lysates revealed that inhibition of Gαq pathway signaling was incomplete. RNAseq analysis of 10 UM cell lines with various GNAQ/11 mutations exposed to YM-254890 revealed that GNAQ/11 inhibition led to significant upregulation of endothelin ET(B) receptor (EDNRB) compared to control treatment. EDNRB is a GNAQ/11 coupled receptor, and western blot confirmed that EDNRB protein level was significantly upregulated when mutant GNAQ/11 was inhibited with either YM-254890 or siRNA. The critical role of endothelin signaling in mediating adaptive resistance to Gαq inhibition was confirmed by demonstrating (1) expression of the EDNRB ligand endothelin 1 in liver metastases of the xenograft model; (2) pharmacological or genetic inhibition of EDNRB was able to break resistance. We also found that the therapeutic efficacy of YM-254890 can be subverted by acquiring additional mutations in the pathway. Upon chronic growth suppression of a GNA11Q209L mutant UM cell line a resistant clone emerged that was demonstrated to harbor a novel GNA11F75Y mutation, affecting the YM-254890 binding site. Concordantly, an engineered GNA11 with the two mutations in cis was resistant to the compound. Our data suggest that targeting mutant GNAQ/11 is promising but will require combinatorial targeting of EDNR signaling and possibly other pathways to reach maximal clinical efficacy.
Citation Format: Jiafang Ma, Boris C. Bastian, Xu Chen. Adaptive and acquired resistance to GNAQ/11 inhibition in uveal melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1812.
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Affiliation(s)
- Jiafang Ma
- University of California, San Francisco, San Francisco, CA
| | | | - Xu Chen
- University of California, San Francisco, San Francisco, CA
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22
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Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- A Hunter Shain
- University of California, San Francisco, Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, Box 3111, San Francisco, CA, 94143, USA
| | - Boris C Bastian
- University of California, San Francisco, Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, Box 3111, San Francisco, CA, 94143, USA.
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Raghavan SS, Peternel S, Mully TW, North JP, Pincus LB, LeBoit PE, McCalmont TH, Bastian BC, Yeh I. Spitz melanoma is a distinct subset of spitzoid melanoma. Mod Pathol 2020; 33:1122-1134. [PMID: 31900433 PMCID: PMC7286778 DOI: 10.1038/s41379-019-0445-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/28/2019] [Indexed: 01/20/2023]
Abstract
Melanomas that have histopathologic features that overlap with those of Spitz nevus are referred to as spitzoid melanomas. However, the diagnostic concept is used inconsistently and genomic analyses suggest it is a heterogeneous category. Spitz tumors, the spectrum of melanocytic neoplasms extending from Spitz nevi to their malignant counterpart Spitz melanoma, are defined in the 2018 WHO classification of skin tumors by the presence of specific genetic alterations, such as kinase fusions or HRAS mutations. It is unclear what fraction of "spitzoid melanomas" defined solely by their histopathologic features belong to the category of Spitz melanoma or to other melanoma subtypes. We assembled a cohort of 25 spitzoid melanomas diagnosed at a single institution over an 8-year period and performed high-coverage DNA sequencing of 480 cancer related genes. Transcriptome wide RNA sequencing was performed for select cases. Only nine cases (36%) had genetic alterations characteristic of Spitz melanoma, including HRAS mutation or fusion involving BRAF, ALK, NTRK1, or MAP3K8. The remaining cases were divided into those with an MAPK activating mutation and those without an MAPK activating mutation. Both Spitz melanoma and spitzoid melanomas in which an MAPK-activating mutation could not be identified tended to occur in younger patients on skin with little solar elastosis, infrequently harbored TERT promoter mutations, and had a lower burden of pathogenic mutations than spitzoid melanomas with non-Spitz MAPK-activating mutations. The MAPK-activating mutations identified affected non-V600 residues of BRAF as well as NRAS, MAP2K1/2, NF1, and KIT, while BRAF V600 mutations, the most common mutations in melanomas of the WHO low-CSD category, were entirely absent. While the "spitzoid melanomas" comprising our cohort were enriched for bona fide Spitz melanomas, the majority of melanomas fell outside of the genetically defined category of Spitz melanomas, indicating that histomorphology is an unreliable predictor of Spitz lineage.
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Affiliation(s)
| | - Sandra Peternel
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
- Department of Dermatovenerology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Thaddeus W Mully
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey P North
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Laura B Pincus
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Philip E LeBoit
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Timothy H McCalmont
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, CA, USA.
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Natesan D, Martell H, Devine P, Stohr BA, Grenert JP, Van Ziffle J, Joseph NM, Bastian BC, Umetsu SE, Onodera C, Chan E, Desai A, Wong AC, Porten SP, Chou J, Friedlander TW, Small EJ, Fong L, Sweet-Cordero EA, Koshkin VS. Correlation of tumor mutational burden (TMB) with molecular profiling and clinical characteristics in patients with bladder cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e17025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e17025 Background: Bladder cancers (BC) are frequently highly mutated. Next generation sequencing (NGS) can both shed light on mutational burden and the specific alterations that provide insights into the underlying biology of individual tumors. Methods: We retrospectively reviewed BC cases assessed with UCSF500, an institutional NGS assay that uses hybrid capture enrichment of target DNA to interrogate approximately 500 frequently mutated cancer genes. Hypermutated tumors were defined as having TMB > 10 mutations/Mb. Fisher’s exact test was used to compare patients (pts) with hypermutated (HM) and non-hypermutated (NHM) tumors. Results: From 2015 to 2019, 74 pts with BC underwent UCSF500 testing; 48 pts were evaluable for TMB, of which 19 pts (40%) had HM tumors. 17/19 pts were evaluable for mutational signatures; all 17 had APOBEC signatures. Signatures were not assessed in NHM tumors due to low TMB. Clinicopathologic characteristics and most common alterations in the two groups are listed in the table. More HM pts had responses to immunotherapy (IO) treatment (86% vs 40%, p = 0.13). Conclusions: In this single-institution BC cohort, HM tumors were common and APOBEC mutational signature was the common underlying biology in HM tumors. There were relevant differences in common alterations between HM and NHM tumors, including more FGFR3 mutations in NHM tumors. HM status and APOBEC signature were suggested as relevant predictive biomarkers of response to IO, which should be investigated further in larger BC cohorts. [Table: see text]
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Affiliation(s)
- Divya Natesan
- University of California, San Francisco, San Francisco, CA
| | - Henry Martell
- University of California San Francisco, San Francisco, CA
| | - Patrick Devine
- University of California San Francisco, San Francisco, CA
| | - Bradley A. Stohr
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | | | | | | | | | - Sarah E Umetsu
- University of California, San Francisco, Department of Pathology, San Francisco, CA
| | | | - Emily Chan
- University of California San Francisco, San Francisco, CA
| | - Arpita Desai
- University of California, San Francisco, San Francisco, CA
| | | | - Sima P. Porten
- University of California, San Francisco, San Francisco, CA
| | - Jonathan Chou
- University of California San Francisco, San Francisco, CA
| | | | - Eric Jay Small
- University of California San Francisco, San Francisco, CA
| | - Lawrence Fong
- University of California San Francisco, San Francisco, CA
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25
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Houlier A, Pissaloux D, Masse I, Tirode F, Karanian M, Pincus LB, McCalmont TH, LeBoit PE, Bastian BC, Yeh I, de la Fouchardière A. Melanocytic tumors with MAP3K8 fusions: report of 33 cases with morphological-genetic correlations. Mod Pathol 2020; 33:846-857. [PMID: 31719662 DOI: 10.1038/s41379-019-0384-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023]
Abstract
We report a series of 33 skin tumors harboring a gene fusion of the MAP3K8 gene, which encodes a serine/threonine kinase. The MAP3K8 fusions were identified by RNA sequencing in 28 cases and by break-apart FISH in five cases. Cases in which fusion genes were fully characterized demonstrated a fusion of the 5' part of MAP3K8 comprising exons 1-8 in frame to one of several partner genes at the 3' end. The fusion genes invariably encoded the intact kinase domain of MAP3K8, but not the inhibitory domain at the C-terminus. In 13 (46%) of the sequenced cases, the 3' fusion partner was SVIL. Other recurrent 3' partners were DIP2C and UBL3, with additional fusion partners that occurred only in a single tumor. Clinically, the lesions appeared mainly in young adults (2-59 years of age; median = 18), most commonly involving the lower limbs (55%). Five cases were diagnosed as Spitz nevus, 13 as atypical Spitz tumor, and 15 as malignant Spitz tumor. Atypical and malignant cases more commonly occurred in younger patients. Atypical Spitz tumors and malignant Spitz tumors cases tended to show epidermal ulceration (32%), a dermal component with giant multinucleated cells (32%), and clusters of pigmented cells in the dermis (32%). Moreover, in atypical and malignant cases, a frequent inactivation of CDKN2A (21/26; 77%) was identified either by p16 immunohistochemistry, FISH, or comparative genomic hybridization. Gene expression analysis revealed that MAP3K8 expression levels were significantly elevated compared to a control group of 57 Spitz lesions harboring other known kinase fusions. Clinical follow-up revealed regional nodal involvement in two of six cases, in which sentinel lymph node biopsy was performed but no distant metastatic disease after a median follow-up time of 6 months.
