1
|
Du R, Li K, Guo K, Chen Z, Zhao X, Han L, Bian H. Two decades of a protooncogene TBL1XR1: from a transcription modulator to cancer therapeutic target. Front Oncol 2024; 14:1309687. [PMID: 38347836 PMCID: PMC10859502 DOI: 10.3389/fonc.2024.1309687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
Transducin beta-like 1X-related protein 1 (TBL1XR1) was discovered two decades ago and was implicated as part of the nuclear transcription corepressor complex. Over the past 20 years, the emerging oncogenic function of TBL1XR1 in cancer development has been discovered. Recent studies have highlighted that the genetic aberrations of TBL1XR1 in cancers, especially in hematologic tumors, are closely associated with tumorigenesis. In solid tumors, TBL1XR1 is proposed to be a promising prognostic biomarker due to the correlation between abnormal expression and clinicopathological parameters. Post-transcriptional and post-translational modification are responsible for the expression and function of TBL1XR1 in cancer. TBL1XR1 exerts its functional role in various processes that involves cell cycle and apoptosis, cell proliferation, resistance to chemotherapy and radiotherapy, cell migration and invasion, stemness and angiogenesis. Multitude of cancer-related signaling cascades like Wnt-β-catenin, PI3K/AKT, ERK, VEGF, NF-κB, STAT3 and gonadal hormone signaling pathways are tightly modulated by TBL1XR1. This review provided a comprehensive overview of TBL1XR1 in tumorigenesis, shedding new light on TBL1XR1 as a promising diagnostic biomarker and druggable target in cancer.
Collapse
Affiliation(s)
- Ruijuan Du
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
- Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Kai Li
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
- Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, Nanyang, Henan, China
| | - KeLei Guo
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
- Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Zhiguo Chen
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Xulin Zhao
- Oncology Department, Nanyang First People’s Hospital, Nan Yang, Henan, China
| | - Li Han
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
- Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Hua Bian
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, Henan, China
- Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, Nanyang, Henan, China
| |
Collapse
|
2
|
Wu G, Yoshida N, Liu J, Zhang X, Xiong Y, Heavican-Foral TB, Mandato E, Liu H, Nelson GM, Yang L, Chen R, Donovan KA, Jones MK, Roshal M, Zhang Y, Xu R, Nirmal AJ, Jain S, Leahy C, Jones KL, Stevenson KE, Galasso N, Ganesan N, Chang T, Wu WC, Louissaint A, Debaize L, Yoon H, Cin PD, Chan WC, Sui SJH, Ng SY, Feldman AL, Horwitz SM, Adelman K, Fischer ES, Chen CW, Weinstock DM, Brown M. TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence. Sci Transl Med 2023; 15:eadi7244. [PMID: 37729434 PMCID: PMC11014717 DOI: 10.1126/scitranslmed.adi7244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Gene fusions involving tumor protein p63 gene (TP63) occur in multiple T and B cell lymphomas and portend a dismal prognosis for patients. The function and mechanisms of TP63 fusions remain unclear, and there is no target therapy for patients with lymphoma harboring TP63 fusions. Here, we show that TP63 fusions act as bona fide oncogenes and are essential for fusion-positive lymphomas. Transgenic mice expressing TBL1XR1::TP63, the most common TP63 fusion, develop diverse lymphomas that recapitulate multiple human T and B cell lymphomas. Here, we identify that TP63 fusions coordinate the recruitment of two epigenetic modifying complexes, the nuclear receptor corepressor (NCoR)-histone deacetylase 3 (HDAC3) by the N-terminal TP63 fusion partner and the lysine methyltransferase 2D (KMT2D) by the C-terminal TP63 component, which are both required for fusion-dependent survival. TBL1XR1::TP63 localization at enhancers drives a unique cell state that involves up-regulation of MYC and the polycomb repressor complex 2 (PRC2) components EED and EZH2. Inhibiting EZH2 with the therapeutic agent valemetostat is highly effective at treating transgenic lymphoma murine models, xenografts, and patient-derived xenografts harboring TP63 fusions. One patient with TP63-rearranged lymphoma showed a rapid response to valemetostat treatment. In summary, TP63 fusions link partner components that, together, coordinate multiple epigenetic complexes, resulting in therapeutic vulnerability to EZH2 inhibition.
Collapse
Affiliation(s)
- Gongwei Wu
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Noriaki Yoshida
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Current address: Merck Research Laboratories, Boston, MA
02215, USA
| | - Jihe Liu
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School
of Public Health, Boston, MA 02115, USA
| | - Xiaoyang Zhang
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge,
MA 02142, USA
- Department of Oncological Sciences, Huntsman Cancer
Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tayla B. Heavican-Foral
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Elisa Mandato
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Huiyun Liu
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Geoffrey M. Nelson
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lu Yang
- Department of Systems Biology, City of Hope Comprehensive
Cancer Center, Monrovia, CA 91016, USA
| | - Renee Chen
- Department of Systems Biology, City of Hope Comprehensive
Cancer Center, Monrovia, CA 91016, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Marcus K. Jones
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Ran Xu
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ajit J. Nirmal
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Salvia Jain
- Massachusetts General Hospital Cancer Center, Boston, MA
02114, USA
| | - Catharine Leahy
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kristen L. Jones
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kristen E. Stevenson
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Natasha Galasso
- Department of Medicine, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Nivetha Ganesan
- Department of Medicine, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Tiffany Chang
- Department of Medicine, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Wen-Chao Wu
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Abner Louissaint
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Massachusetts General Hospital,
Boston, MA 02114, USA
| | - Lydie Debaize
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hojong Yoon
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115, USA
| | - Wing C. Chan
- Department of Pathology, City of Hope Medical Center,
Duarte, CA 91010, USA
| | - Shannan J. Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School
of Public Health, Boston, MA 02115, USA
| | - Samuel Y. Ng
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Division of Hematopathology, Mayo Clinic College of
Medicine, Rochester, MN 55905, USA
| | - Andrew L. Feldman
- Current address: Department of Clinical Studies,
Radiation Effects Research Foundation, Hiroshima, 7320815, Japan
| | - Steven M. Horwitz
- Department of Medicine, Memorial Sloan Kettering Cancer
Center, New York, NY 10065, USA
| | - Karen Adelman
- Broad Institute of MIT and Harvard University, Cambridge,
MA 02142, USA
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chun-Wei Chen
- Department of Systems Biology, City of Hope Comprehensive
Cancer Center, Monrovia, CA 91016, USA
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge,
MA 02142, USA
- Current address: Merck Research Laboratories, Boston, MA
02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
3
|
Lewis NE, Sardana R, Dogan A. Mature T-cell and NK-cell lymphomas: updates on molecular genetic features. Int J Hematol 2023; 117:475-491. [PMID: 36637656 DOI: 10.1007/s12185-023-03537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023]
Abstract
Mature T-cell and NK-cell lymphomas are a heterogeneous group of rare and typically aggressive neoplasms. Diagnosis and subclassification have historically relied primarily on the integration of clinical, histologic, and immunophenotypic features, which often overlap. The widespread application of a variety of genomic techniques in recent years has provided extensive insight into the pathobiology of these diseases, allowing for more precise diagnostic classification, improved prognostication, and development of novel therapies. In this review, we summarize the genomic features of the most common types of mature T-cell and NK-cell lymphomas with a particular focus on the contribution of genomics to biologic insight, classification, risk stratification, and select therapies in the context of the recently published International Consensus and updated World Health Organization classification systems.
Collapse
Affiliation(s)
- Natasha E Lewis
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Rohan Sardana
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| |
Collapse
|
4
|
Yenamandra AK, Smith RB, Senaratne TN, Kang SHL, Fink JM, Corboy G, Hodge CA, Lu X, Mathew S, Crocker S, Fang M. Evidence-based review of genomic aberrations in diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS): Report from the cancer genomics consortium lymphoma working group. Cancer Genet 2022; 268-269:1-21. [PMID: 35970109 DOI: 10.1016/j.cancergen.2022.07.006] [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: 05/02/2022] [Revised: 06/26/2022] [Accepted: 07/31/2022] [Indexed: 01/25/2023]
Abstract
Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). The 2016 World Health Organization (WHO) classification defined DLBCL, NOS and its subtypes based on clinical findings, morphology, immunophenotype, and genetics. However, even within the WHO subtypes, it is clear that additional clinical and genetic heterogeneity exists. Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. We gathered an international group of experts to review the current literature on DLBCL, NOS, with respect to genomic aberrations and the role they may play in the diagnosis, prognosis and therapeutic decisions. We comprehensively surveyed clinical laboratory directors/professionals about their genetic testing practices for DLBCL, NOS. The survey results indicated that a variety of diagnostic approaches were being utilized and that there was an overwhelming interest in further standardization of routine genetic testing along with the incorporation of new genetic testing modalities to help guide a precision medicine approach. Additionally, we present a comprehensive literature summary on the most clinically relevant genomic aberrations in DLBCL, NOS. Based upon the survey results and literature review, we propose a standardized, tiered testing approach which will help laboratories optimize genomic testing in order to provide the maximum information to guide patient care.
