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Mahipal A, Storandt MH, Teslow EA, Jaeger E, Stoppler MC, Jin Z, Chakrabarti S. Frequency of Common and Uncommon BRAF Alterations among Colorectal and Non-Colorectal Gastrointestinal Malignancies. Cancers (Basel) 2024; 16:1823. [PMID: 38791902 PMCID: PMC11119877 DOI: 10.3390/cancers16101823] [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: 03/15/2024] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND The predictive and prognostic role of BRAF alterations has been evaluated in colorectal cancer (CRC); however, BRAF alterations have not been fully characterized in non-CRC gastrointestinal (GI) malignancies. In the present study, we report the frequency and spectrum of BRAF alterations among patients with non-CRC GI malignancies. METHODS Patients with CRC and non-CRC GI malignancies who underwent somatic tumor profiling via a tissue-based or liquid-based assay were included in this study. Gain-of-function BRAF alterations were defined as pathogenic/likely pathogenic somatic short variants (SVs), copy number amplifications ≥8, or fusions (RNA or DNA). RESULTS Among 51,560 patients with somatic profiling, 40% had CRC and 60% had non-CRC GI malignancies. BRAF GOF alterations were seen more frequently in CRC (8.9%) compared to non-CRC GI malignancies (2.2%) (p < 0.001). Non-CRC GI malignancies with the highest prevalence of BRAF GOF alterations were bile duct cancers (4.1%) and small intestine cancers (4.0%). Among BRAF GOF alterations, class II (28% vs. 6.8%, p < 0.001) and class III (23% vs. 14%, p < 0.001) were more common in non-CRC GI malignancies. Among class II alterations, rates of BRAF amplifications (3.1% vs. 0.3%, p < 0.001) and BRAF fusions (12% vs. 2.2%, p < 0.001) were higher in non-CRC GI malignancies compared to CRC. CONCLUSIONS Non-CRC GI malignancies demonstrate a distinct BRAF alteration profile compared to CRC, with a higher frequency of class II and III mutations, and more specifically, a higher incidence of BRAF fusions. Future studies should evaluate clinical implications for the management of non-CRC GI patients with BRAF alterations, especially BRAF fusions.
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Affiliation(s)
- Amit Mahipal
- Department of Medical Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA;
| | | | - Emily A. Teslow
- Tempus AI, Chicago, IL 60654, USA; (E.A.T.); (E.J.); (M.C.S.)
| | - Ellen Jaeger
- Tempus AI, Chicago, IL 60654, USA; (E.A.T.); (E.J.); (M.C.S.)
| | | | - Zhaohui Jin
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Sakti Chakrabarti
- Department of Medical Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA;
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Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581321. [PMID: 38746140 PMCID: PMC11092447 DOI: 10.1101/2024.02.20.581321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreMode's prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.
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3
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Kozyra P, Pitucha M. Revisiting the Role of B-RAF Kinase as a Therapeutic Target in Melanoma. Curr Med Chem 2024; 31:2003-2020. [PMID: 37855341 DOI: 10.2174/0109298673258495231011065225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/19/2023] [Accepted: 08/17/2023] [Indexed: 10/20/2023]
Abstract
Malignant melanoma is the rarest but most aggressive and deadly skin cancer. Melanoma is the result of a malignant transformation of melanocytes, which leads to their uncontrolled proliferation. Mutations in the mitogen-activated protein kinase (MAPK) pathway, which are crucial for the control of cellular processes, such as apoptosis, division, growth, differentiation, and migration, are one of its most common causes. BRAF kinase, as one of the known targets of this pathway, has been known for many years as a prominent molecular target in melanoma therapy, and the following mini-review outlines the state-of-the-art knowledge regarding its structure, mutations and mechanisms.
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Affiliation(s)
- Paweł Kozyra
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, Lublin, PL, 20093, Poland
| | - Monika Pitucha
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, Lublin, PL-20093, Poland
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4
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Castellani G, Buccarelli M, Arasi MB, Rossi S, Pisanu ME, Bellenghi M, Lintas C, Tabolacci C. BRAF Mutations in Melanoma: Biological Aspects, Therapeutic Implications, and Circulating Biomarkers. Cancers (Basel) 2023; 15:4026. [PMID: 37627054 PMCID: PMC10452867 DOI: 10.3390/cancers15164026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Melanoma is an aggressive form of skin cancer resulting from the malignant transformation of melanocytes. Recent therapeutic approaches, including targeted therapy and immunotherapy, have improved the prognosis and outcome of melanoma patients. BRAF is one of the most frequently mutated oncogenes recognised in melanoma. The most frequent oncogenic BRAF mutations consist of a single point mutation at codon 600 (mostly V600E) that leads to constitutive activation of the BRAF/MEK/ERK (MAPK) signalling pathway. Therefore, mutated BRAF has become a useful target for molecular therapy and the use of BRAF kinase inhibitors has shown promising results. However, several resistance mechanisms invariably develop leading to therapeutic failure. The aim of this manuscript is to review the role of BRAF mutational status in the pathogenesis of melanoma and its impact on differentiation and inflammation. Moreover, this review focuses on the mechanisms responsible for resistance to targeted therapies in BRAF-mutated melanoma and provides an overview of circulating biomarkers including circulating tumour cells, circulating tumour DNA, and non-coding RNAs.
