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Chidambaram A, Prabhakaran R, Sivasamy S, Kanagasabai T, Thekkumalai M, Singh A, Tyagi MS, Dhandayuthapani S. Male Breast Cancer: Current Scenario and Future Perspectives. Technol Cancer Res Treat 2024; 23:15330338241261836. [PMID: 39043043 DOI: 10.1177/15330338241261836] [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] [Indexed: 07/25/2024] Open
Abstract
Male breast cancer (MBC), one of the rare types of cancer among men where the global incidence rate is 1.8% of all breast cancers cases with a yearly increase in a pace of 1.1%. Since the last 10 years, the incidence has been increased from 7.2% to 10.3% and the mortality rate was decreased from 11% to 3.8%. Nevertheless, the rate of diagnoses has been expected to be around 2.6% in the near future, still there is a great lack in studies to characterize the MBC including the developed countries. Based on our search, it is evidenced from the literature that the number of risk factors for the cause of MBC are significant, which includes the increase in age, family genetic history, mutations in specific genes due to various environmental impacts, hormonal imbalance and unregulated expression receptors for specific hormones of high levels of estrogen or androgen receptors compared to females. MBCs are broadly classified into ductal and lobular carcinomas with further sub-types, with some of the symptoms including a lump or swelling in the breast, redness of flaky skin in the breast, irritation and nipple discharge that is similar to the female breast cancer (FBC). The most common diagnostic tools currently in use are the ultrasound guided sonography, mammography, and biopsies. Treatment modalities for MBC include surgery, radiotherapy, chemotherapy, hormonal therapy, and targeted therapies. However, the guidelines followed for the diagnosis and treatment modalities of MBC are mostly based on FBC that is due to the lack of prospective studies related to MBC. However, there are distinct clinical and molecular features of MBC, it is a need to develop different clinical methods with more multinational approaches to help oncologist to improve care for MBC patients.
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Affiliation(s)
- Anitha Chidambaram
- Department of Biochemistry, PRIST Deemed to be University, Thanjavur, TN, India
| | - Rajkumar Prabhakaran
- Central Research Facility, Santosh Deemed to be University, Ghaziabad, UP, India
| | - Sivabalan Sivasamy
- Central Research Facility, Santosh Deemed to be University, Ghaziabad, UP, India
| | - Thanigaivelan Kanagasabai
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, USA
| | - Malarvili Thekkumalai
- Department of Biochemistry, Center for Distance Education, Bharathidasan University, Tiruchirappalli, TN, India
| | - Ankit Singh
- Department of Community Medicine, United Institute of Medical Sciences, Prayagraj, UP, India
| | - Mayurika S Tyagi
- Department of Immuno Hematology and Blood Transfusion, Santosh Deemed to be University, Ghaziabad, UP, India
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Lampson BL, Gupta A, Tyekucheva S, Mashima K, Petráčková A, Wang Z, Wojciechowska N, Shaughnessy CJ, Baker PO, Fernandes SM, Shupe S, Machado JH, Fardoun R, Kim AS, Brown JR. Rare Germline ATM Variants Influence the Development of Chronic Lymphocytic Leukemia. J Clin Oncol 2023; 41:1116-1128. [PMID: 36315919 PMCID: PMC9928739 DOI: 10.1200/jco.22.00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Germline missense variants of unknown significance in cancer-related genes are increasingly being identified with the expanding use of next-generation sequencing. The ataxia telangiectasia-mutated (ATM) gene on chromosome 11 has more than 1,000 germline missense variants of unknown significance and is a tumor suppressor. We aimed to determine if rare germline ATM variants are more frequent in chronic lymphocytic leukemia (CLL) compared with other hematologic malignancies and if they influence the clinical characteristics of CLL. METHODS We identified 3,128 patients (including 825 patients with CLL) in our hematologic malignancy clinic who had received clinical-grade sequencing of the entire coding region of ATM. We ascertained the comparative frequencies of germline ATM variants in categories of hematologic neoplasms, and, in patients with CLL, we determined whether these variants affected CLL-associated characteristics such as somatic 11q deletion. RESULTS Rare germline ATM variants are present in 24% of patients with CLL, significantly greater than that in patients with other lymphoid malignancies (16% prevalence), myeloid disease (15%), or no hematologic neoplasm (14%). Patients with CLL with germline ATM variants are younger at diagnosis and twice as likely to have 11q deletion. The ATM variant p.L2307F is present in 3% of patients with CLL, is associated with a three-fold increase in rates of somatic 11q deletion, and is a hypomorph in cell-based assays. CONCLUSION Germline ATM variants cluster within CLL and affect the phenotype of CLL that develops, implying that some of these variants (such as ATM p.L2307F) have functional significance and should not be ignored. Further studies are needed to determine whether these variants affect the response to therapy or account for some of the inherited risk of CLL.
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Affiliation(s)
- Benjamin L. Lampson
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aditi Gupta
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Kiyomi Mashima
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna Petráčková
- Department of Immunology, Palacký University, Olomouc, Czech Republic
| | - Zixu Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Current Address: Wrocław Medical University, Wrocław, Poland
| | - Conner J. Shaughnessy
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter O. Baker
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stacey M. Fernandes
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha Shupe
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John-Hanson Machado
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rayan Fardoun
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jennifer R. Brown
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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Kariri YA, Joseph C, Alsaleem MA, Elsharawy KA, Alsaeed S, Toss MS, Mongan NP, Green AR, Rakha EA. Mechanistic and Clinical Evidence Supports a Key Role for Cell Division Cycle Associated 5 (CDCA5) as an Independent Predictor of Outcome in Invasive Breast Cancer. Cancers (Basel) 2022; 14:cancers14225643. [PMID: 36428736 PMCID: PMC9688237 DOI: 10.3390/cancers14225643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cell Division Cycle Associated 5 (CDCA5) plays a role in the phosphoinositide 3-kinase (PI3K)/AKT/mTOR signalling pathway involving cell division, cancer cell migration and apoptosis. This study aims to assess the prognostic and biological value of CDCA5 in breast cancer (BC). METHODS The biological and prognostic value of CDCA5 were evaluated at mRNA (n = 5109) and protein levels (n = 614) utilizing multiple well-characterized early stage BC cohorts. The effects of CDCA5 knockdown (KD) on multiple oncogenic assays were assessed in vitro using a panel of BC cell lines. RESULTS this study examined cohorts showed that high CDCA5 expression was correlated with features characteristic of aggressive behavior and poor prognosis, including the presence of high grade, large tumor size, lymphovascular invasion (LVI), hormone receptor negativity and HER2 positivity. High CDCA5 expression, at both mRNA and protein levels, was associated with shorter BC-specific survival independent of other variables (p = 0.034, Hazard ratio (HR) = 1.6, 95% CI; 1.1-2.3). In line with the clinical data, in vitro models indicated that CDCA5 depletion results in a marked decrease in BC cell invasion and migration abilities and a significant accumulation of the BC cells in the G2/M-phase. CONCLUSIONS These results provide evidence that CDCA5 plays an important role in BC development and metastasis and could be used as a potential biomarker to predict disease progression in BC.
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Affiliation(s)
- Yousif A. Kariri
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Clinical Laboratory Science, Faculty of Applied Medical Science, Shaqra University, Shaqra 11961, Saudi Arabia
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
| | - Chitra Joseph
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
| | - Mansour A. Alsaleem
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Applied Medical Science, Applied College, Qassim University, Unayzah 56435, Saudi Arabia
| | - Khloud A. Elsharawy
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Zoology, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | - Sami Alsaeed
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- Department of Clinical Laboratory Science, Faculty of Applied Medical Sciences, Northern Border University, Arar 73244, Saudi Arabia
| | - Michael S. Toss
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
| | - Nigel P. Mongan
- Biodiscovery Institute, Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew R. Green
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
| | - Emad A. Rakha
- Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham Breast Cancer Research Centre, Nottingham NG7 2RD, UK
- School of Medicine, Nottingham City Hospital, Nottingham University Hospitals NHS Trust and The University of Nottingham, Nottingham NG5 1PB, UK
- Correspondence: or ; Tel.: +44-0115-9691169; Fax: +44-0115-9627768
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4
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Chat V, Ferguson R, Morales L, Kirchhoff T. Ultra Low-Coverage Whole-Genome Sequencing as an Alternative to Genotyping Arrays in Genome-Wide Association Studies. Front Genet 2022; 12:790445. [PMID: 35251117 PMCID: PMC8889143 DOI: 10.3389/fgene.2021.790445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
An array-based genotyping approach has been the standard practice for genome-wide association studies (GWASs); however, as sequencing costs plummet over the past years, ultra low-coverage whole-genome sequencing (ulcWGS <0.5× coverage) has emerged as a promising alternative that provides superior genomic coverage with substantial reduction of genotyping cost. To evaluate the potential utility of ulcWGS, we performed a whole-genome sequencing (WGS) of 72 European individuals to a target coverage of 0.4× and compared its performance with the widely used Infinium Global Screening Multi-Disease Array (GSA-MD). We showed that the number of variants captured by ulcWGS is comparable with imputed GSA-MD platform, particularly for low-frequency (95.5%) and common variants (99.9%), with high imputation R2 accuracy (mean 0.93 for SNPs and 0.86 for indels). Using deep-coverage 30× WGS as the “truth” genotypes, we found that ulcWGS has higher overall nonreference genotype concordance compared with imputed GSA-MD for both SNPs (0.90 vs. 0.88) and indels (0.86 vs. 0.83). In addition, ulcWGS proved to be as sensitive as the genotyping-based method in sex imputation and ancestry prediction producing similar principal component (PC) scores. Our findings provide important evidence that the cost efficient ulcWGS of <0.5× generates high genotype accuracy, outperforming the standard genotyping arrays, making it an attractive alternative to the array-based method in next-generation GWAS design.