Collapse
Affiliation(s)
- Ashwini K Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37215, United States.
| | | | - T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, United States
| | - Sung-Hae L Kang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, United States
| | - James M Fink
- Department of Pathology and Laboratory Medicine, Hennepin Healthcare, Minneapolis, MN, United States
| | - Gregory Corboy
- Haematology, Pathology Queensland, Herston, Queensland, Australia; Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; School of Clinical Sciences, Monash University, Clayton, Vic, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Vic, Australia
| | - Casey A Hodge
- Department of Pathology and Immunology, Barnes Jewish Hospital, St. Louis, MO, United States
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Susan Mathew
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Kingston Health Sciences Centre, Queen's University, Kingston, ON, Canada
| | - Min Fang
- Fred Hutchinson Cancer Center and University of Washington, Seattle, WA, United States
| |
Collapse
|
5
|
Nagel S, Pommerenke C, Quentmeier H, Meyer C, Kaufmann M, MacLeod RAF. Genomic Aberrations Generate Fusion Gene FOXK2::TP63 and Activate NFKB1 in Cutaneous T-Cell Lymphoma. Biomedicines 2022; 10:biomedicines10082038. [PMID: 36009586 PMCID: PMC9406051 DOI: 10.3390/biomedicines10082038] [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: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a severe lymphoid malignancy with a worse prognosis lacking curative treatment regimens. Several gene mutations and deregulated pathways, including NFkB signaling, have been implicated in its pathogenesis. Accordingly, CTCL cell line HUT-78 reportedly contains mutated NFKB2, which is constitutively activated via partial gene deletion, also demonstrating that genomic rearrangements cause driving mutations in this malignancy. Here, along with HUT-78, we analyzed CTCL cell line HH to identify additional aberrations underlying gene deregulation. Karyotyping and genomic profiling of HH showed several rearrangements worthy of detailed investigation. Corresponding to the established karyotype, RNA-seq data and PCR analysis confirmed the presence of t(3;17)(q28;q25), generating a novel fusion gene, FOXK2::TP63. Furthermore, chromosomal rearrangement t(1;4)(p32;q25) was connected to amplification at 4q24–26, affecting aberrant NFKB1 overexpression thereat. Transcription factor binding-site analysis and knockdown experiments demonstrated that IRF4 contributed to NFKB1 expression. Within the same amplicon, we identified amplification and overexpression of NFkB signaling activator CAMK2D (4q26) and p53-inhibitor UBE2D3 (4q24). Genomic profiling data for HUT-78 detailed a deletion at 10q25 underlying reported NFKB2 activation. Moreover, amplifications of ID1 (20q11) and IKZF2 (2q34) in this cell line drove overexpression of these NK cell differentiation factors and possibly thus formed corresponding lineage characteristics. Target gene analysis for NFKB1 via siRNA-mediated knockdown in HH revealed activation of TP63, MIR155, and NOTCH pathway component RBPJ. Finally, treatment of HH with NFkB inhibitor demonstrated a role for NFkB in supporting proliferation, while usage of inhibitor DAPT showed significant survival effects via the NOTCH pathway. Collectively, our data suggest that NFkB and/or NOTCH inhibitors may represent reasonable treatment options for subsets of CTCL patients.
Collapse
|
6
|
Zhuang Y, Che J, Wu M, Guo Y, Xu Y, Dong X, Yang H. Altered pathways and targeted therapy in double hit lymphoma. J Hematol Oncol 2022; 15:26. [PMID: 35303910 PMCID: PMC8932183 DOI: 10.1186/s13045-022-01249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
High-grade B-cell lymphoma with translocations involving MYC and BCL2 or BCL6, usually referred to as double hit lymphoma (DHL), is an aggressive hematological malignance with distinct genetic features and poor clinical prognosis. Current standard chemoimmunotherapy fails to confer satisfying outcomes and few targeted therapeutics are available for the treatment against DHL. Recently, the delineating of the genetic landscape in tumors has provided insight into both biology and targeted therapies. Therefore, it is essential to understand the altered signaling pathways of DHL to develop treatment strategies with better clinical benefits. Herein, we summarized the genetic alterations in the two DHL subtypes (DHL-BCL2 and DHL-BCL6). We further elucidate their implications on cellular processes, including anti-apoptosis, epigenetic regulations, B-cell receptor signaling, and immune escape. Ongoing and potential therapeutic strategies and targeted drugs steered by these alterations were reviewed accordingly. Based on these findings, we also discuss the therapeutic vulnerabilities that coincide with these genetic changes. We believe that the understanding of the DHL studies will provide insight into this disease and capacitate the finding of more effective treatment strategies.
Collapse
Affiliation(s)
- Yuxin Zhuang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Yu Guo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Yongjin Xu
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People’s Republic of China
| | - Haiyan Yang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| |
Collapse
|
7
|
Matsumoto Y, Tsukamoto T, Chinen Y, Shimura Y, Sasaki N, Nagoshi H, Sato R, Adachi H, Nakano M, Horiike S, Kuroda J, Taki T, Tashiro K, Taniwaki M. Detection of novel and recurrent conjoined genes in non-Hodgkin B-cell lymphoma. J Clin Exp Hematop 2021; 61:71-77. [PMID: 33883344 PMCID: PMC8265495 DOI: 10.3960/jslrt.20033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For this study, we investigated comprehensive expression of conjoined genes (CGs) in
non-Hodgkin B-cell lymphoma (B-NHL) cell line KPUM-UH1 by using paired-end RNA sequencing.
Furthermore, we analyzed the expression of these transcripts in an additional 21 cell lines, 37
primary samples of various malignancies and peripheral blood mononuclear cells of four normal
individuals. Seventeen CGs were detected in KPUM-UH1: CTBS-GNG5,
SRP9-EPHX1, RMND5A-ANAPC, OTX1-EHBP1,
ATF2-CHN1, PRKAA1-TTC33, LARP1-MRPL22,
LOC105379697-BAK1, TIAM2-SCAF8,
SPAG1-VPS13B, WBP1L-CNNM2, NARS2-GAB2,
CTSC-RAB38, VAMP1-CD27-AS1, LRRC37A2-NSF,
UBA2-WTIP and ZNF600-ZNF611. To our knowledge, 10 of these
genes have not been previously reported. The various characteristics of the CGs included in-
and out-of-frame fusions, chimeras involving non-coding RNA and transcript variants. A finding
of note was that LARP1-MRPL2 was characterized as in-frame fusion and was
recurrently expressed in B-NHL samples. In this study, variety of CGs was expressed both in
malignant and normal cells, some of which might be specific to lymphoma.
Collapse
Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Sato
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroko Adachi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University Faculty of Health Science, Tokyo, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| |
Collapse
|
8
|
Wang HY, Sokol ES, Goodman AM, Feldman AL, Mulroney CM. Case Report: Multiple Chromosomal Translocations Including Novel CIITA-CREBBP Fusion and Mutations in a Follicular Lymphoma. Front Oncol 2021; 11:620435. [PMID: 33777766 PMCID: PMC7988195 DOI: 10.3389/fonc.2021.620435] [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: 10/22/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenesis of follicular lymphoma is a multi-step process, in which chromosomal translocation between immunoglobulin heavy chain (IgH) and anti-apoptotic B-cell lymphoma 2 (BCL2), namely IgH-BCL2, is an earliest step, followed by other genetic/genomic alterations including but not limited to mutation of CREB binding protein (CREBBP). MHC class II transactivator (CIITA) is a transcription regulator responsible for expression of MHC class II molecules including HLA-DR in human. We report herein a novel fusion gene involving CIITA and CREBBP in a patient with a low-grade follicular lymphoma (FL) but with high Ki-67 proliferation index. In addition, our patient also harbors CREBBP mutation. Together, we postulate that total loss of CREBBP function may contribute, in part, to the lymphoma genesis. Furthermore, this patient has addition rare (TBL1XR1-TP63) and common (IgH-BCL2) chromosomal translocations and multiple mutations including BCL2, BRAF, MUTYH, and STAT6.