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Affiliation(s)
- Giorgia Castellani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Maria Beatrice Arasi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Stefania Rossi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Maria Elena Pisanu
- High Resolution NMR Unit, Core Facilities, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Maria Bellenghi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Carla Lintas
- Research Unit of Medical Genetics, Department of Medicine, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Operative Research Unit of Medical Genetics, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Claudio Tabolacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
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5
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Kong WM, Guo YJ, Ma J, Shi C. BTN2A1-BRAF fusion may be a novel mechanism of resistance to osimertinib in lung adenocarcinoma: a case report. Transl Cancer Res 2023; 12:186-193. [PMID: 36760378 PMCID: PMC9906054 DOI: 10.21037/tcr-22-2060] [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: 08/16/2022] [Accepted: 12/06/2022] [Indexed: 01/10/2023]
Abstract
Background Non-small cell lung cancer (NSCLC) is one of the most common malignancies in the world. Osimertinib is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) indicated for NSCLC that effectively targets sensitive epidermal growth factor receptor mutation and exon20 T790M. Despite initially impressive outcomes, acquired resistance (AR) develops rapidly, typically within 9-13 months, and the mechanisms of resistance are not fully understood. Over the past years, EGFR-TKI and programmed cell death-ligand 1 (PD-L1) inhibitors have been widely used to treat for patients with advanced lung adenocarcinoma. Case Description Herein we report a middle-aged female who suffered from lung adenocarcinoma based on the pathological diagnosis. Epidermal growth factor receptor exon 19 deletion was detected by next-generation sequencing (NGS). After the patient underwent a series of treatments, including osimertinib, BTN2A1-BRAF fusion was identified. After assessing PD-L1 expression by immunohistochemistry (IHC), the patient was switched to duvalizumab, a PD-L1 inhibitor, but no significant improvements were observed. NGS and IHC assays were conducted to analyze the biopsy and blood samples obtained during treatment. Conclusions This case substantiates that the acquisition of BTN2A1-BRAF fusion potentially serves as a mechanism of AR to osimertinib in NSCLC. Patients with sensitive epidermal growth factor receptor mutation derive minimal benefit from PD-L1 inhibitors irrespective of the degree of PD-L1 expression in the tumor tissue in IHC. Our case provides a new train of thought for treating this patient population.
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Affiliation(s)
- Wei-Min Kong
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yong-Jun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China;,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China;,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Chao Shi
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China;,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
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Roosen M, Odé Z, Bunt J, Kool M. The oncogenic fusion landscape in pediatric CNS neoplasms. Acta Neuropathol 2022; 143:427-451. [PMID: 35169893 PMCID: PMC8960661 DOI: 10.1007/s00401-022-02405-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 01/09/2023]
Abstract
Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.
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Affiliation(s)
- Mieke Roosen
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Zelda Odé
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Jens Bunt
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands.
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany.
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7
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Li J, Lu H, Ng PKS, Pantazi A, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric-Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. A functional genomic approach to actionable gene fusions for precision oncology. SCIENCE ADVANCES 2022; 8:eabm2382. [PMID: 35138907 PMCID: PMC8827659 DOI: 10.1126/sciadv.abm2382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 06/01/2023]
Abstract
Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize ~100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology.
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Affiliation(s)
- Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Carman Ka Man Ip
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bianca Amador
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Tran
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Christopher A. Bristow
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Semin Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael Parfenov
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jiabin Tang
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Sahil Seth
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Harshad S. Mahadeshwar
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dong Zeng
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Alexei Protopopov
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan G. Seidman
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Chad J. Creighton
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiling Lu
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Kenna R. Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of MD Anderson Cancer Center, Houston, TX, USA
- Dell Medical School, The University of Texas Austin, Austin, TX, USA
| | - Kenneth L. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Gordon B. Mills
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health Sciences University, Portland, OR, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
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8
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Functional characterization of NPM1-TYK2 fusion oncogene. NPJ Precis Oncol 2022; 6:3. [PMID: 35042970 PMCID: PMC8766497 DOI: 10.1038/s41698-021-00246-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/16/2021] [Indexed: 11/08/2022] Open
Abstract
Gene fusions are known to drive many human cancers. Therefore, the functional characterization of newly discovered fusions is critical to understanding the oncobiology of these tumors and to enable therapeutic development. NPM1–TYK2 is a novel fusion identified in CD30 + lymphoproliferative disorders, and here we present the functional evaluation of this fusion gene as an oncogene. The chimeric protein consists of the amino-terminus of nucleophosmin 1 (NPM1) and the carboxyl-terminus of tyrosine kinase 2 (TYK2), including the kinase domain. Using in vitro lymphoid cell transformation assays and in vivo tumorigenic xenograft models we present direct evidence that the fusion gene is an oncogene. NPM1 fusion partner provides the critical homodimerization needed for the fusion kinase constitutive activation and downstream signaling that are responsible for cell transformation. As a result, our studies identify NPM1–TYK2 as a novel fusion oncogene and suggest that inhibition of fusion homodimerization could be a precision therapeutic approach in cutaneous T-cell lymphoma patients expressing this chimera.
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Nagasawa S, Ikeda K, Shintani D, Yang C, Takeda S, Hasegawa K, Horie K, Inoue S. Identification of a Novel Oncogenic Fusion Gene SPON1-TRIM29 in Clinical Ovarian Cancer That Promotes Cell and Tumor Growth and Enhances Chemoresistance in A2780 Cells. Int J Mol Sci 2022; 23:689. [PMID: 35054873 PMCID: PMC8776205 DOI: 10.3390/ijms23020689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
Gene structure alterations, such as chromosomal rearrangements that develop fusion genes, often contribute to tumorigenesis. It has been shown that the fusion genes identified in public RNA-sequencing datasets are mainly derived from intrachromosomal rearrangements. In this study, we explored fusion transcripts in clinical ovarian cancer specimens based on our RNA-sequencing data. We successfully identified an in-frame fusion transcript SPON1-TRIM29 in chromosome 11 from a recurrent tumor specimen of high-grade serous carcinoma (HGSC), which was not detected in the corresponding primary carcinoma, and validated the expression of the identical fusion transcript in another tumor from a distinct HGSC patient. Ovarian cancer A2780 cells stably expressing SPON1-TRIM29 exhibited an increase in cell growth, whereas a decrease in apoptosis was observed, even in the presence of anticancer drugs. The siRNA-mediated silencing of SPON1-TRIM29 fusion transcript substantially impaired the enhanced growth of A2780 cells expressing the chimeric gene treated with anticancer drugs. Moreover, a subcutaneous xenograft model using athymic mice indicated that SPON1-TRIM29-expressing A2780 cells rapidly generated tumors in vivo compared to control cells, whose growth was significantly repressed by the fusion-specific siRNA administration. Overall, the SPON1-TRIM29 fusion gene could be involved in carcinogenesis and chemotherapy resistance in ovarian cancer, and offers potential use as a diagnostic and therapeutic target for the disease with the fusion transcript.
