1
|
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: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
2
|
Kim D, Khan AU, Compres EV, Zhang B, Sunshine JC, Quan VL, Gerami P. BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases. J Cutan Pathol 2020; 47:1132-1142. [PMID: 32776349 DOI: 10.1111/cup.13842] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND Fusions involving the BRAF gene are responsible for 5% of Spitz neoplasms. To better characterize them, we report the clinical, morphological, and genomic findings of six BRAF fusion Spitz tumors. METHODS The morphological, clinical, and molecular findings of six BRAF fusion Spitz neoplasms assessed by next generation sequencing (NGS) were compared to a control set of Spitz without BRAF fusions. RESULTS BRAF fusion Spitz tumors had frequent predominance of epithelioid morphology (4/6 cases), frequent high-grade nuclear atypia and pleomorphism (5/6 cases), and a frequent desmoplastic base (3/6 cases). Five of six cases were diagnosed as atypical Spitz tumor and one as Spitz nevus. All cases had uneventful clinical follow-up. There were five different fusion partners, with CLIP2 being the most frequent. Secondary pathogenic mutations were frequent and chromosomal copy number changes were seen in three of six cases by an NGS platform. CONCLUSIONS BRAF fusions Spitz usually have epithelioid morphology, high-grade nuclear atypia, and desmoplasia. Chromosomal copy number changes are not infrequent. While our cases had uneventful follow-up, a meta-analysis of the literature suggests that among the fusion subtypes associated with Spitz tumors, they are among the subgroups more likely to develop distant metastasis.
Collapse
Affiliation(s)
- Daniel Kim
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ayesha U Khan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Elsy V Compres
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Bin Zhang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Joel C Sunshine
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Victor L Quan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| |
Collapse
|
3
|
Botton T, Passeron T, Rocchi S. Comment on 'Testing for BRAF fusions in patients with advanced BRAF/NRAS/KIT wild-type melanomas permits to identify patients who could benefit of anti-MEK targeted therapy'. J Clin Pathol 2019; 73:524-525. [PMID: 31852719 DOI: 10.1136/jclinpath-2019-206366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/04/2022]
Affiliation(s)
- Thomas Botton
- INSERM U1065, Team 12, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, Nice, France
| | - Thierry Passeron
- INSERM U1065, Team 12, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, Nice, France
| | - Stéphane Rocchi
- INSERM U1065, Team 12, Centre Méditerranéen de Médecine Moléculaire, Université Côte d'Azur, Nice, France
| |
Collapse
|
4
|
Lim HC, Montesion M, Botton T, Collisson EA, Umetsu SE, Behr SC, Gordan JD, Stephens PJ, Kelley RK. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in BRCA1-Mutant Cholangiocarcinoma Harboring a Novel YWHAZ-BRAF Fusion. Oncologist 2018; 23:998-1003. [PMID: 29622700 DOI: 10.1634/theoncologist.2017-0645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/12/2018] [Indexed: 01/07/2023] Open
Abstract
Biliary tract cancers such as cholangiocarcinoma represent a heterogeneous group of cancers that can be difficult to diagnose. Recent comprehensive genomic analyses in large cholangiocarcinoma cohorts have defined important molecular subgroups within cholangiocarcinoma that may relate to anatomic location and etiology [1], [2], [3], [4] and may predict responsiveness to targeted therapies in development [5], [6], [7]. These emerging data highlight the potential for tumor genomics to inform diagnosis and treatment options in this challenging tumor type. We report the case of a patient with a germline BRCA1 mutation who presented with a cholangiocarcinoma driven by the novel YWHAZ-BRAF fusion. Hybrid capture-based DNA sequencing and copy number analysis performed as part of clinical care demonstrated that two later-occurring tumors were clonally derived from the primary cholangiocarcinoma rather than distinct new primaries, revealing an unusual pattern of late metachronous metastasis. We discuss the clinical significance of these genetic alterations and their relevance to therapeutic strategies. KEY POINTS Hybrid capture-based next-generation DNA sequencing assays can provide diagnostic clarity in patients with unusual patterns of metastasis and recurrence in which the pathologic diagnosis is ambiguous.To our knowledge, this is the first reported case of a YWHAZ-BRAF fusion in pancreaticobiliary cancer, and a very rare case of cholangiocarcinoma in the setting of a germline BRCA1 mutation.The patient's BRCA1 mutation and YWHAZ-BRAF fusion constitute potential targets for future therapy.