Collapse
Affiliation(s)
- Huan-You Wang
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health System, La Jolla, CA, United States
| | | | - Aaron M Goodman
- Division of Blood and Bone Marrow Transplant, Department of Medicine, University of California San Diego Health System, La Jolla, CA, United States
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Carolyn M Mulroney
- Division of Blood and Bone Marrow Transplant, Department of Medicine, University of California San Diego Health System, La Jolla, CA, United States
| |
Collapse
|
9
|
TBL1XR1-JAK2: a novel fusion in a pediatric T cell acute lymphoblastic leukemia patient with increased absolute eosinophil count. J Hematop 2020. [DOI: 10.1007/s12308-020-00413-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
10
|
Mannan A, Muhsen IN, Barragán E, Sanz MA, Mohty M, Hashmi SK, Aljurf M. Genotypic and Phenotypic Characteristics of Acute Promyelocytic Leukemia Translocation Variants. Hematol Oncol Stem Cell Ther 2020; 13:189-201. [PMID: 32473106 DOI: 10.1016/j.hemonc.2020.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Acute promyelocytic leukemia (APL) is a special disease entity of acute myeloid leukemia (AML). The clinical use of all-trans retinoic acid (ATRA) has transformed APL into the most curable form of AML. The majority of APL cases are characterized by the fusion gene PML-RARA. Although the PML-RARA fusion gene can be detected in almost all APL cases, translocation variants of APL have been reported. To date, this is the most comprehensive review of these translocations, discussing 15 different variants. Reviewed genes involved in APL variants include: ZBTB16, NPM, NuMA, STAT5b, PRKAR1A, FIP1L1, BCOR, NABP1, TBLR1, GTF2I, IRF2BP2, FNDC3B, ADAMDTS17, STAT3, and TFG. The genotypic and phenotypic features of APL translocations are summarized. All reported studies were either case reports or case series indicating the rarity of these entities and limiting the ability to drive conclusions regarding their characteristics. However, reported variants have shown variable clinical and morphological features, with diverse responsiveness to ATRA.
Collapse
Affiliation(s)
- Abdul Mannan
- Betsi Cadwaladr University Health Board, Bangor, UK
| | - Ibrahim N Muhsen
- Department of Medicine, Houston Methodist Hospital, Houston, TX, USA.
| | - Eva Barragán
- Department of Hematology, Hospital Universitari i Politecnic La Fe, Valencia, Spain; Department of Medicine, University of Valencia, Valencia, Spain; Centro de Investigación Biomédica en Red de Cáncer, Instituto Carlos III, Madrid, Spain
| | - Miguel A Sanz
- Department of Hematology, Hospital Universitari i Politecnic La Fe, Valencia, Spain; Department of Medicine, University of Valencia, Valencia, Spain; Centro de Investigación Biomédica en Red de Cáncer, Instituto Carlos III, Madrid, Spain
| | | | - Shahrukh K Hashmi
- Oncology Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mahmoud Aljurf
- Oncology Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| |
Collapse
|
11
|
Wang L, Zhao H, Zhang L, Luo H, Chen Q, Zuo X. HSP90AA1, ADRB2, TBL1XR1 and HSPB1 are chronic obstructive pulmonary disease-related genes that facilitate squamous cell lung cancer progression. Oncol Lett 2020; 19:2115-2122. [PMID: 32194709 PMCID: PMC7039115 DOI: 10.3892/ol.2020.11318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/12/2019] [Indexed: 12/28/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) and squamous cell lung carcinoma (SCC) are smoking-related diseases. However, the connection between the two is poorly understood. Microarray gene expression profiles in bronchial epithelium from patients with SCC with or without COPD were downloaded from the Gene Expression Omnibus repository. Differentially expressed genes associated with COPD and SCC were identified and visualized using the Advanced Network Merger module in Cytoscape. COPD-associated genes in SCC progression were further identified using the BisoGenet plug-in in Cytoscape. The genetic interaction network was predicted using the Network Analysis function. Heat shock protein 90 α family class A member 1 (HSP90AA1), adrenoceptor β2 (ADRB2), transducin β like 1 X-linked receptor 1 (TBL1XR1) and heat shock protein family B (small) member 1 (HSPB1) were identified to be differentially expressed in SCC and COPD cases. The overall survival rate associated with the gene signatures was investigated using clinical samples from patients with SCC and COPD from the PROGgene database. The results suggest that the pathogenesis of SCC caused by COPD is regulated by HSP90AA1, ADRB2, TBL1XR1 and HSPB1. These genes may serve as potential therapeutic targets for the treatment of patients with COPD-related SCC.
Collapse
Affiliation(s)
- Lijing Wang
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hongjun Zhao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Lemeng Zhang
- Department of Thoracic Oncology, Hunan Cancer Hospital, Central South University, Changsha, Hunan 410008, P.R. China.,Department of Thoracic Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Qiong Chen
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| |
Collapse
|
12
|
Peterson JF, Pearce KE, Meyer RG, Greipp PT, Knudson RA, Baughn LB, Ketterling RP, Feldman AL. Fluorescence in-situ hybridisation for TP63 rearrangements in T cell lymphomas: single-site experience of 470 patients and implications for clinical testing. Histopathology 2020; 76:481-485. [PMID: 31557339 DOI: 10.1111/his.14005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/15/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022]
Abstract
AIMS The aims of this study were to review our 5-year experience with clinical FISH testing for TP63 rearrangements using both TP63 break-apart (BAP) and TBL1XR1/TP63 dual-fusion (D-FISH) probes to evaluate the frequency of TP63 rearrangements and the distribution of TBL1XR1 vs. alternate partner loci, and to assess whether both probe sets are necessary in all cases undergoing FISH testing. METHODS AND RESULTS A retrospective review of the Mayo Clinic cytogenetic database identified 470 patients evaluated by FISH testing for TP63 rearrangements in formalin-fixed paraffin-embedded (FFPE) tissue using both BAP and D-FISH probes. Of these, 25 (5.3%) had TP63 rearrangements. All samples were being investigated for anaplastic large-cell lymphoma or other T cell lymphoma subtypes. A TBL1XR1 partner was identified by D-FISH in 12 (48%) of 25 cases. All cases positive by TBL1XR1/TP63 D-FISH were also positive by TP63 BAP FISH. CONCLUSION This is the largest series of TP63 rearrangements to date. The frequency of positive results among cases referred to a large reference laboratory for TP63 FISH testing was 5.3%. Approximately half of TP63 rearrangements have a TBL1XR1 partner. TP63 BAP FISH testing is sufficient for up-front testing of FFPE tissue samples. However, because of the genomic proximity of the TP63 and TBL1XR1 loci, we recommend reflex TBL1XR1/TP63 D-FISH testing in positive and equivocal cases.
Collapse
Affiliation(s)
- Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Knudson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
13
|
Hapgood G, Ben-Neriah S, Mottok A, Lee DG, Robert K, Villa D, Sehn LH, Connors JM, Gascoyne RD, Feldman AL, Farinha P, Steidl C, Scott DW, Slack GW, Savage KJ. Identification of high-risk DUSP22-rearranged ALK-negative anaplastic large cell lymphoma. Br J Haematol 2019; 186:e28-e31. [PMID: 30873584 PMCID: PMC7679007 DOI: 10.1111/bjh.15860] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Greg Hapgood
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| | - Susana Ben-Neriah
- Department of Lymphoid Cancer Research, BC Cancer Centre for Lymphoid Cancer, Vancouver, Canada
| | - Anja Mottok
- Department of Lymphoid Cancer Research, BC Cancer Centre for Lymphoid Cancer, Vancouver, Canada
| | - Derrick G Lee
- Cancer Control Research, BC Cancer Research Center and Department of Math, Statistics and Computational Science, St. Francis Xavier University, Antigonish, Canada
| | - Kridel Robert
- Department of Lymphoid Cancer Research, BC Cancer Centre for Lymphoid Cancer, Vancouver, Canada
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Diego Villa
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| | - Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| | - Joseph M Connors
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| | - Randy D Gascoyne
- BC Cancer Centre for Lymphoid Cancer and the Department of Pathology, Vancouver, Canada
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer and the Department of Pathology, Vancouver, Canada
| | - Christian Steidl
- Department of Lymphoid Cancer Research, BC Cancer Centre for Lymphoid Cancer, Vancouver, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer and the Department of Pathology, Vancouver, Canada
| | - Kerry J Savage
- BC Cancer Centre for Lymphoid Cancer and the Department of Medical Oncology, Vancouver, Canada
| |
Collapse
|
14
|
Mlynarczyk C, Fontán L, Melnick A. Germinal center-derived lymphomas: The darkest side of humoral immunity. Immunol Rev 2019; 288:214-239. [PMID: 30874354 PMCID: PMC6518944 DOI: 10.1111/imr.12755] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 02/06/2023]
Abstract
One of the unusual features of germinal center (GC) B cells is that they manifest many hallmarks of cancer cells. Accordingly, most B-cell neoplasms originate from the GC reaction, and characteristically display abundant point mutations, structural genomic lesions, and clonal diversity from the genetic and epigenetic standpoints. The dominant biological theme of GC-derived lymphomas is mutation of genes involved in epigenetic regulation and immune receptor signaling, which come into play at critical transitional stages of the GC reaction. Hence, mechanistic studies of these mutations reveal fundamental insight into the biology of the normal and malignant GC B cell. The BCL6 transcription factor plays a central role in establishing the GC phenotype in B cells, and most lymphomas are dependent on BCL6 to maintain survival, proliferation, and perhaps immune evasion. Many lymphoma mutations have the commonality of enhancing the oncogenic functions of BCL6, or overcoming some of its tumor suppressive effects. Herein, we discuss how unique features of the GC reaction create vulnerabilities that select for particular lymphoma mutations. We examine the interplay between epigenetic programming, metabolism, signaling, and immune regulatory mechanisms in lymphoma, and discuss how these are leading to novel precision therapy strategies to treat lymphoma patients.