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Affiliation(s)
- Saya Nagasawa
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Daisuke Shintani
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Chiujung Yang
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan;
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan; (D.S.); (K.H.)
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
| | - Satoshi Inoue
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (S.N.); (K.I.); (C.Y.)
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
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10
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Chew SM, Lucas M, Brady M, Kelly CM. SKAP2-BRAF fusion and response to an MEK inhibitor in a patient with metastatic melanoma resistant to immunotherapy. BMJ Case Rep 2021; 14:14/6/e238494. [PMID: 34167970 PMCID: PMC8230919 DOI: 10.1136/bcr-2020-238494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A woman in her 40s presented to the emergency department with headache and unintentional weight loss in September 2018. Investigations revealed a widely metastatic pan-negative melanoma of unknown primary. She had multiple lines of treatment including combination immunotherapy and chemotherapy. Next-generation sequencing identified an SKAP2-BRAF fusion protein, and she was commenced on an MEK inhibitor in September 2019 with a partial response seen on restaging scans after 6 weeks and a dramatic fall in her lactate dehydrogenase from 2248 IU/L to 576 IU/L. Unfortunately, the response was not maintained and she died from progression of her cancer in January 2020. SKAP2-BRAF fusions have a dimerisation domain that paradoxically activates the mitogen-activated protein kinase pathway, resulting in hyperproliferation if first-generation or second-generation BRAF inhibitors are used. Our knowledge is limited regarding the complex effects of targeted therapy in rare BRAF fusion proteins.
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Affiliation(s)
- Sonya Minmin Chew
- Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Mairi Lucas
- Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Michelle Brady
- Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
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11
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A Methodological Framework to Discover Pharmacogenomic Interactions Based on Random Forests. Genes (Basel) 2021; 12:genes12060933. [PMID: 34207374 PMCID: PMC8235396 DOI: 10.3390/genes12060933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
The identification of genomic alterations in tumor tissues, including somatic mutations, deletions, and gene amplifications, produces large amounts of data, which can be correlated with a diversity of therapeutic responses. We aimed to provide a methodological framework to discover pharmacogenomic interactions based on Random Forests. We matched two databases from the Cancer Cell Line Encyclopaedia (CCLE) project, and the Genomics of Drug Sensitivity in Cancer (GDSC) project. For a total of 648 shared cell lines, we considered 48,270 gene alterations from CCLE as input features and the area under the dose-response curve (AUC) for 265 drugs from GDSC as the outcomes. A three-step reduction to 501 alterations was performed, selecting known driver genes and excluding very frequent/infrequent alterations and redundant ones. For each model, we used the concordance correlation coefficient (CCC) for assessing the predictive performance, and permutation importance for assessing the contribution of each alteration. In a reasonable computational time (56 min), we identified 12 compounds whose response was at least fairly sensitive (CCC > 20) to the alteration profiles. Some diversities were found in the sets of influential alterations, providing clues to discover significant drug-gene interactions. The proposed methodological framework can be helpful for mining pharmacogenomic interactions.
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12
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Ottaviano M, Giunta EF, Tortora M, Curvietto M, Attademo L, Bosso D, Cardalesi C, Rosanova M, De Placido P, Pietroluongo E, Riccio V, Mucci B, Parola S, Vitale MG, Palmieri G, Daniele B, Simeone E. BRAF Gene and Melanoma: Back to the Future. Int J Mol Sci 2021; 22:ijms22073474. [PMID: 33801689 PMCID: PMC8037827 DOI: 10.3390/ijms22073474] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
As widely acknowledged, 40-50% of all melanoma patients harbour an activating BRAF mutation (mostly BRAF V600E). The identification of the RAS-RAF-MEK-ERK (MAP kinase) signalling pathway and its targeting has represented a valuable milestone for the advanced and, more recently, for the completely resected stage III and IV melanoma therapy management. However, despite progress in BRAF-mutant melanoma treatment, the two different approaches approved so far for metastatic disease, immunotherapy and BRAF+MEK inhibitors, allow a 5-year survival of no more than 60%, and most patients relapse during treatment due to acquired mechanisms of resistance. Deep insight into BRAF gene biology is fundamental to describe the acquired resistance mechanisms (primary and secondary) and to understand the molecular pathways that are now being investigated in preclinical and clinical studies with the aim of improving outcomes in BRAF-mutant patients.
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Affiliation(s)
- Margaret Ottaviano
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
- CRCTR Coordinating Rare Tumors Reference Center of Campania Region, 80131 Naples, Italy; (M.T.); (G.P.)
- Correspondence:
| | - Emilio Francesco Giunta
- Department of Precision Medicine, Università Degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy;
| | - Marianna Tortora
- CRCTR Coordinating Rare Tumors Reference Center of Campania Region, 80131 Naples, Italy; (M.T.); (G.P.)
| | - Marcello Curvietto
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy; (M.C.); (M.G.V.); (E.S.)
| | - Laura Attademo
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
| | - Davide Bosso
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
| | - Cinzia Cardalesi
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
| | - Mario Rosanova
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
| | - Pietro De Placido
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
| | - Erica Pietroluongo
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
| | - Vittorio Riccio
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
| | - Brigitta Mucci
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
| | - Sara Parola
- Department of Clinical Medicine and Surgery, Università Degli Studi di Napoli “Federico II”, 80131 Naples, Italy; (P.D.P.); (E.P.); (V.R.); (B.M.); (S.P.)
| | - Maria Grazia Vitale
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy; (M.C.); (M.G.V.); (E.S.)
| | - Giovannella Palmieri
- CRCTR Coordinating Rare Tumors Reference Center of Campania Region, 80131 Naples, Italy; (M.T.); (G.P.)
| | - Bruno Daniele
- Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (L.A.); (D.B.); (C.C.); (M.R.); (B.D.)
| | - Ester Simeone
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy; (M.C.); (M.G.V.); (E.S.)
