1
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Witte H, Künstner A, Gebauer N. Update: The molecular spectrum of virus-associated high-grade B-cell non-Hodgkin lymphomas. Blood Rev 2024; 65:101172. [PMID: 38267313 DOI: 10.1016/j.blre.2024.101172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
The vast spectrum of aggressive B-cell non-Hodgkin neoplasms (B-NHL) encompasses several infrequent entities occurring in association with viral infections, posing diagnostic challenges for practitioners. In the emerging era of precision oncology, the molecular characterization of malignancies has acquired paramount significance. The pathophysiological comprehension of specific entities and the identification of targeted therapeutic options have seen rapid development. However, owing to their rarity, not all entities have undergone exhaustive molecular characterization. Considerable heterogeneity exists in the extant body of work, both in terms of employed methodologies and the scale of cases studied. Presently, therapeutic strategies are predominantly derived from observations in diffuse large B-cell lymphoma (DLBCL), the most prevalent subset of aggressive B-NHL. Ongoing investigations into the molecular profiles of these uncommon virus-associated entities are progressively facilitating a clearer distinction from DLBCL, ultimately paving the way towards individualized therapeutic approaches. This review consolidates the current molecular insights into aggressive and virus-associated B-NHL, taking into consideration the recently updated 5th edition of the WHO classification of hematolymphoid tumors (WHO-5HAEM) and the International Consensus Classification (ICC). Additionally, potential therapeutically targetable susceptibilities are highlighted, offering a comprehensive overview of the present scientific landscape in the field.
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Affiliation(s)
- H Witte
- Department of Hematology and Oncology, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081 Ulm, Germany; Department of Hematology and Oncology, University Hospital Schleswig-Holstein (UKSH) Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
| | - A Künstner
- University Cancer Center Schleswig-Holstein (UCCSH), Ratzeburger Allee 160, 23538 Lübeck, Germany; Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - N Gebauer
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein (UKSH) Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; University Cancer Center Schleswig-Holstein (UCCSH), Ratzeburger Allee 160, 23538 Lübeck, Germany
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2
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, Alonso de la Vega A, Proehl J, Holzhauer AM, Seeman ZJ, Liu X, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases. Cell Rep Med 2023; 4:101211. [PMID: 37797615 PMCID: PMC10591044 DOI: 10.1016/j.xcrm.2023.101211] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many cancers. However, despite years of work, a causal relationship has yet to be established in vivo. Here, we report a murine model that expresses tumor-like levels of human APOBEC3B. Animals expressing full-body APOBEC3B appear to develop normally. However, adult males manifest infertility, and older animals of both sexes show accelerated rates of carcinogenesis, visual and molecular tumor heterogeneity, and metastasis. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Enrichment for APOBEC3B-attributable single base substitution mutations also associates with elevated levels of insertion-deletion mutations and structural variations. APOBEC3B catalytic activity is required for all of these phenotypes. Together, these studies provide a cause-and-effect demonstration that human APOBEC3B is capable of driving both tumor initiation and evolution in vivo.
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Lene Alsøe
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hilde Nilsen
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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3
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Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
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Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, de la Vega AA, Proehl J, Holzhauer AM, Seeman ZJ, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529970. [PMID: 36865194 PMCID: PMC9980288 DOI: 10.1101/2023.02.24.529970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many different cancers. Despite over 10 years of work, a causal relationship has yet to be established between APOBEC3B and any stage of carcinogenesis. Here we report a murine model that expresses tumor-like levels of human APOBEC3B after Cre-mediated recombination. Animals appear to develop normally with full-body expression of APOBEC3B. However, adult males manifest infertility and older animals of both sexes show accelerated rates of tumorigenesis (mostly lymphomas or hepatocellular carcinomas). Interestingly, primary tumors also show overt heterogeneity, and a subset spreads to secondary sites. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Elevated levels of structural variation and insertion-deletion mutations also accumulate in these tumors. Together, these studies provide the first cause-and-effect demonstration that human APOBEC3B is an oncoprotein capable of causing a wide range of genetic changes and driving tumor formation in vivo .