Collapse
Affiliation(s)
- Coraline Mlynarczyk
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Lorena Fontán
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Ari Melnick
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| |
Collapse
|
15
|
Jacobsen ED, Weinstock DM. Challenges and implications of genomics for T-cell lymphomas. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2018; 2018:63-68. [PMID: 30504292 PMCID: PMC6246015 DOI: 10.1182/asheducation-2018.1.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Treatment outcomes for patients with peripheral T-cell lymphomas (PTCLs) and advanced-stage cutaneous T-cell lymphomas (CTCLs) remain poor. The past few years have witnessed an explosion in our understanding of the genetics of these diverse malignancies. Many subtypes harbor highly recurrent mutations, including single-nucleotide variants, insertions/deletions, and chromosomal rearrangements, that affect T-cell receptor signaling, costimulatory molecules, JAK/STAT and phosphatidylinositol 3-kinase pathways, transcription factors, and epigenetic modifiers. An important subset of these mutations is included within commercially available, multigene panels and, in rare circumstances, indicate therapeutic targets. However, current preclinical and clinical evidence suggests that only a minority of mutations identified in TCLs indicate biologic dependence. With a few exceptions that we highlight, mutations identified in TCLs should not be routinely used to select targeted therapies outside of a clinical trial. Participation in trials and publication of both positive and negative results remain the most important mechanisms for improving patient outcomes.
Collapse
MESH Headings
- Genomics/methods
- Humans
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Lymphoma, T-Cell, Peripheral/therapy
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/genetics
Collapse
Affiliation(s)
- Eric D. Jacobsen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA; and
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA; and
- Broad Institute of MIT and Harvard, Cambridge, MA
| |
Collapse
|
16
|
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun 2018; 9:4001. [PMID: 30275490 PMCID: PMC6167379 DOI: 10.1038/s41467-018-06354-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3′ UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics. The driver mutations for the two main molecular subgroups of diffuse large B-cell lymphoma (DLBCL) are poorly defined. Here, an integrative genomics analysis identifies 3′ UTR NFKBIZ mutations within the activated B-cell DLBCL subgroup and small FCGR2B amplifications in the germinal centre B-cell DLBCL subgroup.
Collapse
|
17
|
Hyeon J, Lee B, Shin SH, Yoo HY, Kim SJ, Kim WS, Park WY, Ko YH. Targeted deep sequencing of gastric marginal zone lymphoma identified alterations of TRAF3 and TNFAIP3 that were mutually exclusive for MALT1 rearrangement. Mod Pathol 2018; 31:1418-1428. [PMID: 29765142 DOI: 10.1038/s41379-018-0064-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 11/10/2022]
Abstract
Gastric extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue is a distinct entity in that Helicobacter pylori infection plays the most important causative role in the development of the disease. To investigate the genomic alteration in gastric marginal zone lymphoma that was resistant to the H. pylori eradication therapy, we analyzed 19 cases of the gastric marginal zone lymphoma using fluorescence in situ hybridization for MALT1, BCL10 rearrangement, and targeted sequencing using an Illumina platform. Major genetic alterations affected genes involved in nuclear factor (NF)-κB pathway activation and included MALT1 rearrangement (39%), and somatic mutations of TRAF3 (21%), TNFAIP3 (16%), and NOTCH1 (16%). In the MALT1 rearrangement-negative group, disruptive somatic mutations of TRAF3 were the most common alterations (4/12, 33%), followed by somatic mutations of TNFAIP3 (3/12, 25%), and NOTCH1 (3/12, 25%). The present study confirms that genes involved in activation of NF-κB-signaling pathways are a major driver in oncogenesis of H. pylori eradication-resistant gastric marginal zone lymphoma and revealed that TRAF3 mutation is a major contributor in MALT1 rearrangement-negative gastric marginal zone lymphoma.
Collapse
Affiliation(s)
- Jiyeon Hyeon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Lee
- Samsung Genome Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - So-Hyun Shin
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hae Yong Yoo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Seok Jin Kim
- Division of hematology-oncology, Department of Internal medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Seog Kim
- Division of hematology-oncology, Department of Internal medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea.
| | - Young-Hyeh Ko
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|
18
|
Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med 2018; 24:679-690. [PMID: 29713087 DOI: 10.1038/s41591-018-0016-8] [Citation(s) in RCA: 1161] [Impact Index Per Article: 193.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B cell (ABC) and germinal center B cell (GCB) subtypes. We carried out a comprehensive genetic analysis of 304 primary DLBCLs and identified low-frequency alterations, captured recurrent mutations, somatic copy number alterations, and structural variants, and defined coordinate signatures in patients with available outcome data. We integrated these genetic drivers using consensus clustering and identified five robust DLBCL subsets, including a previously unrecognized group of low-risk ABC-DLBCLs of extrafollicular/marginal zone origin; two distinct subsets of GCB-DLBCLs with different outcomes and targetable alterations; and an ABC/GCB-independent group with biallelic inactivation of TP53, CDKN2A loss, and associated genomic instability. The genetic features of the newly characterized subsets, their mutational signatures, and the temporal ordering of identified alterations provide new insights into DLBCL pathogenesis. The coordinate genetic signatures also predict outcome independent of the clinical International Prognostic Index and suggest new combination treatment strategies. More broadly, our results provide a roadmap for an actionable DLBCL classification.
Collapse
|
19
|
Amin AD, Peters TL, Li L, Rajan SS, Choudhari R, Puvvada SD, Schatz JH. Diffuse large B-cell lymphoma: can genomics improve treatment options for a curable cancer? Cold Spring Harb Mol Case Stud 2017; 3:a001719. [PMID: 28487884 PMCID: PMC5411687 DOI: 10.1101/mcs.a001719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gene-expression profiling and next-generation sequencing have defined diffuse large B-cell lymphoma (DLBCL), the most common lymphoma diagnosis, as a heterogeneous group of subentities. Despite ongoing explosions of data illuminating disparate pathogenic mechanisms, however, the five-drug chemoimmunotherapy combination R-CHOP remains the frontline standard treatment. This has not changed in 15 years, since the anti-CD20 monoclonal antibody rituximab was added to the CHOP backbone, which first entered use in the 1970s. At least a third of patients are not cured by R-CHOP, and relapsed or refractory DLBCL is fatal in ∼90%. Targeted small-molecule inhibitors against distinct molecular pathways activated in different subgroups of DLBCL have so far translated poorly into the clinic, justifying the ongoing reliance on R-CHOP and other long-established chemotherapy-driven combinations. New drugs and improved identification of biomarkers in real time, however, show potential to change the situation eventually, despite some recent setbacks. Here, we review established and putative molecular drivers of DLBCL identified through large-scale genomics, highlighting among other things the care that must be taken when differentiating drivers from passengers, which is influenced by the promiscuity of activation-induced cytidine deaminase. Furthermore, we discuss why, despite having so much genomic data available, it has been difficult to move toward personalized medicine for this umbrella disorder and some steps that may be taken to hasten the process.
Collapse
Affiliation(s)
- Amit Dipak Amin
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Tara L Peters
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Lingxiao Li
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soumya Sundara Rajan
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Ramesh Choudhari
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soham D Puvvada
- Department of Medicine, Division of Hematology-Oncology, University of Arizona Comprehensive Cancer Center, Tucson, Arizona 85719, USA
| | - Jonathan H Schatz
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| |
Collapse
|
20
|
Rosenquist R, Beà S, Du MQ, Nadel B, Pan-Hammarström Q. Genetic landscape and deregulated pathways in B-cell lymphoid malignancies. J Intern Med 2017. [PMID: 28631441 DOI: 10.1111/joim.12633] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the introduction of next-generation sequencing, the genetic landscape of the complex group of B-cell lymphoid malignancies has rapidly been unravelled in recent years. This has provided important information about recurrent genetic events and identified key pathways deregulated in each lymphoma subtype. In parallel, there has been intense search and development of novel types of targeted therapy that 'hit' central mechanisms in lymphoma pathobiology, such as BTK, PI3K or BCL2 inhibitors. In this review, we will outline the current view of the genetic landscape of selected entities: follicular lymphoma, diffuse large B-cell lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and marginal zone lymphoma. We will detail recurrent alterations affecting important signalling pathways, that is the B-cell receptor/NF-κB pathway, NOTCH signalling, JAK-STAT signalling, p53/DNA damage response, apoptosis and cell cycle regulation, as well as other perhaps unexpected cellular processes, such as immune regulation, cell migration, epigenetic regulation and RNA processing. Whilst many of these pathways/processes are commonly altered in different lymphoid tumors, albeit at varying frequencies, others are preferentially targeted in selected B-cell malignancies. Some of these genetic lesions are either involved in disease ontogeny or linked to the evolution of each disease and/or specific clinicobiological features, and some of them have been demonstrated to have prognostic and even predictive impact. Future work is especially needed to understand the therapy-resistant disease, particularly in patients treated with targeted therapy, and to identify novel targets and therapeutic strategies in order to realize true precision medicine in this clinically heterogeneous patient group.