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13
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Miyanaga A, Matsumoto M, Beck JA, Horikawa I, Oike T, Okayama H, Tanaka H, Burkett SS, Robles AI, Khan M, Lissa D, Seike M, Gemma A, Mano H, Harris CC. EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells. BMC Cancer 2021; 21:310. [PMID: 33761896 PMCID: PMC7992817 DOI: 10.1186/s12885-021-07905-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Chromosomal inversions involving anaplastic lymphoma kinase (ALK) and echinoderm microtubule associated protein like 4 (EML4) generate a fusion protein EML4-ALK in non-small cell lung cancer (NSCLC). The understanding of EML4-ALK function can be improved by a functional study using normal human cells. METHODS Here we for the first time conduct such study to examine the effects of EML4-ALK on cell proliferation, cellular senescence, DNA damage, gene expression profiles and transformed phenotypes. RESULTS The lentiviral expression of EML4-ALK in mortal, normal human fibroblasts caused, through its constitutive ALK kinase activity, an early induction of cellular senescence with accumulated DNA damage, upregulation of p16INK4A and p21WAF1, and senescence-associated β-galactosidase (SA-β-gal) activity. In contrast, when EML4-ALK was expressed in normal human fibroblasts transduced with telomerase reverse transcriptase (hTERT), which is activated in the vast majority of NSCLC, the cells showed accelerated proliferation and acquired anchorage-independent growth ability in soft-agar medium, without accumulated DNA damage, chromosome aberration, nor p53 mutation. EML4-ALK induced the phosphorylation of STAT3 in both mortal and hTERT-transduced cells, but RNA sequencing analysis suggested that the different signaling pathways contributed to the different phenotypic outcomes in these cells. While EML4-ALK also induced anchorage-independent growth in hTERT-immortalized human bronchial epithelial cells in vitro, the expression of EML4-ALK alone did not cause detectable in vivo tumorigenicity in immunodeficient mice. CONCLUSIONS Our data indicate that the expression of hTERT is critical for EML4-ALK to manifest its in vitro transforming activity in human cells. This study provides the isogenic pairs of human cells with and without EML4-ALK expression.
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Affiliation(s)
- Akihiko Miyanaga
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masaru Matsumoto
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Jessica A Beck
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Izumi Horikawa
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Takahiro Oike
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Hirokazu Okayama
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Hiromi Tanaka
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sandra S Burkett
- Molecular Cytogenetic Core Facility, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Mohammed Khan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Delphine Lissa
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA
| | - Masahiro Seike
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Akihiko Gemma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 3068A, Bethesda, MD, 20892, USA.
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14
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The Fusion Gene Landscape in Taiwanese Patients with Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13061343. [PMID: 33809651 PMCID: PMC8002233 DOI: 10.3390/cancers13061343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/05/2021] [Accepted: 03/14/2021] [Indexed: 01/23/2023] Open
Abstract
Simple Summary Human cancer genomes show a variety of alterations, such as single base changes, deletions, insertions, copy number changes, and gene fusions. Analyzing fusion gene transcripts may yield a novel and effective approach for selecting cancer treatments. However, few comprehensive analyses of gene fusions in non-small cell lung cancer (NSCLC) patients have been performed. Here, we characterized the fusion gene landscape of NSCLC in a case study of Taiwanese lung cancer patients. We concluded that some fusion genes likely play driver roles in carcinogenesis, while others act as passengers. We demonstrated that by using RNA-sequencing to detect gene fusion events, putative therapeutic drug targets could be identified, potentially leading to more precise therapies for NSCLC. Abstract Background: Analyzing fusion gene transcripts may yield an effective approach for selecting cancer treatments. However, few comprehensive analyses of fusions in non-small cell lung cancer (NSCLC) patients have been performed. Methods: We enrolled 54 patients with NSCLC, and performed RNA-sequencing (RNA-Seq). STAR (Spliced Transcripts Alignment to a Reference)-Fusion was used to identify fusions. Results: Of the 218 fusions discovered, 24 had been reported and the rest were novel. Three fusions had the highest occurrence rates. After integrating our gene expression and fusion data, we found that samples harboring fusions containing ASXL1, CACNA1A, EEF1A1, and RET also exhibited increased expression of these genes. We then searched for mutations and fusions in cancer driver genes in each sample and found that nine patients carried both mutations and fusions in cancer driver genes. Furthermore, we found a trend for mutual exclusivity between gene fusions and mutations in the same gene, with the exception of DMD, and we found that EGFR mutations are associated with the number of fusion genes. Finally, we identified kinase gene fusions, and potentially druggable fusions, which may play roles in lung cancer therapy. Conclusion: The clinical use of RNA-Seq for detecting driver fusion genes may play an important role in the treatment of lung cancer.
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15
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Liu M, Chen P, Hu HY, Ou-Yang DJ, Khushbu RA, Tan HL, Huang P, Chang S. Kinase gene fusions: roles and therapeutic value in progressive and refractory papillary thyroid cancer. J Cancer Res Clin Oncol 2021; 147:323-337. [PMID: 33387037 DOI: 10.1007/s00432-020-03491-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022]
Abstract
The incidence of papillary thyroid cancer (PTC), the major type of thyroid cancer, is increasing rapidly around the world, and its pathogenesis is still unclear. There is poor prognosis for PTC involved in rapidly progressive tumors and resistance to radioiodine therapy. Kinase gene fusions have been discovered to be present in a wide variety of malignant tumors, and an increasing number of novel types have been detected in PTC, especially progressive tumors. As a tumor-driving event, kinase fusions are constitutively activated or overexpress their kinase function, conferring oncogenic potential, and their frequency is second only to BRAFV600E mutation in PTC. Diverse forms of kinase fusions have been observed and are associated with specific pathological features of PTC (usually at an advanced stage), and clinical trials of therapeutic strategies targeting kinase gene fusions are feasible for radioiodine-resistant PTC. This review summarizes the roles of kinase gene fusions in PTC and the value of clinical therapy of targeting fusions in progressive or refractory PTC, and discusses the future perspectives and challenges related to kinase gene fusions in PTC patients.