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Affiliation(s)
- Vylyny Chat
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Robert Ferguson
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Leah Morales
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
- *Correspondence: Tomas Kirchhoff,
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Wang H, Yang B, Cai X, Cheng X, Shen N, Liu L, Li J, Wang Y, He H, Ying P, Li B, Lu Z, Yang N, Wang X, Zhang F, Li Y, Wang W, Ning C, Zhu Y, Chang J, Miao X, Tian J, Zhong R. Hepatocellular carcinoma risk variant modulates lncRNA HLA-DQB1-AS1 expression via a long-range enhancer-promoter interaction. Carcinogenesis 2021; 42:1347-1356. [PMID: 34665859 DOI: 10.1093/carcin/bgab095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Substantial evidence highlighted the critical role of long non-coding RNAs (lncRNA) in driving hepatocarcinogenesis. We hypothesized that functional variants in genome-wide association studies (GWASs) associated loci might alter the expression levels of lncRNAs and contribute to the development of hepatocellular carcinoma (HCC). Here, we prioritized potentially cis-expression quantitative trait loci-based single nucleotide polymorphism (SNP)-lncRNA association together with the physical interaction by the analyses from Hi-C data in GWAS loci of chronic hepatitis B and HCC. Subsequently, by leveraging two-stage case-control study (1738 hepatitis B [HBV]) related HCC cases and 1988 HBV persistent carriers) and biological assays, we identified that rs2647046 was significantly associated with HCC risk (odds ratio = 1.26, 95% CI = 1.11 to 1.43, P = 4.14 × 10-4). Luciferase reporter assays and electrophoretic mobility shift assays showed that rs2647046 A allele significantly increased transcriptional activity via influencing transcript factor binding affinity. Allele-specific chromosome conformation capture assays revealed that enhancer with rs2647046 interacted with the HLA-DQB1-AS1 promoter to allele-specifically influence its expression by CTCF-mediated long-range loop. Cell proliferation assays indicated that HLA-DQB1-AS1 is a potential oncogene in HCC. Our study showed HLA-DQB1-AS1 regulated by a causal SNP in a long-range interaction manner conferred the susceptibility to HCC, suggesting an important mechanism of modulating lncRNA expression for risk-associated SNPs in the etiology of HCC.
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Affiliation(s)
- Haoxue Wang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Beifang Yang
- Hubei Institute for Infectious Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Xiaomin Cai
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiang Cheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Wang
- Department of Virology, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei, China
| | - Heng He
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Pingting Ying
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Bin Li
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Ying Zhu
- School of Health Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiaoping Miao
- School of Health Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Jianbo Tian
- School of Health Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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6
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Thorball CW, Oudot-Mellakh T, Ehsan N, Hammer C, Santoni FA, Niay J, Costagliola D, Goujard C, Meyer L, Wang SS, Hussain SK, Theodorou I, Cavassini M, Rauch A, Battegay M, Hoffmann M, Schmid P, Bernasconi E, Günthard HF, Mohammadi P, McLaren PJ, Rabkin CS, Besson C, Fellay J. Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma. Haematologica 2021; 106:2233-2241. [PMID: 32675224 PMCID: PMC8327743 DOI: 10.3324/haematol.2020.247023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 11/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is associated with an increased risk of non-Hodgkin lymphoma (NHL). Even in the era of suppressive antiretroviral treatment, HIV-infected individuals remain at higher risk of developing NHL compared to the general population. In order to identify potential genetic risk loci, we performed case-control genome-wide association studies and a meta-analysis across three cohorts of HIV-infected patients of European ancestry, including a total of 278 cases and 1,924 matched controls. We observed a significant association with NHL susceptibility in the C-X-C motif chemokine ligand 12 (CXCL12) region on chromosome 10. A fine mapping analysis identified rs7919208 as the most likely causal variant (P=4.77e-11), with the G>A polymorphism creating a new transcription factor binding site for BATF and JUND. These results suggest a modulatory role of CXCL12 regulation in the increased susceptibility to NHL observed in the HIV-infected population.
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Affiliation(s)
- Christian W Thorball
- Ecole Polytechnique Federale de Lausanne, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tiphaine Oudot-Mellakh
- Centre de genetique moleculaire et chromosomique, GH La Pitié Salpetriere, Paris, France
| | - Nava Ehsan
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Christian Hammer
- Dept. of Cancer Immunology and Human Genetics, Genentech, South San Francisco, CA, USA
| | - Federico A Santoni
- Dept. of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Switzerland
| | - Jonathan Niay
- Centre de genetique moleculaire et chromosomique, GH La Pitié Salpetriere, Paris, France
| | | | - Cécile Goujard
- Paris-Sud University and Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | | | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | - Shehnaz K Hussain
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ioannis Theodorou
- Centre de genetique moleculaire et chromosomique, GH La Pitié Salpetriere, Paris, France
| | - Matthias Cavassini
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Andri Rauch
- Dept. of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland
| | - Manuel Battegay
- Dept. of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital Olten, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital of Lugano, Lugano, Switzerland
| | | | | | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Caroline Besson
- Department of Hematology and Oncology, Hospital of Versailles, Le Chesnay, France
| | - Jacques Fellay
- Ecole Polytechnique Federale de Lausanne and University of Lausanne, Switzerland
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7
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Waller RG, Klein RJ, Vijai J, McKay JD, Clay-Gilmour A, Wei X, Madsen MJ, Sborov DW, Curtin K, Slager SL, Offit K, Vachon CM, Lipkin SM, Dumontet C, Camp NJ. Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes. Hum Mol Genet 2021; 30:1142-1153. [PMID: 33751038 PMCID: PMC8188404 DOI: 10.1093/hmg/ddab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/14/2022] Open
Abstract
Inherited genetic risk factors play a role in multiple myeloma (MM), yet considerable missing heritability exists. Rare risk variants at genome-wide association study (GWAS) loci are a new avenue to explore. Pleiotropy between lymphoid neoplasms (LNs) has been suggested in family history and genetic studies, but no studies have interrogated sequencing for pleiotropic genes or rare risk variants. Sequencing genetically enriched cases can help discover rarer variants. We analyzed exome sequencing in familial or early-onset MM cases to identify rare, functionally relevant variants near GWAS loci for a range of LNs. A total of 149 distinct and significant LN GWAS loci have been published. We identified six recurrent, rare, potentially deleterious variants within 5 kb of significant GWAS single nucleotide polymorphisms in 75 MM cases. Mutations were observed in BTNL2, EOMES, TNFRSF13B, IRF8, ACOXL and TSPAN32. All six genes replicated in an independent set of 255 early-onset MM or familial MM or precursor cases. Expansion of our analyses to the full length of these six genes resulted in a list of 39 rare and deleterious variants, seven of which segregated in MM families. Three genes also had significant rare variant burden in 733 sporadic MM cases compared with 935 control individuals: IRF8 (P = 1.0 × 10-6), EOMES (P = 6.0 × 10-6) and BTNL2 (P = 2.1 × 10-3). Together, our results implicate six genes in MM risk, provide support for genetic pleiotropy between LN subtypes and demonstrate the utility of sequencing genetically enriched cases to identify functionally relevant variants near GWAS loci.
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MESH Headings
- Acyl-CoA Oxidase/genetics
- Butyrophilins/genetics
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Hodgkin Disease/genetics
- Hodgkin Disease/pathology
- Humans
- Interferon Regulatory Factors/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphocytes/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Multiple Myeloma/genetics
- Multiple Myeloma/pathology
- Polymorphism, Single Nucleotide/genetics
- Risk Factors
- T-Box Domain Proteins/genetics
- Tetraspanins/genetics
- Transmembrane Activator and CAML Interactor Protein/genetics
- Exome Sequencing
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Affiliation(s)
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY 10029-5674, USA
| | - Joseph Vijai
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - James D McKay
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, 69372 Lyon Cedex 08, France
| | - Alyssa Clay-Gilmour
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaomu Wei
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael J Madsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Douglas W Sborov
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Karen Curtin
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Susan L Slager
- Department of Health Sciences, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Celine M Vachon
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Charles Dumontet
- INSERM 1052, CNRS 5286, University of Lyon, 69361 Lyon Cedex 07, France
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
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8
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Sutton E, De Santis D, Hay L, McKinnon E, D'Orsogna L, Joske D. Correlating HLA associations with follicular lymphoma in an Australian data set: A pilot study. HLA 2020; 96:192-193. [PMID: 32342606 DOI: 10.1111/tan.13918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/11/2020] [Accepted: 04/22/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Edwina Sutton
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Louise Hay
- Department of Haematology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Elizabeth McKinnon
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - D Joske
- Department of Haematology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
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9
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Zhong C, Cozen W, Bolanos R, Song J, Wang SS. The role of HLA variation in lymphoma aetiology and survival. J Intern Med 2019; 286:154-180. [PMID: 31155783 DOI: 10.1111/joim.12911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epidemiologic and laboratory evidence has consistently supported a strong inflammatory and immune component for lymphoma aetiology. These studies have consistently implicated variation in the immune gene, human leucocyte antigen (HLA), to be associated with lymphoma risk. In this review, we summarize the historical and recent evidence of HLA in both lymphoma aetiology and survival. The recent momentum in uncovering HLA associations has been propelled by the conduct of genome-wide association studies (GWAS), which has permitted the evaluation of imputed HLA alleles in much larger sample sizes than historically feasible with allelotyping studies. Based on the culmination of smaller HLA typing studies and larger GWAS, we now recognize several HLA associations with Hodgkin (HL) and non-Hodgkin lymphomas (NHLs) and their subtypes. Although other genetic variants have also been implicated with lymphoma risk, it is notable that HLA associations have been reported in every NHL and HL subtype evaluated to date. Both HLA class I and class II alleles have been linked with NHL and HL risk. It is notable that the associations identified are largely specific to each lymphoma subtype. However, pleiotropic HLA associations have also been observed. For example, rs10484561, which is in linkage disequilibrium with HLA-DRB1*01:01˜DQA1*01:01˜DQB1*05:01, has been implicated in increased FL and DLBCL risk. Opposing HLA associations across subtypes have also been reported, such as for HLA-A*01:01 which is associated with increased risk of EBV-positive cHL but decreased risk of EBV-negative cHL and chronic lymphocytic leukaemia/small cell lymphoma. Due to extensive linkage disequilibrium and allele/haplotypic variation across race/ethnicities, identification of causal alleles/haplotypes remains challenging. Follow-up functional studies are needed to identify the specific immunological pathways responsible in the multifactorial aetiology of HL and NHL. Correlative studies linking HLA alleles with known molecular subtypes and HLA expression in the tumours are also needed. Finally, additional association studies investigating HLA diversity and lymphoma survival are also required to replicate initial associations reported to date.
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Affiliation(s)
- C Zhong
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute and Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - W Cozen
- Genetic Epidemiology Center, Department of Preventive Medicine, Keck School of Medicine of USC, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - R Bolanos
- Genetic Epidemiology Center, Department of Preventive Medicine, Keck School of Medicine of USC, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - J Song
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - S S Wang
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute and Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
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10
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Immunomodulatory germline variation associated with the development of multiple primary melanoma (MPM). Sci Rep 2019; 9:10173. [PMID: 31308438 PMCID: PMC6629847 DOI: 10.1038/s41598-019-46665-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022] Open
Abstract
Multiple primary melanoma (MPM) has been associated with a higher 10-year mortality risk compared to patients with single primary melanoma (SPM). Given that 3–8% of patients with SPM develop additional primary melanomas, new markers predictive of MPM risk are needed. Based on the evidence that the immune system may regulate melanoma progression, we explored whether germline genetic variants controlling the expression of 41 immunomodulatory genes modulate the risk of MPM compared to patients with SPM or healthy controls. By genotyping these 41 variants in 977 melanoma patients, we found that rs2071304, linked to the expression of SPI1, was strongly associated with MPM risk reduction (OR = 0.60; 95% CI = 0.45–0.81; p = 0.0007) when compared to patients with SPM. Furthermore, we showed that rs6695772, a variant affecting expression of BATF3, is also associated with MPM-specific survival (HR = 3.42; 95% CI = 1.57–7.42; p = 0.0019). These findings provide evidence that the genetic variation in immunomodulatory pathways may contribute to the development of secondary primary melanomas and also associates with MPM survival. The study suggests that inherited host immunity may play an important role in MPM development.