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, Ohio, USA, 43210
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
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5
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Jain MD, Ziccheddu B, Coughlin CA, Faramand R, Griswold AJ, Reid KM, Menges M, Zhang Y, Cen L, Wang X, Hussaini M, Landgren O, Davila ML, Schatz JH, Locke FL, Maura F. Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma. Blood 2022; 140:491-503. [PMID: 35476848 PMCID: PMC9353150 DOI: 10.1182/blood.2021015008] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/20/2022] Open
Abstract
CD19-directed chimeric antigen receptor (CAR-19) T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. Although host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients with relapsed disease retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 patients with CAR-19-treated large B-cell lymphoma. We found that the pretreatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients for whom CAR T-cell therapy failed. Pretreatment reduced expression or monoallelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are related to multiple mechanisms. Our study showed that tumor-intrinsic genomic alterations are key among the complex interplay of factors that underlie CAR-19 efficacy and resistance for large B-cell lymphomas.
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Affiliation(s)
- Michael D Jain
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Bachisio Ziccheddu
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Caroline A Coughlin
- Medical Scientist Training Program
- Sheila and David Fuente Graduate Program in Cancer Biology, and
| | - Rawan Faramand
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Kayla M Reid
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Meghan Menges
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | | | - Ling Cen
- Department of Biostatistics and Bioinformatics and
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics and
| | - Mohammad Hussaini
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Ola Landgren
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Marco L Davila
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Jonathan H Schatz
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Frederick L Locke
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Francesco Maura
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
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6
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Li Z, Liang H, Zhang S, Luo W. A practical framework RNMF for exploring the association between mutational signatures and genes using gene cumulative contribution abundance. Cancer Med 2022; 11:4053-4069. [PMID: 35575002 PMCID: PMC9636515 DOI: 10.1002/cam4.4717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background Mutational signatures are somatic mutation patterns enriching operational mutational processes, which can provide abundant information about the mechanism of cancer. However, understanding of the pathogenic biological processes is still limited, such as the association between mutational signatures and genes. Methods We developed a simple and practical R package called RNMF (https://github.com/zhenzhang‐li/RNMF) for mutational signature analysis, including a key model of cumulative contribution abundance (CCA), which was designed to highlight the association between mutational signatures and genes and then applying it to a meta‐analysis of 1073 individuals with esophageal squamous cell carcinoma (ESCC). Results We revealed a number of known and previously undescribed SBS or ID signatures, and we found that APOBEC signatures (SBS2* and SBS13*) were closely associated with PIK3CA mutation, especially the E545k mutation. Furthermore, we found that age signature is closely related to the frequent mutation of TP53, of which R342* is highlighted due to strongly linked to age signature. In addition, the CCA matrix image data of genes in the signatures New, SBS3*, and SBS17b* were helpful for the preliminary evaluation of shortened survival outcome. These results can be extended to estimate the distribution of mutations or features, and study the potential impact of clinical factors. Conclusions In a word, RNMF can successfully achieve the correlation analysis of mutational signatures and genes, proving a strong theoretical basis for the study of mutational processes during tumor development.
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Affiliation(s)
- Zhenzhang Li
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Cloud and Gene AI Research Institute, Guangzhou, China
| | - Haihua Liang
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Shaoan Zhang
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wen Luo
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China
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7
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Cesarman E, Chadburn A, Rubinstein PG. KSHV/HHV8-mediated hematologic diseases. Blood 2022; 139:1013-1025. [PMID: 34479367 PMCID: PMC8854683 DOI: 10.1182/blood.2020005470] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Kaposi sarcoma (KS) herpesvirus (KSHV), also known as human herpesvirus 8, is the causal agent of KS but is also pathogenetically related to several lymphoproliferative disorders, including primary effusion lymphoma (PEL)/extracavitary (EC) PEL, KSHV-associated multicentric Castleman disease (MCD), KSHV+ diffuse large B-cell lymphoma, and germinotropic lymphoproliferative disorder. These different KSHV-associated diseases may co-occur and may have overlapping features. KSHV, similar to Epstein-Barr virus (EBV), is a lymphotropic gammaherpesvirus that is preferentially present in abnormal lymphoid proliferations occurring in immunecompromised individuals. Notably, both KSHV and EBV can infect and transform the same B cell, which is frequently seen in KSHV+ EBV+ PEL/EC-PEL. The mechanisms by which KSHV leads to lymphoproliferative disorders is thought to be related to the expression of a few transforming viral genes that can affect cellular proliferation and survival. There are critical differences between KSHV-MCD and PEL/EC-PEL, the 2 most common KSHV-associated lymphoid proliferations, including viral associations, patterns of viral gene expression, and cellular differentiation stage reflected by the phenotype and genotype of the infected abnormal B cells. Advances in treatment have improved outcomes, but mortality rates remain high. Our deepening understanding of KSHV biology, clinical features of KSHV-associated diseases, and newer clinical interventions should lead to improved and increasingly targeted therapeutic interventions.