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Affiliation(s)
- Mian Liu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Pei Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Hui-Yu Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Deng-Jie Ou-Yang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Rooh-Afza Khushbu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Hai-Long Tan
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Peng Huang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Shi Chang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
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16
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Pekova B, Sykorova V, Dvorakova S, Vaclavikova E, Moravcova J, Katra R, Astl J, Vlcek P, Kodetova D, Vcelak J, Bendlova B. RET, NTRK, ALK, BRAF, and MET Fusions in a Large Cohort of Pediatric Papillary Thyroid Carcinomas. Thyroid 2020; 30:1771-1780. [PMID: 32495721 DOI: 10.1089/thy.2019.0802] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Background: Pediatric papillary thyroid carcinoma (PTC) is a rare malignancy, but with increasing incidence. Pediatric PTCs have distinct clinical and pathological features and even the molecular profile differs from adult PTCs. Somatic point mutations in pediatric PTCs have been previously described and studied, but complex information about fusion genes is lacking. The aim of this study was to identify different fusion genes in a large cohort of pediatric PTCs and to correlate them with clinical and pathological data of patients. Methods: The cohort consisted of 93 pediatric PTC patients (6-20 years old). DNA and RNA were extracted from fresh frozen tissue samples, followed by DNA and RNA-targeted next-generation sequencing analyses. Fusion gene-positive samples were verified by real-time polymerase chain reaction. Results: A genetic alteration was found in 72/93 (77.4%) pediatric PTC cases. In 52/93 (55.9%) pediatric PTC patients, a fusion gene was detected. Twenty different types of RET, NTRK3, ALK, NTRK1, BRAF, and MET fusions were found, of which five novel, TPR/RET, IKBKG/RET, BBIP1/RET, OPTN/BRAF, and EML4/MET, rearrangements were identified and a CUL1/BRAF rearrangement that has not been previously described in thyroid cancer. Fusion gene-positive PTCs were significantly associated with the mixture of classical and follicular variants of PTC, extrathyroidal extension, higher T classification, lymph node and distant metastases, chronic lymphocytic thyroiditis, and frequent occurrence of psammoma bodies compared with fusion gene-negative PTCs. Fusion-positive patients also received more doses of radioiodine therapy. The most common fusion genes were the RET fusions, followed by NTRK3 fusions. RET fusions were associated with more frequent lymph node and distant metastases and psammoma bodies, and NTRK3 fusions were associated with the follicular variant of PTC. Conclusions: Fusion genes were the most common genetic alterations in pediatric PTCs. Fusion gene-positive PTCs were associated with more aggressive disease than fusion gene-negative PTCs.
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Affiliation(s)
- Barbora Pekova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Vlasta Sykorova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Sarka Dvorakova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Eliska Vaclavikova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Jitka Moravcova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Rami Katra
- Department of Ear, Nose and Throat, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Jaromir Astl
- Department of Otorhinolaryngology and Maxillofacial Surgery, 3rd Faculty of Medicine, Military University Hospital, Prague, Czech Republic
| | - Petr Vlcek
- Department of Nuclear Medicine and Endocrinology, and 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Daniela Kodetova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Josef Vcelak
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
| | - Bela Bendlova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic
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17
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Lee Y, Choi Y, Seo GH, Kim GH, Choi IH, Keum C, Ko JM, Cheon CK, Jeon J, Choi JH, Yoo HW, Lee BH. Clinical and molecular spectra of BRAF-associated RASopathy. J Hum Genet 2020; 66:389-399. [PMID: 33040082 DOI: 10.1038/s10038-020-00852-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 01/13/2023]
Abstract
Noonan syndrome (NS) and cardio-facio-cutaneous (CFC) syndrome are the most common subtypes of RASopathy. As an effector of Ras, BRAF is one of the molecules responsible for RASopathy. We investigated the phenotypic and genotypic features of 26 patients with BRAF-associated RASopathy. The clinical diagnoses were CFC (n = 21, 80.8%), NS (n = 3, 11.5%), NS/CFC (n = 1, 3.8%), and undefined syndromic intellectual disability (ID) (n = 1, 3.8%). The mostly shared phenotypes were ID (90.5%), cutaneous manifestations (84.6%), congenital heart defects (76.9%), short stature (76.9%), and dysmorphic features such as short neck (65.4%) and low-set ears (65.4%). Importantly, moderate to severe ID (57.1%) and epilepsy (26.9%) were noted. Eighteen different missense mutations were found, including a novel mutation, p.Phe498Tyr. p.Gln257Arg (n = 9, 34.6%) was the most common mutation, and the mutations were clustered in the cysteine-rich domain or protein kinase domain. A review of previously reported cases along with our findings revealed the existence of multiple sub-phenotypes of RASopathy within a single genotype, indicating that BRAF-associated RASopathy is not variant-specific. Our study further delineated the diverse and expanded clinical phenotypes of BRAF-associated RASopathy with their molecular genetic characteristics.
