1
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Belpaire M, Taminiau A, Geerts D, Rezsohazy R. HOXA1, a breast cancer oncogene. Biochim Biophys Acta Rev Cancer 2022; 1877:188747. [PMID: 35675857 DOI: 10.1016/j.bbcan.2022.188747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/27/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
More than 25 years ago, the first literature records mentioned HOXA1 expression in human breast cancer. A few years later, HOXA1 was confirmed as a proper oncogene in mammary tissue. In the following two decades, molecular data about the mode of action of the HOXA1 protein, the factors contributing to activate and maintain HOXA1 gene expression and the identity of its target genes have accumulated and provide a wider view on the association of this transcription factor to breast oncogenesis. Large-scale transcriptomic data gathered from wide cohorts of patients further allowed refining the relationship between breast cancer type and HOXA1 expression. Several recent reports have reviewed the connection between cancer hallmarks and the biology of HOX genes in general. Here we take HOXA1 as a paradigm and propose an extensive overview of the molecular data centered on this oncoprotein, from what its expression modulators, to the interactors contributing to its oncogenic activities, and to the pathways and genes it controls. The data converge to an intricate picture that answers questions on the multi-modality of its oncogene activities, point towards better understanding of breast cancer aetiology and thereby provides an appraisal for treatment opportunities.
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Affiliation(s)
- Magali Belpaire
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium
| | - Arnaud Taminiau
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium
| | - Dirk Geerts
- Heart Failure Research Center, Amsterdam University Medical Center (AMC), Universiteit van Amsterdam, Amsterdam, the Netherlands.
| | - René Rezsohazy
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium.
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2
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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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3
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Lin Y, Yin P, Zhu Z, Peng Y, Li M, Li J, Liang L, Yu X. Epigenome-wide association study and network analysis for IgA Nephropathy from CD19 + B-cell in Chinese Population. Epigenetics 2021; 16:1283-1294. [PMID: 33319642 DOI: 10.1080/15592294.2020.1861171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
IgA nephropathy (IgAN) is the most common primary glomerular disease in China and worldwide. The proliferation of B cells is known to be associated with both risk and prognosis of IgAN, but the epigenetic mechanism underlying this association is unknown. In this study we carried out the first Epigenome-wide Association Study (EWAS) by using the latest Infinium Methylation EPIC BeadChip on 184 B cell-specific samples (92 case/control pairs) for Chinese IgAN population. After rigorous data normalization and residual batch effect correction, linear mixed effect model was used to detect methylation CpG sites associated with IgAN adjusting for age, gender and smoking. False discovery rate (FDR) less than 10% was used to account for multiple testing. Weighted gene co-methylation networks were generated to identify gene modules highly correlated with IgAN. A permutation test was performed to account for the potential effect of overfitting. After adjusting clinical covariates and potential technical batch effects, three CpGs corresponding to PCDH17, TERT, WDR82 genes and three in the intergenic regions passed the genome-wide significant threshold. Methylation network analysis identified an additional IgAN associated gene module, containing 72 significant CpGs including GALNT6, IQSEC1, CDC16 and SYS1, involved in the pathway related to tubular atrophy/interstitial fibrosis of IgAN. These results suggested important DNA methylation and gene targets in CD19+ B cells for the pathogenesis of IgAN.
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Affiliation(s)
- Yifei Lin
- Precision Medicine Center, Department of Urology, Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China.,Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Peiran Yin
- Department of Nephrology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yuan Peng
- Department of Nephrology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ming Li
- Department of Nephrology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Li
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Xueqing Yu
- Department of Nephrology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Nephrology, Guangdong Provincial People's Hospital, Guangzhou, China
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4
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Tracking the Genetic Susceptibility Background of B-Cell Non-Hodgkin's Lymphomas from Genome-Wide Association Studies. Int J Mol Sci 2020; 22:ijms22010122. [PMID: 33374413 PMCID: PMC7795678 DOI: 10.3390/ijms22010122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
B-cell non-Hodgkin’s lymphoma (NHL) risk associations had been mainly attributed to family history of the disease, inflammation, and immune components including human leukocyte antigen (HLA) genetic variations. Nevertheless, a broad range of genome-wide association studies (GWAS) have shed light into the identification of several genetic variants presumptively associated with B-cell NHL etiologies, survival or shared genetic risk with other diseases. The present review aims to overview HLA structure and diversity and summarize the evidence of genetic variations, by GWAS, on five NHL subtypes (diffuse large B-cell lymphoma DLBCL, follicular lymphoma FL, chronic lymphocytic leukemia CLL, marginal zone lymphoma MZL, and primary central nervous system lymphoma PCNSL). Evidence indicates that the HLA zygosity status in B-cell NHL might promote immune escape and that genome-wide significance variants can give biological insight but also potential therapeutic markers such as WEE1 in DLBCL. However, additional studies are needed, especially for non-DLBCL, to replicate the associations found to date.