Collapse
Affiliation(s)
- Huat C Lim
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Thomas Botton
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Spencer C Behr
- Department of Radiology, University of California, San Francisco, San Francisco, California, USA
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | | | - Robin K Kelley
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
5
|
Next-Generation Sequencing Reveals Pathway Activations and New Routes to Targeted Therapies in Cutaneous Metastatic Melanoma. Am J Dermatopathol 2017; 39:1-13. [PMID: 28045747 DOI: 10.1097/dad.0000000000000729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test. METHODS NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials. RESULTS The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7). CONCLUSION Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.
Collapse
|
6
|
Yeh I. Recent advances in molecular genetics of melanoma progression: implications for diagnosis and treatment. F1000Res 2016; 5. [PMID: 27408703 PMCID: PMC4926755 DOI: 10.12688/f1000research.8247.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 11/20/2022] Open
Abstract
According to the multi-step carcinogenesis model of cancer, initiation results in a benign tumor and subsequent genetic alterations lead to tumor progression and the acquisition of the hallmarks of cancer. This article will review recent discoveries in our understanding of initiation and progression in melanocytic neoplasia and the impact on diagnostic dermatopathology.
Collapse
Affiliation(s)
- Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
7
|
Kong BY, Carlino MS, Menzies AM. Biology and treatment of BRAF mutant metastatic melanoma. Melanoma Manag 2016; 3:33-45. [PMID: 30190871 DOI: 10.2217/mmt.15.38] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/12/2015] [Indexed: 12/31/2022] Open
Abstract
BRAF inhibitors were among the first systemic therapies to show clinical benefit in metastatic melanoma. Here, we review the spectrum of BRAF mutations in melanoma, their role in oncogenesis, clinicopathological associations and response to treatment. The differing biology and clinical features of V600E- and V600K-mutated melanoma are outlined. The molecular changes associated with BRAF fusion genes and their response to targeted therapies, as well as the role of immunotherapy in treatment sequencing with targeted therapies are discussed.
Collapse
Affiliation(s)
- Benjamin Y Kong
- Crown Princess Mary Cancer Care Centre, Westmead, Sydney, NSW 2145, Australia.,Crown Princess Mary Cancer Care Centre, Westmead, Sydney, NSW 2145, Australia
| | - Matteo S Carlino
- Crown Princess Mary Cancer Care Centre, Westmead, Sydney, NSW 2145, Australia.,Melanoma Institute Australia, North Sydney, NSW 2060, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Crown Princess Mary Cancer Care Centre, Westmead, Sydney, NSW 2145, Australia.,Melanoma Institute Australia, North Sydney, NSW 2060, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, North Sydney, NSW 2060, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Royal North Shore Hospital, Sydney, NSW 2065, Australia.,Melanoma Institute Australia, North Sydney, NSW 2060, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Royal North Shore Hospital, Sydney, NSW 2065, Australia
| |
Collapse
|
8
|
Ross JS, Wang K, Chmielecki J, Gay L, Johnson A, Chudnovsky J, Yelensky R, Lipson D, Ali SM, Elvin JA, Vergilio JA, Roels S, Miller VA, Nakamura BN, Gray A, Wong MK, Stephens PJ. The distribution of BRAF gene fusions in solid tumors and response to targeted therapy. Int J Cancer 2015; 138:881-90. [PMID: 26314551 PMCID: PMC5049644 DOI: 10.1002/ijc.29825] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 08/16/2015] [Accepted: 08/19/2015] [Indexed: 12/12/2022]
Abstract
Although the BRAF V600E base substitution is an approved target for the BRAF inhibitors in melanoma, BRAF gene fusions have not been investigated as anticancer drug targets. In our study, a wide variety of tumors underwent comprehensive genomic profiling for hundreds of known cancer genes using the FoundationOne™ or FoundationOne Heme™ comprehensive genomic profiling assays. BRAF fusions involving the intact in-frame BRAF kinase domain were observed in 55 (0.3%) of 20,573 tumors, across 12 distinct tumor types, including 20 novel BRAF fusions. These comprised 29 unique 5' fusion partners, of which 31% (9) were known and 69% (20) were novel. BRAF fusions included 3% (14/531) of melanomas; 2% (15/701) of gliomas; 1.0% (3/294) of thyroid cancers; 0.3% (3/1,062) pancreatic carcinomas; 0.2% (8/4,013) nonsmall-cell lung cancers and 0.2% (4/2,154) of colorectal cancers, and were enriched in pilocytic (30%) vs. nonpilocytic gliomas (1%; p < 0.0001), Spitzoid (75%) vs. nonSpitzoid melanomas (1%; p = 0.0001), acinar (67%) vs. nonacinar pancreatic cancers (<1%; p < 0.0001) and papillary (3%) vs. nonpapillary thyroid cancers (0%; p < 0.03). Clinical responses to trametinib and sorafenib are presented. In conclusion, BRAF fusions are rare driver alterations in a wide variety of malignant neoplasms, but enriched in Spitzoid melanoma, pilocytic astrocytomas, pancreatic acinar and papillary thyroid cancers.