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Affiliation(s)
- Yena Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yunha Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - In Hee Choi
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Chong Kun Cheon
- Department of Pediatrics, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jihyun Jeon
- Department of Pediatrics, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, South Korea
| | - Jin-Ho Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Han-Wook Yoo
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea.,Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea. .,Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
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18
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Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020. [PMID: 33033246 DOI: 10.1038/s41467-020-18875-x.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
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Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain. .,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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19
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Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020; 11:5060. [PMID: 33033246 PMCID: PMC7544871 DOI: 10.1038/s41467-020-18875-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
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Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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20
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Cho WC, Shin YK, Na YS, Ryu MH, Ku JL, Kang YK. The role of novel fusion genes in human GIST cell lines derived from imatinib-resistant GIST patients: A therapeutic potential of fusion gene. Biochem Biophys Res Commun 2020; 529:699-706. [PMID: 32736695 DOI: 10.1016/j.bbrc.2020.05.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/24/2020] [Indexed: 01/18/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is the most common sarcoma in the gastrointestinal (GI) tract. Approximately 85% of the GIST is associated with a c-KIT mutation. A few GISTs show mutations in the gene encoding platelet-derived growth factor receptor alpha (PDGFR α or PDGFRA) without c-KIT gene mutation. GIST without c-KIT or PDGFRA mutations, which called wild type GIST, is about 5-10% of the total GIST. Fusion genes were also reported as one of the factors associated with carcinogenesis and drug resistance. With five cell lines derived from imatinib-resistant patients, novel fusion genes were identified from RNA sequencing and both physiological role and therapeutic potential were elucidated. Next-generation sequencing (NGS) analysis and lentiviral transduction were used to effect of fusion gene on GISTs. All the GIST cell lines carried c-KIT-positivity. Three different fusion gene analysis methods were used to find candidate fusion genes, including EIF3K-ACTN4, SYNCRIP-SNX14 and EXOC2-AK7. A novel interchromosomal fusion gene of the candidates, especially EXOC2-AK7, was confirmed in both tissue and cell line. The transduction of fusion gene increased the proliferation compared with the control group. Additionally, the fusion gene increased wound coverage capability. The fusion gene-transduced cell lines were more sensitive than the control group in the treatment of imatinib. In conclusion, five different imatinib-resistant GIST cell lines including the EXOC2-AK7 fusion gene derived from GIST-R5 represent important research tools for the investigation of cancer cell mechanisms underlying drug resistance and genetic variation. Furthermore, our study may facilitate pre-clinical studies of new therapeutic strategies.
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Affiliation(s)
- Woo-Cheol Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Young-Kyoung Shin
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Young-Soon Na
- Asan Institute for Life Science, Asan Medical Center, Seoul, 05505, South Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Ja-Lok Ku
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea; Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea.
| | - Yoon-Koo Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea.
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21
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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: 60] [Impact Index Per Article: 15.0] [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.
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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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22
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Tsang YH, Wang Y, Kong K, Grzeskowiak C, Zagorodna O, Dogruluk T, Lu H, Villafane N, Bhavana VH, Moreno D, Elsea SH, Liang H, Mills GB, Scott KL. Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression. eLife 2020; 9:48963. [PMID: 32270762 PMCID: PMC7164953 DOI: 10.7554/elife.48963] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/06/2020] [Indexed: 12/19/2022] Open
Abstract
The melanoma-associated antigen family A (MAGEA) antigens are expressed in a wide variety of malignant tumors but not in adult somatic cells, rendering them attractive targets for cancer immunotherapy. Here we show that a number of cancer-associated MAGEA mutants that undergo proteasome-dependent degradation in vitro could negatively impact their utility as immunotherapeutic targets. Importantly, in pancreatic ductal adenocarcinoma cell models, MAGEA6 suppresses macroautophagy (autophagy). The inhibition of autophagy is released upon MAGEA6 degradation, which can be induced by nutrient deficiency or by acquisition of cancer-associated mutations. Using xenograft mouse models, we demonstrated that inhibition of autophagy is critical for tumor initiation whereas reinstitution of autophagy as a consequence of MAGEA6 degradation contributes to tumor progression. These findings could inform cancer immunotherapeutic strategies for targeting MAGEA antigens and provide mechanistic insight into the divergent roles of MAGEA6 during pancreatic cancer initiation and progression.
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Affiliation(s)
- Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Cell, Develop & Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Caitlin Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Nicole Villafane
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, United States
| | | | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, United States.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Gordon B Mills
- Cell, Develop & Cancer Biology, Oregon Health & Science University, Portland, United States.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
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23
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Stangl C, Post JB, van Roosmalen MJ, Hami N, Verlaan-Klink I, Vos HR, van Es RM, Koudijs MJ, Voest EE, Snippert HJG, Kloosterman WP. Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity. Mol Cancer Res 2020; 18:537-548. [PMID: 31911540 DOI: 10.1158/1541-7786.mcr-19-0529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/13/2019] [Accepted: 01/02/2020] [Indexed: 11/16/2022]
Abstract
Fusion genes can be oncogenic drivers in a variety of cancer types and represent potential targets for targeted therapy. The BRAF gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2%-3% throughout different cancers. However, BRAF fusions rarely occur in the same gene configuration, potentially challenging personalized therapy design. In particular, the impact of the wide variety of fusion partners on the oncogenic role of BRAF during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare BRAF fusions containing various partner genes (AGAP3, DLG1, and TRIM24) with respect to cellular behavior, downstream signaling activation, and response to targeted therapies. We demonstrate that 5' fusion partners mainly promote canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region. In addition, the 5' partner of BRAF fusions influences their subcellular localization and intracellular signaling capacity, revealing distinct subsets of affected signaling pathways and altered gene expression. Presence of the different BRAF fusions resulted in varying sensitivities to combinatorial inhibition of MEK and the EGF receptor family. However, all BRAF fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that BRAF fusions should be screened alongside other MAPK pathway alterations to identify patients with metastatic colorectal cancer to exclude from anti-EGFR-targeted treatment. IMPLICATIONS: Although intracellular signaling and sensitivity to targeted therapies of BRAF fusion genes are influenced by their 5' fusion partner, we show that all investigated BRAF fusions confer resistance to clinically relevant EGFR inhibition.