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Affiliation(s)
- Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Paul G Rubinstein
- Section of Hematology/Oncology, Department of Medicine, John H. Stroger Jr Hospital of Cook County, Chicago, IL; and
- Department of Medicine, Ruth M. Rothstein CORE Center, Rush University Medical Center, Chicago, IL
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8
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Vendramini E, Bomben R, Pozzo F, Bittolo T, Tissino E, Gattei V, Zucchetto A. KRAS and RAS-MAPK Pathway Deregulation in Mature B Cell Lymphoproliferative Disorders. Cancers (Basel) 2022; 14:666. [PMID: 35158933 PMCID: PMC8833570 DOI: 10.3390/cancers14030666] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
KRAS mutations account for the most frequent mutations in human cancers, and are generally correlated with disease aggressiveness, poor prognosis, and poor response to therapies. KRAS is required for adult hematopoiesis and plays a key role in B cell development and mature B cell proliferation and survival, proved to be critical for B cell receptor-induced ERK pathway activation. In mature B cell neoplasms, commonly seen in adults, KRAS and RAS-MAPK pathway aberrations occur in a relevant fraction of patients, reaching high recurrence in some specific subtypes like multiple myeloma and hairy cell leukemia. As inhibitors targeting the RAS-MAPK pathway are being developed and improved, it is of outmost importance to precisely identify all subgroups of patients that could potentially benefit from their use. Herein, we review the role of KRAS and RAS-MAPK signaling in malignant hematopoiesis, focusing on mature B cell lymphoproliferative disorders. We discuss KRAS and RAS-MAPK pathway aberrations describing type, incidence, mutual exclusion with other genetic abnormalities, and association with prognosis. We review the current therapeutic strategies applied in mature B cell neoplasms to counteract RAS-MAPK signaling in pre-clinical and clinical studies, including most promising combination therapies. We finally present an overview of genetically engineered mouse models bearing KRAS and RAS-MAPK pathway aberrations in the hematopoietic compartment, which are valuable tools in the understanding of cancer biology and etiology.
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Affiliation(s)
- Elena Vendramini
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (R.B.); (F.P.); (T.B.); (E.T.); (V.G.); (A.Z.)
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9
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Aschacher T, Wolf B, Aschacher O, Enzmann F, Laszlo V, Messner B, Türkcan A, Weis S, Spiegl-Kreinecker S, Holzmann K, Laufer G, Ehrlich M, Bergmann M. Long interspersed element-1 ribonucleoprotein particles protect telomeric ends in alternative lengthening of telomeres dependent cells. Neoplasia 2019; 22:61-75. [PMID: 31846834 PMCID: PMC6920197 DOI: 10.1016/j.neo.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022] Open
Abstract
Malignant cells ensure telomere maintenance by the alternative lengthening of telomeres (ALT) in the absence of telomerase activity (TA). The retrotransposons "long interspersed nuclear element-1" (LINE-1, L1) are expressed in malignant cells and are primarily known to contribute to complex karyotypes. Here we demonstrate that LINE-1 ribonucleoprotein particles (L1-RNPs) expression is significantly higher in ALT+- versus in TA+-human glioma. Analyzing a role of L1-RNP in ALT, we show that L1-RNPs bind to telomeric repeat containing RNA (TERRA), which is critical for telomere stabilization and which is overexpressed in ALT+ cells. In turn, L1-RNP knockdown (KD) abrogated the nuclear retention of TERRA, resulted in increased telomeric DNA damage, decreased cell growth and reduced expression of ALT characteristics such as c-circles and PML-bodies. L1-RNP KD also decreased the expression of Shelterin- and the ALT-regulating protein Topoisomerase IIIα (TopoIIIα) indicating a more general role of L1-RNPs in supporting telomeric integrity in ALT. Our findings suggest an impact of L1-RNP on telomere stability in ALT+ dependent tumor cells. As L1-RNPs are rarely expressed in normal adult human tissue those elements might serve as a novel target for tumor ablative therapy.