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Affiliation(s)
- Aurelie Houlier
- Department of Biopathology, Centre Léon Bérard, Lyon, France.,University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Daniel Pissaloux
- Department of Biopathology, Centre Léon Bérard, Lyon, France.,University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Ingrid Masse
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Franck Tirode
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Marie Karanian
- Department of Biopathology, Centre Léon Bérard, Lyon, France.,University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France
| | - Laura B Pincus
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Timothy H McCalmont
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Philip E LeBoit
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Boris C Bastian
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Iwei Yeh
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Arnaud de la Fouchardière
- Department of Biopathology, Centre Léon Bérard, Lyon, France. .,University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5286, INSERM U1052, Cancer Research Centre of Lyon, Lyon, France.
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Elder DE, Bastian BC, Cree IA, Massi D, Scolyer RA. The 2018 World Health Organization Classification of Cutaneous, Mucosal, and Uveal Melanoma: Detailed Analysis of 9 Distinct Subtypes Defined by Their Evolutionary Pathway. Arch Pathol Lab Med 2020; 144:500-522. [PMID: 32057276 DOI: 10.5858/arpa.2019-0561-ra] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— There have been major advances in the understanding of melanoma since the last revision of the World Health Organization (WHO) classification in 2006. OBJECTIVE.— To discuss development of the 9 distinct types of melanoma and distinguishing them by their epidemiology, clinical and histologic morphology, and genomic characteristics. Each melanoma subtype is placed at the end of an evolutionary pathway that is rooted in its respective precursor, wherever appropriate and feasible, based on currently known data. Each precursor has a variable risk of progression culminating in its fully evolved, invasive melanoma. DATA SOURCES.— This review is based on the "Melanocytic Tumours" section of the 4th edition of the WHO Classification of Skin Tumours, published in 2018. CONCLUSIONS.— Melanomas were divided into those etiologically related to sun exposure and those that are not, as determined by their mutational signatures, anatomic site, and epidemiology. Melanomas on the sun-exposed skin were further divided by the histopathologic degree of cumulative solar damage (CSD) of the surrounding skin, into low and high CSD, on the basis of degree of associated solar elastosis. Low-CSD melanomas include superficial spreading melanomas and high-CSD melanomas incorporate lentigo maligna and desmoplastic melanomas. The "nonsolar" category includes acral melanomas, some melanomas in congenital nevi, melanomas in blue nevi, Spitz melanomas, mucosal melanomas, and uveal melanomas. The general term melanocytoma is proposed to encompass "intermediate" tumors that have an increased (though still low) probability of disease progression to melanoma.
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Affiliation(s)
- David E Elder
- From the Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia (Dr Elder); the Department of Dermatology, University of California San Francisco, San Francisco (Dr Bastian); International Agency for Research on Cancer, Lyon, France (Dr Cree); Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy (Dr Massi); and the Department of Pathology and Melanoma Institute Australia, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia (Dr Scolyer)
| | - Boris C Bastian
- From the Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia (Dr Elder); the Department of Dermatology, University of California San Francisco, San Francisco (Dr Bastian); International Agency for Research on Cancer, Lyon, France (Dr Cree); Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy (Dr Massi); and the Department of Pathology and Melanoma Institute Australia, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia (Dr Scolyer)
| | - Ian A Cree
- From the Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia (Dr Elder); the Department of Dermatology, University of California San Francisco, San Francisco (Dr Bastian); International Agency for Research on Cancer, Lyon, France (Dr Cree); Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy (Dr Massi); and the Department of Pathology and Melanoma Institute Australia, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia (Dr Scolyer)
| | - Daniela Massi
- From the Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia (Dr Elder); the Department of Dermatology, University of California San Francisco, San Francisco (Dr Bastian); International Agency for Research on Cancer, Lyon, France (Dr Cree); Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy (Dr Massi); and the Department of Pathology and Melanoma Institute Australia, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia (Dr Scolyer)
| | - Richard A Scolyer
- From the Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia (Dr Elder); the Department of Dermatology, University of California San Francisco, San Francisco (Dr Bastian); International Agency for Research on Cancer, Lyon, France (Dr Cree); Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy (Dr Massi); and the Department of Pathology and Melanoma Institute Australia, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia (Dr Scolyer)
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27
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Lee HJ, Pham T, Chang MT, Barnes D, Cai AG, Noubade R, Totpal K, Chen X, Tran C, Hagenbeek T, Wu X, Eastham-Anderson J, Tao J, Lee W, Bastian BC, Carbone M, Webster JD, Dey A. The Tumor Suppressor BAP1 Regulates the Hippo Pathway in Pancreatic Ductal Adenocarcinoma. Cancer Res 2020; 80:1656-1668. [PMID: 31988076 DOI: 10.1158/0008-5472.can-19-1704] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 01/17/2020] [Indexed: 11/16/2022]
Abstract
The deubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with a high risk for mesothelioma and melanocytic tumors. Here, we show that pancreatic intraepithelial neoplasia driven by oncogenic mutant KrasG12D progressed to pancreatic adenocarcinoma in the absence of BAP1. The Hippo pathway was deregulated in BAP1-deficient pancreatic tumors, with the tumor suppressor LATS exhibiting enhanced ubiquitin-dependent proteasomal degradation. Therefore, BAP1 may limit tumor progression by stabilizing LATS and thereby promoting activity of the Hippo tumor suppressor pathway. SIGNIFICANCE: BAP1 is mutated in a broad spectrum of tumors. Pancreatic Bap1 deficiency causes acinar atrophy but combines with oncogenic Ras to produce pancreatic tumors. BAP1-deficient tumors exhibit deregulation of the Hippo pathway.See related commentary by Brekken, p. 1624.
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Affiliation(s)
- Ho-June Lee
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Trang Pham
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Matthew T Chang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California
| | - Dwight Barnes
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Allen G Cai
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Rajkumar Noubade
- Department of Immunology, Genentech, Inc., South San Francisco, California
| | - Klara Totpal
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California
| | - Xu Chen
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Christopher Tran
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Thijs Hagenbeek
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Xiumin Wu
- Translational Immunology, Genentech, Inc., South San Francisco, California
| | | | - Janet Tao
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Wyne Lee
- Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Boris C Bastian
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Michele Carbone
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Joshua D Webster
- Department of Pathology, Genentech, Inc., South San Francisco, California.
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California.
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Torres R, Lang UE, Hejna M, Shelton SJ, Joseph NM, Shain AH, Yeh I, Wei ML, Oldham MC, Bastian BC, Judson-Torres RL. MicroRNA Ratios Distinguish Melanomas from Nevi. J Invest Dermatol 2020; 140:164-173.e7. [PMID: 31580842 PMCID: PMC6926155 DOI: 10.1016/j.jid.2019.06.126] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 12/27/2022]
Abstract
The use of microRNAs as biomarkers has been proposed for many diseases, including the diagnosis of melanoma. Although hundreds of microRNAs have been identified as differentially expressed in melanomas as compared to benign melanocytic lesions, a limited consensus has been achieved across studies, constraining the effective use of these potentially useful markers. In this study, we applied a machine learning-based pipeline to a dataset consisting of genetic features, clinical features, and next-generation microRNA sequencing from micro-dissected formalin-fixed paraffin embedded melanomas and their adjacent benign precursor nevi. We identified patient age and tumor cellularity as variables that frequently confound the measured expression of potentially diagnostic microRNAs. By employing the ratios of microRNAs that were either enriched or depleted in melanoma compared to the nevi as a normalization strategy, we developed a model that classified all the available published cohorts with an area under the receiver operating characteristic curve of 0.98. External validation on an independent cohort classified lesions with 81% sensitivity and 88% specificity and was uninfluenced by the tumor content of the sample or patient age.