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11
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Ryan RJH, Wilcox RA. Ontogeny, Genetics, Molecular Biology, and Classification of B- and T-Cell Non-Hodgkin Lymphoma. Hematol Oncol Clin North Am 2019; 33:553-574. [PMID: 31229154 DOI: 10.1016/j.hoc.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mature B- and T-cell lymphomas are diverse in their biology, etiology, genetics, clinical behavior, and response to specific therapies. Here, we review the principles of diagnostic classification for non-Hodgkin lymphomas, summarize the characteristic features of major entities, and place recent biological and molecular findings in the context of principles that are applicable across the spectrum of mature lymphoid cancers.
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Affiliation(s)
- Russell James Hubbard Ryan
- Department of Pathology, University of Michigan Medical School, 4306 Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5936, USA.
| | - Ryan Alan Wilcox
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, 4310 Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5936, USA
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12
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McMaster ML, Berndt SI, Zhang J, Slager SL, Li SA, Vajdic CM, Smedby KE, Yan H, Birmann BM, Brown EE, Smith A, Kleinstern G, Fansler MM, Mayr C, Zhu B, Chung CC, Park JH, Burdette L, Hicks BD, Hutchinson A, Teras LR, Adami HO, Bracci PM, McKay J, Monnereau A, Link BK, Vermeulen RCH, Ansell SM, Maria A, Diver WR, Melbye M, Ojesina AI, Kraft P, Boffetta P, Clavel J, Giovannucci E, Besson CM, Canzian F, Travis RC, Vineis P, Weiderpass E, Montalvan R, Wang Z, Yeager M, Becker N, Benavente Y, Brennan P, Foretova L, Maynadie M, Nieters A, de Sanjose S, Staines A, Conde L, Riby J, Glimelius B, Hjalgrim H, Pradhan N, Feldman AL, Novak AJ, Lawrence C, Bassig BA, Lan Q, Zheng T, North KE, Tinker LF, Cozen W, Severson RK, Hofmann JN, Zhang Y, Jackson RD, Morton LM, Purdue MP, Chatterjee N, Offit K, Cerhan JR, Chanock SJ, Rothman N, Vijai J, Goldin LR, Skibola CF, Caporaso NE. Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia. Nat Commun 2018; 9:4182. [PMID: 30305637 PMCID: PMC6180091 DOI: 10.1038/s41467-018-06541-2] [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: 11/17/2017] [Accepted: 09/04/2018] [Indexed: 01/07/2023] Open
Abstract
Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P = 1.36 × 10-54) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 × 10-19). Both risk alleles are observed at a low frequency among controls (~2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.
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Affiliation(s)
- Mary L McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Jianqing Zhang
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Shengchao Alfred Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Karin E Smedby
- Department of Medicine, Solna Karolinska Institutet, Stockholm, 17176, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, 17176, Sweden
| | - Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Alex Smith
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, 10021, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Charles C Chung
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Ju-Hyun Park
- Department of Statistics, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Laurie Burdette
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Lauren R Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, 30303, GA, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, NO-0316, Norway
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, 94118, CA, USA
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, 69372, France
| | - Alain Monnereau
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, F-94807, France
- Université Paris Descartes, Paris, 75006, France
- Registry of Hematological Malignancies in Gironde, Institut Bergonié, University of Bordeaux, Inserm, Team EPICENE, UMR 1219, Bordeaux, 33000, France
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, 52242, IA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, 3508 TD, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, 55905, MN, USA
| | - Ann Maria
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, 30303, GA, USA
| | - Mads Melbye
- Division of Health Surveillance and Research, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, 2300, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Akinyemi I Ojesina
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Paolo Boffetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Jacqueline Clavel
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, F-94807, France
- Université Paris Descartes, Paris, 75006, France
| | - Edward Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Caroline M Besson
- Service d'hématologie et Oncologie, Centre Hospitalier de Versailles, Le Chesnay, Inserm U1018, Centre pour la Recherche en Epidémiologie et Santé des Populations (CESP), Villejuif, 78157, France
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, OX3 7LF, UK
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Human Genetics Foundation, Turin, 10126, Italy
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, 9019, Norway
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, 0379, Norway
- Genetic Epidemiology Group, Folkhälsan Research Center and University of Helsinki, Helsinki, 00250, Finland
| | | | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, 38105, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20877, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Baden-Württemberg, Germany
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, 69372, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and MF MU, Brno, 65653, Czech Republic
| | - Marc Maynadie
- EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, 21070, France
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, 79108, Baden-Württemberg, Germany
| | - Silvia de Sanjose
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin, 9, Ireland
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, 94720, CA, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75105, Sweden
| | - Henrik Hjalgrim
- Division of Health Surveillance and Research, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, 2300, Denmark
- Department of Hematology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Nisha Pradhan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, 55905, MN, USA
| | | | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, 02903, RI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, 98117, WA, USA
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, 06520, CT, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, 43210, OH, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
- Ontario Health Study, Toronto, M5S 1C6, ON, Canada
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, 21205, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, 21205, MD, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Lynn R Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, 30322, GA, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
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13
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Ye X, Zhao K, Wu C, Hu P, Fu H. Associations between genetic variants in immunoregulatory genes and risk of non-Hodgkin lymphoma in a Chinese population. Oncotarget 2018; 8:10450-10457. [PMID: 28060727 PMCID: PMC5354671 DOI: 10.18632/oncotarget.14426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 12/13/2016] [Indexed: 11/25/2022] Open
Abstract
We undertook a hospital-based case-control study to examine the associations between single nucleotide polymorphisms (SNPs) in selected immunoregulatory genes and non-Hodgkin lymphoma (NHL) risk in a Chinese population. One hundred and sixty-nine NHL patients diagnosed according to the World Health Organization (WHO) 2001 standard and 421 controls were recruited. Nine SNPs in three genes (IL-10, IL-1RN, and TNF-α) were selected based on predicted functions and previous study findings. Genetic association analysis was performed using the Cochran-Armitage trend test and multiple logistic regression. Four SNPs were associated with an increased risk of overall NHL: odds ratio per minor allele [ORper-minor-allele] and 95% confidence interval [CI] were 2.64 (1.75-3.98) for IL-10 rs1800893, 2.67 (1.72-4.16) for IL-1RN rs4251961, 1.80 (1.24-2.63) for TNF- α rs1800630, and 1.55 (1.02-2.37) for TNF- α rs2229094. These SNPs were also associated with an increased risk of diffuse large B-cell lymphoma (DLBCL). In addition, another SNP (TNF- α rs1041981) was associated with an increased risk of DLBCL (ORper-minor-allele=1.73, 95% CI 1.14-2.61). The findings provide evidence on the role of these immunoregulatory gene variants in NHL etiology.
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Affiliation(s)
- Xibiao Ye
- Department of Community Health Sciences, College of Medicine, Faculty of Health Sciences, University of Manitoba, Canada.,Vaccine and Drug Evaluation Centre, University of Manitoba, Canada.,Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kaiqiong Zhao
- Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Canada
| | - Cuie Wu
- School of Public Health, Fudan University, Shanghai, China
| | - Pingzhao Hu
- Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Canada
| | - Hua Fu
- School of Public Health, Fudan University, Shanghai, China
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14
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Chen X, Ma H, Wang Z, Zhang S, Yang H, Fang Z. EZH2 Palmitoylation Mediated by ZDHHC5 in p53-Mutant Glioma Drives Malignant Development and Progression. Cancer Res 2017; 77:4998-5010. [PMID: 28775165 DOI: 10.1158/0008-5472.can-17-1139] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/30/2017] [Accepted: 07/25/2017] [Indexed: 12/11/2022]
Abstract
Gliomas with mutant p53 occurring in 30% of glioma patients exhibit therapeutic resistance and poor outcomes. In this study, we identify a novel mechanism through which mutant p53 drives cancer cell survival and malignant growth. We documented overexpression of the zinc finger protein ZDHHC5 in glioma compared with normal brain tissue and that this event tightly correlated with p53 mutations. Mechanistic investigations revealed that mutant p53 transcriptionally upregulated ZDHHC5 along with the nuclear transcription factor NF-Y. These events contributed to the development of glioma by promoting the self-renewal capacity and tumorigenicity of glioma stem-like cells, by altering the palmitoylation and phosphorylation status of the tumor suppressor EZH2. Taken together, our work highlighted ZDHHC5 as a candidate therapeutic target for management of p53-mutated gliomas. Cancer Res; 77(18); 4998-5010. ©2017 AACR.
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Affiliation(s)
- Xueran Chen
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China. .,Cancer Hospital, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Huihui Ma
- Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China.,Department of Radiation Oncology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Zhen Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China.,Cancer Hospital, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Shangrong Zhang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China.,Cancer Hospital, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Haoran Yang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China.,Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Zhiyou Fang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China. .,Cancer Hospital, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
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15
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Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1. Sci Rep 2017; 7:6725. [PMID: 28751734 PMCID: PMC5532274 DOI: 10.1038/s41598-017-06810-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
Nephrotic syndrome (NS) occurs when the glomerular filtration barrier becomes excessively permeable leading to massive proteinuria. In childhood NS, immune system dysregulation has been implicated and increasing evidence points to the central role of podocytes in the pathogenesis. Children with NS are typically treated with an empiric course of glucocorticoid (Gc) therapy; a class of steroids that are activating ligands for the glucocorticoid receptor (GR) transcription factor. Although Gc-therapy has been the cornerstone of NS management for decades, the mechanism of action, and target cell, remain poorly understood. We tested the hypothesis that Gc acts directly on the podocyte to produce clinically useful effects without involvement of the immune system. In human podocytes, we demonstrated that the basic GR-signalling mechanism is intact and that Gc induced an increase in podocyte barrier function. Defining the GR-cistrome identified Gc regulation of motility genes. These findings were functionally validated with live-cell imaging. We demonstrated that treatment with Gc reduced the activity of the pro-migratory small GTPase regulator Rac1. Furthermore, Rac1 inhibition had a direct, protective effect on podocyte barrier function. Our studies reveal a new mechanism for Gc action directly on the podocyte, with translational relevance to designing new selective synthetic Gc molecules.
