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Riaud M, Maxwell J, Soria-Bretones I, Dankner M, Li M, Rose AAN. The role of CRAF in cancer progression: from molecular mechanisms to precision therapies. Nat Rev Cancer 2024; 24:105-122. [PMID: 38195917 DOI: 10.1038/s41568-023-00650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
The RAF family of kinases includes key activators of the pro-tumourigenic mitogen-activated protein kinase pathway. Hyperactivation of RAF proteins, particularly BRAF and CRAF, drives tumour progression and drug resistance in many types of cancer. Although BRAF is the most studied RAF protein, partially owing to its high mutation incidence in melanoma, the role of CRAF in tumourigenesis and drug resistance is becoming increasingly clinically relevant. Here, we summarize the main known regulatory mechanisms and gene alterations that contribute to CRAF activity, highlighting the different oncogenic roles of CRAF, and categorize RAF1 (CRAF) mutations according to the effect on kinase activity. Additionally, we emphasize the effect that CRAF alterations may have on drug resistance and how precision therapies could effectively target CRAF-dependent tumours. Here, we discuss preclinical and clinical findings that may lead to improved treatments for all types of oncogenic RAF1 alterations in cancer.
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Affiliation(s)
- Melody Riaud
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Isabel Soria-Bretones
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Dankner
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Meredith Li
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - April A N Rose
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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Lim SH, Jung J, Hong JY, Kim ST, Park SH, Park JO, Kim KM, Lee J. Prevalence of RAF1 Aberrations in Metastatic Cancer Patients: Real-World Data. Biomedicines 2023; 11:3264. [PMID: 38137485 PMCID: PMC10740931 DOI: 10.3390/biomedicines11123264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
PURPOSE Therapeutic targeting of RAF1 is a promising cancer treatment, but the relationship between clinical features and RAF1 aberrations in terms of the MAPK signaling pathway is poorly understood in various solid tumors. METHODS Between October 2019 and June 2023 at Samsung Medical Center, 3895 patients with metastatic solid cancers underwent next-generation sequencing (NGS) using TruSight Oncology 500 (TSO500) assays as routine clinical practice. We surveyed the incidence of RAF1 aberrations including mutations (single-nucleotide variants [SNVs]), amplifications (copy number variation), and fusions. RESULTS Among the 3895 metastatic cancer patients, 77 (2.0%) exhibited RAF1 aberrations. Of these 77 patients, 44 (1.1%) had RAF1 mutations (SNV), 25 (0.6%) had RAF1 amplifications, and 10 (0.3%) had RAF1 fusions. Among the 10 patients with RAF1 fusions, concurrent RAF1 amplifications and RAF1 mutations were detected in one patient each. The most common tumor types were bladder cancer (11.5%), followed by ampulla of Vater (AoV) cancer (5.3%), melanoma (3.0%), gallbladder (GB) cancer (2.6%), and gastric (2.3%) cancer. Microsatellite instability high (MSI-H) tumors were observed in five of 76 patients (6.6%) with RAF1 aberrations, while MSI-H tumors were found in only 2.1% of patients with wild-type RAF1 cancers (p < 0.0001). CONCLUSION We demonstrated that approximately 2.0% of patients with metastatic solid cancers have RAF1 aberrations according to NGS of tumor specimens.
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Affiliation(s)
- Sung Hee Lim
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
| | - Jaeyun Jung
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
- Experimental Therapeutics Development Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Jung Young Hong
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
| | - Seung Tae Kim
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
| | - Se Hoon Park
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
| | - Joon Oh Park
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
| | - Kyoung-Mee Kim
- Samsung Medical Center, Department of Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea;
| | - Jeeyun Lee
- Samsung Medical Center, Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (S.H.L.); (J.J.); (J.Y.H.); (S.T.K.); (S.H.P.); (J.O.P.)