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Affiliation(s)
- Rodrigo Torres
- Department of Dermatology, University of California, San Francisco, California, USA
| | - Ursula E Lang
- Department of Dermatology, University of California, San Francisco, California, USA; Department of Pathology, University of California, San Francisco, California, USA
| | - Miroslav Hejna
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Samuel J Shelton
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Nancy M Joseph
- Department of Pathology, University of California, San Francisco, California, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, California, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, California, USA; Department of Pathology, University of California, San Francisco, California, USA
| | - Maria L Wei
- Department of Dermatology, University of California, San Francisco, California, USA; San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Michael C Oldham
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, California, USA; Department of Pathology, University of California, San Francisco, California, USA
| | - Robert L Judson-Torres
- Department of Dermatology, University of California, San Francisco, California, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA; Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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Afshar AR, Pekmezci M, Bloomer MM, Cadenas NJ, Stevers M, Banerjee A, Roy R, Olshen AB, Van Ziffle J, Onodera C, Devine WP, Grenert JP, Bastian BC, Solomon DA, Damato BE. Next-Generation Sequencing of Retinoblastoma Identifies Pathogenic Alterations beyond RB1 Inactivation That Correlate with Aggressive Histopathologic Features. Ophthalmology 2019; 127:804-813. [PMID: 32139107 DOI: 10.1016/j.ophtha.2019.12.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To determine the usefulness of a comprehensive, targeted-capture next-generation sequencing (NGS) assay for the clinical management of children undergoing enucleation for retinoblastoma. DESIGN Cohort study. PARTICIPANTS Thirty-two children with retinoblastoma. METHODS We performed targeted NGS using the UCSF500 Cancer Panel (University of California, San Francisco, San Francisco, CA) on formalin-fixed, paraffin-embedded tumor tissue along with constitutional DNA isolated from peripheral blood, buccal swab, or uninvolved optic nerve. Peripheral blood samples were also sent to a commercial laboratory for germline RB1 mutation testing. MAIN OUTCOME MEASURES Presence or absence of germline RB1 mutation or deletion, tumor genetic profile, and association of genetic alterations with clinicopathologic features. RESULTS Germline mutation or deletion of the RB1 gene was identified in all children with bilateral retinoblastoma (n = 12), and these NGS results were 100% concordant with commercial germline RB1 mutation analysis. In tumor tissue tested with NGS, biallelic inactivation of RB1 was identified in 28 tumors and focal MYCN amplification was identified in 4 tumors (2 with wild-type RB1 and 2 with biallelic RB1 inactivation). Additional likely pathogenic alterations beyond RB1 were identified in 13 tumors (41%), several of which have not been reported previously in retinoblastoma. These included focal amplifications of MDM4 and RAF1, as well as damaging mutations involving BCOR, ARID1A, MGA, FAT1, and ATRX. The presence of additional likely pathogenetic mutations beyond RB1 inactivation was associated with aggressive histopathologic features, including higher histologic grade and anaplasia, and also with both unilateral and sporadic disease. CONCLUSIONS Comprehensive NGS analysis reliably detects relevant mutations, amplifications, and chromosomal copy number changes in retinoblastoma. The presence of genetic alterations beyond RB1 inactivation correlates with aggressive histopathologic features.
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Affiliation(s)
- Armin R Afshar
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.
| | - Melike Pekmezci
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Michele M Bloomer
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Nicola J Cadenas
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, California
| | - Meredith Stevers
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Anuradha Banerjee
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Division of Hematology-Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California
| | - Adam B Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Courtney Onodera
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - W Patrick Devine
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - James P Grenert
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California; Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - David A Solomon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Bertil E Damato
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Burbidge TE, Bastian BC, Guo D, Li H, Morris DG, Monzon JG, Leung G, Yang H, Cheng T. Association of Indoor Tanning Exposure With Age at Melanoma Diagnosis and BRAF V600E Mutations. J Natl Cancer Inst 2019; 111:1228-1231. [PMID: 30923800 DOI: 10.1093/jnci/djz048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 02/21/2019] [Accepted: 03/26/2019] [Indexed: 02/03/2023] Open
Abstract
There is limited information on how indoor tanning promotes melanoma development. We investigated indoor tanning use in patients with melanomas in sun-exposed skin and studied the clinicopathological and molecular characteristics in relation to indoor tanning exposure. Patients from a multidisciplinary clinic for cutaneous cancers completed standardized questionnaires on risk factors for melanoma as a component of medical history at their initial consultations. For this study, we included patients from December 2013 to May 2015. The 114 patients who reported indoor tanning exposure were younger at diagnosis than the 222 patients who did not (51.5 vs 64.0 years, two-sided P < .001). BRAF V600E genotype was more prevalent in ever-users than in nonusers (42.9% vs 28.3%, two-sided P = .04) and higher in ever-users who initiated indoor tanning prior to age 25 years compared with age 25 years or older (62.2% vs 31.1%, two-sided P = .003). There were more melanomas in intermittently sun-exposed skin in ever-users than nonusers (65.7% vs 51.9%, respectively, two-sided P = .02). Our data suggest indoor tanning may promote melanomas that arise in skin with low-chronic sun-induced damage through BRAF V600E-mediated melanomagenesis.
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Fernandez KS, Turski ML, Shah AT, Bastian BC, Horvai A, Hardee S, Sweet-Cordero EA. Ewing sarcoma in a child with neurofibromatosis type 1. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004580. [PMID: 31645347 PMCID: PMC6824249 DOI: 10.1101/mcs.a004580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/28/2019] [Indexed: 12/02/2022] Open
Abstract
We report here on a case of Ewing sarcoma (ES) occurring in a child with neurofibromatosis type 1. The sarcoma had an EWSR1-ERG translocation as well as loss of the remaining wild-type allele of NF1. Loss of the NF1 wild-type allele in the tumor suggests that activation of the Ras pathway contributed to its evolution. Review of available public data suggests that secondary mutations in the Ras pathway are found in ∼3% of ESs. This case suggests that Ras pathway activation may play a role in tumor progression in a subset of ESs.
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Affiliation(s)
- Karen S Fernandez
- Division of Hematology/Oncology, Valley Children's Hospital, Madera, California 93636, USA
| | - Michelle L Turski
- Molecular Oncology Initiative, University of California, San Francisco, San Francisco, California 94158, USA
| | - Avanthi Tayi Shah
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California 94158, USA
| | - Boris C Bastian
- Departments of Dermatology and Pathology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Andrew Horvai
- Department of Pathology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Steven Hardee
- Division of Pathology, Valley Children's Hospital, Madera, California 93636, USA
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California 94158, USA
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32
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Yeh I, Jorgenson E, Shen L, Xu M, North JP, Shain AH, Reuss D, Wu H, Robinson WA, Olshen A, von Deimling A, Kwok PY, Bastian BC, Asgari MM. Targeted Genomic Profiling of Acral Melanoma. J Natl Cancer Inst 2019; 111:1068-1077. [PMID: 30657954 PMCID: PMC6792090 DOI: 10.1093/jnci/djz005] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Acral melanoma is a rare type of melanoma that affects world populations irrespective of skin color and has worse survival than other cutaneous melanomas. It has relatively few single nucleotide mutations without the UV signature of cutaneous melanomas, but instead has a genetic landscape characterized by structural rearrangements and amplifications. BRAF mutations are less common than in other cutaneous melanomas, and knowledge about alternative therapeutic targets is incomplete. METHODS To identify alternative therapeutic targets, we performed targeted deep-sequencing on 122 acral melanomas. We confirmed the loss of the tumor suppressors p16 and NF1 by immunohistochemistry in select cases. RESULTS In addition to BRAF (21.3%), NRAS (27.9%), and KIT (11.5%) mutations, we identified a broad array of MAPK pathway activating alterations, including fusions of BRAF (2.5%), NTRK3 (2.5%), ALK (0.8%), and PRKCA (0.8%), which can be targeted by available inhibitors. Inactivation of NF1 occurred in 18 cases (14.8%). Inactivation of the NF1 cooperating factor SPRED1 occurred in eight cases (6.6%) as an alternative mechanism of disrupting the negative regulation of RAS. Amplifications recurrently affected narrow loci containing PAK1 and GAB2 (n = 27, 22.1%), CDK4 (n = 27, 22.1%), CCND1 (n = 24, 19.7%), EP300 (n = 20, 16.4%), YAP1 (n = 15, 12.3%), MDM2 (n = 13, 10.7%), and TERT (n = 13, 10.7%) providing additional and possibly complementary therapeutic targets. Acral melanomas with BRAFV600E mutations harbored fewer genomic amplifications and were more common in patients with European ancestry. CONCLUSION Our findings support a new, molecularly based subclassification of acral melanoma with potential therapeutic implications: BRAFV600E mutant acral melanomas with characteristics similar to nonacral melanomas that could benefit from BRAF inhibitor therapy, and non-BRAFV600E mutant acral melanomas. Acral melanomas without BRAFV600E mutations harbor a broad array of therapeutically relevant alterations. Expanded molecular profiling would increase the detection of potentially targetable alterations for this subtype of acral melanoma.