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5
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LNX1/LNX2 proteins: functions in neuronal signalling and beyond. Neuronal Signal 2018; 2:NS20170191. [PMID: 32714586 PMCID: PMC7373230 DOI: 10.1042/ns20170191] [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: 04/02/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022] Open
Abstract
Ligand of NUMB Protein X1 and X2 (LNX1 and LNX2) are E3 ubiquitin ligases, named for their ability to interact with and promote the degradation of the cell fate determinant protein NUMB. On this basis they are thought to play a role in modulating NUMB/NOTCH signalling during processes such as cortical neurogenesis. However, LNX1/2 proteins can bind, via their four PDZ (PSD95, DLGA, ZO-1) domains, to an extraordinarily large number of other proteins besides NUMB. Many of these interactions suggest additional roles for LNX1/2 proteins in the nervous system in areas such as synapse formation, neurotransmission and regulating neuroglial function. Twenty years on from their initial discovery, I discuss here the putative neuronal functions of LNX1/2 proteins in light of the anxiety-related phenotype of double knockout mice lacking LNX1 and LNX2 in the central nervous system (CNS). I also review what is known about non-neuronal roles of LNX1/2 proteins, including their roles in embryonic patterning and pancreas development in zebrafish and their possible involvement in colorectal cancer (CRC), osteoclast differentiation and immune function in mammals. The emerging picture places LNX1/2 proteins as potential regulators of multiple cellular signalling processes, but in many cases the physiological significance of such roles remains only partly validated and needs to be considered in the context of the tight control of LNX1/2 protein levels in vivo.
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6
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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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7
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Zhai K, Chang J, Hu J, Wu C, Lin D. Germline variation in the 3'-untranslated region of the POU2AF1 gene is associated with susceptibility to lymphoma. Mol Carcinog 2017; 56:1945-1952. [PMID: 28345816 DOI: 10.1002/mc.22652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 03/05/2017] [Accepted: 03/23/2017] [Indexed: 01/06/2023]
Abstract
Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls. Compared with individuals with the rs1042752TT genotype, those with the rs1042752CC genotype had a higher risk of lymphoma (OR = 2.14, 95% CI: 1.55-2.95, P < 0.001), even in stratified analysis for non-Hodgkin lymphoma (OR = 4.58, 95% CI: 2.38-8.81, P < 0.001), B-cell lymphoma (OR = 4.89, 95% CI: 2.46-9.73, P < 0.001), T-cell lymphoma (OR = 4.20, 95% CI: 1.76-10.05, P = 0.001), and Hodgkin lymphoma (OR = 3.62, 95% CI: 1.25-10.46, P = 0.018). Similar results were also observed in a recessive genetic model. Database findings suggested that rs1042752 might affect the interaction of POU2AF1 mRNA with hsa-miR-633. Functional assays confirmed that rs1042752C altered the binding site of hsa-miR-633 and increased POU2AF1 expression in Ramos, HuT 102, and Jurkat E6-1 cell lines. These findings demonstrate for the first time that functional polymorphism in the 3'-UTR of POU2AF1 is associated with susceptibility, and that SNP interaction with hsa-miR-633 affects gene expression and increases the risk of lymphoma.
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Affiliation(s)
- Kan Zhai
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinlong Hu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
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8
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Kagemoto K, Urabe Y, Miwata T, Oka S, Ochi H, Kitadai Y, Tanaka S, Chayama K. ADH1B and ALDH2 are associated with metachronous SCC after endoscopic submucosal dissection of esophageal squamous cell carcinoma. Cancer Med 2016; 5:1397-404. [PMID: 27038040 PMCID: PMC4944865 DOI: 10.1002/cam4.705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/31/2016] [Accepted: 02/22/2016] [Indexed: 11/29/2022] Open
Abstract
A previous genome‐wide association study identified two novel esophageal squamous cell carcinoma (ESCC) susceptibility genes, ADH1B and ALDH2. We investigated the characteristics of ESCC, and the relationship between metachronous esophageal and/or pharyngeal squamous cell carcinoma (SCC) and the ADH1B & ALDH2 risk alleles. One hundred and seventeen superficial ESCC patients who underwent treatment with endoscopic submucosal dissection (ESD) were followed up using endoscopy for ≥12 months. First, we performed a replication analysis to confirm the relationship between ESCC and the ADH1B & ALDH2 risk alleles using 117 superficial ESCC cases and 1125 healthy controls. Next, we investigated the incidence and genetic/environmental factors associated with metachronous SCC development after ESD. We also analyzed the potential risk factors for metachronous SCC development using Cox's proportional hazards model. rs1229984 GG located on ADH1B and rs671 GA located on ALDH2 were significantly associated with ESCC progression (P = 7.93 × 10−4 and P = 1.04 × 10−5). Patients with rs1229984 GG, those with rs671 GA, smokers, heavy alcohol drinkers (44 g/day ethanol), and presence of multiple Lugol‐voiding lesions (LVLs) developed metachronous SCC more frequently (P = 3.20 × 10−3, 7.00 × 10−4, 4.00 × 10−4, 2.15 × 10−2, and 4.41 × 10−3, respectively), with hazard ratios were 2.84 (95% confidence interval [CI] = 1.43–5.63), 4.57 (95% CI = 1.80–15.42), 4.84 (95% CI = 1.89–16.41), and 2.34 (95% CI = 1.12–5.31), respectively. Multiple logistic regression analysis revealed that rs1229984 GG, rs671 GA, and smoking status were independently associated with the risk of developing metachronous SCCs after ESD. Moreover, we found cumulative effects of these two genetic factors (rs1229984 GG and rs671 GA) and one environmental factor (tobacco smoking) which appear to increase metachrous SCCs after ESD of ESCC risk approximately nearly 12‐fold. Our findings elucidated the crucial role of multiple genetic variations in ADH1B and ALDH2 as biomarkers of metachronous ESCC.