Collapse
Affiliation(s)
- R Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - S Beà
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), CIBER de Cáncer, Barcelona, Spain
| | - M-Q Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - B Nadel
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | - Q Pan-Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
| |
Collapse
|
21
|
MicroRNA profile for health risk assessment: Environmental exposure to persistent organic pollutants strongly affects the human blood microRNA machinery. Sci Rep 2017; 7:9262. [PMID: 28835693 PMCID: PMC5569060 DOI: 10.1038/s41598-017-10167-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 08/04/2017] [Indexed: 12/24/2022] Open
Abstract
Persistent organic pollutants (POPs) are synthetic chemical substances that accumulate in our environment. POPs such as polychlorinated biphenyls (PCBs), hexachlorobenzene (HCB) and dichlorodiphenyltrichloroethane (DDT) have been classified as carcinogenic to humans and animals. Due to their resistance to biodegradation humans are still exposed to these compounds worldwide. We aim to evaluate the miRNA and transcriptomic response of a human population exposed to POPs. The miRNA and transcriptomic response was measured in blood of healthy subjects by microarray technology and associated with the serum concentrations of six PCB congeners, DDE (a common DDT metabolite), and HCB. A total of 93 miRNA levels appeared significantly associated with the POP-exposure (FDR < 0.05). The miRNA profile includes four tumor suppressor miRNAs, namely miR-193a-3p, miR-152, miR-31-5p and miR-34a-5p. Integration of the miRNA profile with the transcriptome profile suggests an interaction with oncogenes such as MYC, CCND1, BCL2 and VEGFA. We have shown that exposure to POPs is associated with human miRNA and transcriptomic responses. The identified miRNAs and target genes are related to various types of cancer and involved in relevant signaling pathways like wnt and p53. Therefore, these miRNAs may have great potential to contribute to biomarker-based environmental health risk assessment.
Collapse
|
22
|
The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP. Oncotarget 2017; 8:17038-17049. [PMID: 28152507 PMCID: PMC5370020 DOI: 10.18632/oncotarget.14928] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022] Open
Abstract
Ocular marginal zone lymphoma is a common type of low-grade B-cell lymphoma. To investigate the genomic changes that occur in ocular marginal zone lymphoma, we analyzed 10 cases of ocular marginal zone lymphoma using whole-genome and RNA sequencing and an additional 38 cases using targeted sequencing. Major genetic alterations affecting genes involved in nuclear factor (NF)-κB pathway activation (60%), chromatin modification and transcriptional regulation (44%), and B-cell differentiation (23%) were identified. In whole-genome sequencing, the 6q23.3 region containing TNFAIP3 was deleted in 5 samples (50%). In addition, 5 structural variation breakpoints in the first intron of IL20RA located in the 6q23.3 region was found in 3 samples (30%). In targeted sequencing, a disruptive mutation of TNFAIP3 was the most common alteration (54%), followed by mutations of TBL1XR1 (18%), cAMP response element binding proteins (CREBBP) (17%) and KMT2D (6%). All TBL1XR1 mutations were located within the WD40 domain, and TBL1XR1 mutants transfected into 293T cells increased TBL1XR1 binding with nuclear receptor corepressor (NCoR), leading to increased degradation of NCoR and the activation of NF-κB and JUN target genes. This study confirms genes involving in the activation of the NF-kB signaling pathway is the major driver in the oncogenesis of ocular MZL.
Collapse
|
23
|
Fang X, Xiu B, Yang Z, Qiu W, Zhang L, Zhang S, Wu Y, Zhu X, Chen X, Xie S, Yi X, Liang A, Zeng Y. The expression and clinical relevance of PD-1, PD-L1, and TP63 in patients with diffuse large B-cell lymphoma. Medicine (Baltimore) 2017; 96:e6398. [PMID: 28403071 PMCID: PMC5403068 DOI: 10.1097/md.0000000000006398] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Latest study showed that a novel translocation between programmed cell death ligand 1 (PD-L1) (cluster of differentiation 274) and TP63 (tumor protein 63) can be found in diffuse large B-cell lymphoma (DLBCL), resulting in their conjunct overexpression in tumor cells at RNA level. However, the expressed pattern of these 2 genes at protein level in DLBCL remains largely unknown, and the clinical relevance of PD-L1 and TP63 expression in DLBCL are also unclear.Tumor tissues from 76 Chinese DLBCL patients were immunostained for programmed cell death 1 (PD-1), PD-L1, and TP63 using the EnVision system. Clinical relevance of PD-1, PD-L1, and TP63 in 74 DLBCL were analyzed by chi-square test, the Kaplan-Meier curves with log rank test, and Cox's proportional hazards regression model.PD-1 was mainly expressed in tumor-infiltrating lymphocytes (TILs) of 39.5% patients. PD-L1 was expressed in tumor cells of 26.3% patients, and TP63 was immunostained in nucleoli of tumor cells of 31.6% cases. PD-1 expression was significantly associated with the patients' gender and B symptoms (P = 0.032, P = 0.026). DLBCL with PD-L1 or TP63 expression in tumor cells showed low International Prognostic Index (IPI) score (P = 0.007, P = 0.009). PD-1 TILs was related to prolonged overall survival rate (OS) of DLBCL patients (P = 0.02), whereas PD-L1 expression was associated with worse clinical outcome of patients (P = 0.049). Immunoreactivity of TP63 was not correlated with patients' survival time. Besides, PD-1 expression, patients' age, Ann Arbor stage, and IPI score were significant prognostic markers for OS, but PD-L1 and TP63 had no prognostic significance.PD-1, PD-L1, and TP63 are frequently expressed in DLBCL. PD-1/PD-L1/TP63 blockade may be a potential therapeutic strategy for some patients.
Collapse
MESH Headings
- Adult
- Age Factors
- Aged
- Aged, 80 and over
- Asian People/genetics
- B7-H1 Antigen/metabolism
- Biomarkers, Tumor/genetics
- Chi-Square Distribution
- China
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Kaplan-Meier Estimate
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Male
- Middle Aged
- Neoplasm Staging
- Prognosis
- Programmed Cell Death 1 Receptor/metabolism
- Proportional Hazards Models
- Severity of Illness Index
- Survival Rate
- Transcription Factors/metabolism
- Treatment Outcome
- Tumor Suppressor Proteins/metabolism
Collapse
Affiliation(s)
| | | | - Zhizhang Yang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN
| | - Weizhe Qiu
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Long Zhang
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Suxia Zhang
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yunjin Wu
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuyou Zhu
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue Chen
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Suhong Xie
- Department of Laboratory, Shanghai Zhongliu Hospital, Shanghai Fudan University School of Medicine, Shanghai, China
| | - Xianghua Yi
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Yu Zeng
- Deparment of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
24
|
Abstract
Diffuse large B-cell lymphoma (DLBCL) is divided into germinal center B-like (GCB) DLBCL and activated B-like (ABC) DLBCL. In recent years, whole genome sequencing (WGS), whole exome sequencing (WES), and transcriptome sequencing (RNA-seq) have been performed for samples from many patients with DLBCL. Here, I present a review of the results of next generation sequencing data for DLBCL. Somatic mutations show a low identity between studies with only 10-20% gene overlap. DLBCL is a disease that results from various molecular pathogeneses. Mutations in genes involved in chromatin remodeling were found in the GCB subtype. Mutations in members of B-cell receptor (BCR) signaling and the NF-κB pathway (MYD88) were found in the ABC subtype. The MYD88 L265P mutation was observed in 29% of ABC DLBCL cases. EZH2 mutations were observed in 21.7% of GCB DLBCL cases. WGS indicated that inactivating mutations in GNA13 (Gα protein) were prevalent in GCB DLBCL cases. In addition, S1PR2 is a target of aberrant somatic hypermutation. In recent years, samples from patients with relapsed and refractory DLBCL were analyzed. The activation of the NF-κB pathway is associated with treatment resistance in DLBCL. Further clarification of the molecular pathogenesis of DLBCL is expected to lead to the development of individualized treatment for the disease.
Collapse
Affiliation(s)
- Akito Dobashi
- Pathology Project for Molecular Targets, The Cancer Institute, Japanese Foundation for Cancer Research
| |
Collapse
|
25
|
Expression of p63 protein in anaplastic large cell lymphoma: implications for genetic subtyping. Hum Pathol 2017; 64:19-27. [PMID: 28153507 DOI: 10.1016/j.humpath.2017.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/28/2016] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
Abstract
Anaplastic large cell lymphomas (ALCLs) are CD30-positive T-cell non-Hodgkin lymphomas that bear chromosomal rearrangements of the TP53 homologue TP63 in a subset of cases that demonstrate aggressive clinical behavior. In the present study, we examined the relationship between p63 protein expression by immunohistochemistry and the results of fluorescence in situ hybridization using TP63 probes in 116 ALCLs. We also determined the relative expression of full-length TAp63 and truncated ΔNp63 isoforms (eg, p40) in ALCL cell lines and a subset of clinical cases. Overall, 35.3% of ALCLs were positive for p63 protein. Primary cutaneous and anaplastic lymphoma kinase-negative ALCLs were positive more frequently than anaplastic lymphoma kinase-positive ALCLs (P=.0034). As previously reported, cases with TP63 gene rearrangements expressed p63 uniformly. p63 expression in nonrearranged cases was associated with extra copies of TP63 on 3q28 (P<.0001). Extra copies of TP63 correlated with extra copies of the DUSP22 locus on 6p25.3 (P<.0001). Results of immunohistochemistry, Western blotting, and RNA sequencing indicated that p63 expression in nonrearranged cases was entirely attributable to TAp63 isoforms. Taken together, these findings indicate that ALCLs without TP63 rearrangements may express TAp63 isoforms of p63 and that this expression is associated with extra copies of TP63, probably due to widespread genomic copy number abnormalities rather than focal gains. Immunohistochemistry for p63 in ALCL is not specific for TP63 rearrangements but is useful clinically as a screening test to select cases for further testing by fluorescence in situ hybridization. Immunohistochemistry for ΔNp63 (p40) is not informative in the evaluation of ALCL.