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Affiliation(s)
- Iwei Yeh
- Correspondence to: Iwei Yeh, MD, PhD, Departments of Dermatology and Pathology, 1701 Divisadero St. Ste. 280, San Francisco, CA 94115 (e-mail: )
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33
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Rotow JK, Gui P, Wu W, Raymond VM, Lanman RB, Kaye FJ, Peled N, Fece de la Cruz F, Nadres B, Corcoran RB, Yeh I, Bastian BC, Starostik P, Newsom K, Olivas VR, Wolff AM, Fraser JS, Collisson EA, McCoach CE, Camidge DR, Pacheco J, Bazhenova L, Li T, Bivona TG, Blakely CM. Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clin Cancer Res 2019; 26:439-449. [PMID: 31548343 DOI: 10.1158/1078-0432.ccr-19-1667] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 09/10/2019] [Indexed: 01/07/2023]
Abstract
PURPOSE Although patients with advanced-stage non-small cell lung cancers (NSCLC) harboring MET exon 14 skipping mutations (METex14) often benefit from MET tyrosine kinase inhibitor (TKI) treatment, clinical benefit is limited by primary and acquired drug resistance. The molecular basis for this resistance remains incompletely understood. EXPERIMENTAL DESIGN Targeted sequencing analysis was performed on cell-free circulating tumor DNA obtained from 289 patients with advanced-stage METex14-mutated NSCLC. RESULTS Prominent co-occurring RAS-MAPK pathway gene alterations (e.g., in KRAS, NF1) were detected in NSCLCs with METex14 skipping alterations as compared with EGFR-mutated NSCLCs. There was an association between decreased MET TKI treatment response and RAS-MAPK pathway co-occurring alterations. In a preclinical model expressing a canonical METex14 mutation, KRAS overexpression or NF1 downregulation hyperactivated MAPK signaling to promote MET TKI resistance. This resistance was overcome by cotreatment with crizotinib and the MEK inhibitor trametinib. CONCLUSIONS Our study provides a genomic landscape of co-occurring alterations in advanced-stage METex14-mutated NSCLC and suggests a potential combination therapy strategy targeting MAPK pathway signaling to enhance clinical outcomes.
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Affiliation(s)
- Julia K Rotow
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | - Frederic J Kaye
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Nir Peled
- Soroka Medical Center, Ben-Gurion University, Beer-Sheva, Israel
| | - Ferran Fece de la Cruz
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brandon Nadres
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Kimberly Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, California
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | | | - Tianhong Li
- Department of Internal Medicine, University of California, Davis, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
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34
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Leachman SA, Hornyak TJ, Barsh G, Bastian BC, Brash DE, Cleaver JE, Cooper CD, D'Orazio JA, Fujita M, Holmen SL, Indra AK, Kraemer KH, Le Poole IC, Lo RS, Lund AW, Manga P, Pavan WJ, Setaluri V, Stemwedel CE, Kulesz-Martin MF. Melanoma to Vitiligo: The Melanocyte in Biology & Medicine-Joint Montagna Symposium on the Biology of Skin/PanAmerican Society for Pigment Cell Research Annual Meeting. J Invest Dermatol 2019; 140:269-274. [PMID: 31348921 DOI: 10.1016/j.jid.2019.03.1164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Sancy A Leachman
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Thomas J Hornyak
- Research and Development Service, VA Maryland Health Care System, Baltimore, Maryland; Departments of Dermatology and Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - Douglas E Brash
- Departments of Therapeutic Radiology and Dermatology and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - James E Cleaver
- Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - Cynthia D Cooper
- School of Molecular Biosciences and College of Arts and Sciences, Washington State University Vancouver, Vancouver, Washington
| | - John A D'Orazio
- The Markey Cancer Center and the Departments of Toxicology and Cancer Biology and Pediatrics, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Mayumi Fujita
- Departments of Dermatology and Immunology & Microbiology, University of Colorado School of Medicine, Aurora, Colorado; Denver VA Medical Center, Denver, Colorado
| | - Sheri L Holmen
- Huntsman Cancer Institute and Departments of Oncological Sciences and Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Arup K Indra
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon; Department of Pharmaceutical Sciences, College of Pharmacy, Linus Pauling Institute, and Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - I Caroline Le Poole
- Oncology Research Institute, Loyola University Chicago, Maywood, Illinois; Departments of Dermatology and Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
| | - Amanda W Lund
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon; Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon
| | - Prashiela Manga
- Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, New York
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Clara E Stemwedel
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon
| | - Molly F Kulesz-Martin
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon.
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35
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Newell F, Kong Y, Wilmott JS, Johansson PA, Ferguson PM, Cui C, Li Z, Kazakoff SH, Burke H, Dodds TJ, Patch AM, Nones K, Tembe V, Shang P, van der Weyden L, Wong K, Holmes O, Lo S, Leonard C, Wood S, Xu Q, Rawson RV, Mukhopadhyay P, Dummer R, Levesque MP, Jönsson G, Wang X, Yeh I, Wu H, Joseph N, Bastian BC, Long GV, Spillane AJ, Shannon KF, Thompson JF, Saw RPM, Adams DJ, Si L, Pearson JV, Hayward NK, Waddell N, Mann GJ, Guo J, Scolyer RA. Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets. Nat Commun 2019; 10:3163. [PMID: 31320640 PMCID: PMC6639323 DOI: 10.1038/s41467-019-11107-x] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
Knowledge of key drivers and therapeutic targets in mucosal melanoma is limited due to the paucity of comprehensive mutation data on this rare tumor type. To better understand the genomic landscape of mucosal melanoma, here we describe whole genome sequencing analysis of 67 tumors and validation of driver gene mutations by exome sequencing of 45 tumors. Tumors have a low point mutation burden and high numbers of structural variants, including recurrent structural rearrangements targeting TERT, CDK4 and MDM2. Significantly mutated genes are NRAS, BRAF, NF1, KIT, SF3B1, TP53, SPRED1, ATRX, HLA-A and CHD8. SF3B1 mutations occur more commonly in female genital and anorectal melanomas and CTNNB1 mutations implicate a role for WNT signaling defects in the genesis of some mucosal melanomas. TERT aberrations and ATRX mutations are associated with alterations in telomere length. Mutation profiles of the majority of mucosal melanomas suggest potential susceptibility to CDK4/6 and/or MEK inhibitors.
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Affiliation(s)
- Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Yan Kong
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Chuanliang Cui
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Zhongwu Li
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Hazel Burke
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Tristan J Dodds
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Varsha Tembe
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Ping Shang
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kim Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Serigne Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Robert V Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | | | - Reinhard Dummer
- Dermatology Clinic, University Hospital Zürich, University of Zurich, Zurich, 8091, Switzerland
| | - Mitchell P Levesque
- Dermatology Clinic, University Hospital Zürich, University of Zurich, Zurich, 8091, Switzerland
| | - Göran Jönsson
- Department of Oncology, Clinical Sciences, Lund University, Lund, 221 85, Sweden
| | - Xuan Wang
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Iwei Yeh
- Departments of Dermatology and Pathology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Hong Wu
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Nancy Joseph
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Boris C Bastian
- Departments of Dermatology and Pathology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Royal North Shore and Mater Hospitals, Sydney, NSW, 2065, Australia
| | - Andrew J Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Lu Si
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Jun Guo
- Department of Renal Cancer and Melanoma, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.
- Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.
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36
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Afshar AR, Damato BE, Stewart JM, Zablotska LB, Roy R, Olshen AB, Joseph NM, Bastian BC. Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis. Transl Vis Sci Technol 2019; 8:18. [PMID: 31024753 PMCID: PMC6472431 DOI: 10.1167/tvst.8.2.18] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/12/2019] [Indexed: 12/30/2022] Open
Abstract
Purpose To clinically use the UCSF500, a pancancer, next-generation sequencing assay in uveal melanoma (UM) and to correlate results with gene expression profiling (GEP) and predictive factors for metastasis. Methods Cohort study. Tumor samples of adult UM patients were analyzed with the UCSF500 and GEP. Main outcomes were copy number changes in chromosomes 1, 3, 6, and 8 and mutations in GNAQ, GNA11, SF3B1, EIF1AX, BAP1, SRSF2, U2AF1, and PLCB4. Chromosome 3 loss (a metastasis predictor) was tested for correlation with GEP class, tumor characteristics (largest basal diameter, thickness, ciliary body involvement, and extraocular extension), and histology (presence of epithelioid cells, closed loops, and mitotic count). Results The 62 patients had a mean age of 59 years (range, 24–89 years). Chromosome 3 loss was detected in 30 patients and was associated with larger basal tumor diameter (Wilcoxon rank sum test, P = 0.015), greater thickness (Wilcoxon rank sum test, P = 0.016) and tumor, node, metastasis stage (Fisher test, P = 0.006), epithelioid cytology (Fisher test, P < 0.001), BAP1 mutation (Fisher test, P < 0.001), and chromosome 8q gain (Fisher test, P < 0.001). Class 2 tumors were much more likely to have chromosome 3 loss than class 1 (odds ratio, 121; P < 0.001). Eleven patients developed metastatic UM, of which five died during the study. All metastatic cases had chromosome 3 loss, 8 gain, BAP1 mutation, and class 2 GEP. Five class 1 tumors had chromosome 3 loss. Conclusions UCSF500 detects chromosomal copy number changes and missense mutations that correlate strongly with metastasis predictors, including GEP. Translational Relevance Next-generation sequencing of UM should enhance survival prognostication.