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Affiliation(s)
- Thomas Aschacher
- Cardiac Surgery Research Laboratory, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Brigitte Wolf
- Surgical Research Laboratories, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Olivia Aschacher
- Department of Plastic and Reconstructive Surgery, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Florian Enzmann
- Department of Vascular and Endovascular Surgery, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020 Salzburg, Austria
| | - Viktoria Laszlo
- Surgical Research Laboratories, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Barbara Messner
- Cardiac Surgery Research Laboratory, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Adrian Türkcan
- Surgical Research Laboratories, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Serge Weis
- Division of Neuropathology, Neuromed Campus, Kepler University Hospital, 4020 Linz, Austria
| | - Sabine Spiegl-Kreinecker
- University Clinic for Neurosurgery, Neuromed Campus, Kepler University Hospital, Johannes Kepler University, Linz, Austria
| | - Klaus Holzmann
- Department of Cancer Research, Borschkegasse 8a, 1090 Vienna, Austria; Comprehensive Cancer Centre, Medical University of Vienna, Austria
| | - Günther Laufer
- Cardiac Surgery Research Laboratory, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Marek Ehrlich
- Cardiac Surgery Research Laboratory, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Michael Bergmann
- Surgical Research Laboratories, Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria; Comprehensive Cancer Centre, Medical University of Vienna, Austria.
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10
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Matsutani T, Ueno Y, Fukunaga T, Hamada M. Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinformatics 2019; 35:4543-4552. [PMID: 30993319 PMCID: PMC6853711 DOI: 10.1093/bioinformatics/btz266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a 'mutation signature.' Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches (e.g. non-negative matrix factorization and latent Dirichlet allocation) revealed a number of mutation signatures. Nonetheless, strictly speaking, these existing approaches employ an ad hoc method or incorrect approximation to estimate the number of mutation signatures, and the whole picture of mutation signatures is unclear. RESULTS In this study, we present a novel method for estimating the number of mutation signatures-latent Dirichlet allocation with variational Bayes inference (VB-LDA)-where variational lower bounds are utilized for finding a plausible number of mutation patterns. In addition, we performed cluster analyses for estimated mutation signatures to extract novel mutation signatures that appear in multiple primary lesions. In a simulation with artificial data, we confirmed that our method estimated the correct number of mutation signatures. Furthermore, applying our method in combination with clustering procedures for real mutation data revealed many interesting mutation signatures that have not been previously reported. AVAILABILITY AND IMPLEMENTATION All the predicted mutation signatures with clustering results are freely available at http://www.f.waseda.jp/mhamada/MS/index.html. All the C++ source code and python scripts utilized in this study can be downloaded on the Internet (https://github.com/qkirikigaku/MS_LDA). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Taro Matsutani
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
| | - Yuki Ueno
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
| | - Tsukasa Fukunaga
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model 2019; 59:2264-2273. [PMID: 30130104 PMCID: PMC6644697 DOI: 10.1021/acs.jcim.8b00427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Özlem Demir
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Daniel A Harki
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
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Biology and management of primary effusion lymphoma. Blood 2018; 132:1879-1888. [DOI: 10.1182/blood-2018-03-791426] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/24/2018] [Indexed: 12/14/2022] Open
Abstract
Abstract
Primary effusion lymphoma (PEL) is a rare B-cell malignancy that most often occurs in immunocompromised patients, such as HIV-infected individuals and patients receiving organ transplantation. The main characteristic of PEL is neoplastic effusions in body cavities without detectable tumor masses. The onset of the disease is associated with latent infection of human herpes virus 8/Kaposi sarcoma–associated herpes virus, and the normal counterpart of tumor cells is B cells with plasmablastic differentiation. A condition of immunodeficiency and a usual absence of CD20 expression lead to the expectation of the lack of efficacy of anti-CD20 monoclonal antibody; clinical outcomes of the disease remain extremely poor, with an overall survival at 1 year of ∼30%. Although recent progress in antiretroviral therapy has improved outcomes of HIV-infected patients, its benefit is still limited in patients with PEL. Furthermore, the usual high expression of programmed death ligand 1 in tumor cells, one of the most important immune-checkpoint molecules, results in the immune escape of tumor cells from the host immune defense, which could be the underlying mechanism of poor treatment efficacy. Molecular-targeted therapies for the activating pathways in PEL, including NF-κB, JAK/STAT, and phosphatidylinositol 3-kinase/AKT, have emerged to treat this intractable disease. A combination of immunological recovery from immune deficiency, overcoming the immune escape, and the development of more effective drugs will be vital for improving the outcomes of PEL patients in the future.