Collapse
|
26
|
p63 expression confers significantly better survival outcomes in high-risk diffuse large B-cell lymphoma and demonstrates p53-like and p53-independent tumor suppressor function. Aging (Albany NY) 2016; 8:345-65. [PMID: 26878872 PMCID: PMC4789587 DOI: 10.18632/aging.100898] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The role of p53 family member, p63 in oncogenesis is the subject of controversy. Limited research has been done on the clinical implications of p63 expression in diffuse large B-cell lymphoma (DLBCL). In this study, we assessed p63 expression in de novo DLBCL samples (n=795) by immunohistochemistry with a pan-p63-monoclonal antibody and correlated it with other clinicopathologic factors and clinical outcomes. p63 expression was observed in 42.5% of DLBCL, did not correlate with p53 levels, but correlated with p21, MDM2, p16INK4A, Ki-67, Bcl-6, IRF4/MUM-1 and CD30 expression, REL gains, and BCL6 translocation. p63 was an independent favorable prognostic factor in DLBCL, which was most significant in patients with International Prognostic Index (IPI) >2, and in activated-B-cell–like DLBCL patients with wide-type TP53. The prognostic impact in germinal-center-B-cell–like DLBCL was not apparent, which was likely due to the association of p63 expression with high-risk IPI, and potential presence of ∆Np63 isoform in TP63 rearranged patients (a mere speculation). Gene expression profiling suggested that p63 has both overlapping and distinct functions compared with p53, and that p63 and mutated p53 antagonize each other. In summary, p63 has p53-like and p53-independent functions and favorable prognostic impact, however this protective effect can be abolished by TP53 mutations.
Collapse
|
27
|
Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas. Blood 2016; 127:3026-34. [DOI: 10.1182/blood-2015-12-686550] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/17/2016] [Indexed: 12/16/2022] Open
Abstract
Key Points
Translocations between PD-L1 and the IGH locus represent a genetic mechanism of PD-L1 overexpression in DLBCL. Genetic alterations in the PD-L1/PDL-2 locus are mainly associated with the non-GCB subtype of DLBCL.
Collapse
|
28
|
Dubois S, Jardin F. The role of next-generation sequencing in understanding the genomic basis of diffuse large B cell lymphoma and advancing targeted therapies. Expert Rev Hematol 2016; 9:255-69. [PMID: 26652775 DOI: 10.1586/17474086.2016.1130616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Next Generation Sequencing (NGS) has redefined the genetic landscape of Diffuse Large B-Cell Lymphoma (DLBCL) by identifying recurrent somatic mutations. Importantly, in some cases these mutations impact potentially actionable targets, thus affording novel personalized therapy opportunities. At the forefront of today's precision therapy era, how to best incorporate NGS into daily clinical practice is of primordial concern, in order to tailor patient's treatment regimens according to their individual mutational profiles. With the advent of cell-free DNA sequencing, which provides a sensitive and less invasive means of monitoring DLBCL patients, the clinical feasibility of NGS has been greatly improved. This article reviews the current landscape of DLBCL mutations, as well as the targeted therapies developed to counter their effects, and discusses how best to utilize NGS data for treatment decision-making.
Collapse
Affiliation(s)
- Sydney Dubois
- a Inserm U918, Centre Henri Becquerel , Université de Rouen, IRIB , Rouen , France
| | - Fabrice Jardin
- a Inserm U918, Centre Henri Becquerel , Université de Rouen, IRIB , Rouen , France.,b Department of Hematology , Centre Henri Becquerel , Rouen , France
| |
Collapse
|
29
|
Panagopoulos I, Gorunova L, Bjerkehagen B, Lobmaier I, Heim S. Fusion of the TBL1XR1 and HMGA1 genes in splenic hemangioma with t(3;6)(q26;p21). Int J Oncol 2015; 48:1242-50. [PMID: 26708416 PMCID: PMC4750536 DOI: 10.3892/ijo.2015.3310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/26/2015] [Indexed: 11/06/2022] Open
Abstract
RNA-sequencing of a splenic hemangioma with the karyotype 45~47,XX,t(3;6)(q26;p21) showed that this translocation generated a chimeric TBL1XR1-HMGA1 gene. This is the first time that this tumor has been subjected to genetic analysis, but the finding of an acquired clonal chromosome abnormality in cells cultured from the lesion and the presence of the TBL1XR1-HMGA1 fusion in them strongly favor the conclusion that splenic hemangiomas are of a neoplastic nature. Genomic PCR confirmed the presence of the TBL1XR1-HMGA1 fusion gene, and RT-PCR together with Sanger sequencing verified the presence of the fusion transcripts. The molecular consequences of the t(3;6) would be substantial. The cells carrying the translocation would retain only one functional copy of the wild-type TBL1XR1 gene while the other, rearranged allele could produce a putative truncated form of TBL1XR1 protein containing the LiSH and F-box-like domains. In the TBL1XR1-HMGA1 fusion transcript, furthermore, untranslated exons of HMGA1 are replaced by the first 5 exons of the TBL1XR1 gene. The result is that the entire coding region of HMGA1 comes under the control of the TBL1XR1 promoter, bringing about dysregulation of HMGA1. This is reminiscent of similar pathogenetic mechanisms involving high mobility genes in benign connective tissue tumors such as lipomas and leiomyomas.
Collapse
Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ingvild Lobmaier
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
30
|
Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements. PLoS One 2015; 10:e0139360. [PMID: 26422229 PMCID: PMC4589387 DOI: 10.1371/journal.pone.0139360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/10/2015] [Indexed: 11/19/2022] Open
Abstract
Though numerous polymorphisms have been associated with risk of developing lymphoma, how these variants function to promote tumorigenesis is poorly understood. Here, we report that lymphoma risk SNPs, especially in the non-Hodgkin's lymphoma subtype chronic lymphocytic leukemia, are significantly enriched for co-localization with epigenetic marks of active gene regulation. These enrichments were seen in a lymphoid-specific manner for numerous ENCODE datasets, including DNase-hypersensitivity as well as multiple segmentation-defined enhancer regions. Furthermore, we identify putatively functional SNPs that are both in regulatory elements in lymphocytes and are associated with gene expression changes in blood. We developed an algorithm, UES, that uses a Monte Carlo simulation approach to calculate the enrichment of previously identified risk SNPs in various functional elements. This multiscale approach integrating multiple datasets helps disentangle the underlying biology of lymphoma, and more broadly, is generally applicable to GWAS results from other diseases as well.
Collapse
|
31
|
Abstract
Germinal centres (GCs) are involved in the selection of B cells secreting high-affinity antibodies and are also the origin of most human B cell lymphomas. Recent progress has been made in identifying the functionally relevant stages of the GC and the complex trafficking mechanisms of B cells within the GC. These studies have identified transcription factors and signalling pathways that regulate distinct phases of GC development. Notably, these factors and pathways are hijacked during tumorigenesis, as revealed by analyses of the genetic lesions associated with various types of B cell lymphomas. This Review focuses on recent insights into the mechanisms that regulate GC development and that are relevant for human B cell lymphomagenesis.
Collapse
Affiliation(s)
- Katia Basso
- 1] Institute for Cancer Genetics, Columbia University. [2] Department of Pathology and Cell Biology, Columbia University
| | - Riccardo Dalla-Favera
- 1] Institute for Cancer Genetics, Columbia University. [2] Department of Pathology and Cell Biology, Columbia University. [3] Department of Genetics and Development, Columbia University. [4] Department of Microbiology and Immunology, Columbia University. [5] The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| |
Collapse
|
32
|
Li JY, Daniels G, Wang J, Zhang X. TBL1XR1 in physiological and pathological states. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2015; 3:13-23. [PMID: 26069883 PMCID: PMC4446378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Transducin (beta)-like 1X related protein 1 (TBL1XR1/TBLR1) is an integral subunit of the NCoR (nuclear receptor corepressor) and SMRT (silencing mediator of retinoic acid and thyroid hormone receptors) repressor complexes. It is an evolutionally conserved protein that shares high similarity across all species. TBL1XR1 is essential for transcriptional repression mediated by unliganded nuclear receptors (NRs) and othe regulated transcription factors (TFs). However, it can also act as a transcription activator through the recruitment of the ubiquitin-conjugating/19S proteasome complex that mediates the exchange of corepressors for coactivators. TBL1XR1 is required for the activation of multiple intracellular signaling pathways. TBL1XR1 germline mutations and recurrent mutations are linked to intellectual disability. Upregulation of TBL1XR1 is observed in a variety of solid tumors, which is associated with advanced tumor stage, metastasis and poor prognosis. A variety of genomic alterations, such as translocation, deletion and mutation have been identified in many types of neoplasms. Loss of TBL1XR1 in B-lymphoblastic leukemia disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance. However, the mechanisms of other types of genomic changes in tumorogenesis are still not clear. A pre-clinical study has shown that the disruption of the interaction between TBL1X and β-catenin using a small molecule can inhibit the growth of AML stem and blast cells both in vitro and in vivo. These findings shed light on the therapeutic potentials of targeting TBL1XR1 related proteins in cancer treatment.