Collapse
Affiliation(s)
- Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA.,Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY
| | - Kai Wang
- Foundation Medicine, Inc., Cambridge, MA
| | | | - Laurie Gay
- Foundation Medicine, Inc., Cambridge, MA
| | | | | | | | | | | | | | | | | | | | - Brooke N Nakamura
- Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Adam Gray
- Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Michael K Wong
- Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | | |
Collapse
|
9
|
Menzies AM, Yeh I, Botton T, Bastian BC, Scolyer RA, Long GV. Clinical activity of the MEK inhibitor trametinib in metastatic melanoma containing BRAF kinase fusion. Pigment Cell Melanoma Res 2015; 28:607-10. [PMID: 26072686 PMCID: PMC4539279 DOI: 10.1111/pcmr.12388] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexander M Menzies
- Melanoma Institute Australia, Sydney, NSW, Australia
- The University of Sydney, Sydney, NSW, Australia
| | - Iwei Yeh
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Thomas Botton
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Richard A Scolyer
- Melanoma Institute Australia, Sydney, NSW, Australia
- The University of Sydney, Sydney, NSW, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, Sydney, NSW, Australia
- The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
10
|
Klammer M, Dybowski JN, Hoffmann D, Schaab C. Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib. PLoS One 2015; 10:e0128542. [PMID: 26083411 PMCID: PMC4470654 DOI: 10.1371/journal.pone.0128542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/26/2015] [Indexed: 01/17/2023] Open
Abstract
Multivariate biomarkers that can predict the effectiveness of targeted therapy in individual patients are highly desired. Previous biomarker discovery studies have largely focused on the identification of single biomarker signatures, aimed at maximizing prediction accuracy. Here, we present a different approach that identifies multiple biomarkers by simultaneously optimizing their predictive power, number of features, and proximity to the drug target in a protein-protein interaction network. To this end, we incorporated NSGA-II, a fast and elitist multi-objective optimization algorithm that is based on the principle of Pareto optimality, into the biomarker discovery workflow. The method was applied to quantitative phosphoproteome data of 19 non-small cell lung cancer (NSCLC) cell lines from a previous biomarker study. The algorithm successfully identified a total of 77 candidate biomarker signatures predicting response to treatment with dasatinib. Through filtering and similarity clustering, this set was trimmed to four final biomarker signatures, which then were validated on an independent set of breast cancer cell lines. All four candidates reached the same good prediction accuracy (83%) as the originally published biomarker. Although the newly discovered signatures were diverse in their composition and in their size, the central protein of the originally published signature — integrin β4 (ITGB4) — was also present in all four Pareto signatures, confirming its pivotal role in predicting dasatinib response in NSCLC cell lines. In summary, the method presented here allows for a robust and simultaneous identification of multiple multivariate biomarkers that are optimized for prediction performance, size, and relevance.
Collapse
Affiliation(s)
- Martin Klammer
- Evotec (München) GmbH, Dept. of Bioinformatics, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - J. Nikolaj Dybowski
- Evotec (München) GmbH, Dept. of Bioinformatics, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - Daniel Hoffmann
- Center for Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 1-4, 45141 Essen, Germany
| | - Christoph Schaab
- Evotec (München) GmbH, Dept. of Bioinformatics, Am Klopferspitz 19a, 82152 Martinsried, Germany
- Max-Plack Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- * E-mail:
| |
Collapse
|
11
|
Okura R, Yoshioka H, Yoshioka M, Hiromasa K, Nishio D, Nakamura M. Expression of AID in malignant melanoma with BRAF(V600E) mutation. Exp Dermatol 2014; 23:347-8. [PMID: 24684646 DOI: 10.1111/exd.12402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2014] [Indexed: 01/14/2023]
Abstract
BRAF-activating somatic mutations often exist in malignant melanoma. The underlying molecular mechanism of somatic BRAF mutation inductions remained to be clear. Activation-induced cytidine deaminase (AID), a member of a cytidine deaminase family, and APOBEC3B induce somatic mutations and recently have been indicated to be involved in the pathomechanism of several kinds of cancers. The aim of this study was to explore the expression level of AID and APOBEC3B in BRAF-mutation- containing malignant melanoma. Immunohistochemical study demonstrated that 9 of 10 malignant melanomas with high AID expression had BRAF(V600E) mutation. Eight of them developed multiorgan metastases or multiple lymph node metastases afterwards. Although the size of the patient panel was small, the results indicate that there might be an association between AID expression and BRAF mutation in melanoma.