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Liu F, Wang Z, Zhou X, Liu Q, Chen G, Xiao H, Yin W, Nakamura S, Rao H. Genetic heterogeneity and mutational signature in Chinese Epstein-Barr virus-positive diffuse large B-cell lymphoma. PLoS One 2018; 13:e0201546. [PMID: 30106962 PMCID: PMC6091946 DOI: 10.1371/journal.pone.0201546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/17/2018] [Indexed: 01/19/2023] Open
Abstract
Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (EBV+ DLBCL) is typically an aggressive tumor in elderly patients. However, in a subset of young patients, EBV+ DLBCL follows a relatively indolent clinical course and exhibits a good response to chemotherapy. This lymphoma comprises polymorphous lymphoma and large cell lymphomas subtypes, with the latter subtype showing a significantly poorer prognosis. It is unknown whether the genetic background differs between age groups and histopathological subtypes. To investigate the genetic basis, heterogeneity, and recurrently mutated genes in EBV+ DLBCL, we performed whole-exome sequencing of DNA from 11 tissue samples of this lymphoma. Sequencing revealed that the most common substitution was the transition C>T/G>A. Genetic features—including the numbers of mutated genes in exonic region, single-nucleotide variants (SNV), and indels—did not significantly differ between age groups or histological subtypes. Matching with the COSMIC database revealed that the main mutational signature was signature 3, which is associated with failure of DNA double-strand break-repair by homologous recombination. Mutant-Allele Tumor Heterogeneity (MATH) scores showed that EBV+ DLBCL exhibited broad intratumor heterogeneity, and were positively correlated with Ann Arbor Stage and ≥2 extranodal lesion sites. We identified 57 selected recurrently mutated genes. The most commonly mutated five genes—LNP1 (11/11), PRSS3 (10/11), MUC3A (9/11), FADS6 (9/11), and TRAK1 (8/11)—were validated by Sanger sequencing. These mutated genes have not previously been identified. Overall, our present results demonstrate the tremendous genetic heterogeneity underlying EBV+ DLBCLs, and highlight the need for personalized therapeutic approaches to treating these patients.
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Affiliation(s)
- Fang Liu
- Department of Pathology, Foshan Hospital, Sun Yat-sen University, Foshan, Guangdong Province, China
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shannxi Province, China
| | - Xiaoge Zhou
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qing Liu
- Department of Pathology, Foshan Hospital, Sun Yat-sen University, Foshan, Guangdong Province, China
| | - Gang Chen
- Department of Pathology, Fujian province Cancer Hospital, Fuzhou, Fujian Province, China
| | - Hualiang Xiao
- Daping Hospital, Army Medical University, Chongqing, China
| | - Weihua Yin
- Department of Pathology, Shenzhen Hospital, Peking University, Shenzhen, Guangdong Province, China
| | - Shigeo Nakamura
- Department of Pathology and Clinical Laboratories, Nagoya University Hospital, Nagoya, Japan
| | - Huilan Rao
- Department of Pathology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
- * E-mail:
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Temko D, Tomlinson IPM, Severini S, Schuster-Böckler B, Graham TA. The effects of mutational processes and selection on driver mutations across cancer types. Nat Commun 2018; 9:1857. [PMID: 29748584 PMCID: PMC5945620 DOI: 10.1038/s41467-018-04208-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 04/11/2018] [Indexed: 11/17/2022] Open
Abstract
Epidemiological evidence has long associated environmental mutagens with increased cancer risk. However, links between specific mutation-causing processes and the acquisition of individual driver mutations have remained obscure. Here we have used public cancer sequencing data from 11,336 cancers of various types to infer the independent effects of mutation and selection on the set of driver mutations in a cancer type. First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer types. Second, we quantify differential selection between well-known alternative driver mutations, including differences in selection between distinct mutant residues in the same gene. These results show that while mutational processes have a large role in determining which driver mutations are present in a cancer, the role of selection frequently dominates.
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Affiliation(s)
- Daniel Temko
- Evolution and Cancer laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Sq, London, EC1M 6BQ, UK.
- Department of Computer Science, University College London, London, WC1E 6BT, UK.
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Gower Street, London, WC1E 6BT, UK.
| | - Ian P M Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Simone Severini
- Department of Computer Science, University College London, London, WC1E 6BT, UK
- Institute of Natural Sciences, Shanghai Jiao Tong University, Dong Chuan Road, Minhang District, Shanghai, 200240, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Dr, Oxford, OX3 7DQ, USA.
| | - Trevor A Graham
- Evolution and Cancer laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Sq, London, EC1M 6BQ, UK.