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3
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Moran JMT, Le LP, Nardi V, Golas J, Farahani AA, Signorelli S, Onozato ML, Foreman RK, Duncan LM, Lawrence DP, Lennerz JK, Dias-Santagata D, Hoang MP. Identification of fusions with potential clinical significance in melanoma. Mod Pathol 2022; 35:1837-1847. [PMID: 35871080 DOI: 10.1038/s41379-022-01138-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022]
Abstract
Though uncommon in melanoma, gene fusions may have therapeutic implications. Next generation sequencing-based clinical assays, designed to detect relevant gene fusions, mutations, and copy number changes, were performed on 750 melanomas (375 primary and 375 metastases) at our institution from 2014-2021. These included 599 (80%) cutaneous, 38 (5%) acral, 11 (1.5%) anorectal, 23 (3%) sinonasal, 27 (3.6%) eye (uveal/ conjunctiva), 11 (1.5%) genital (vulva/penile), and 41 (5.5%) melanomas of unknown primary. Sixteen fusions (2%) were detected in samples from 16 patients: 12/599 (2%) cutaneous, 2/38 (5%) acral, 1/9 (11%) vulva, 1/23(4.3%) sinonasal; and 12/16 (75%) fusions were potentially targetable. We identified two novel rearrangements: NAGS::MAST2 and NOTCH1::GNB1; and two fusions that have been reported in other malignancies but not in melanoma: CANT1::ETV4 (prostate cancer) and CCDC6::RET (thyroid cancer). Additional fusions, previously reported in melanoma, included: EML4::ALK, MLPH::ALK, AGAP3::BRAF, AGK::BRAF, CDH3::BRAF, CCT8::BRAF, DIP2B::BRAF, EFNB1::RAF1, LRCH3::RAF1, MAP4::RAF1, RUFY1::RAF1, and ADCY2::TERT. Fusion positive melanomas harbored recurrent alterations in TERT and CDKN2A, among others. Gene fusions were exceedingly rare (0.2%) in BRAF/RAS/NF1-mutant tumors and were detected in 5.6% of triple wild-type melanomas. Interestingly, gene rearrangements were significantly enriched within the subset of triple wild-type melanomas that harbor TERT promoter mutations (18% versus 2%, p < 0.0001). Thirteen (81%) patients were treated with immunotherapy for metastatic disease or in the adjuvant setting. Six of 12 (50%) patients with potentially actionable fusions progressed on immunotherapy, and 3/6 (50%) were treated with targeted agents (ALK and MEK inhibitors), 2 off-label and 1 as part of a clinical trial. One patient with an AGAP3::BRAF fusion positive melanoma experienced a 30-month long response to trametinib. We show that, detecting fusions, especially in triple wild-type melanomas with TERT promoter mutations, may have a clinically significant impact in patients with advanced disease who have failed front-line immunotherapy.
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Affiliation(s)
- Jakob M T Moran
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Josephine Golas
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander A Farahani
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sylvia Signorelli
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maristela L Onozato
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruth K Foreman
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lyn M Duncan
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donald P Lawrence
- Division of Medical Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Darabi S, Elliott A, Braxton DR, Zeng J, Hodges K, Poorman K, Swensen J, Shanthappa BU, Hinton JP, Gibney GT, Moser J, Phung T, Atkins MB, In GK, Korn WM, Eisenberg BL, Demeure MJ. Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions. Cancers (Basel) 2022; 14:cancers14061505. [PMID: 35326655 PMCID: PMC8946593 DOI: 10.3390/cancers14061505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Malignant melanoma is a complex disease that is estimated to claim over 7000 lives in the United States in 2021. Although recent advances in genomic technology have helped with the identification of driver variants, molecular studies and clinical trials have often focused on prevalent alterations, such as the BRAF-V600E mutation. With the inclusion of whole transcriptome sequencing, molecular profiling of melanomas has identified gene fusions and revealed gene expression profiles that are consistent with the activation of signaling pathways by common driver mutations. Patients harboring such fusions may benefit from currently approved targeted therapies and should be considered in the design of future clinical trials to further personalize treatments for patients with malignant melanoma. Abstract Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.