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Affiliation(s)
- Kenichi Kagemoto
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | - Yuji Urabe
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan.,Department of Regeneration and Medicine Medical center for Translation and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Tomohiro Miwata
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | - Shiro Oka
- Department of Endoscopy, Hiroshima University Hospital, Hiroshima, Japan
| | - Hidenori Ochi
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | - Yasuhiko Kitadai
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | - Shinji Tanaka
- Department of Endoscopy, Hiroshima University Hospital, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
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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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10
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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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11
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Chang ET, Boffetta P, Adami HO, Mandel JS. A critical review of the epidemiology of Agent Orange or 2,3,7,8-tetrachlorodibenzo-p-dioxin and lymphoid malignancies. Ann Epidemiol 2015; 25:275-292.e30. [DOI: 10.1016/j.annepidem.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/06/2015] [Accepted: 01/09/2015] [Indexed: 12/20/2022]
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12
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Kuksin CA, Minter LM. The Link between Autoimmunity and Lymphoma: Does NOTCH Signaling Play a Contributing Role? Front Oncol 2015; 5:51. [PMID: 25759795 PMCID: PMC4338678 DOI: 10.3389/fonc.2015.00051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022] Open
Abstract
An association between certain autoimmune conditions and increased risk of developing lymphoma is well documented. Recent evidence points to NOTCH signaling as a strong driver of autoimmunity. Furthermore, a role for NOTCH in various lymphomas, including classical Hodgkin lymphoma, non-Hodgkin lymphoma, and T cell lymphoma has also been described. In this mini-review, we will outline what is known about involvement of NOTCH signaling in those autoimmune conditions, such as rheumatoid arthritis and primary Sjörgren’s syndrome, which show an increased risk for subsequent diagnosis of lymphoma. Furthermore, we will detail what is known about the lymphomas associated with these autoimmune conditions and how aberrant or sustained NOTCH signaling in the immune cells that mediate these diseases may contribute to lymphoma.
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Affiliation(s)
- Christina Arieta Kuksin
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst , Amherst, MA , USA
| | - Lisa M Minter
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst , Amherst, MA , USA ; Program in Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, MA , USA
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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: 129] [Impact Index Per Article: 12.9] [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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14
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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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15
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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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16
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Genome-wide association studies of cancer predisposition. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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17
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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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18
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Urabe Y, Ochi H, Kato N, Kumar V, Takahashi A, Muroyama R, Hosono N, Otsuka M, Tateishi R, Lo PHY, Tanikawa C, Omata M, Koike K, Miki D, Abe H, Kamatani N, Toyota J, Kumada H, Kubo M, Chayama K, Nakamura Y, Matsuda K. A genome-wide association study of HCV-induced liver cirrhosis in the Japanese population identifies novel susceptibility loci at the MHC region. J Hepatol 2013; 58:875-82. [PMID: 23321320 DOI: 10.1016/j.jhep.2012.12.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 12/15/2012] [Accepted: 12/24/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS We performed a genome-wide association study (GWAS) of hepatitis C virus (HCV)-induced liver cirrhosis (LC) to identify predictive biomarkers for the risk of LC in patients with chronic hepatitis C (CHC). METHODS A total of 682 HCV-induced LC cases and 1045 CHC patients of Japanese origin were genotyped by Illumina Human Hap 610-Quad bead Chip. RESULTS Eight SNPs which showed possible associations (p<1.0 × 10(-5)) at the GWAS stage were further genotyped using 936 LC cases and 3809 CHC patients. We found that two SNPs within the major histocompatibility complex (MHC) region on chromosome 6p21, rs910049 and rs3135363, were significantly associated with the progression from CHC to LC (pcombined=9.15 × 10(-11) and 1.45 × 10(-10), odds ratio (OR)=1.46 and 1.37, respectively). We also found that HLA-DQA1(*)0601 and HLA-DRB1(*)0405 were associated with the progression from CHC to LC (p=4.53 × 10(-4) and 1.54 × 10(-4) with OR=2.80 and 1.45, respectively). Multiple logistic regression analysis revealed that rs3135363, rs910049, and HLA-DQA1(*)0601 were independently associated with the risk of HCV-induced LC. In addition, individuals with four or more risk alleles for these three loci have a 2.83-fold higher risk for LC than those with no risk allele, indicating the cumulative effects of these variations. CONCLUSIONS Our findings elucidated the crucial roles of multiple genetic variations within the MHC region as prognostic/predictive biomarkers for CHC patients.