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16
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Law PJ, Sud A, Mitchell JS, Henrion M, Orlando G, Lenive O, Broderick P, Speedy HE, Johnson DC, Kaiser M, Weinhold N, Cooke R, Sunter NJ, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Carmichael J, Bailey JR, Pratt G, Rahman T, Pepper C, Fegan C, von Strandmann EP, Engert A, Försti A, Chen B, Filho MIDS, Thomsen H, Hoffmann P, Noethen MM, Eisele L, Jöckel KH, Allan JM, Swerdlow AJ, Goldschmidt H, Catovsky D, Morgan GJ, Hemminki K, Houlston RS. Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. Sci Rep 2017; 7:41071. [PMID: 28112199 PMCID: PMC5253627 DOI: 10.1038/srep41071] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/14/2016] [Indexed: 02/08/2023] Open
Abstract
B-cell malignancies (BCM) originate from the same cell of origin, but at different maturation stages and have distinct clinical phenotypes. Although genetic risk variants for individual BCMs have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. We explored genome-wide association studies of chronic lymphocytic leukaemia (CLL, N = 1,842), Hodgkin lymphoma (HL, N = 1,465) and multiple myeloma (MM, N = 3,790). We identified a novel pleiotropic risk locus at 3q22.2 (NCK1, rs11715604, P = 1.60 × 10-9) with opposing effects between CLL (P = 1.97 × 10-8) and HL (P = 3.31 × 10-3). Eight established non-HLA risk loci showed pleiotropic associations. Within the HLA region, Ser37 + Phe37 in HLA-DRB1 (P = 1.84 × 10-12) was associated with increased CLL and HL risk (P = 4.68 × 10-12), and reduced MM risk (P = 1.12 × 10-2), and Gly70 in HLA-DQB1 (P = 3.15 × 10-10) showed opposing effects between CLL (P = 3.52 × 10-3) and HL (P = 3.41 × 10-9). By integrating eQTL, Hi-C and ChIP-seq data, we show that the pleiotropic risk loci are enriched for B-cell regulatory elements, as well as an over-representation of binding of key B-cell transcription factors. These data identify shared biological pathways influencing the development of CLL, HL and MM. The identification of these risk loci furthers our understanding of the aetiological basis of BCMs.
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Affiliation(s)
- Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Jonathan S. Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - David C. Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nicola J. Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Graham H. Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Geoffrey Summerfield
- Department of Haematology, Queen Elizabeth Hospital, Gateshead, Newcastle upon Tyne, UK
| | - Robert J. Harris
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Andrew R. Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - David J. Allsup
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Jonathan Carmichael
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - James R. Bailey
- Queens Centre for Haematology and Oncology, Castle Hill Hospital, Hull and East Yorkshire NHS Trust, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Thahira Rahman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | | | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | | | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland
| | - Markus M. Noethen
- Institute of Human Genetics, University of Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Germany
| | | | | | - James M. Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center of Tumor Diseases, Heidelberg, Germany
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gareth J. Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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17
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Uçar F, Sönmez M, Ermantaş N, Özbaş HM, Cansız A, Balcı M, Yılmazz M. The associations of HLA-A, -B, DRB1 alleles and haplotypes in Turkish lymphoma patients. Gene 2016; 586:263-7. [DOI: 10.1016/j.gene.2016.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/06/2016] [Indexed: 01/21/2023]
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18
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Nielsen KR, Steffensen R, Bendtsen MD, Rodrigo-Domingo M, Baech J, Haunstrup TM, Bergkvist KS, Schmitz A, Boedker JS, Johansen P, Dybkaeær K, Boeøgsted M, Johnsen HE. Inherited Inflammatory Response Genes Are Associated with B-Cell Non-Hodgkin's Lymphoma Risk and Survival. PLoS One 2015; 10:e0139329. [PMID: 26448050 PMCID: PMC4598167 DOI: 10.1371/journal.pone.0139329] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Malignant B-cell clones are affected by both acquired genetic alterations and by inherited genetic variations changing the inflammatory tumour microenvironment. METHODS We investigated 50 inflammatory response gene polymorphisms in 355 B-cell non-Hodgkin's lymphoma (B-NHL) samples encompassing 216 diffuse large B cell lymphoma (DLBCL) and 139 follicular lymphoma (FL) and 307 controls. The effect of single genes and haplotypes were investigated and gene-expression analysis was applied for selected genes. Since interaction between risk genes can have a large impact on phenotype, two-way gene-gene interaction analysis was included. RESULTS We found inherited SNPs in genes critical for inflammatory pathways; TLR9, IL4, TAP2, IL2RA, FCGR2A, TNFA, IL10RB, GALNT12, IL12A and IL1B were significantly associated with disease risk and SELE, IL1RN, TNFA, TAP2, MBL2, IL5, CX3CR1, CHI3L1 and IL12A were, associated with overall survival (OS) in specific diagnostic entities of B-NHL. We discovered noteworthy interactions between DLBCL risk alleles on IL10 and IL4RA and FL risk alleles on IL4RA and IL4. In relation to OS, a highly significant interaction was observed in DLBCL for IL4RA (rs1805010) * IL10 (rs1800890) (HR = 0.11 (0.02-0.50)). Finally, we explored the expression of risk genes from the gene-gene interaction analysis in normal B-cell subtypes showing a different expression of IL4RA, IL10, IL10RB genes supporting a pathogenetic effect of these interactions in the germinal center. CONCLUSIONS The present findings support the importance of inflammatory genes in B-cell lymphomas. We found association between polymorphic sites in inflammatory response genes and risk as well as outcome in B-NHL and suggest an effect of gene-gene interactions during the stepwise oncogenesis.
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MESH Headings
- Aged
- Alleles
- Female
- Genotype
- Haplotypes
- Humans
- Interleukin-10/genetics
- Interleukin-10/metabolism
- Interleukin-10 Receptor beta Subunit/genetics
- Interleukin-10 Receptor beta Subunit/metabolism
- Interleukin-4/genetics
- Interleukin-4/metabolism
- Interleukin-4 Receptor alpha Subunit/genetics
- Interleukin-4 Receptor alpha Subunit/metabolism
- Linkage Disequilibrium
- Lymphoma, Follicular/etiology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/mortality
- Lymphoma, Large B-Cell, Diffuse/etiology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Male
- Middle Aged
- Odds Ratio
- Polymorphism, Single Nucleotide
- Proportional Hazards Models
- Risk
- Survival Analysis
- Transcriptome
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Affiliation(s)
- Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - John Baech
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Thure Mors Haunstrup
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Preben Johansen
- Department of Haematopathology, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkaeær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Martin Boeøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- * E-mail:
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19
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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.
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20
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Familial predisposition and genetic risk factors for lymphoma. Blood 2015; 126:2265-73. [PMID: 26405224 DOI: 10.1182/blood-2015-04-537498] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/11/2015] [Indexed: 02/06/2023] Open
Abstract
Our understanding of familial predisposition to lymphoma (collectively defined as non-Hodgkin lymphoma [NHL], Hodgkin lymphoma [HL], and chronic lymphocytic leukemia [CLL]) outside of rare hereditary syndromes has progressed rapidly during the last decade. First-degree relatives of NHL, HL, and CLL patients have an ∼1.7-fold, 3.1-fold, and 8.5-fold elevated risk of developing NHL, HL, and CLL, respectively. These familial risks are elevated for multiple lymphoma subtypes and do not appear to be confounded by nongenetic risk factors, suggesting at least some shared genetic etiology across the lymphoma subtypes. However, a family history of a specific subtype is most strongly associated with risk for that subtype, supporting subtype-specific genetic factors. Although candidate gene studies have had limited success in identifying susceptibility loci, genome-wide association studies (GWAS) have successfully identified 67 single nucleotide polymorphisms from 41 loci, predominately associated with specific subtypes. In general, these GWAS-discovered loci are common (minor allele frequency >5%), have small effect sizes (odds ratios, 0.60-2.0), and are of largely unknown function. The relatively low incidence of lymphoma, modest familial risk, and the lack of a screening test and associated intervention, all argue against active clinical surveillance for lymphoma in affected families at this time.
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21
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Koff JL, Chihara D, Phan A, Nastoupil LJ, Williams JN, Flowers CR. To Each Its Own: Linking the Biology and Epidemiology of NHL Subtypes. Curr Hematol Malig Rep 2015; 10:244-55. [PMID: 26104907 PMCID: PMC5738916 DOI: 10.1007/s11899-015-0267-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Non-Hodgkin lymphoma (NHL) constitutes a diverse group of more than 40 subtypes, each characterized by distinct biologic and clinical features. Until recently, pinpointing genetic and epidemiologic risk factors for individual subtypes has been limited by the relative rarity of each. However, several large pooled case-control studies have provided sufficient statistical power for detecting etiologic differences and commonalities between subtypes and thus yield new insight into their unique epidemiologic backgrounds. Here, we review the subtype-specific medical, lifestyle, and biologic components identified in these studies, which suggest that a complex interplay between host genetics, autoimmune disorders, modifiable risk factors, and occupation contributes to lymphomagenesis.
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Affiliation(s)
- Jean L Koff
- Winship Cancer Institute, Emory University School of Medicine, 1365 Clifton Rd NE, Building B, Suite 4302, Atlanta, GA, USA,
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22
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Nielsen KR, Steffensen R, Haunstrup TM, Bødker JS, Dybkær K, Baech J, Bøgsted M, Johnsen HE. Inherited variation in immune response genes in follicular lymphoma and diffuse large B-cell lymphoma. Leuk Lymphoma 2015; 56:3257-66. [PMID: 26044172 DOI: 10.3109/10428194.2015.1058936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) both depend on immune-mediated survival and proliferation signals from the tumor microenvironment. Inherited genetic variation influences this complex interaction. A total of 89 studies investigating immune-response genes in DLBCL and FL were critically reviewed. Relatively consistent association exists for variation in the tumor necrosis factor alpha (TNFA) and interleukin-10 loci and DLBCL risk; for DLBCL outcome association with the TNFA locus exists. Variations at chromosome 6p31-32 were associated with FL risk. Importantly, individual risk alleles have been shown to interact with each other. We suggest that the pathogenetic impact of polymorphic genes should include gene-gene interaction analysis and should be validated in preclinical model systems of normal B lymphopoiesis and B-cell malignancies. In the future, large cohort studies of interactions and genome-wide association studies are needed to extend the present findings and explore new risk alleles to be studied in preclinical models.