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Affiliation(s)
- Armin R Afshar
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.,Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Bertil E Damato
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.,Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Jay M Stewart
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Lydia B Zablotska
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Ritu Roy
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Computational Biology and Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Adam B Olshen
- Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Computational Biology and Informatics, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy M Joseph
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
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37
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Webster JD, Pham TH, Wu X, Hughes NW, Li Z, Totpal K, Lee HJ, Calses PC, Chaurushiya MS, Stawiski EW, Modrusan Z, Chang MT, Tran C, Lee WP, Chalasani S, Hung J, Sharma N, Chan S, Hotzel K, Talevich E, Shain A, Xu M, Lill J, Dixit VM, Bastian BC, Dey A. The tumor suppressor BAP1 cooperates with BRAFV600E to promote tumor formation in cutaneous melanoma. Pigment Cell Melanoma Res 2019; 32:269-279. [PMID: 30156010 DOI: 10.1111/pcmr.12735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/19/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022]
Abstract
The deubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with a high risk of mesothelioma and melanocytic tumors. Here, we show that Bap1 deletion in melanocytes cooperates with the constitutively active, oncogenic form of BRAF (BRAFV600E ) and UV to cause melanoma in mice, albeit at very low frequency. In addition, Bap1-null melanoma cells derived from mouse tumors are more aggressive and colonize and grow at distant sites more than their wild-type counterparts. Molecularly, Bap1-null melanoma cell lines have increased DNA damage measured by γH2aX and hyperubiquitination of histone H2a. Therapeutically, these Bap1-null tumors are completely responsive to BRAF- and MEK-targeted therapies. Therefore, BAP1 functions as a tumor suppressor and limits tumor progression in melanoma.
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Affiliation(s)
- Joshua D Webster
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Trang H Pham
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Nicolas W Hughes
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Zhongwu Li
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Klara Totpal
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California
| | - Ho-June Lee
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Philamer C Calses
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Mira S Chaurushiya
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, California
| | - Eric W Stawiski
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California
| | - Matthew T Chang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California
| | - Christopher Tran
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Sreedevi Chalasani
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Jeffrey Hung
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Neeraj Sharma
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Sara Chan
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Kathy Hotzel
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Eric Talevich
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Alan Shain
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Mengshu Xu
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jennie Lill
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, California
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, California
| | - Boris C Bastian
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
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38
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Wong K, van der Weyden L, Schott CR, Foote A, Constantino-Casas F, Smith S, Dobson JM, Murchison EP, Wu H, Yeh I, Fullen DR, Joseph N, Bastian BC, Patel RM, Martincorena I, Robles-Espinoza CD, Iyer V, Kuijjer ML, Arends MJ, Brenn T, Harms PW, Wood GA, Adams DJ. Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nat Commun 2019; 10:353. [PMID: 30664638 PMCID: PMC6341101 DOI: 10.1038/s41467-018-08081-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023] Open
Abstract
Mucosal melanoma is a rare and poorly characterized subtype of human melanoma. Here we perform a cross-species analysis by sequencing tumor-germline pairs from 46 primary human muscosal, 65 primary canine oral and 28 primary equine melanoma cases from mucosal sites. Analysis of these data reveals recurrently mutated driver genes shared between species such as NRAS, FAT4, PTPRJ, TP53 and PTEN, and pathogenic germline alleles of BRCA1, BRCA2 and TP53. We identify a UV mutation signature in a small number of samples, including human cases from the lip and nasal mucosa. A cross-species comparative analysis of recurrent copy number alterations identifies several candidate drivers including MDM2, B2M, KNSTRN and BUB1B. Comparison of somatic mutations in recurrences and metastases to those in the primary tumor suggests pervasive intra-tumor heterogeneity. Collectively, these studies suggest a convergence of some genetic changes in mucosal melanomas between species but also distinctly different paths to tumorigenesis.
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Affiliation(s)
- Kim Wong
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Louise van der Weyden
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Courtney R Schott
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - Alastair Foote
- Rossdales Equine Hospital and Diagnostic Centre, High Street, Newmarket, Suffolk, CB8 8JS, UK
| | - Fernando Constantino-Casas
- Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Sionagh Smith
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jane M Dobson
- Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Elizabeth P Murchison
- Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Hong Wu
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, 94143, USA
| | - Iwei Yeh
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, 94143, USA
| | - Douglas R Fullen
- Departments of Pathology and Dermatology, University of Michigan Medical School, 3261 Medical Science I, 1301 Catherine, Ann Arbor, MI, 48109-5602, USA
| | - Nancy Joseph
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, 94143, USA
| | - Boris C Bastian
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, 94143, USA
| | - Rajiv M Patel
- Departments of Pathology and Dermatology, University of Michigan Medical School, 3261 Medical Science I, 1301 Catherine, Ann Arbor, MI, 48109-5602, USA
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Carla Daniela Robles-Espinoza
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, Santiago de Querétaro, 76230, Mexico
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Marieke L Kuijjer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, 0349, Oslo, Norway
| | - Mark J Arends
- University of Edinburgh, Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Genetics & Molecular Medicine, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Thomas Brenn
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine and Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, T2L 2K8, Canada
| | - Paul W Harms
- Departments of Pathology and Dermatology, University of Michigan Medical School, 3261 Medical Science I, 1301 Catherine, Ann Arbor, MI, 48109-5602, USA
| | - Geoffrey A Wood
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Phillips JJ, Gong H, Chen K, Joseph NM, van Ziffle J, Bastian BC, Grenert JP, Kline CN, Mueller S, Banerjee A, Nicolaides T, Gupta N, Berger MS, Lee HS, Pekmezci M, Tihan T, Bollen AW, Perry A, Shieh JT, Solomon DA. The genetic landscape of anaplastic pleomorphic xanthoastrocytoma. Brain Pathol 2019; 29:85-96. [PMID: 30051528 PMCID: PMC7837273 DOI: 10.1111/bpa.12639] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Pleomorphic xanthoastrocytoma (PXA) is an astrocytic neoplasm that is typically well circumscribed and can have a relatively favorable prognosis. Tumor progression to anaplastic PXA (WHO grade III), however, is associated with a more aggressive biologic behavior and worse prognosis. The factors that drive anaplastic progression are largely unknown. We performed comprehensive genomic profiling on a set of 23 PXAs from 19 patients, including 15 with anaplastic PXA. Four patients had tumor tissue from multiple recurrences, including two with anaplastic progression. We find that PXAs are genetically defined by the combination of CDKN2A biallelic inactivation and RAF alterations that were present in all 19 cases, most commonly as CDKN2A homozygous deletion and BRAF p.V600E mutation but also occasionally BRAF or RAF1 fusions or other rearrangements. The third most commonly altered gene in anaplastic PXA was TERT, with 47% (7/15) harboring TERT alterations, either gene amplification (n = 2) or promoter hotspot mutation (n = 5). In tumor pairs analyzed before and after anaplastic progression, two had increased copy number alterations and one had TERT promoter mutation at recurrence. Less commonly altered genes included TP53, BCOR, BCORL1, ARID1A, ATRX, PTEN, and BCL6. All PXA in this cohort were IDH and histone H3 wildtype, and did not contain alterations in EGFR. Genetic profiling performed on six regions from the same tumor identified intratumoral genomic heterogeneity, likely reflecting clonal evolution during tumor progression. Overall, anaplastic PXA is characterized by the combination of CDKN2A biallelic inactivation and oncogenic RAF kinase signaling as well as a relatively small number of additional genetic alterations, with the most common being TERT amplification or promoter mutation. These data define a distinct molecular profile for PXA and suggest additional genetic alterations, including TERT, may be associated with anaplastic progression.