Collapse
Affiliation(s)
- Risa Okura
- Department of Dermatology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | | | | | | | | |
Collapse
|
12
|
Affiliation(s)
- Thomas Botton
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Iwei Yeh
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 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.
| |
Collapse
|
13
|
Chmielecki J, Hutchinson KE, Frampton GM, Chalmers ZR, Johnson A, Shi C, Elvin J, Ali SM, Ross JS, Basturk O, Balasubramanian S, Lipson D, Yelensky R, Pao W, Miller VA, Klimstra DS, Stephens PJ. Comprehensive genomic profiling of pancreatic acinar cell carcinomas identifies recurrent RAF fusions and frequent inactivation of DNA repair genes. Cancer Discov 2014; 4:1398-405. [PMID: 25266736 DOI: 10.1158/2159-8290.cd-14-0617] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
UNLABELLED Pancreatic acinar cell carcinomas (PACC) account for approximately 1% (∼500 cases) of pancreatic cancer diagnoses annually in the United States. Oncogenic therapuetic targets have proven elusive in this disease, and chemotherapy and radiotherapy have demonstrated limited efficacy against these tumors. Comprehensive genomic profiling of a large series of PACCs (n=44) identified recurrent rearrangements involving BRAF and RAF1 (CRAF) in approximately 23% of tumors. The most prevalent fusion, SND1-BRAF, resulted in activation of the MAPK pathway, which was abrogated with MEK inhibition. SND1-BRAF-transformed cells were sensitive to treatment with the MEK inhibitor trametinib. PACCs lacking RAF rearrangements were significantly enriched for genomic alterations, causing inactivation of DNA repair genes (45%); these genomic alterations have been associated with sensitivity to platinum-based therapies and PARP inhibitors. Collectively, these results identify potentially actionable genomic alterations in the majority of PACCs and provide a rationale for using personalized therapies in this disease. SIGNIFICANCE PACC is genomically distinct from other pancreatic cancers. Fusions in RAF genes and mutually exclusive inactivation of DNA repair genes represent novel potential therapeutic targets that are altered in over two thirds of these tumors.
Collapse
Affiliation(s)
| | | | | | | | | | - Chanjuan Shi
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Julia Elvin
- Foundation Medicine, Cambridge, Massachusetts
| | - Siraj M Ali
- Foundation Medicine, Cambridge, Massachusetts
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, Massachusetts. Albany Medical College, Albany, New York
| | - Olca Basturk
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - William Pao
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | | |
Collapse
|
14
|
Bergamaschi D. Is Mcl-1L the new anti-apoptotic effector of B-RAFV(600E) in melanoma? Exp Dermatol 2014; 23:94. [PMID: 24372788 DOI: 10.1111/exd.12312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 12/24/2022]
Abstract
A recent report has unveiled a novel mechanism by which oncogenic BRAF signalling might trigger apoptotic resistance in melanoma by selectively affecting the expression of Bcl-2 family member Mcl-1L (Exp Dermatol 2013: 22: 767). Correlation of Mcl-1 splice variants and B-RAF mutational status was determined in a panel of melanoma cell lines. In vivo validation of this mechanism, which is supported by recent literature, might provide novel therapeutic approaches such as the use of targeted Mcl-1 inhibitors to improve outcome in melanoma.
Collapse
Affiliation(s)
- Daniele Bergamaschi
- Centre for Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, UK
| |
Collapse
|
15
|
Abstract
Recent efforts in genomic research have enabled the characterization of molecular mechanisms underlying many types of cancers, ushering novel approaches for diagnosis and therapeutics. Melanoma is a molecularly heterogeneous disease, as many genetic alterations have been identified and the clinical features can vary. Although discoveries of frequent mutations including BRAF have already made clinically significant impact on patient care, there is a growing body of literature suggesting a role for additional mutations, driver and passenger types, in disease pathophysiology. Although some mutations have been strongly associated with clinical phenotypes of melanomas (such as physical distribution or morphologic subtype), the function or implications of many of the recently identified mutations remains less clear. The phenotypic and clinical impact of genomic mutations in melanoma remains a promising opportunity for progress in the care of melanoma patients.