Collapse
Affiliation(s)
- Jian Yi Li
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| | - Garrett Daniels
- Department of Pathology, New York University School of MedicineNew York, USA
| | - Jing Wang
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| | - Xinmin Zhang
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| |
Collapse
|
33
|
[The progress of diagnostic and prognostic molecular markers of lymphoma]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2015; 36:354-7. [PMID: 25916304 PMCID: PMC7342629 DOI: 10.3760/cma.j.issn.0253-2727.2015.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
34
|
Twa DDW, Mottok A, Chan FC, Ben-Neriah S, Woolcock BW, Tan KL, Mungall AJ, McDonald H, Zhao Y, Lim RS, Nelson BH, Milne K, Shah SP, Morin RD, Marra MA, Scott DW, Gascoyne RD, Steidl C. Recurrent genomic rearrangements in primary testicular lymphoma. J Pathol 2015; 236:136-41. [DOI: 10.1002/path.4522] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/05/2015] [Accepted: 02/18/2015] [Indexed: 02/06/2023]
Affiliation(s)
- David DW Twa
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
| | - Anja Mottok
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
| | - Fong Chun Chan
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Bioinformatics Training Programme; University of British Columbia; Vancouver BC Canada
| | - Susana Ben-Neriah
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
| | - Bruce W Woolcock
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
| | - King L Tan
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
| | - Andrew J Mungall
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver BC Canada
| | - Helen McDonald
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver BC Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver BC Canada
| | - Raymond S Lim
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
| | - Brad H Nelson
- Deeley Research Centre; BC Cancer Agency; Victoria BC Canada
- Department of Medical Genetics; University of British Columbia; Vancouver BC Canada
| | - Katy Milne
- Deeley Research Centre; BC Cancer Agency; Victoria BC Canada
| | - Sohrab P Shah
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Bioinformatics Training Programme; University of British Columbia; Vancouver BC Canada
| | - Ryan D Morin
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Department of Molecular Biology and Biochemistry; Simon Fraser University; Vancouver BC Canada
| | - Marco A Marra
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver BC Canada
| | - David W Scott
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
| | - Randy D Gascoyne
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
| | - Christian Steidl
- Department of Lymphoid Cancer Research; BC Cancer Agency; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
| |
Collapse
|
35
|
Chromosomal rearrangements and copy number abnormalities of TP63 correlate with p63 protein expression in lung adenocarcinoma. Mod Pathol 2015; 28:359-66. [PMID: 25189640 DOI: 10.1038/modpathol.2014.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 07/14/2014] [Accepted: 07/30/2014] [Indexed: 01/09/2023]
Abstract
The TP63 gene encodes a member of the p53 family of transcription factors. Although TP53 is a well-known tumor suppressor gene, the role of p63 in tumorigenesis is controversial. Our group recently identified novel chromosomal rearrangements involving TP63 in approximately 6% of peripheral T-cell lymphomas, which correlated with a p63+/p40- immunohistochemical profile. As a subset of lung adenocarcinomas are p63+/p40-, we undertook the current study to examine the presence of TP63 rearrangements and correlate with p63/p40 expression. Next-generation sequencing was used to identify genomic rearrangements of TP63 in 37 adenocarcinomas. Confirmatory fluorescence in-situ hybridization (FISH) using a break-apart probe to the TP63 gene region and immunohistochemistry for p63 and p40 were performed on adenocarcinomas with TP63 rearrangements identified by mate-pair sequencing. Immunohistochemistry for p63 and p40 was performed on 45 additional adenocarcinomas, and FISH was performed on all adenocarcinomas with p63 positivity. TP63 rearrangement was identified in two adenocarcinoma specimens from a single patient. The rearrangement resulted in a complex rearrangement of 3q that fused B3GALNT1 at the 3' intron to TP63. FISH confirmed the rearrangement in both tumors. Immunohistochemistry staining for p63 was diffuse (>80% cells+) and p40 was negative. Of the 44 additional adenocarcinomas, 13 (30%) showed p63 expression; p40 was negative in all cases. No case showed rearrangement of TP63 by a break-apart FISH. However, extra copies of the intact TP63 locus were seen in the p63-positive areas of all 12 cases, with copy numbers ranging from three to seven. We have identified a novel chromosomal rearrangement involving TP63 in a p63+/p40- lung adenocarcinoma. Break-apart FISH testing can be used to diagnose this finding. Immunohistochemistry for p63 was not specific for this rearrangement, as nearly 33% of adenocarcinomas expressed p63. Additional copies of the intact TP63 locus were also a common finding and correlated with immunohistochemistry positivity for p63.
Collapse
|
36
|
Xing X, Feldman AL. Anaplastic large cell lymphomas: ALK positive, ALK negative, and primary cutaneous. Adv Anat Pathol 2015; 22:29-49. [PMID: 25461779 DOI: 10.1097/pap.0000000000000047] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Anaplastic large cell lymphomas (ALCLs) comprise a group of CD30-positive non-Hodgkin lymphomas that generally are of T-cell origin and share common morphologic and phenotypic characteristics. The World Health Organization recognizes 3 entities: primary cutaneous ALCL (pcALCL), anaplastic lymphoma kinase (ALK)-positive ALCL, and, provisionally, ALK-negative ALCL. Despite overlapping pathologic features, these tumors differ in clinical behavior and genetics. pcALCL presents in the skin and, while it may involve locoregional lymph nodes, rarely disseminates. Outcomes typically are excellent. ALK-positive ALCL and ALK-negative ALCL are systemic diseases. ALK-positive ALCLs consistently have chromosomal rearrangements involving the ALK gene with varied gene partners, and generally have a favorable prognosis. ALK-negative ALCLs lack ALK rearrangements and their genetic and clinical features are more variable. A subset of ALK-negative ALCLs has rearrangements in or near the DUSP22 gene and has a favorable prognosis similar to that of ALK-positive ALCL. DUSP22 rearrangements also are seen in a subset of pcALCLs. In this review, we discuss the clinical, morphologic, phenotypic, genetic, and biological features of ALCLs.
Collapse
|
37
|
Bohers E, Mareschal S, Bertrand P, Viailly PJ, Dubois S, Maingonnat C, Ruminy P, Tilly H, Jardin F. Activating somatic mutations in diffuse large B-cell lymphomas: lessons from next generation sequencing and key elements in the precision medicine era. Leuk Lymphoma 2014; 56:1213-22. [DOI: 10.3109/10428194.2014.941836] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
38
|
Shindiapina P, Brown JR, Danilov AV. A new hope: novel therapeutic approaches to treatment of chronic lymphocytic leukaemia with defects in TP53. Br J Haematol 2014; 167:149-61. [PMID: 25040077 DOI: 10.1111/bjh.13042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is an indolent B-cell malignancy with heterogeneous outcomes. Chromosomal abnormalities in CLL are predictive of the natural disease course; del(11q) and del(17p) are recognized as high risk genetic lesions. Del(17p) is associated with an impaired function of TP53, a key tumour suppressor, and is particularly problematic. Such patients respond poorly to chemo-immunotherapy and have significantly shorter survival compared to patients with standard and low-risk cytogenetics. While TP53 pathway defects are rare at initial diagnosis, their frequency increases in relapsed CLL. Until very recently, this group of patients represented an unmet clinical need with few therapeutic options. However, the advent of targeted therapies has expanded the drug armamentarium and introduced new hope for these highly refractory patients. Agents that target B-cell receptor signalling, BH3-mimetics and others induce apoptosis of the neoplastic B-cells in a TP53-independent manner. Their use in the clinic is associated with remarkable activity in patients with del(17p). In this review we discuss the frequency and clinical significance of del(17p) and genetic mutations leading to disrupted TP53, the putative role of other TP53 homologues, and the results of key clinical trials involving both conventional chemotherapy and novel agents.