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Affiliation(s)
| | - Rudi Steffensen
- a Department of Clinical Immunology , Aalborg University Hospital , Denmark
| | | | | | - Karen Dybkær
- b Department of Haematology , Aalborg University Hospital.,c Clinical Cancer Research Center, Aalborg University Hospital , Denmark and Department of Clinical Medicine , Aalborg University , Denmark
| | - John Baech
- a Department of Clinical Immunology , Aalborg University Hospital , Denmark
| | - Martin Bøgsted
- b Department of Haematology , Aalborg University Hospital.,c Clinical Cancer Research Center, Aalborg University Hospital , Denmark and Department of Clinical Medicine , Aalborg University , Denmark
| | - Hans Erik Johnsen
- b Department of Haematology , Aalborg University Hospital.,c Clinical Cancer Research Center, Aalborg University Hospital , Denmark and Department of Clinical Medicine , Aalborg University , Denmark
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23
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Vijai J, Wang Z, Berndt SI, Skibola CF, Slager SL, de Sanjose S, Melbye M, Glimelius B, Bracci PM, Conde L, Birmann BM, Wang SS, Brooks-Wilson AR, Lan Q, de Bakker PIW, Vermeulen RCH, Portlock C, Ansell SM, Link BK, Riby J, North KE, Gu J, Hjalgrim H, Cozen W, Becker N, Teras LR, Spinelli JJ, Turner J, Zhang Y, Purdue MP, Giles GG, Kelly RS, Zeleniuch-Jacquotte A, Ennas MG, Monnereau A, Bertrand KA, Albanes D, Lightfoot T, Yeager M, Chung CC, Burdett L, Hutchinson A, Lawrence C, Montalvan R, Liang L, Huang J, Ma B, Villano DJ, Maria A, Corines M, Thomas T, Novak AJ, Dogan A, Liebow M, Thompson CA, Witzig TE, Habermann TM, Weiner GJ, Smith MT, Holly EA, Jackson RD, Tinker LF, Ye Y, Adami HO, Smedby KE, De Roos AJ, Hartge P, Morton LM, Severson RK, Benavente Y, Boffetta P, Brennan P, Foretova L, Maynadie M, McKay J, Staines A, Diver WR, Vajdic CM, Armstrong BK, Kricker A, Zheng T, Holford TR, Severi G, Vineis P, Ferri GM, Ricco R, Miligi L, Clavel J, Giovannucci E, Kraft P, Virtamo J, Smith A, Kane E, Roman E, Chiu BCH, Fraumeni JF, Wu X, Cerhan JR, Offit K, Chanock SJ, Rothman N, Nieters A. A genome-wide association study of marginal zone lymphoma shows association to the HLA region. Nat Commun 2015; 6:5751. [PMID: 25569183 PMCID: PMC4287989 DOI: 10.1038/ncomms6751] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 11/04/2014] [Indexed: 01/07/2023] Open
Abstract
Marginal zone lymphoma (MZL) is the third most common subtype of B-cell non-Hodgkin lymphoma. Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. This is the first evidence that genetic variation in the major histocompatibility complex influences MZL susceptibility.
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Affiliation(s)
- Joseph Vijai
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20877, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Christine F. Skibola
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama 35233, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California 94720, USA
| | - Susan L. Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Silvia de Sanjose
- Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d’Oncologia, IDIBELL, Barcelona 8907, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona 8036, Spain
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Bengt Glimelius
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm 17176, Sweden
- Department of Radiology, Oncology and Radiation Science, Uppsala University, Uppsala 75105, Sweden
| | - Paige M. Bracci
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California 94118, USA
| | - Lucia Conde
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama 35233, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California 94720, USA
| | - Brenda M. Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sophia S. Wang
- Department of Cancer Etiology, City of Hope Beckman Research Institute, Duarte, California 91030, USA
| | - Angela R. Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z1L3
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada V5A1S6
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Paul I. W. de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Roel C. H. Vermeulen
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, The Netherlands
| | - Carol Portlock
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Stephen M. Ansell
- Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Brian K. Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama 35233, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California 94720, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jian Gu
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Lauren R. Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - John J. Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z1L3
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z3
| | - Jenny Turner
- Pathology, Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Macquarie Park, New South Wales 2113, Australia
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, USA
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3053, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, Victoria 3010, Australia
| | - Rachel S. Kelly
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, New York 10016, USA
- Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Maria Grazia Ennas
- Department of Biomedical Science, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Alain Monnereau
- Environmental Epidemiology of Cancer Group, Inserm, Centre for research in Epidemiology and Population Health (CESP), U1018, Villejuif F-94807, France
- UMRS 1018, Univ Paris Sud, Villejuif F-94807, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux 33076, France
| | - Kimberly A. Bertrand
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Tracy Lightfoot
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20877, USA
| | - Charles C. Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20877, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20877, USA
| | | | | | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Baoshan Ma
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Danylo J. Villano
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Maria
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Marina Corines
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Tinu Thomas
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anne J. Novak
- Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Mark Liebow
- Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | - Thomas E. Witzig
- Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | - George J. Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Martyn T. Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California 94720, USA
| | - Elizabeth A. Holly
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California 94118, USA
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, Ohio 43210, USA
| | - Lesley F. Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98117, USA
| | - Yuanqing Ye
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hans-Olov Adami
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Karin E. Smedby
- Department of Medicine Solna, Karolinska Institutet, Stockholm 17176, Sweden
| | - Anneclaire J. De Roos
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98117, USA
- Department of Environmental and Occupational Health, Drexel University School of Public Health, Philadelphia, Pennsylvania 19104, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Richard K. Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Yolanda Benavente
- Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d’Oncologia, IDIBELL, Barcelona 8907, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona 8036, Spain
| | - Paolo Boffetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Paul Brennan
- Group of Genetic Epidemiology, Section of Genetics, International Agency for Research on Cancer, Lyon 69372, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and MF MU, Brno 65653, Czech Republic
| | - Marc Maynadie
- EA 4184, Registre des Hémopathies Malignes de Côte d’Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - James McKay
- Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer, Lyon 69372, France
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin 9, Ireland
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Claire M. Vajdic
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Bruce K. Armstrong
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tongzhang Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, USA
| | - Theodore R. Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06520, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3053, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, Victoria 3010, Australia
- Human Genetics Foundation, Turin 10126, Italy
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
- Human Genetics Foundation, Turin 10126, Italy
| | - Giovanni M. Ferri
- Interdisciplinary Department of Medicine, University of Bari, Bari 70124, Italy
| | - Rosalia Ricco
- Department of Pathological Anatomy, University of Bari, Bari 70124, Italy
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence 50139, Italy
| | - Jacqueline Clavel
- Environmental Epidemiology of Cancer Group, Inserm, Centre for research in Epidemiology and Population Health (CESP), U1018, Villejuif F-94807, France
- UMRS 1018, Univ Paris Sud, Villejuif F-94807, France
| | - Edward Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Alex Smith
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Brian C. H. Chiu
- Department of Health Studies, University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph F. Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Xifeng Wu
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - James R. Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Alexandra Nieters
- Center For Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg 79108, Germany
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24
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Cerhan JR, Berndt SI, Vijai J, Ghesquières H, McKay J, Wang SS, Wang Z, Yeager M, Conde L, de Bakker PIW, Nieters A, Cox D, Burdett L, Monnereau A, Flowers CR, De Roos AJ, Brooks-Wilson AR, Lan Q, Severi G, Melbye M, Gu J, Jackson RD, Kane E, Teras LR, Purdue MP, Vajdic CM, Spinelli JJ, Giles GG, Albanes D, Kelly RS, Zucca M, Bertrand KA, Zeleniuch-Jacquotte A, Lawrence C, Hutchinson A, Zhi D, Habermann TM, Link BK, Novak AJ, Dogan A, Asmann YW, Liebow M, Thompson CA, Ansell SM, Witzig TE, Weiner GJ, Veron AS, Zelenika D, Tilly H, Haioun C, Molina TJ, Hjalgrim H, Glimelius B, Adami HO, Bracci PM, Riby J, Smith MT, Holly EA, Cozen W, Hartge P, Morton LM, Severson RK, Tinker LF, North KE, Becker N, Benavente Y, Boffetta P, Brennan P, Foretova L, Maynadie M, Staines A, Lightfoot T, Crouch S, Smith A, Roman E, Diver WR, Offit K, Zelenetz A, Klein RJ, Villano DJ, Zheng T, Zhang Y, Holford TR, Kricker A, Turner J, Southey MC, Clavel J, Virtamo J, Weinstein S, Riboli E, Vineis P, Kaaks R, Trichopoulos D, Vermeulen RCH, Boeing H, Tjonneland A, Angelucci E, Di Lollo S, Rais M, Birmann BM, Laden F, Giovannucci E, Kraft P, Huang J, Ma B, Ye Y, Chiu BCH, Sampson J, Liang L, Park JH, Chung CC, Weisenburger DD, Chatterjee N, Fraumeni JF, Slager SL, Wu X, de Sanjose S, Smedby KE, Salles G, Skibola CF, Rothman N, Chanock SJ. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma. Nat Genet 2014; 46:1233-8. [PMID: 25261932 PMCID: PMC4213349 DOI: 10.1038/ng.3105] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/04/2014] [Indexed: 12/14/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 × 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 × 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 × 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 × 10(-13) and 3.63 × 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.