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Affiliation(s)
- Joanna J. Phillips
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
| | - Henry Gong
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
| | - Katharine Chen
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
| | - Nancy M. Joseph
- Clinical Cancer Genomics LaboratoryUniversity of California San FranciscoSan FranciscoCA
- Department of PathologyUniversity of California San FranciscoSan FranciscoCA
| | - Jessica van Ziffle
- Clinical Cancer Genomics LaboratoryUniversity of California San FranciscoSan FranciscoCA
| | - Boris C. Bastian
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
- Clinical Cancer Genomics LaboratoryUniversity of California San FranciscoSan FranciscoCA
| | - James P. Grenert
- Clinical Cancer Genomics LaboratoryUniversity of California San FranciscoSan FranciscoCA
- Department of PathologyUniversity of California San FranciscoSan FranciscoCA
| | - Cassie N. Kline
- Division of Pediatric Hematology/OncologyDepartment of PediatricsUniversity of California San FranciscoSan FranciscoCA
| | - Sabine Mueller
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Division of Pediatric Hematology/OncologyDepartment of PediatricsUniversity of California San FranciscoSan FranciscoCA
| | - Anuradha Banerjee
- Division of Pediatric Hematology/OncologyDepartment of PediatricsUniversity of California San FranciscoSan FranciscoCA
| | - Theodore Nicolaides
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Division of Pediatric Hematology/OncologyDepartment of PediatricsUniversity of California San FranciscoSan FranciscoCA
| | - Nalin Gupta
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
| | - Mitchel S. Berger
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
| | - Han S. Lee
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
| | - Melike Pekmezci
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
| | - Tarik Tihan
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
| | - Andrew W. Bollen
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
| | - Arie Perry
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCA
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
| | - Joseph T.C. Shieh
- Department of PediatricsDivision of Medical GeneticsUniversity of California San FranciscoSan FranciscoCA
- Institute for Human GeneticsUniversity of CaliforniaSan FranciscoCA
| | - David A. Solomon
- Division of NeuropathologyDepartment of PathologyUniversity of California San FranciscoSan FranciscoCA
- Helen Diller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
- Clinical Cancer Genomics LaboratoryUniversity of California San FranciscoSan FranciscoCA
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40
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López GY, Van Ziffle J, Onodera C, Grenert JP, Yeh I, Bastian BC, Clarke J, Oberheim Bush NA, Taylor J, Chang S, Butowski N, Banerjee A, Mueller S, Kline C, Torkildson J, Samuel D, Siongco A, Raffel C, Gupta N, Kunwar S, Mummaneni P, Aghi M, Theodosopoulos P, Berger M, Phillips JJ, Pekmezci M, Tihan T, Bollen AW, Perry A, Solomon DA. The genetic landscape of gliomas arising after therapeutic radiation. Acta Neuropathol 2019; 137:139-150. [PMID: 30196423 DOI: 10.1007/s00401-018-1906-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 11/26/2022]
Abstract
Radiotherapy improves survival for common childhood cancers such as medulloblastoma, leukemia, and germ cell tumors. Unfortunately, long-term survivors suffer sequelae that can include secondary neoplasia. Gliomas are common secondary neoplasms after cranial or craniospinal radiation, most often manifesting as high-grade astrocytomas with poor clinical outcomes. Here, we performed genetic profiling on a cohort of 12 gliomas arising after therapeutic radiation to determine their molecular pathogenesis and assess for differences in genomic signature compared to their spontaneous counterparts. We identified a high frequency of TP53 mutations, CDK4 amplification or CDKN2A homozygous deletion, and amplifications or rearrangements involving receptor tyrosine kinase and Ras-Raf-MAP kinase pathway genes including PDGFRA, MET, BRAF, and RRAS2. Notably, all tumors lacked alterations in IDH1, IDH2, H3F3A, HIST1H3B, HIST1H3C, TERT (including promoter region), and PTEN, which genetically define the major subtypes of diffuse gliomas in children and adults. All gliomas in this cohort had very low somatic mutation burden (less than three somatic single nucleotide variants or small indels per Mb). The ten high-grade gliomas demonstrated markedly aneuploid genomes, with significantly increased quantity of intrachromosomal copy number breakpoints and focal amplifications/homozygous deletions compared to spontaneous high-grade gliomas, likely as a result of DNA double-strand breaks induced by gamma radiation. Together, these findings demonstrate a distinct molecular pathogenesis of secondary gliomas arising after radiation therapy and identify a genomic signature that may aid in differentiating these tumors from their spontaneous counterparts.
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Affiliation(s)
- Giselle Y López
- Department of Pathology, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - Courtney Onodera
- Department of Pathology, University of California, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - James P Grenert
- Department of Pathology, University of California, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Pathology, University of California, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Pathology, University of California, San Francisco, CA, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Jennifer Clarke
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Jennie Taylor
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Susan Chang
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Nicholas Butowski
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Anuradha Banerjee
- Division of Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Sabine Mueller
- Department of Neurology, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Cassie Kline
- Department of Neurology, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Joseph Torkildson
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Aleli Siongco
- Department of Pathology, Valley Children's Hospital, Madera, CA, USA
| | - Corey Raffel
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Sandeep Kunwar
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Praveen Mummaneni
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Manish Aghi
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Mitchel Berger
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Pathology, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, CA, USA.
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA.
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41
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Ablain J, Xu M, Rothschild H, Jordan RC, Mito JK, Daniels BH, Bell CF, Joseph NM, Wu H, Bastian BC, Zon LI, Yeh I. Human tumor genomics and zebrafish modeling identify SPRED1 loss as a driver of mucosal melanoma. Science 2018; 362:1055-1060. [PMID: 30385465 DOI: 10.1126/science.aau6509] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
Abstract
Melanomas originating from mucosal surfaces have low mutation burden, genomic instability, and poor prognosis. To identify potential driver genes, we sequenced hundreds of cancer-related genes in 43 human mucosal melanomas, cataloging point mutations, amplifications, and deletions. The SPRED1 gene, which encodes a negative regulator of mitogen-activated protein kinase (MAPK) signaling, was inactivated in 37% of the tumors. Four distinct genotypes were associated with SPRED1 loss. Using a rapid, tissue-specific CRISPR technique to model these genotypes in zebrafish, we found that SPRED1 functions as a tumor suppressor, particularly in the context of KIT mutations. SPRED1 knockdown caused MAPK activation, increased cell proliferation, and conferred resistance to drugs inhibiting KIT tyrosine kinase activity. These findings provide a rationale for MAPK inhibition in SPRED1-deficient melanomas and introduce a zebrafish modeling approach that can be used more generally to dissect genetic interactions in cancer.
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Affiliation(s)
- Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mengshu Xu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Harriet Rothschild
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Richard C Jordan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey K Mito
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Brianne H Daniels
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caitlin F Bell
- Department of Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Nancy M Joseph
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hong Wu
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Boston Children's Hospital and Harvard University, Boston, MA 02115, USA
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. .,Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
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42
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Lee J, Putnam AR, Chesier SH, Banerjee A, Raffel C, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Perry A, Solomon DA. Oligodendrogliomas, IDH-mutant and 1p/19q-codeleted, arising during teenage years often lack TERT promoter mutation that is typical of their adult counterparts. Acta Neuropathol Commun 2018; 6:95. [PMID: 30231927 PMCID: PMC6145350 DOI: 10.1186/s40478-018-0598-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/10/2022] Open
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43
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Solomon DA, Korshunov A, Sill M, Jones DTW, Kool M, Pfister SM, Fan X, Bannykh S, Hu J, Danielpour M, Li R, Johnston J, Cham E, Cooney T, Sun PP, Oberheim Bush NA, McDermott M, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Villanueva-Meyer JE, Pekmezci M, Bollen AW, Perry A. Myxoid glioneuronal tumor of the septum pellucidum and lateral ventricle is defined by a recurrent PDGFRA p.K385 mutation and DNT-like methylation profile. Acta Neuropathol 2018; 136:339-343. [PMID: 30006677 DOI: 10.1007/s00401-018-1883-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
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44
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Zeng H, Jorapur A, Shain AH, Lang UE, Torres R, Zhang Y, McNeal AS, Botton T, Lin J, Donne M, Bastian IN, Yu R, North JP, Pincus L, Ruben BS, Joseph NM, Yeh I, Bastian BC, Judson RL. Bi-allelic Loss of CDKN2A Initiates Melanoma Invasion via BRN2 Activation. Cancer Cell 2018; 34:56-68.e9. [PMID: 29990501 PMCID: PMC6084788 DOI: 10.1016/j.ccell.2018.05.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 02/12/2018] [Accepted: 05/30/2018] [Indexed: 02/03/2023]
Abstract
Loss of the CDKN2A tumor suppressor is associated with melanoma metastasis, but the mechanisms connecting the phenomena are unknown. Using CRISPR-Cas9 to engineer a cellular model of melanoma initiation from primary human melanocytes, we discovered that a lineage-restricted transcription factor, BRN2, is downstream of CDKN2A and directly regulated by E2F1. In a cohort of melanocytic tumors that capture distinct progression stages, we observed that CDKN2A loss coincides with both the onset of invasive behavior and increased BRN2 expression. Loss of the CDKN2A protein product p16INK4A permitted metastatic dissemination of human melanoma lines in mice, a phenotype rescued by inhibition of BRN2. These results demonstrate a mechanism by which CDKN2A suppresses the initiation of melanoma invasion through inhibition of BRN2.