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Affiliation(s)
- Christina Stangl
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Division of Molecular Oncology, Netherlands Cancer Institute, and Oncode Institute, Amsterdam, the Netherlands
| | - Jasmin B Post
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, the Netherlands
| | - Nizar Hami
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Ingrid Verlaan-Klink
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Marco J Koudijs
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Center for Personalized Cancer Treatment, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emile E Voest
- Division of Molecular Oncology, Netherlands Cancer Institute, and Oncode Institute, Amsterdam, the Netherlands.
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - W P Kloosterman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands. .,Cyclomics, Utrecht, the Netherlands.,Frame Cancer Therapeutics, Amsterdam, the Netherlands
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24
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Weinberg F, Griffin R, Fröhlich M, Heining C, Braun S, Spohr C, Iconomou M, Hollek V, Röring M, Horak P, Kreutzfeldt S, Warsow G, Hutter B, Uhrig S, Neumann O, Reuss D, Heiland DH, von Kalle C, Weichert W, Stenzinger A, Brors B, Glimm H, Fröhling S, Brummer T. Identification and characterization of a BRAF fusion oncoprotein with retained autoinhibitory domains. Oncogene 2019; 39:814-832. [PMID: 31558800 DOI: 10.1038/s41388-019-1021-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022]
Abstract
Fusion proteins involving the BRAF serine/threonine kinase occur in many cancers. The oncogenic potential of BRAF fusions has been attributed to the loss of critical N-terminal domains that mediate BRAF autoinhibition. We used whole-exome and RNA sequencing in a patient with glioblastoma multiforme to identify a rearrangement between TTYH3, encoding a membrane-resident, calcium-activated chloride channel, and BRAF intron 1, resulting in a TTYH3-BRAF fusion protein that retained all features essential for BRAF autoinhibition. Accordingly, the BRAF moiety of the fusion protein alone, which represents full-length BRAF without the amino acids encoded by exon 1 (BRAFΔE1), did not induce MEK/ERK phosphorylation or transformation. Likewise, neither the TTYH3 moiety of the fusion protein nor full-length TTYH3 provoked ERK pathway activity or transformation. In contrast, TTYH3-BRAF displayed increased MEK phosphorylation potential and transforming activity, which were caused by TTYH3-mediated tethering of near-full-length BRAF to the (endo)membrane system. Consistent with this mechanism, a synthetic approach, in which BRAFΔE1 was tethered to the membrane by fusing it to the cytoplasmic tail of CD8 also induced transformation. Furthermore, we demonstrate that TTYH3-BRAF signals largely independent of a functional RAS binding domain, but requires an intact BRAF dimer interface and activation loop phosphorylation sites. Cells expressing TTYH3-BRAF exhibited increased MEK/ERK signaling, which was blocked by clinically achievable concentrations of sorafenib, trametinib, and the paradox breaker PLX8394. These data provide the first example of a fully autoinhibited BRAF protein whose oncogenic potential is dictated by a distinct fusion partner and not by a structural change in BRAF itself.
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Affiliation(s)
- Florian Weinberg
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martina Fröhlich
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Christoph Heining
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Heidelberg, Germany.,University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Mary Iconomou
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Viola Hollek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Horak
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Gregor Warsow
- Omics IT and Data Management Core Facility, DKFZ, Heidelberg, Germany.,Division of Theoretical Bioinformatics, DKFZ, Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Sebastian Uhrig
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Olaf Neumann
- DKTK, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Reuss
- DKTK, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Translational NeuroOncology Research Group, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany.,DKTK, Munich, Germany
| | - Albrecht Stenzinger
- DKTK, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Heidelberg, Germany.,University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany. .,DKTK, Heidelberg, Germany.
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany. .,Comprehensive Cancer Centre Freiburg, University of Freiburg, Freiburg, Germany. .,DKTK Partner Site Freiburg and DKFZ, Heidelberg, Germany.
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25
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Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep 2019; 23:227-238.e3. [PMID: 29617662 PMCID: PMC5916809 DOI: 10.1016/j.celrep.2018.03.050] [Citation(s) in RCA: 334] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/25/2018] [Accepted: 03/13/2018] [Indexed: 12/11/2022] Open
Abstract
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.
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Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang FM, Martinez-Ledesma E, Lee SH, Zheng S, Verhaak RGW. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res 2019; 46:D1144-D1149. [PMID: 29099951 PMCID: PMC5753333 DOI: 10.1093/nar/gkx1018] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/17/2017] [Indexed: 01/29/2023] Open
Abstract
Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as a means of validation. We observed that 65% of transcript fusions were associated with a chromosomal alteration, which is annotated in the portal. Other features of the portal include links to SNP array-based copy number levels and mutational patterns, exon and transcript level expressions of the partner genes, and a network-based centrality score for prioritizing functional fusions. Our portal aims to be a broadly applicable and user friendly resource for cancer gene annotation and is publicly available at http://www.tumorfusions.org.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Program in Bioinformatics and Biostatistics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Qianghu Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Samirkumar Amin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Frederick M Lang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emmanuel Martinez-Ledesma
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Soo Hyun Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siyuan Zheng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Zhou Y, Sinha S, Schwartz JL, Adami GR. A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA. BMC Cancer 2019; 19:607. [PMID: 31221127 PMCID: PMC6587277 DOI: 10.1186/s12885-019-5789-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/31/2019] [Indexed: 01/17/2023] Open
Abstract