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Affiliation(s)
- Sourat Darabi
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Correspondence:
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - David R. Braxton
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
| | - Jia Zeng
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kurt Hodges
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kelsey Poorman
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Jeff Swensen
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Basavaraja U. Shanthappa
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - James P. Hinton
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Geoffrey T. Gibney
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Justin Moser
- Honor Health Research Institute, Scottsdale, AZ 85258, USA;
| | - Thuy Phung
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA;
| | - Michael B. Atkins
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Gino K. In
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Wolfgang M. Korn
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Burton L. Eisenberg
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Michael J. Demeure
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Translational Genomics Research Institution, Phoenix, AZ 85004, USA
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Fusco MJ, Saeed-Vafa D, Carballido EM, Boyle TA, Malafa M, Blue KL, Teer JK, Walko CM, McLeod HL, Hicks JK, Extermann M, Fleming JB, Knepper TC, Kim DW. Identification of Targetable Gene Fusions and Structural Rearrangements to Foster Precision Medicine in KRAS Wild-Type Pancreatic Cancer. JCO Precis Oncol 2021; 5:PO.20.00265. [PMID: 34250383 PMCID: PMC8232071 DOI: 10.1200/po.20.00265] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023] Open
Abstract
It has recently been described that alternative oncogenic drivers may be found in KRAS wild-type (KRAS WT) pancreatic cancers. This study aimed to determine the incidence of targetable gene fusions present in KRAS WT pancreatic adenocarcinoma and response to targeted therapy. METHODS One hundred consecutive patients with pancreatic adenocarcinoma who underwent targeted next-generation sequencing using DNA sequencing with RNA sequencing (n = 47) or without RNA sequencing (n = 53) at a single institution were included in the study. The frequency and landscape of targetable fusions in KRAS WT pancreatic adenocarcinoma was characterized and compared with the frequency of fusions in KRAS-mutated (KRAS MUT) pancreatic adenocarcinoma. Results were validated in two independent cohorts using data from AACR GENIE (n = 1,252) and TCGA (n = 150). The clinical history of fusion-positive patients who received targeted treatment is described. RESULTS Pancreatic cancers from 13 of 100 patients (13%) were found to be KRAS WT. Targetable fusions were identified in 4/13 (31%) KRAS WT tumors compared with 0/87 (0%) KRAS MUT pancreatic adenocarcinomas (P = .0002). One patient with a novel MET fusion had a complete response to targeted therapy with crizotinib that is ongoing at 12+ months of treatment. In the validation cohorts, gene fusions were identified in 18/97 (19%) and 2/10 (20%) KRAS WT tumors reported in the AACR GENIE and TCGA cohorts, respectively. CONCLUSION Oncogene fusions are present in KRAS WT pancreatic adenocarcinomas at an increased frequency when compared with KRAS MUT pancreatic adenocarcinomas. As these fusions may be susceptible to targeted therapy, molecular analyses for the detection of fusions in KRAS WT pancreatic adenocarcinomas may warrant increased consideration.