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Affiliation(s)
- Hanlin Zeng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Aparna Jorapur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - A Hunter Shain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Ursula E Lang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Rodrigo Torres
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Yuntian Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Andrew S McNeal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Thomas Botton
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Donne
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ingmar N Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Richard Yu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Faculty of Medicine, University of British Columbia, Vancouver, BC V6T1Z3, Canada
| | - Jeffrey P North
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Laura Pincus
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Beth S Ruben
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Palo Alto Medical Foundation, Palo Alto, CA 94301, USA
| | - Nancy M Joseph
- Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA.
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Shain AH, Joseph NM, Yu R, Benhamida J, Liu S, Prow T, Ruben B, North J, Pincus L, Yeh I, Judson R, Bastian BC. Genomic and Transcriptomic Analysis Reveals Incremental Disruption of Key Signaling Pathways during Melanoma Evolution. Cancer Cell 2018; 34:45-55.e4. [PMID: 29990500 PMCID: PMC6319271 DOI: 10.1016/j.ccell.2018.06.005] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 03/02/2018] [Accepted: 06/08/2018] [Indexed: 12/30/2022]
Abstract
We elucidated genomic and transcriptomic changes that accompany the evolution of melanoma from pre-malignant lesions by sequencing DNA and RNA from primary melanomas and their adjacent precursors, as well as matched primary tumors and regional metastases. In total, we analyzed 230 histopathologically distinct areas of melanocytic neoplasia from 82 patients. Somatic alterations sequentially induced mitogen-activated protein kinase (MAPK) pathway activation, upregulation of telomerase, modulation of the chromatin landscape, G1/S checkpoint override, ramp-up of MAPK signaling, disruption of the p53 pathway, and activation of the PI3K pathway; no mutations were specifically associated with metastatic progression, as these pathways were perturbed during the evolution of primary melanomas. UV radiation-induced point mutations steadily increased until melanoma invasion, at which point copy-number alterations also became prevalent.
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Affiliation(s)
- A Hunter Shain
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA.
| | - Nancy M Joseph
- University of California San Francisco, Department of Pathology, San Francisco, CA, USA
| | - Richard Yu
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Jamal Benhamida
- University of California San Francisco, Department of Pathology, San Francisco, CA, USA
| | - Shanshan Liu
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Tarl Prow
- Future Industries Institute, University of South Australia, Adelaide, SA, Australia
| | - Beth Ruben
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA; Palo Alto Medical Foundation, Palo Alto, CA, USA
| | - Jeffrey North
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA
| | - Laura Pincus
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA
| | - Iwei Yeh
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA
| | - Robert Judson
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Boris C Bastian
- University of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA.
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Shain AH, Joseph NM, Yu R, Benhamida J, Liu S, Prow T, Ruben B, North J, Pincus L, Yeh I, Judson R, Bastian BC. Abstract NG07: Genomic and transcriptomic analysis reveals incremental disruption of key signaling pathways during melanoma evolution. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-ng07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Thousands of tumors have been sequenced through large-scale genomic profiling efforts, and from these studies the mutational drivers of most tumor subtypes have been catalogued. Nevertheless, the order in which these mutations occur is poorly understood. This is because most tumors are sequenced at a late stage, revealing only the aftermaths of the evolutionary processes that led to their transformation. A better understanding of tumor evolution would reveal biomarkers for progression and identify crucial steps in tumorigenesis, which could be subject to future treatments. In order to delineate the evolution of melanoma, we identified cases of melanomas that were adjacent to their intact, remnant precursors (e.g. a melanoma adjacent to a nevus from which it originated). We separately microdissected the precursor and descendent areas from these cases and performed matched DNA- and RNA- sequencing on the microdissected tissues. From these data, we were able to infer the order of genetic alterations that occur during the evolution of each melanoma and the transcriptomic changes that accompanied these mutations. In total, we analyzed 230 histopathologically distinct areas (normal, precursor, and descendent tissues) from 82 patients. Somatic alterations known to activate MAP-kinase signaling occurred at the earliest stages and continued to accumulate as individual tumors evolved, indicating that MAPK signaling ramps up during progression. TERT promoter mutations were detectable in 52% of intermediate stage lesions and 85% of melanomas, regardless of tumor thickness. Telomerase expression strongly correlated with the presence of a promoter mutation, confirming that telomerase is upregulated early during progression. The transition from the benign to the malignant state was marked by the emergence of mutations affecting genes involved in chromatin remodeling and accompanied by downregulation of genes modulated by polycomb repressive complex-2 (PRC2). Mono-allelic inactivation of G1/S checkpoint genes were occasionally found in earlier histopathologic stages, whereas bi-allelic alterations, predicted to ablate checkpoint function, occurred at or after the transition to invasive melanoma. p53- and PI3-kinase pathway mutations appeared later, only becoming evident in thicker primary melanomas. Comparisons between paired primary melanomas and metastases did not reveal oncogenic alterations specifically associated with metastatic progression. The types of somatic alterations further revealed the mutational forces that shaped each melanoma during its progression. Point mutations with signatures of UV-radiation induced DNA damage were more common in the trunks of the phylogenetic trees and tended to occur prior to the transition to invasive melanoma. In contrast, copy number alterations were more branchial and tended to occur at or after the transition to invasive melanoma. In aggregate, these patterns indicate that UV radiation is the predominant mutagen shaping melanocytic neoplasms until the transition to invasive melanoma, at which point chromosomal instability prevails. Overall, this study delineates the sequential order in which key signaling pathways are disrupted during melanoma evolution, highlighting replicative senescence, G1/S arrest, and chromatin organization as barriers that have to be overcome for the transition to melanoma, whereas amplification of MAPK signaling and inactivation of the p53 and PI3-kinase pathways are associated with the progression to more advanced primaries.
Citation Format: A. Hunter Shain, Nancy M. Joseph, Richard Yu, Jamal Benhamida, Shanshan Liu, Tarl Prow, Beth Ruben, Jeffrey North, Laura Pincus, Iwei Yeh, Robert Judson, Boris C. Bastian. Genomic and transcriptomic analysis reveals incremental disruption of key signaling pathways during melanoma evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr NG07.
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Affiliation(s)
| | | | - Richard Yu
- 1University of California San Francisco, San Francisco, CA
| | | | - Shanshan Liu
- 1University of California San Francisco, San Francisco, CA
| | - Tarl Prow
- 2University of South Australia, Adelaide, Australia
| | - Beth Ruben
- 1University of California San Francisco, San Francisco, CA
| | - Jeffrey North
- 1University of California San Francisco, San Francisco, CA
| | - Laura Pincus
- 1University of California San Francisco, San Francisco, CA
| | - Iwei Yeh
- 1University of California San Francisco, San Francisco, CA
| | - Robert Judson
- 1University of California San Francisco, San Francisco, CA
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Zeng H, Jorapur A, Shain AH, Lang UE, Torres R, Zhang Y, Botton T, Lin J, Mcneal AS, Donne M, Bastian IN, North J, Pincus L, Yu R, Ruben BS, Joseph N, Ye I, Bastian BC, Judson RL. Abstract 5518: Bi-allelic loss of CDKN2A initiates melanoma invasion and metastasis via E2F1-BRN2 axis. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
CDKN2A acts as a critical tumor suppressor in melanoma, as evidenced by frequent loss of function mutations and deletion. Loss of CDKN2A is believed to permit escape from senescent pre-neoplastic cell populations through relieve of a cell cycle block mediated by its two gene products. We performed a comprehensive analysis of CDKN2A gene status, mRNA and protein expression levels of p16 and p14 in a cohort of melanomas and their adjacent pre-neoplastic lesions and observed that bi-allelic CDKN2A loss coincides with the progression stage when primary melanomas become invasive. In melanoma lines, p16INK4A, one of the protein products of the CDKN2A locus, is a potent barrier to metastasis, independent of its known role inhibiting cell proliferation. We genetically engineered primary human melanocytes to harbor CDKN2A deletions and/or BRAF V600E mutation at their endogenous BRAF locus. Using this physiologic model for the early phases of neoplastic transformation, we found no evidence for BRAF-induced senescence, rather observing that p16INK4A loss activates a master regulator of melanoma invasion, BRN2, through Rb-E2F1 pathway. These results demonstrate that one of the most frequently altered genes across human cancers, CDKN2A, has an unexpected novel role in inhibiting cellular invasion through lineage specific transcription factors and acts as an essential gatekeeper of early metastatic dissemination.