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Affiliation(s)
- James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Hervé Ghesquières
- 1] Department of Hematology, Centre Léon Bérard, Lyon, France. [2] Laboratoire de Biologie Moléculaire de la Cellule, UMR 5239, CNRS, Pierre-Benite, France
| | - James McKay
- Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Sophia S Wang
- Department of Cancer Etiology, City of Hope Beckman Research Institute, Duarte, California, USA
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland, USA
| | - Lucia Conde
- 1] Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama, USA. [2] Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California, USA
| | - Paul I W de Bakker
- 1] Department of Medical Genetics and of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | | | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland, USA
| | - Alain Monnereau
- 1] Environmental Epidemiology of Cancer Group, INSERM, Centre for Research in Epidemiology and Population Health (CESP), Villejuif, France. [2] UMRS 1018, Université Paris Sud, Villejuif, France. [3] Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, Bordeaux, France
| | - Christopher R Flowers
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Anneclaire J De Roos
- 1] Department of Environmental and Occupational Health, Drexel University School of Public Health, Philadelphia, Pennsylvania, USA. [2] Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Angela R Brooks-Wilson
- 1] Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Gianluca Severi
- 1] Human Genetics Foundation, Turin, Italy. [2] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [3] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, Victoria, Australia
| | - Mads Melbye
- 1] Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark. [2] Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, Ohio, USA
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, UK
| | - Lauren R Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Claire M Vajdic
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - John J Spinelli
- 1] Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Graham G Giles
- 1] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [2] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, Victoria, Australia
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Rachel S Kelly
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Medical Research Council (MRC)-Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Mariagrazia Zucca
- Department of Biomedical Science, University of Cagliari, Monserrato, Italy
| | - Kimberly A Bertrand
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Anne Zeleniuch-Jacquotte
- 1] Department of Population Health, New York University School of Medicine, New York, New York, USA. [2] Cancer Institute, New York University School of Medicine, New York, New York, USA
| | | | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland, USA
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Anne J Novak
- Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ahmet Dogan
- Department of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yan W Asmann
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, Florida, USA
| | - Mark Liebow
- Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Thomas E Witzig
- Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | | | | | | | - Corinne Haioun
- Department of Hematology, Centre Hospitalier Universitaire (CHU) Henri Mondor, Creteil, France
| | - Thierry Jo Molina
- Department of Pathology, Necker Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Bengt Glimelius
- 1] Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden. [2] Department of Radiology, Oncology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Hans-Olov Adami
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Jacques Riby
- 1] Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama, USA. [2] Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Wendy Cozen
- 1] Department of Preventive Medicine, University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kari E North
- 1] Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yolanda Benavente
- 1] Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d'Oncologia, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain. [2] Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Paolo Boffetta
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paul Brennan
- Group of Genetic Epidemiology, Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic
| | - Marc Maynadie
- Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin, Ireland
| | | | - Simon Crouch
- Department of Health Sciences, University of York, York, UK
| | - Alex Smith
- Department of Health Sciences, University of York, York, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, UK
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Andrew Zelenetz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Robert J Klein
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Danylo J Villano
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Tongzhang Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne Kricker
- Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia
| | - Jenny Turner
- 1] Pathology, Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales, Australia. [2] Department of Histopathology, Douglass Hanly Moir Pathology, Macquarie Park, New South Wales, Australia
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Jacqueline Clavel
- 1] Environmental Epidemiology of Cancer Group, INSERM, Centre for Research in Epidemiology and Population Health (CESP), Villejuif, France. [2] UMRS 1018, Université Paris Sud, Villejuif, France
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Paolo Vineis
- 1] Human Genetics Foundation, Turin, Italy. [2] Medical Research Council (MRC)-Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dimitrios Trichopoulos
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece. [3] Hellenic Health Foundation, Athens, Greece
| | - Roel C H Vermeulen
- 1] Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Heiner Boeing
- Department of Epidemiology, German Institute for Human Nutrition, Potsdam, Germany
| | | | - Emanuele Angelucci
- Hematology Unit, Ospedale Oncologico di Riferimento Regionale A. Businco, Cagliari, Italy
| | - Simonetta Di Lollo
- Department of Surgery and Translational Medicine, Section of Anatomo-Pathology, University of Florence, Florence, Italy
| | - Marco Rais
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Italy
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francine Laden
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [3] Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Edward Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [3] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Peter Kraft
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Baoshan Ma
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] College of Information Science and Technology, Dalian Maritime University, Dalian, China
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Brian C H Chiu
- Department of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Liming Liang
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Dennis D Weisenburger
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Silvia de Sanjose
- 1] Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d'Oncologia, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain. [2] Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Karin E Smedby
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Gilles Salles
- 1] Laboratoire de Biologie Moléculaire de la Cellule, UMR 5239, CNRS, Pierre-Benite, France. [2] Department of Hematology, Hospices Civils de Lyon, Pierre-Benite, France. [3] Department of Hematology, Université Lyon 1, Pierre-Benite, France
| | - Christine F Skibola
- 1] Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, Alabama, USA. [2] Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, California, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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25
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Skibola CF, Berndt SI, Vijai J, Conde L, Wang Z, Yeager M, de Bakker PIW, Birmann BM, Vajdic CM, Foo JN, Bracci PM, Vermeulen RCH, Slager SL, de Sanjose S, Wang SS, Linet MS, Salles G, Lan Q, Severi G, Hjalgrim H, Lightfoot T, Melbye M, Gu J, Ghesquières H, Link BK, Morton LM, Holly EA, Smith A, Tinker LF, Teras LR, Kricker A, Becker N, Purdue MP, Spinelli JJ, Zhang Y, Giles GG, Vineis P, Monnereau A, Bertrand KA, Albanes D, Zeleniuch-Jacquotte A, Gabbas A, Chung CC, Burdett L, Hutchinson A, Lawrence C, Montalvan R, Liang L, Huang J, Ma B, Liu J, Adami HO, Glimelius B, Ye Y, Nowakowski GS, Dogan A, Thompson CA, Habermann TM, Novak AJ, Liebow M, Witzig TE, Weiner GJ, Schenk M, Hartge P, De Roos AJ, Cozen W, Zhi D, Akers NK, Riby J, Smith MT, Lacher M, Villano DJ, Maria A, Roman E, Kane E, Jackson RD, North KE, Diver WR, Turner J, Armstrong BK, Benavente Y, Boffetta P, Brennan P, Foretova L, Maynadie M, Staines A, McKay J, Brooks-Wilson AR, Zheng T, Holford TR, Chamosa S, Kaaks R, Kelly RS, Ohlsson B, Travis RC, Weiderpass E, Clavel J, Giovannucci E, Kraft P, Virtamo J, Mazza P, Cocco P, Ennas MG, Chiu BCH, Fraumeni JF, Nieters A, Offit K, Wu X, Cerhan JR, Smedby KE, Chanock SJ, Rothman N. Genome-wide association study identifies five susceptibility loci for follicular lymphoma outside the HLA region. Am J Hum Genet 2014; 95:462-71. [PMID: 25279986 PMCID: PMC4185120 DOI: 10.1016/j.ajhg.2014.09.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/10/2014] [Indexed: 11/20/2022] Open
Abstract
Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10(-20)) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10(-11)) near ETS1; 3q28 (rs6444305, p = 1.10 × 10(-10)) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10(-10)) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10(-8)) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRβ1 multiallelic amino acids at positions 11, 13, 28, and 30 that were associated with FL risk (pomnibus = 4.20 × 10(-67) to 2.67 × 10(-70)). Additional independent signals included rs17203612 in HLA class II (odds ratio [OR(per-allele)] = 1.44; p = 4.59 × 10(-16)) and rs3130437 in HLA class I (OR(per-allele) = 1.23; p = 8.23 × 10(-9)). Our findings further expand the number of loci associated with FL and provide evidence that multiple common variants outside the HLA region make a significant contribution to FL risk.
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Affiliation(s)
- Christine F Skibola
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, AL 35233, USA; Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA 94720, USA.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lucia Conde
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, AL 35233, USA; Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA 94720, USA
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD 20877, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD 20877, USA
| | - Paul I W de Bakker
- Department of Medical Genetics and of Epidemiology, University Medical Center Utrecht, Utrecht 3584 CG, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, the Netherlands
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Claire M Vajdic
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jia-Nee Foo
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Paige M Bracci
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Roel C H Vermeulen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Silvia de Sanjose
- Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d'Oncologia, IDIBELL, Barcelona 8907, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona 8036, Spain
| | - Sophia S Wang
- Department of Cancer Etiology, City of Hope Beckman Research Institute, Duarte, CA 91030, USA
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gilles Salles
- Department of Hematology, Hospices Civils de Lyon, Pierre benite Cedex 69495, France; Department of Hematology, Université Lyon-1, Pierre benite Cedex 69495, France; Laboratoire de Biologie Moléculaire de la Cellule UMR 5239, Centre National de la Recherche Scientifique, Pierre benite Cedex 69495, France
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gianluca Severi
- Human Genetics Foundation, Turin 10126, Italy; Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3053, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, VIC 3010, Australia
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Tracy Lightfoot
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jian Gu
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Hervé Ghesquières
- Laboratoire de Biologie Moléculaire de la Cellule UMR 5239, Centre National de la Recherche Scientifique, Pierre benite Cedex 69495, France; Department of Hematology, Centre Léon Bérard, Lyon 69008, France
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Elizabeth A Holly
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Alex Smith
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98117, USA
| | - Lauren R Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3053, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, VIC 3010, Australia
| | - Paolo Vineis
- Human Genetics Foundation, Turin 10126, Italy; MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Alain Monnereau
- Environmental Epidemiology of Cancer Group, Inserm, Centre for Research in Epidemiology and Population Health (CESP), U1018, Villejuif Cedex 94807, France; UMRS 1018, Université Paris Sud, Villejuif Cedex 94807, France; Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux Cedex 33076, France
| | - Kimberly A Bertrand
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY 10016, USA; Cancer Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD 20877, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD 20877, USA
| | | | | | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Baoshan Ma
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; College of Information Science and Technology, Dalian Maritime University, Dalian, Liaoning Province 116026, China
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Hans-Olov Adami
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Bengt Glimelius
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm 17176, Sweden; Department of Radiology, Oncology and Radiation Science, Uppsala University, Uppsala 75105, Sweden
| | - Yuanqing Ye
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | | | - Anne J Novak
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mark Liebow
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas E Witzig
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Maryjean Schenk
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anneclaire J De Roos
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98117, USA; Department of Environmental and Occupational Health, Drexel University School of Public Health, Philadelphia, PA 19104, USA
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Nicholas K Akers
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA 94720, USA
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, Birmingham, AL 35233, USA; Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA 94720, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA 94720, USA
| | - Mortimer Lacher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danylo J Villano
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ann Maria
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH 43210, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Jenny Turner
- Department of Anatomical Pathology, Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia; Department of Histopathology, Douglass Hanly Moir Pathology, Macquarie Park, NSW 2113, Australia
| | - Bruce K Armstrong
- Sydney School of Public Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yolanda Benavente
- Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Programme, Institut Catala d'Oncologia, IDIBELL, Barcelona 8907, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona 8036, Spain
| | - Paolo Boffetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul Brennan
- Group of Genetic Epidemiology, Section of Genetics, International Agency for Research on Cancer, Lyon 69372, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and MF MU, Brno 656 53, Czech Republic
| | - Marc Maynadie
- EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin 9, Ireland
| | - James McKay
- Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer, Lyon 69372, France
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Tongzhang Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
| | - Saioa Chamosa
- Health Department, BioDonostia Research Institute, Basque Region 20014, Spain
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany
| | - Rachel S Kelly
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Bodil Ohlsson
- Department of Clinical Sciences, Division of Internal Medicine, Skåne University Hospital, Lund University, Malmö 205 02, Sweden
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden; Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Breivika 9037, Norway; Cancer Registry of Norway, Oslo 0304, Norway; Department of Genetic Epidemiology, Folkhalsan Research Center, Helsinki 00250, Finland
| | - Jacqueline Clavel
- Environmental Epidemiology of Cancer Group, Inserm, Centre for Research in Epidemiology and Population Health (CESP), U1018, Villejuif Cedex 94807, France; UMRS 1018, Université Paris Sud, Villejuif Cedex 94807, France
| | - Edward Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Patrizio Mazza
- Department of Hematology, Ospedale Nord, Taranto 74100, Italy
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Maria Grazia Ennas
- Department of Biomedical Science, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Brian C H Chiu
- Department of Health Studies, University of Chicago, Chicago, IL 60637, USA
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg 79108, Germany
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xifeng Wu
- Department of Epidemiology, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Karin E Smedby
- Department of Medicine Solna, Karolinska Institutet, Stockholm 17176, Sweden
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Kelly RS, Vineis P. Biomarkers of susceptibility to chemical carcinogens: the example of non-Hodgkin lymphomas. Br Med Bull 2014; 111:89-100. [PMID: 25114269 DOI: 10.1093/bmb/ldu015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Genetic susceptibly to suspected chemical and environmental carcinogens may modify the response to exposure. The aim of this review was to explore the issues involved in the study of gene-environment interactions, and to consider the use of susceptibility biomarkers in cancer epidemiology, using non-Hodgkin lymphoma (NHL) as an example. SOURCES OF DATA PubMed, EMBASE and Web of Science were searched for peer-reviewed articles considering biomarkers of susceptibility to chemical, agricultural and industrial carcinogens in the aetiology of NHL. AREAS OF AGREEMENT The results suggest a modifying role for genetic susceptibility to a number of occupational and environmental exposures including organochlorines, chlorinated solvents, chlordanes and benzene in the aetiology of NHL. The potential importance of these gene-environment interactions in NHL may help to explain the lack of definitive carcinogens identified to date for this malignancy. AREAS OF CONTROVERSY Although a large number of genetic variants and gene-environment interactions have been explored for NHL, to date replication is lacking and therefore the findings remain to be validated. GROWING POINTS AND AREAS TIMELY FOR DEVELOPING RESEARCH These findings highlight the need for novel standardized methodologies in the study of genetic susceptibility to chemical carcinogens.