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Affiliation(s)
- Michael J. Fusco
- Department of Individualized Cancer Management Section of Precision Oncology, Moffitt Cancer Center, Tampa, FL
| | | | | | - Theresa A. Boyle
- Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Kirsten L. Blue
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Jamie K. Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL
| | - Christine M. Walko
- Department of Individualized Cancer Management Section of Precision Oncology, Moffitt Cancer Center, Tampa, FL
| | - Howard L. McLeod
- Geriatric Oncology Consortium, Tampa, FL
- USF Taneja College of Pharmacy, Tampa, FL
| | - J. Kevin Hicks
- Department of Individualized Cancer Management Section of Precision Oncology, Moffitt Cancer Center, Tampa, FL
| | - Martine Extermann
- Department of Senior Adult Oncology, Moffitt Cancer Center, Tampa, FL
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Todd C. Knepper
- Department of Individualized Cancer Management Section of Precision Oncology, Moffitt Cancer Center, Tampa, FL
| | - Dae Won Kim
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
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Rankin A, Johnson A, Roos A, Kannan G, Knipstein J, Britt N, Rosenzweig M, Haberberger J, Pavlick D, Severson E, Vergilio J, Squillace R, Erlich R, Sathyan P, Cramer S, Kram D, Ross J, Miller V, Reddy P, Alexander B, Ali SM, Ramkissoon S. Targetable BRAF and RAF1 Alterations in Advanced Pediatric Cancers. Oncologist 2021; 26:e153-e163. [PMID: 32918774 PMCID: PMC7794197 DOI: 10.1002/onco.13519] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
RAF family protein kinases signal through the MAPK pathway to orchestrate cellular proliferation, survival, and transformation. Identifying BRAF alterations in pediatric cancers is critically important as therapeutic agents targeting BRAF or MEK may be incorporated into the clinical management of these patients. In this study, we performed comprehensive genomic profiling on 3,633 pediatric cancer samples and identified a cohort of 221 (6.1%) cases with known or novel alterations in BRAF or RAF1 detected in extracranial solid tumors, brain tumors, or hematological malignancies. Eighty percent (176/221) of these tumors had a known-activating short variant (98, 55.7%), fusion (72, 40.9%), or insertion/deletion (6, 3.4%). Among BRAF altered cancers, the most common tumor types were brain tumors (74.4%), solid tumors (10.8%), hematological malignancies (9.1%), sarcomas (3.4%), and extracranial embryonal tumors (2.3%). RAF1 fusions containing intact RAF1 kinase domain (encoded by exons 10-17) were identified in seven tumors, including two novel fusions TMF1-RAF1 and SOX6-RAF1. Additionally, we highlight a subset of patients with brain tumor with positive clinical response to BRAF inhibitors, demonstrating the rationale for incorporating precision medicine into pediatric oncology. IMPLICATIONS FOR PRACTICE: Precision medicine has not yet gained a strong foothold in pediatric cancers. This study describes the landscape of BRAF and RAF1 genomic alterations across a diverse spectrum of pediatric cancers, primarily brain tumors, but also encompassing melanoma, sarcoma, several types of hematologic malignancy, and others. Given the availability of multiple U.S. Food and Drug Administration-approved BRAF inhibitors, identification of these alterations may assist with treatment decision making, as described here in three cases of pediatric cancer.
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Affiliation(s)
| | | | - Alison Roos
- Foundation Medicine Inc.CambridgeMassachusettsUSA
| | - Geoffrey Kannan
- Center for Cancer and Blood Disorders, Pediatric Specialists of VirginiaFalls ChurchVirginiaUSA
| | - Jeffrey Knipstein
- Pediatric Hematology/Oncology/BMT, Medical College of WisconsinMilwaukeeWisconsinUSA
| | | | | | | | - Dean Pavlick
- Foundation Medicine Inc.CambridgeMassachusettsUSA
| | | | | | | | | | | | - Stuart Cramer
- University of South Carolina School of MedicineColumbiaSouth CarolinaUSA
| | - David Kram
- Wake Forest Pediatric OncologyWinston‐SalemNorth CarolinaUSA
| | - Jeffrey Ross
- Foundation Medicine Inc.CambridgeMassachusettsUSA
- SUNY Upstate Medical UniversitySyracuseNew YorkUSA
| | - Vince Miller
- Foundation Medicine Inc.CambridgeMassachusettsUSA
| | | | | | - Siraj M. Ali
- Foundation Medicine Inc.CambridgeMassachusettsUSA
| | - Shakti Ramkissoon
- Foundation Medicine Inc.MorrisvilleNorthCarolinaUSA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
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7
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Lee SJ, Hong JY, Kim K, Kim KM, Kang SY, Lee T, Kim ST, Park SH, Park YS, Lim HY, Kang WK, Lee J, Park JO. Detection of Fusion Genes Using a Targeted RNA Sequencing Panel in Gastrointestinal and Rare Cancers. JOURNAL OF ONCOLOGY 2020; 2020:4659062. [PMID: 32411236 PMCID: PMC7204148 DOI: 10.1155/2020/4659062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/09/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022]
Abstract