Citation Format: Hanlin Zeng, Aparna Jorapur, A. Hunter Shain, Ursula E. Lang, Rodrigo Torres, Yuntian Zhang, Thomas Botton, Jue Lin, Andrew S. Mcneal, Matthew Donne, Ingmar N. Bastian, Jeffrey North, Laura Pincus, Richard Yu, Beth S. Ruben, Nancy Joseph, Iwei Ye, Boris C. Bastian, Robert L. Judson. Bi-allelic loss of CDKN2A initiates melanoma invasion and metastasis via E2F1-BRN2 axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5518.
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Affiliation(s)
- Hanlin Zeng
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Aparna Jorapur
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - A. Hunter Shain
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Ursula E. Lang
- 2Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Rodrigo Torres
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Yuntian Zhang
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Thomas Botton
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Jue Lin
- 3Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Andrew S. Mcneal
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Matthew Donne
- 4Department of Anatomy, University of California San Francisco. San Francisco, San Francisco, CA
| | - Ingmar N. Bastian
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Jeffrey North
- 5Department of Dermatology, University of California San Francisco, San Francisco, CA
| | - Laura Pincus
- 5Department of Dermatology, University of California San Francisco, San Francisco, CA
| | - Richard Yu
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Beth S. Ruben
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Nancy Joseph
- 2Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Iwei Ye
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Boris C. Bastian
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
| | - Robert L. Judson
- 1Helen Diller Family Comprehensive Cancer Center. University of California San Francisco, San Francisco, CA
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Pekmezci M, Villanueva-Meyer JE, Goode B, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Chamyan G, Maher OM, Khatib Z, Kleinschmidt-DeMasters BK, Samuel D, Mueller S, Banerjee A, Clarke JL, Cooney T, Torkildson J, Gupta N, Theodosopoulos P, Chang EF, Berger M, Bollen AW, Perry A, Tihan T, Solomon DA. The genetic landscape of ganglioglioma. Acta Neuropathol Commun 2018; 6:47. [PMID: 29880043 PMCID: PMC5992851 DOI: 10.1186/s40478-018-0551-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 05/27/2018] [Indexed: 12/11/2022] Open
Abstract
Ganglioglioma is the most common epilepsy-associated neoplasm that accounts for approximately 2% of all primary brain tumors. While a subset of gangliogliomas are known to harbor the activating p.V600E mutation in the BRAF oncogene, the genetic alterations responsible for the remainder are largely unknown, as is the spectrum of any additional cooperating gene mutations or copy number alterations. We performed targeted next-generation sequencing that provides comprehensive assessment of mutations, gene fusions, and copy number alterations on a cohort of 40 gangliogliomas. Thirty-six harbored mutations predicted to activate the MAP kinase signaling pathway, including 18 with BRAF p.V600E mutation, 5 with variant BRAF mutation (including 4 cases with novel in-frame insertions at p.R506 in the β3-αC loop of the kinase domain), 4 with BRAF fusion, 2 with KRAS mutation, 1 with RAF1 fusion, 1 with biallelic NF1 mutation, and 5 with FGFR1/2 alterations. Three gangliogliomas with BRAF p.V600E mutation had concurrent CDKN2A homozygous deletion and one additionally harbored a subclonal mutation in PTEN. Otherwise, no additional pathogenic mutations, fusions, amplifications, or deletions were identified in any of the other tumors. Amongst the 4 gangliogliomas without canonical MAP kinase pathway alterations identified, one epilepsy-associated tumor in the temporal lobe of a young child was found to harbor a novel ABL2-GAB2 gene fusion. The underlying genetic alterations did not show significant association with patient age or disease progression/recurrence in this cohort. Together, this study highlights that ganglioglioma is characterized by genetic alterations that activate the MAP kinase pathway, with only a small subset of cases that harbor additional pathogenic alterations such as CDKN2A deletion.
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Iorgulescu JB, Van Ziffle J, Stevers M, Grenert JP, Bastian BC, Chavez L, Stichel D, Buchhalter I, Samuel D, Nicolaides T, Banerjee A, Mueller S, Gupta N, Tihan T, Bollen AW, Northcott PA, Kool M, Pfister S, Korshunov A, Perry A, Solomon DA. Deep sequencing of WNT-activated medulloblastomas reveals secondary SHH pathway activation. Acta Neuropathol 2018; 135:635-638. [PMID: 29435664 DOI: 10.1007/s00401-018-1819-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022]
Affiliation(s)
- J Bryan Iorgulescu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - Meredith Stevers
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - James P Grenert
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA
| | - Lukas Chavez
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - David Samuel
- Division of Pediatric Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Theodore Nicolaides
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Anuradha Banerjee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Sabine Mueller
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Marcel Kool
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, CA, USA.
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50
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Kline CN, Joseph NM, Grenert JP, van Ziffle J, Talevich E, Onodera C, Aboian M, Cha S, Raleigh DR, Braunstein S, Torkildson J, Samuel D, Bloomer M, Campomanes AGDA, Banerjee A, Butowski N, Raffel C, Tihan T, Bollen AW, Phillips JJ, Korn WM, Yeh I, Bastian BC, Gupta N, Mueller S, Perry A, Nicolaides T, Solomon DA. Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy. Neuro Oncol 2018; 19:699-709. [PMID: 28453743 DOI: 10.1093/neuonc/now254] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/04/2016] [Indexed: 12/25/2022] Open
Abstract
Background Molecular profiling is revolutionizing cancer diagnostics and leading to personalized therapeutic approaches. Herein we describe our clinical experience performing targeted sequencing for 31 pediatric neuro-oncology patients. Methods We sequenced 510 cancer-associated genes from tumor and peripheral blood to identify germline and somatic mutations, structural variants, and copy number changes. Results Genomic profiling was performed on 31 patients with tumors including 11 high-grade gliomas, 8 medulloblastomas, 6 low-grade gliomas, 1 embryonal tumor with multilayered rosettes, 1 pineoblastoma, 1 uveal ganglioneuroma, 1 choroid plexus carcinoma, 1 chordoma, and 1 high-grade neuroepithelial tumor. In 25 cases (81%), results impacted patient management by: (i) clarifying diagnosis, (ii) identifying pathogenic germline mutations, or (iii) detecting potentially targetable alterations. The pathologic diagnosis was amended after genomic profiling for 6 patients (19%), including a high-grade glioma to pilocytic astrocytoma, medulloblastoma to pineoblastoma, ependymoma to high-grade glioma, and medulloblastoma to CNS high-grade neuroepithelial tumor with BCOR alteration. Multiple patients had pathogenic germline mutations, many of which were previously unsuspected. Potentially targetable alterations were identified in 19 patients (61%). Additionally, novel likely pathogenic alterations were identified in 3 cases: an in-frame RAF1 fusion in a BRAF wild-type pleomorphic xanthoastrocytoma, an inactivating ASXL1 mutation in a histone H3 wild-type diffuse pontine glioma, and an in-frame deletion within exon 2 of MAP2K1 in a low-grade astrocytic neoplasm. Conclusions Our experience demonstrates the significant impact of molecular profiling on diagnosis and treatment of pediatric brain tumors and confirms its feasibility for use at the time of diagnosis or recurrence.
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Affiliation(s)
- Cassie N Kline
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Nancy M Joseph
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - James P Grenert
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Jessica van Ziffle
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Eric Talevich
- Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Courtney Onodera
- Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Mariam Aboian
- Department of Radiology, UCSF, San Francisco, California, USA
| | - Soonmee Cha
- Department of Radiology, UCSF, San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - David R Raleigh
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Steve Braunstein
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Joseph Torkildson
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland,Oakland, California, USA
| | - David Samuel
- Division of Pediatric Hematology/Oncology, Valley Children's Hospital, Madera, California, USA
| | - Michelle Bloomer
- Department of Ophthalmology, UCSF, San Francisco, California, USA
| | | | - Anuradha Banerjee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco (UCSF), San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Nicholas Butowski
- Division of Neuro-Oncology, Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Corey Raffel
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Tarik Tihan
- Department of Pathology, UCSF, San Francisco, California, USA
| | - Andrew W Bollen
- Department of Pathology, UCSF, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Pathology, UCSF, San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - W Michael Korn
- Divisions of Gastroenterology and Medical Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Iwei Yeh
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Boris C Bastian
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Sabine Mueller
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco (UCSF), San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Arie Perry
- Department of Pathology, UCSF, San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Theodore Nicolaides
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco (UCSF), San Francisco, California, USA.,Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, UCSF, San Francisco, California, USA.,Clinical Cancer Genomics Laboratory, UCSF, San Francisco, California, USA
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