Collapse
Affiliation(s)
- Elena B Hawryluk
- Dermatology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115 Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Hensin Tsao
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| |
Collapse
|
16
|
McKee CS, Hill DS, Redfern CPF, Armstrong JL, Lovat PE. Oncogenic BRAF signalling increases Mcl-1 expression in cutaneous metastatic melanoma. Exp Dermatol 2013; 22:767-9. [PMID: 24118207 DOI: 10.1111/exd.12254] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2013] [Indexed: 11/29/2022]
Abstract
The Bcl-2 family member Mcl-1 is essential for melanoma survival; however, the influence of oncogenic BRAF signalling remains elusive. In this study, Mcl-1 splice variant expression was determined in a panel of melanoma cell lines in relation to BRAF mutational status. Mcl-1L mRNA expression was increased in melanoma cells compared with primary melanocytes with significantly increased mRNA and protein expression observed in BRAF(V600E) mutant melanoma cells. Although no change in Mcl-1S mRNA was observed, Mcl-1S protein expression also increased in BRAF mutant melanoma cells. Additionally, while over-expression of mutant BRAF(V600E) increased both Mcl-1L and Mcl-1S expression, inhibition of hyperactive BRAF signalling resulted in decreased Mcl-1L expression. These studies suggest that the regulation of Mcl-1 expression by BRAF signalling is increased by oncogenic activation of BRAF, revealing a mechanism of apoptotic resistance which may be overcome by the use of more specifically targeted Mcl-1 inhibitors.
Collapse
Affiliation(s)
- Christopher S McKee
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | | | | | | | | |
Collapse
|
17
|
Botton T, Yeh I, Nelson T, Vemula SS, Sparatta A, Garrido MC, Allegra M, Rocchi S, Bahadoran P, McCalmont TH, LeBoit PE, Burton EA, Bollag G, Ballotti R, Bastian BC. Recurrent BRAF kinase fusions in melanocytic tumors offer an opportunity for targeted therapy. Pigment Cell Melanoma Res 2013; 26:845-51. [PMID: 23890088 DOI: 10.1111/pcmr.12148] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/19/2013] [Indexed: 11/30/2022]
Abstract
BRAF is the most prevalent oncogene and an important therapeutic target in melanoma. In some cancers, BRAF is activated by rearrangements that fuse its kinase domain to 5' partner genes. We examined 848 comparative genomic hybridization profiles of melanocytic tumors and found copy number transitions within BRAF in 10 tumors, of which six could be further characterized by sequencing. In all, the BRAF kinase domain was fused in-frame to six N-terminal partners. No other mutations were identified in melanoma oncogenes. One of the seven melanoma cell lines without known oncogenic mutations harbored a similar BRAF fusion, which constitutively activated the MAP kinase pathway. Sorafenib, but not vemurafenib, could block MAP kinase pathway activation and proliferation of the cell line at clinically relevant concentrations, whereas BRAF(V) (600E) mutant melanoma cell lines were significantly more sensitive to vemurafenib. The patient from whom the cell line was derived showed a durable clinical response to sorafenib.
Collapse
Affiliation(s)
- Thomas Botton
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Kunz M, Dannemann M, Kelso J. High-throughput sequencing of the melanoma genome. Exp Dermatol 2012; 22:10-7. [PMID: 23174022 DOI: 10.1111/exd.12054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2012] [Indexed: 12/16/2022]
Abstract
Next-generation sequencing technologies are now common for whole-genome, whole-exome and whole-transcriptome sequencing (RNA-seq) of tumors to identify point mutations, structural or copy number alterations and changes in gene expression. A substantial number of studies have already been performed for melanoma. One study analysed eight melanoma cell lines with RNA-Seq technology and identified 11 novel melanoma gene fusions. Whole-exome sequencing of seven melanoma cell lines identified overlapping gain of function mutations in MAP2K1 (MEK1) and MAP2K2 (MEK2) genes. Integrative sequencing of cutaneous melanoma metastases using different sequencing platforms revealed a new somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C (a CDK4 inhibitor). These latter sequencing-based discoveries may be used to motivate the inclusion of the affected patients into clinical trials with specific signalling pathway inhibitors. Taken together, we are at the beginning of an era with new sequencing technologies providing a more comprehensive view of cancer mutational landscapes and hereby a better understanding of their pathogenesis. This will also open interesting perspectives for new treatment approaches and clinical trial designs.
Collapse
Affiliation(s)
- Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany.
| | | | | |
Collapse
|