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Affiliation(s)
- Rachel S Kelly
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK HuGef Foundation, Torino, Italy
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Copy number variation analysis on a non-Hodgkin lymphoma case-control study identifies an 11q25 duplication associated with diffuse large B-cell lymphoma. PLoS One 2014; 9:e105382. [PMID: 25133503 PMCID: PMC4136881 DOI: 10.1371/journal.pone.0105382] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/23/2014] [Indexed: 11/19/2022] Open
Abstract
Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the LOC283177 long non-coding RNA that was further confirmed by quantitative PCR. For chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), known somatic deletions were identified on chromosomes 13q14, 11q22-23, 14q32 and 22q11.22. Our study shows that GWAS data can be used to identify germline CNVs associated with disease risk for DLBCL and somatic CNVs for CLL/SLL.
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Rendleman J, Antipin Y, Reva B, Adaniel C, Przybylo JA, Dutra-Clarke A, Hansen N, Heguy A, Huberman K, Borsu L, Paltiel O, Ben-Yehuda D, Brown JR, Freedman AS, Sander C, Zelenetz A, Klein RJ, Shao Y, Lacher M, Vijai J, Offit K, Kirchhoff T. Genetic variation in DNA repair pathways and risk of non-Hodgkin's lymphoma. PLoS One 2014; 9:e101685. [PMID: 25010664 PMCID: PMC4092067 DOI: 10.1371/journal.pone.0101685] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 06/10/2014] [Indexed: 01/27/2023] Open
Abstract
Molecular and genetic evidence suggests that DNA repair pathways may contribute to lymphoma susceptibility. Several studies have examined the association of DNA repair genes with lymphoma risk, but the findings from these reports have been inconsistent. Here we provide the results of a focused analysis of genetic variation in DNA repair genes and their association with the risk of non-Hodgkin's lymphoma (NHL). With a population of 1,297 NHL cases and 1,946 controls, we have performed a two-stage case/control association analysis of 446 single nucleotide polymorphisms (SNPs) tagging the genetic variation in 81 DNA repair genes. We found the most significant association with NHL risk in the ATM locus for rs227060 (OR = 1.27, 95% CI: 1.13-1.43, p = 6.77×10(-5)), which remained significant after adjustment for multiple testing. In a subtype-specific analysis, associations were also observed for the ATM locus among both diffuse large B-cell lymphomas (DLBCL) and small lymphocytic lymphomas (SLL), however there was no association observed among follicular lymphomas (FL). In addition, our study provides suggestive evidence of an interaction between SNPs in MRE11A and NBS1 associated with NHL risk (OR = 0.51, 95% CI: 0.34-0.77, p = 0.0002). Finally, an imputation analysis using the 1,000 Genomes Project data combined with a functional prediction analysis revealed the presence of biologically relevant variants that correlate with the observed association signals. While the findings generated here warrant independent validation, the results of our large study suggest that ATM may be a novel locus associated with the risk of multiple subtypes of NHL.
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Affiliation(s)
- Justin Rendleman
- NYU School of Medicine, New York University, New York, New York, United States of America
| | - Yevgeniy Antipin
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Boris Reva
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Christina Adaniel
- NYU School of Medicine, New York University, New York, New York, United States of America
| | - Jennifer A. Przybylo
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ana Dutra-Clarke
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Nichole Hansen
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Adriana Heguy
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Kety Huberman
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Laetitia Borsu
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ora Paltiel
- Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dina Ben-Yehuda
- Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Jennifer R. Brown
- Dana Farber Cancer Center, Harvard University, Boston, Massachusetts, United States of America
| | - Arnold S. Freedman
- Dana Farber Cancer Center, Harvard University, Boston, Massachusetts, United States of America
| | - Chris Sander
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Andrew Zelenetz
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Robert J. Klein
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Yongzhao Shao
- NYU School of Medicine, New York University, New York, New York, United States of America
| | - Mortimer Lacher
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Joseph Vijai
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Kenneth Offit
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Tomas Kirchhoff
- NYU School of Medicine, New York University, New York, New York, United States of America
- * E-mail:
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Rodriguez-Fontenla C, Calaza M, Gonzalez A. Genetic distance as an alternative to physical distance for definition of gene units in association studies. BMC Genomics 2014; 15:408. [PMID: 24884992 PMCID: PMC4048458 DOI: 10.1186/1471-2164-15-408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as ±50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances. RESULTS Standardized recombination rates (SRR) from the deCODE recombination map were used as units of genetic distances. We searched for a SRR producing flanking sequences near the ±50 Kb offset that has been common in previous studies. A SRR≥2 was selected because it led to gene extensions with median length=45.3 Kb and the simplicity of an integer value. As expected, boundaries of the genes defined with the ±50 Kb and with the SRR≥2 rules were rarely concordant. The impact of these differences was illustrated with the interpretation of top association signals from two large studies including many hits and their detailed analysis based in different criteria. The definition based in genetic distance was more concordant with the results of these studies than the based in physical distance. In the analysis of 18 top disease associated loci form the first study, the SRR≥2 genes led to a fully concordant interpretation in 17 loci; the ±50 Kb genes only in 6. Interpretation of the 43 putative functional genes of the second study based in the SRR≥2 definition only missed 4 of the genes, whereas the based in the ±50 Kb definition missed 10 genes. CONCLUSIONS A gene definition based on genetic distance led to results more concordant with expert detailed analyses than the commonly used based in physical distance. The genome coordinates for each gene are provided to maintain a simple use of the new definitions.
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Affiliation(s)
| | | | - Antonio Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain.
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Different role of tumor necrosis factor-α polymorphism in non-Hodgkin lymphomas among Caucasian and Asian populations: a meta-analysis. Int J Mol Sci 2014; 15:7684-98. [PMID: 24857911 PMCID: PMC4057699 DOI: 10.3390/ijms15057684] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/15/2014] [Accepted: 04/23/2014] [Indexed: 01/26/2023] Open
Abstract
Tumor necrosis factor-α (TNF-α) is an immunoregulatory cytokine involved in B- and T-cell function, and also plays an important role in inflammation and cancer. TNF-α-308G>A has been associated with constitutively elevated TNF-α expression. Several studies have reported the association between the TNF-α-308G>A polymorphism and non-Hodgkin lymphomas (NHL) risk, however, results are still inconsistent. To solve these conflicts, we conducted the first meta-analysis to assess the effect of TNF-α-308G>A polymorphism on the risk of NHL and various subtypes (additive model) including 10,619 cases and 12,977 controls in Caucasian and Asian populations. Our meta-analysis indicated that TNF-α-308G>A polymorphism is not associated with NHL risk when pooling all studies together (OR=1.06, 95% CI: 0.92-1.23, p=0.413). In stratified analyses, we found TNF-α-308A allele was significantly associated with higher risk of NHL, B-cell lymphomas (BCL), T-cell lymphomas (TCL) and diffuse large B-cell lymphomas (DLBCL) in Caucasians (OR=1.22, 95% CI: 1.06-1.40, p=0.007; OR=1.18, 95% CI: 1.03-1.34, p=0.014; OR=1.20, 95% CI: 1.01-1.42, p=0.040; OR=1.21, 95% CI: 1.11-1.32, p<0.001, respectively). Interestingly, it was associated with decreased risk of NHL, BCL and DLBCL in Asians (OR=0.75, 95% CI: 0.66-0.86, p<0.001; OR=0.70, 95% CI: 0.52-0.94, p=0.018; OR=0.70, 95% CI: 0.57-0.86, p=0.001). These findings also suggest TNF-α might play a distinct role in pathogenesis of NHL in different populations.
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Xie Y, Diao L, Zhang L, Liu C, Xu Z, Liu S. A miR-SNP of the KRT81 gene is associated with the prognosis of non-Hodgkin's lymphoma. Gene 2014; 539:198-202. [PMID: 24530479 DOI: 10.1016/j.gene.2014.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022]
Abstract
MicroRNA (miRNA), which plays an important role in tumorigenesis, can regulate post-transcriptional gene expression by binding to the 3' untranslated regions (3'-UTRs) of messenger RNAs and repressing its translation. Several single nucleotide polymorphisms (SNPs) are considered to have significant impacts on susceptibility of the role these genetic polymorphisms in development of carcinogenesis through that mechanism. But few of them focus their impact on non-Hodgkin's lymphoma (NHL). Therefore, we conducted this study to investigate the associations between the genetic variants and cancer risk or cancer outcome. MiRNA-related single nucleotide polymorphism (miR-SNP) sites rs3660 of KRT81, rs1044129 of RYR3, rs4901706 of f101, and rs1053667 of KIAA0423 were selected and analyzed in 210 patients in NHL to evaluate their association with cancer risk and prognosis. The results indicated that none of them is associated with the cancer risk in NHL. Otherwise KRT81 rs3660 GG type is associated with a shorter survival time (p=0.012), after being assessed by multivariate Cox analyses, its effect on prognosis was verified (p=0.003). It suggests that KRT81 rs3660 GG type is an independent prognostic marker in NHL.
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Affiliation(s)
- Ying Xie
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Lanping Diao
- Department of Hematology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Li Zhang
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Chao Liu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Zengnian Xu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China
| | - Shufeng Liu
- Hebei Key Lab of Laboratory Animal Science, Department of Laboratory Animal Science, Hebei Medical University, Shijiazhuang, PR China.