Successful identification and targeting of oncogenic gene fusion is a major breakthrough in cancer treatment. Here, we investigate the therapeutic implications and feasibility of using a targeted RNA sequencing panel to identify fusion genes in gastrointestinal and rare cancers. From February through December 2017, patients with gastrointestinal, hepatobiliary, gynecologic, sarcoma, or rare cancers were recruited for a clinical sequencing project at Samsung Medical Center (NCT #02593578). The median age of the patients was 58 years (range, 31-81 years), and the male-to-female ratio was 1.3 : 1. A total of 118 patients passed the quality control process for a next-generation sequencing- (NGS-) based targeted sequencing assay. The NGS-based targeted sequencing assay was performed to detect gene fusions in 36-53 cancer-implicated genes. The following cancer types were included in this study: 28 colorectal cancers, 27 biliary tract cancers, 25 gastric cancers, 18 soft tissue sarcomas, 9 pancreatic cancers, 6 ovarian cancers, and 9 other rare cancers. Strong fusion was detected in 25 samples (21.2%). We found that 5.9% (7/118) of patients had known targetable fusion genes involving NTRK1 (n=3), FGFR (n=3), and RET (n=1), and 10.2% (12/118) of patients had potentially targetable fusion genes involving RAF1 (n=4), BRAF (n=2), ALK (n=2), ROS1 (n=1), EGFR (n=1), and CLDN18 (n=2). Thus, we successfully identified a substantial proportion of patients harboring fusion genes by RNA panel sequencing of gastrointestinal/rare cancers. Targetable and potentially targetable involved fusion genes were NTRK1, RET, FGFR3, FGFR2, BRAF, RAF1, ALK, ROS1, and CLDN18. Detection of fusion genes by RNA panel sequencing may be beneficial in refractory patients with gastrointestinal/rare cancers.
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Affiliation(s)
- Su Jin Lee
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Division of Hematology-Oncology, Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Jung Yong Hong
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyung Kim
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - So Young Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Taeyang Lee
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Se Hoon Park
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Suk Park
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ho Yeong Lim
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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McEvoy CR, Xu H, Smith K, Etemadmoghadam D, San Leong H, Choong DY, Byrne DJ, Iravani A, Beck S, Mileshkin L, Tothill RW, Bowtell DD, Bates BM, Nastevski V, Browning J, Bell AH, Khoo C, Desai J, Fellowes AP, Fox SB, Prall OW. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion. J Clin Invest 2019; 129:1940-1945. [PMID: 30835257 PMCID: PMC6486352 DOI: 10.1172/jci123089] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
BRAF and CRAF are critical components of the MAPK signaling pathway which is activated in many cancer types. In approximately 1% of melanomas, BRAF or CRAF are activated through structural arrangements. We describe here a metastatic melanoma with a GOLGA4-RAF1 fusion and pathogenic variants in CTNNB1 and CDKN2A. Anti-CTLA4/anti-PD1 combination immunotherapy failed to control tumor progression. In the absence of other actionable variants the patient was administered MEK inhibitor therapy on the basis of its potential action against RAF1 fusions. This resulted in a profound and clinically significant response. We demonstrated that GOLGA4-RAF1 expression was associated with ERK activation, elevated expression of the RAS/RAF downstream co-effector ETV5, and a high Ki67 index. These findings provide a rationale for the dramatic response to targeted therapy. This study shows that thorough molecular characterization of treatment-resistant cancers can identify therapeutic targets and personalize management, leading to improved patient outcomes.
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Affiliation(s)
- Christopher R. McEvoy
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Huiling Xu
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | | | | | | | | | | | - Amir Iravani
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sophie Beck
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Linda Mileshkin
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Richard W. Tothill
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - David D. Bowtell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | | | | | | | | | - Chloe Khoo
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jayesh Desai
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Department of Surgery, St Vincent’s Hospital, Fitzroy, Australia
- Clinical School, Austin Health, Heidelberg, Australia
- Department of Surgery, Royal Melbourne Hospital, Parkville, Australia
| | - Andrew P. Fellowes
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen B. Fox
- Department of Pathology, and
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
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