Collapse
|
39
|
Carbone A, Gloghini A, Kwong YL, Younes A. Diffuse large B cell lymphoma: using pathologic and molecular biomarkers to define subgroups for novel therapy. Ann Hematol 2014; 93:1263-77. [PMID: 24870942 PMCID: PMC4082139 DOI: 10.1007/s00277-014-2116-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/19/2014] [Indexed: 12/22/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) comprises specific subtypes, disease entities, and other not otherwise specified (NOS) lymphomas. This review will focus on DLBCL NOS because of their prevalence and their heterogeneity with respect to morphology, clinical presentation, biology, and response to treatment. Gene expression profiling of DLBCL NOS has identified molecular subgroups that correlate with prognosis and may have relevance for treatment based on signaling pathways. New technologies have revealed that the "activated B cell" subgroup is linked to activation of the nuclear factor kB (NF-kB) pathway, with mutations found in CD79A/B, CARD11, and MYD88, and loss of function mutations in TNFAIP3. The "germinal center B cell-like" subgroup is linked to mutational changes in EZH2 and CREBBP. Biomarkers that are related to pathways promoting tumor cell growth and survival in DLBCL have been recognized, although their predictive role requires clinical validation. Immunohistochemistry for detecting the expression of these biomarkers is a practical technique that could provide a rational for clinical trial design.
Collapse
Affiliation(s)
- Antonino Carbone
- Department of Pathology, Centro di Riferimento Oncologico (CRO) Aviano, Istituto Nazionale Tumori, IRCCS, Via F. Gallini 2, 33081, Aviano, Italy,
| | | | | | | |
Collapse
|
40
|
TBLR1 fuses to retinoid acid receptor α in a variant t(3;17)(q26;q21) translocation of acute promyelocytic leukemia. Blood 2014; 124:936-45. [PMID: 24782508 DOI: 10.1182/blood-2013-10-528596] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The majority of acute promyelocytic leukemia (APL) cases are characterized by the PML-RARα fusion gene. Although the PML-RARα fusion gene can be detected in >98% of APL cases, RARα is also found to be fused with other partner genes, which are also related to all-trans retinoic acid (ATRA)-dependent transcriptional activity and cell differentiation. In this study, we identified a novel RARα fusion gene, TBLR1-RARα (GenBank KF589333), in a rare case of APL with a t(3;17)(q26;q21),t(7;17)(q11.2;q21) complex chromosomal rearrangement. To our knowledge, TBLR1-RARα is the 10th RARα chimeric gene that has been reported up to now. TBLR1-RARα contained the B-F domains of RARα and exhibited a distinct subcellular localization. It could form homodimers and also heterodimers with retinoid X receptor α. As a result, TBLR1-RARα exhibited diminished transcriptional activity by recruitment of more transcriptional corepressors compared with RARα. In the presence of pharmacologic doses of ATRA, TBLR1-RARα could be degraded, and its homodimerization was abrogated. Moreover, when treated with ATRA, TBLR1-RARα could mediate the dissociation and degradation of transcriptional corepressors, consequent transactivation of RARα target genes, and cell differentiation induction in a dose- and time-dependent manner.
Collapse
|
41
|
Nord KH, Lilljebjörn H, Vezzi F, Nilsson J, Magnusson L, Tayebwa J, de Jong D, Bovée JVMG, Hogendoorn PCW, Szuhai K. GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma. Nat Genet 2014; 46:474-7. [DOI: 10.1038/ng.2927] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/27/2014] [Indexed: 12/14/2022]
|
42
|
Abstract
PURPOSE OF REVIEW Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease featuring heterogeneous genetic, phenotypic, and clinical characteristics. Understanding the basis for this heterogeneity represents a critical step toward further progress in the management of this disease, which remains a clinical challenge in approximately one-third of patients. This review summarizes current knowledge about the molecular pathogenesis of DLBCL, and describes how recent advances in the genomic characterization of this cancer have provided new insights into its biology, revealing several potential targets for improved diagnosis and therapy. RECENT FINDINGS In the past few years, the development of high-resolution technologies has provided significant help in identifying genetic lesions and/or disrupted signaling pathways that are required for DLBCL initiation and progression. These studies uncovered the involvement of cellular programs that had not been previously appreciated, including histone/chromatin remodeling and immune recognition. Alterations in these pathways could favor epigenetic reprogramming and escape from cellular immunity. SUMMARY The identification of genetic alterations that contribute to the malignant transformation of a B cell into a DLBCL is helping to better understand the biology of this disease and to identify critical nodes driving tumor progression or resistance to therapy. The rapid pace at which these discoveries are taking place is poised to have significant impact for patient stratification based on molecular predictors and for the development of rational targeted therapies.
Collapse
|
43
|
Morin RD, Gascoyne RD. Newly Identified Mechanisms in B-Cell Non-Hodgkin Lymphomas Uncovered by Next-Generation Sequencing. Semin Hematol 2013; 50:303-13. [DOI: 10.1053/j.seminhematol.2013.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
44
|
Abstract
Our understanding of the pathogenesis of lymphoid malignancies has been transformed by next-generation sequencing. The studies in this review have used whole-genome, exome, and transcriptome sequencing to identify recurring structural genetic alterations and sequence mutations that target key cellular pathways in acute lymphoblastic leukemia (ALL) and the lymphomas. Although each tumor type is characterized by a unique genomic landscape, several cellular pathways are mutated in multiple tumor types-transcriptional regulation of differentiation, antigen receptor signaling, tyrosine kinase and Ras signaling, and epigenetic modifications-and individual genes are mutated in multiple tumors, notably TCF3, NOTCH1, MYD88, and BRAF. In addition to providing fundamental insights into tumorigenesis, these studies have also identified potential new markers for diagnosis, risk stratification, and therapeutic intervention. Several genetic alterations are intuitively "druggable" with existing agents, for example, kinase-activating lesions in high-risk B-cell ALL, NOTCH1 in both leukemia and lymphoma, and BRAF in hairy cell leukemia. Future sequencing efforts are required to comprehensively define the genetic basis of all lymphoid malignancies, examine the relative roles of germline and somatic variation, dissect the genetic basis of clonal heterogeneity, and chart a course for clinical sequencing and translation to improved therapeutic outcomes.
Collapse
|
45
|
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood 2013; 122:1256-65. [PMID: 23699601 DOI: 10.1182/blood-2013-02-483727] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.
Collapse
|
46
|
Abstract
Since the mapping of the human genome and the advent of next-generation sequencing technology thorough examination of the cancer genome has become a reality. Over the last few years several studies have used next-generation sequencing technology to investigate the genetic landscape of Hodgkin and non-Hodgkin lymphomas, identifying novel genetic mutations and gene rearrangements that have shed new light on the underlying tumor biology in these diseases as well as identifying possible targets for directed therapy. This review covers the major discoveries in lymphoma using next-generation sequencing technology.
Collapse
|
47
|
Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2012; 340:284-95. [PMID: 23174106 DOI: 10.1016/j.canlet.2012.11.025] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 02/06/2023]
Abstract
The advent of next generation sequencing (NGS) technologies has revolutionized the field of genomics, enabling fast and cost-effective generation of genome-scale sequence data with exquisite resolution and accuracy. Over the past years, rapid technological advances led by academic institutions and companies have continued to broaden NGS applications from research to the clinic. A recent crop of discoveries have highlighted the medical impact of NGS technologies on Mendelian and complex diseases, particularly cancer. However, the ever-increasing pace of NGS adoption presents enormous challenges in terms of data processing, storage, management and interpretation as well as sequencing quality control, which hinder the translation from sequence data into clinical practice. In this review, we first summarize the technical characteristics and performance of current NGS platforms. We further highlight advances in the applications of NGS technologies towards the development of clinical diagnostics and therapeutics. Common issues in NGS workflows are also discussed to guide the selection of NGS platforms and pipelines for specific research purposes.
Collapse
Affiliation(s)
- Jiekun Xuan
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China; National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | | | | | | | | |
Collapse
|
48
|
Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas. Blood 2012; 120:2280-9. [PMID: 22855598 DOI: 10.1182/blood-2012-03-419937] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are aggressive malignancies of mature T lymphocytes with 5-year overall survival rates of only ∼ 35%. Improvement in outcomes has been stymied by poor understanding of the genetics and molecular pathogenesis of PTCL, with a resulting paucity of molecular targets for therapy. We developed bioinformatic tools to identify chromosomal rearrangements using genome-wide, next-generation sequencing analysis of mate-pair DNA libraries and applied these tools to 16 PTCL patient tissue samples and 6 PTCL cell lines. Thirteen recurrent abnormalities were identified, of which 5 involved p53-related genes (TP53, TP63, CDKN2A, WWOX, and ANKRD11). Among these abnormalities were novel TP63 rearrangements encoding fusion proteins homologous to ΔNp63, a dominant-negative p63 isoform that inhibits the p53 pathway. TP63 rearrangements were seen in 11 (5.8%) of 190 PTCLs and were associated with inferior overall survival; they also were detected in 2 (1.2%) of 164 diffuse large B-cell lymphomas. As TP53 mutations are rare in PTCL compared with other malignancies, our findings suggest that a constellation of alternate genetic abnormalities may contribute to disruption of p53-associated tumor suppressor function in PTCL.
Collapse
|