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Li J, Jiang R, Liu WS, Liu Q, Xu M, Feng QS, Chen LZ, Bei JX, Chen MY, Zeng YX. A large cohort study reveals the association of elevated peripheral blood lymphocyte-to-monocyte ratio with favorable prognosis in nasopharyngeal carcinoma. PLoS One 2013; 8:e83069. [PMID: 24386144 PMCID: PMC3873908 DOI: 10.1371/journal.pone.0083069] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/08/2013] [Indexed: 02/06/2023] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is an endemic neoplasm in southern China. Although NPC sufferers are sensitive to radiotherapy, 20–30% of patients finally progress with recurrence and metastases. Elevated lymphocyte-to-monocyte ratio (LMR) has been reported to be associated with favorable prognosis in some hematology malignancies, but has not been studied in NPC. The aim of this study was to evaluate whether LMR could predict the prognosis of NPC patients. Methods A retrospective cohort of 1,547 non-metastatic NPC patients was recruited between January 2005 and June 2008. The counts for peripheral lymphocyte and monocyte were retrieved, and the LMR was calculated. Receiver operating characteristic curve analysis, univariate and multivariate COX proportional hazards analyses were applied to evaluate the associations of LMR with overall survival (OS), disease-free survival (DFS), distant metastasis-free survival (DMFS) and loco-regional recurrence-free survival (LRRFS), respectively. Results Univariate analysis revealed that higher LMR level (≥5.220) was significantly associated with superior OS, DFS and DMFS (P values <0.001). The higher lymphocyte count (≥2.145×109/L) was significantly associated with better OS (P = 0.002) and DMFS (P = 0.031), respectively, while the lower monocyte count (<0.475×109/L) was associated with better OS (P = 0.012), DFS (P = 0.011) and DMFS (P = 0.003), respectively. Multivariate Cox proportional hazard analysis showed that higher LMR level was a significantly independent predictor for superior OS (hazard ratio or HR = 0.558, 95% confidence interval or 95% CI = 0.417–0.748; P<0.001), DFS (HR = 0.669, 95% CI = 0.535–0.838; P<0.001) and DMFS (HR = 0.543, 95% CI = 0.403–0.732; P<0.001), respectively. The advanced T and N stages were also independent indicators for worse OS, DFS, and DMFS, except that T stage showed borderline statistical significance for DFS (P = 0.053) and DMFS (P = 0.080). Conclusions The elevated pretreatment peripheral LMR level was a significant favorable factor for NPC prognosis and this easily accessed variable may serve as a potent marker to predict the outcomes of NPC patients.
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Affiliation(s)
- Jing Li
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Rou Jiang
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Wen-Sheng Liu
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Qing Liu
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Epidemiology, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
| | - Miao Xu
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Qi-Sheng Feng
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Li-Zhen Chen
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Jin-Xin Bei
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ming-Yuan Chen
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- * E-mail: (MYC); (YXZ)
| | - Yi-Xin Zeng
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- * E-mail: (MYC); (YXZ)
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Su WH, Hildesheim A, Chang YS. Human leukocyte antigens and epstein-barr virus-associated nasopharyngeal carcinoma: old associations offer new clues into the role of immunity in infection-associated cancers. Front Oncol 2013; 3:299. [PMID: 24367763 PMCID: PMC3856645 DOI: 10.3389/fonc.2013.00299] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/26/2013] [Indexed: 12/18/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV) associated tumor. In addition to EBV, host genetic factors are believed to be important determinants of NPC risk. Of all genes studies to date, human leukocyte antigen (HLA) genes have shown the most consistent evidence for association with NPC, both from candidate-gene studies and genome-wide association studies (GWAS). In this report we summarize results from recent studies that evaluated the association between HLA and NPC, and discuss whether findings reflect direct causal associations for HLA genes and/or indirect associations that mark causal associations with other genes in the gene-dense major histocompatibility (MHC) region where HLA resides. We also compare GWAS results across cancer sites for which strong hits in the MHC region were observed to generate new hypotheses regarding the role of HLA genes in the development of EBV-associated cancers such as NPC. Of note, we report that MHC associations for EBV-associated cancers (NPC, EBV+ Hodgkin lymphoma) are driven by HLA class I genes. In contrast, MHC associations for other viral-associated cancers (cervical cancer, hepatocellular carcinoma) or other hematopoetic cancers (EBV− Hodgkin lymphoma, leukemia, non-Hodgkin lymphomas) are driven by HLA class II genes, and those for other solid tumors with less clear links to infections (lung, testicular, prostate cancers) are driven by non-HLA genes in the MHC region. Future studies should aim to better understand these patterns.
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Affiliation(s)
- Wen-Hui Su
- Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan , Taiwan ; Chang Gung Molecular Medicine Research Center, Chang Gung University , Taoyuan , Taiwan
| | - Allan Hildesheim
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute , Bethesda, MD , USA
| | - Yu-Sun Chang
- Chang Gung Molecular Medicine Research Center, Chang Gung University , Taoyuan , Taiwan
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Sillé FCM, Conde L, Zhang J, Akers NK, Sanchez S, Maltbaek J, Riby JE, Smith MT, Skibola CF. Follicular lymphoma-protective HLA class II variants correlate with increased HLA-DQB1 protein expression. Genes Immun 2013; 15:133-6. [PMID: 24304973 DOI: 10.1038/gene.2013.64] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 11/09/2022]
Abstract
Multiple follicular lymphoma (FL) susceptibility single-nucleotide polymorphisms in the human leukocyte antigen (HLA) class I and II regions have been identified, including rs6457327, rs3117222, rs2647012, rs10484561, rs9268853 and rs2621416. Here we validated previous expression quantitative trait loci results with real-time reverse transcription quantitative PCR and investigated protein expression in B-lymphoblastoid cell lines and primary dendritic cells using flow cytometry, cell-based enzyme-linked immunosorbent assay and western blotting. We confirmed that FL-protective rs2647012-linked variants, in high linkage disequilibrium with the extended haplotype DRB1*15:01-DQA1*01:02-DQB1*06:02, correlate with increased HLA-DQB1 expression. This association remained significant at the protein level and was reproducible across different cell types. We also found that differences in HLA-DQB1 expression were not related to changes in activation markers or class II, major histocompatibility complex, transactivator expression, suggesting the role of an alternative regulatory mechanism. However, functional analysis using RegulomeDB did not reveal any relevant regulatory candidates. Future studies should focus on the clinical relevance of increased HLA-DQB1 protein expression facilitating tumor cell removal through increased immune surveillance.
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Affiliation(s)
- F C M Sillé
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - L Conde
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama, Birmingham, AL, USA
| | - J Zhang
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama, Birmingham, AL, USA
| | - N K Akers
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - S Sanchez
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - J Maltbaek
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - J E Riby
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama, Birmingham, AL, USA
| | - M T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - C F Skibola
- Department of Epidemiology, Comprehensive Cancer Center, University of Alabama, Birmingham, AL, USA
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Foo JN, Smedby KE, Akers NK, Berglund M, Irwan ID, Jia X, Li Y, Conde L, Darabi H, Bracci PM, Melbye M, Adami HO, Glimelius B, Khor CC, Hjalgrim H, Padyukov L, Humphreys K, Enblad G, Skibola CF, de Bakker PIW, Liu J. Coding variants at hexa-allelic amino acid 13 of HLA-DRB1 explain independent SNP associations with follicular lymphoma risk. Am J Hum Genet 2013; 93:167-72. [PMID: 23791106 DOI: 10.1016/j.ajhg.2013.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
Non-Hodgkin lymphoma represents a diverse group of blood malignancies, of which follicular lymphoma (FL) is a common subtype. Previous genome-wide association studies (GWASs) have identified in the human leukocyte antigen (HLA) class II region multiple independent SNPs that are significantly associated with FL risk. To dissect these signals and determine whether coding variants in HLA genes are responsible for the associations, we conducted imputation, HLA typing, and sequencing in three independent populations for a total of 689 cases and 2,446 controls. We identified a hexa-allelic amino acid polymorphism at position 13 of the HLA-DR beta chain that showed the strongest association with FL within the major histocompatibility complex (MHC) region (multiallelic p = 2.3 × 10⁻¹⁵). Out of six possible amino acids that occurred at that position within the population, we classified two as high risk (Tyr and Phe), two as low risk (Ser and Arg), and two as moderate risk (His and Gly). There was a 4.2-fold difference in risk (95% confidence interval = 2.9-6.1) between subjects carrying two alleles encoding high-risk amino acids and those carrying two alleles encoding low-risk amino acids (p = 1.01 × 10⁻¹⁴). This coding variant might explain the complex SNP associations identified by GWASs and suggests a common HLA-DR antigen-driven mechanism for the pathogenesis of FL and rheumatoid arthritis.
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Affiliation(s)
- Jia Nee Foo
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
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Conde L, Foo JN, Riby J, Liu J, Darabi H, Hjalgrim H, Bracci PM, Smedby KE, Skibola CF. X chromosome-wide association study of follicular lymphoma. Br J Haematol 2013; 162:858-62. [PMID: 23795672 DOI: 10.1111/bjh.12438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Conesa-Zamora P, Ruiz-Cosano J, Torres-Moreno D, Español I, Gutiérrez-Meca MD, Trujillo-Santos J, Pérez-Ceballos E, González-Conejero R, Corral J, Vicente V, Pérez-Guillermo M. Polymorphisms in xenobiotic metabolizing genes (EPHX1, NQO1 and PON1) in lymphoma susceptibility: a case control study. BMC Cancer 2013; 13:228. [PMID: 23651475 PMCID: PMC3649938 DOI: 10.1186/1471-2407-13-228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 05/01/2013] [Indexed: 11/14/2022] Open
Abstract
Background The interplay between genetic susceptibility and carcinogenic exposure is important in the development of haematopoietic malignancies. EPHX1, NQO1 and PON1 are three genes encoding proteins directly involved in the detoxification of potential carcinogens. Methods We have studied the prevalence of three functional polymorphisms affecting these genes rs1051740 EPHX1, rs1800566 NQO1 and rs662 PON1 in 215 patients with lymphoma and 214 healthy controls. Results Genotype frequencies for EPHX and NQO1 polymorphisms did not show any correlation with disease. In contrast, the GG genotype in the PON1 polymorphism was found to be strongly associated with the disease (15.3% vs. 4.7%; OR = 3.7 CI (95%): 1.8-7.7; p < 0.001). According to the pathological diagnosis this association was related to follicular (p = 0.004) and diffuse large B-cell (p = 0.016) lymphomas. Conclusions Despite the fact that further confirmation is needed, this study shows that the PON1 GG genotype in rs662 polymorphism could be a risk factor for B-cell lymphomas.
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Affiliation(s)
- Pablo Conesa-Zamora
- Pathology Department, Santa Lucía General University Hospital (HGUSL), 30202, Cartagena, Spain.
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Abstract
Autism spectrum disorder (ASD) is a highly heterogeneous disorder diagnosed based on the presence and severity of core abnormalities in social communication and repetitive behavior, yet several studies converge on immune dysregulation as a feature of ASD. Widespread alterations in immune molecules and responses are seen in the brains and periphery of ASD individuals, and early life immune disruptions are associated with ASD. This chapter discusses immune-related environmental and genetic risk factors for ASD, emphasizing population-wide studies and animal research that reveal potential mechanistic pathways involved in the development of ASD-related symptoms. It further reviews immunologic pathologies seen in ASD individuals and how such abnormalities can impact neurodevelopment and behavior. Finally, it evaluates emerging evidence for an immune contribution to the pathogenesis of ASD and a potential role for immunomodulatory effects in current treatments for ASD.
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Affiliation(s)
- Elaine Y Hsiao
- Division of Biology and Biological Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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