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15
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The ubiquitous 'cancer mutational signature' 5 occurs specifically in cancers with deleted FHIT alleles. Oncotarget 2017; 8:102199-102211. [PMID: 29254236 PMCID: PMC5731946 DOI: 10.18632/oncotarget.22321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/25/2017] [Indexed: 01/22/2023] Open
Abstract
The FHIT gene is located at the fragile FRA3B locus where activation by carcinogen-induced and endogenous replication stress causes FHIT deletions even in normal cells over a lifetime. Our lab has shown that loss of FHIT expression causes genome instability and provides single-strand DNA substrates for APOBEC3B hypermutation, in line with evidence that FHIT locus deletions occur in many cancers. Based on these biological features, we hypothesized that FHIT loss drives development of COSMIC mutational signature 5 and here provide evidence, including data mining of >6,500 TCGA samples, that FHIT is the cancer-associated gene with copy number alterations correlating most significantly with signature 5 mutation rate. In addition, tissues of Fhit-deficient mice exhibit a mutational signature strongly resembling signature 5 (cosine similarity value = 0.89). We conclude that FHIT loss is a molecular determinant for signature 5 mutations, which occur in all cancer types early in cancer development, are clock-like, and accelerated by carcinogen exposure. Loss of FHIT caretaker function may be a predictive and preventive marker for cancer development.
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Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR. Mutational signatures associated with tobacco smoking in human cancer. Science 2016; 354:618-622. [PMID: 27811275 PMCID: PMC6141049 DOI: 10.1126/science.aag0299] [Citation(s) in RCA: 689] [Impact Index Per Article: 86.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Tobacco smoking increases the risk of at least 17 classes of human cancer. We analyzed somatic mutations and DNA methylation in 5243 cancers of types for which tobacco smoking confers an elevated risk. Smoking is associated with increased mutation burdens of multiple distinct mutational signatures, which contribute to different extents in different cancers. One of these signatures, mainly found in cancers derived from tissues directly exposed to tobacco smoke, is attributable to misreplication of DNA damage caused by tobacco carcinogens. Others likely reflect indirect activation of DNA editing by APOBEC cytidine deaminases and of an endogenous clocklike mutational process. Smoking is associated with limited differences in methylation. The results are consistent with the proposition that smoking increases cancer risk by increasing the somatic mutation load, although direct evidence for this mechanism is lacking in some smoking-related cancer types.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87102, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Iñigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Medical Genetics, Addenbrooke's Hospital National Health Service Trust, Cambridge, UK
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Paolo Vineis
- Human Genetics Foundation, 10126 Torino, Italy
- Department of Epidemiology and Biostatistics, Medical Research Council (MRC)-Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - David H Phillips
- King's College London, MRC-PHE Centre for Environment and Health, Analytical and Environmental Sciences Division, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
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Petljak M, Alexandrov LB. Understanding mutagenesis through delineation of mutational signatures in human cancer. Carcinogenesis 2016; 37:531-40. [DOI: 10.1093/carcin/bgw055] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 01/04/2023] Open
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18
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Alexandrov LB, Jones PH, Wedge DC, Sale JE, Campbell PJ, Nik-Zainal S, Stratton MR. Clock-like mutational processes in human somatic cells. Nat Genet 2015; 47:1402-7. [PMID: 26551669 PMCID: PMC4783858 DOI: 10.1038/ng.3441] [Citation(s) in RCA: 664] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 10/14/2015] [Indexed: 12/16/2022]
Abstract
During the course of a lifetime, somatic cells acquire mutations. Different mutational processes may contribute to the mutations accumulated in a cell, with each imprinting a mutational signature on the cell's genome. Some processes generate mutations throughout life at a constant rate in all individuals, and the number of mutations in a cell attributable to these processes will be proportional to the chronological age of the person. Using mutations from 10,250 cancer genomes across 36 cancer types, we investigated clock-like mutational processes that have been operating in normal human cells. Two mutational signatures show clock-like properties. Both exhibit different mutation rates in different tissues. However, their mutation rates are not correlated, indicating that the underlying processes are subject to different biological influences. For one signature, the rate of cell division may influence its mutation rate. This study provides the first survey of clock-like mutational processes operating in human somatic cells.
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Affiliation(s)
- Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Philip H Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Medical Research Council (MRC) Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medical Genetics, Addenbrooke's Hospital National Health Service (NHS) Trust, Cambridge, UK
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