Background The NTRK2 genetic locus encodes neurotrophin membrane receptors that play an important role in normal neural tissue plasticity, growth, and survival. One NTRK2-encoded protein is TrkB-FL, which can regulate multiple pathways relevant to cancer. A second NTRK2 gene mRNA isoform encodes TrkB-T1, a receptor that has a different cytoplasmic domain encoded in a mRNA with a unique 3′ terminal exon. Method Tumors from The Cancer Genome Atlas (TCGA) and other studies were classified according to the expression of a single form of NTRK2 mRNA, TrkB-T1, identified by its unique 3′ terminal exon. Analysis of differentially expressed genes in TrkB-T1 high expressers was done to determine if tumors enriched for TrkB-T1 mRNA were a uniform group independent of anatomic site. Results The mRNA for TrkB-T1 is the most abundant NTRK2 gene mRNA in all squamous cell carcinomas (SCCs) in the TCGA database. Comparison of larynx SCC high TrkB-T1 RNA expressers to low expressers (n = 96) revealed gene expression differences consistent with the high TrkB-T1 tumors being more neural-like. The upregulated genes in the TrkB-T1 RNA high expressers also showed enrichment of pathways involved in retinol metabolism, hedgehog signaling, and the Nfe2l2 response, among other pathways. An examination of oral, esophagus, and lung SCCs (n = 284, 97, 501) showed induction of the same pathways among tumors that expressed high levels of TrkB-T1 mRNA. Proteins associated with regulation of the sonic hedgehog pathway, and the Nfe2l2 response, Tp63, and Keap1 and p62/SQSTM1 proteins, showed differential expression in larynx, oral and lung high TrkB1-T1 expresser SCCs. Unexpectantly, the relationship of high level TrkB-T1 expression to patient outcomes was SCC anatomic site specific. High TrkB-T1 mRNA levels in laryngeal SCC correlated with poor survival, but the opposite was true for lung SCC. This may be because pathways enriched in the TrkB high expressers, like those involving oncogenes NFE2L2, PIK3CA, and SOX2, are known to have SCC anatomic site-specific effects on progression. Conclusions High level TrkB-T1 mRNA is a marker of a distinct SCC subtype enriched for at least 3 pathways relevant to tumor progression: Nfe2l2 response, retinol metabolism, and hedgehog signaling. Electronic supplementary material The online version of this article (10.1186/s12885-019-5789-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yalu Zhou
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Saurabh Sinha
- Department of Computer Science and Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 2122 Siebel Center, 201N. Goodwin Ave, Urbana, IL, USA
| | - Joel L Schwartz
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Guy R Adami
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA.
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Tuna M, Amos CI, Mills GB. Molecular mechanisms and pathobiology of oncogenic fusion transcripts in epithelial tumors. Oncotarget 2019; 10:2095-2111. [PMID: 31007851 PMCID: PMC6459343 DOI: 10.18632/oncotarget.26777] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Recurrent fusion transcripts, which are one of the characteristic hallmarks of cancer, arise either from chromosomal rearrangements or from transcriptional errors in splicing. DNA rearrangements include intrachromosomal or interchromosomal translocation, tandem duplication, deletion, inversion, or result from chromothripsis, which causes complex rearrangements. In addition, fusion proteins can be created through transcriptional read-through. Fusion genes can be transcribed to fusion transcripts and translated to chimeric proteins, with many having demonstrated transforming activities through multiple mechanisms in cells. Fusion proteins represent novel therapeutic targets and diagnostic biomarkers of diagnosis, disease status, or progression. This review focuses on the mechanisms underlying the formation of oncogenic fusion genes and transcripts and their impact on the pathobiology of epithelial tumors.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA.,Precision Oncology, Knight Cancer Institute, Portland, OR, USA
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29
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Turner JA, Bemis JGT, Bagby SM, Capasso A, Yacob BW, Chimed TS, Van Gulick R, Lee H, Tobin R, Tentler JJ, Pitts T, McCarter M, Robinson WA, Couts KL. BRAF fusions identified in melanomas have variable treatment responses and phenotypes. Oncogene 2018; 38:1296-1308. [PMID: 30254212 DOI: 10.1038/s41388-018-0514-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 12/13/2022]
Abstract
Oncogenic BRAF fusions have emerged as an alternate mechanism for BRAF activation in melanomas and other cancers. A number of BRAF fusions with different 5' gene partners and BRAF exon breakpoints have been described, but the effects of different partners and breakpoints on cancer phenotypes and treatment responses has not been well characterized. Targeted RNA sequencing was used to screen 60 melanoma patient-derived xenograft (PDX) models for BRAF fusions. We identified three unique BRAF fusions, including a novel SEPT3-BRAF fusion, occurring in four tumors (4/60, 6.7%), all of which were "pan-negative" (lacking other common mutations) (4/18, 22.2%). The BRAF fusion PDX models showed variable growth rates and responses to MAPK inhibitors in vivo. Overexpression of BRAF fusions identified in our study, as well as other BRAF fusions previously identified in melanomas, resulted in a high degree of variability in 2D proliferation and 3D invasion between the different fusions. While exogenously expressed BRAF fusions all responded to MAPK inhibition in vitro, we observed potential differences in signaling and feedback mechanisms. In summary, BRAF fusions are actionable therapeutic targets, however there are significant differences in phenotypes, treatment responses, and signaling which may be clinically relevant.
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Affiliation(s)
- Jacqueline A Turner
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Judson G T Bemis
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Stacey M Bagby
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Anna Capasso
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Betelehem W Yacob
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Tugs-Saikhan Chimed
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Robert Van Gulick
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Hannah Lee
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA.,Department of Medicine, Internal Medicine Residency Training Program, University of Colorado Denver, Aurora, CO, USA
| | - Richard Tobin
- Division Surgical Oncology, Department of Surgery, University of Colorado Denver, Aurora, CO, USA
| | - John J Tentler
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Todd Pitts
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Martin McCarter
- Division Surgical Oncology, Department of Surgery, University of Colorado Denver, Aurora, CO, USA
| | - William A Robinson
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Kasey L Couts
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, USA.
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30
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Ng PKS, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell 2018; 33:450-462.e10. [PMID: 29533785 PMCID: PMC5926201 DOI: 10.1016/j.ccell.2018.01.021] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.
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Affiliation(s)
- Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shan Shao
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sohini Sengupta
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Zixing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Richard Tran
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie Soewito
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Collin Tokheim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniel Cui Zhou
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Amber M Johnson
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Zeng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carman Ka Man Ip
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Wester
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher P Vellano
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins Medicine, Baltimore, MD 21287, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63108, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lydia Wai Ting Cheung
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenna R Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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