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Affiliation(s)
- Yuji Urabe
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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19
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Qiao Y, Zhou Y, Wu C, Zhai K, Han X, Chen J, Tian X, Chang J, Lu Z, Zhang B, Yu D, Yao J, Shi Y, Tan W, Lin D. Risk of genome-wide association study-identified genetic variants for non-Hodgkin lymphoma in a Chinese population. Carcinogenesis 2013; 34:1516-9. [DOI: 10.1093/carcin/bgt082] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Vijai J, Kirchhoff T, Schrader KA, Brown J, Dutra-Clarke AV, Manschreck C, Hansen N, Rau-Murthy R, Sarrel K, Przybylo J, Shah S, Cheguri S, Stadler Z, Zhang L, Paltiel O, Ben-Yehuda D, Viale A, Portlock C, Straus D, Lipkin SM, Lacher M, Robson M, Klein RJ, Zelenetz A, Offit K. Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. PLoS Genet 2013; 9:e1003220. [PMID: 23349640 PMCID: PMC3547842 DOI: 10.1371/journal.pgen.1003220] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 10/18/2012] [Indexed: 12/31/2022] Open
Abstract
The genetics of lymphoma susceptibility reflect the marked heterogeneity of diseases that comprise this broad phenotype. However, multiple subtypes of lymphoma are observed in some families, suggesting shared pathways of genetic predisposition to these pathologically distinct entities. Using a two-stage GWAS, we tested 530,583 SNPs in 944 cases of lymphoma, including 282 familial cases, and 4,044 public shared controls, followed by genotyping of 50 SNPs in 1,245 cases and 2,596 controls. A novel region on 11q12.1 showed association with combined lymphoma (LYM) subtypes. SNPs in this region included rs12289961 near LPXN, (P(LYM) = 3.89×10(-8), OR = 1.29) and rs948562 (P(LYM) = 5.85×10(-7), OR = 1.29). A SNP in a novel non-HLA region on 6p23 (rs707824, P(NHL) = 5.72×10(-7)) was suggestive of an association conferring susceptibility to lymphoma. Four SNPs, all in a previously reported HLA region, 6p21.32, showed genome-wide significant associations with follicular lymphoma. The most significant association with follicular lymphoma was for rs4530903 (P(FL) = 2.69×10(-12), OR = 1.93). Three novel SNPs near the HLA locus, rs9268853, rs2647046, and rs2621416, demonstrated additional variation contributing toward genetic susceptibility to FL associated with this region. Genes implicated by GWAS were also found to be cis-eQTLs in lymphoblastoid cell lines; candidate genes in these regions have been implicated in hematopoiesis and immune function. These results, showing novel susceptibility regions and allelic heterogeneity, point to the existence of pathways of susceptibility to both shared as well as specific subtypes of lymphoid malignancy.
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Affiliation(s)
- Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Tomas Kirchhoff
- New York University Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Kasmintan A. Schrader
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Jennifer Brown
- Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Ana Virginia Dutra-Clarke
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Christopher Manschreck
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Nichole Hansen
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Rohini Rau-Murthy
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Kara Sarrel
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Jennifer Przybylo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Sohela Shah
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Srujana Cheguri
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Liying Zhang
- Diagnostic Molecular Genetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ora Paltiel
- Department of Hematology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dina Ben-Yehuda
- Department of Hematology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Agnes Viale
- Genomics Core, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Carol Portlock
- Lymphoma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - David Straus
- Lymphoma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Steven M. Lipkin
- Weill Cornell Medical Center, New York, New York, United States of America
| | - Mortimer Lacher
- Lymphoma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Robert J. Klein
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Andrew Zelenetz
- Lymphoma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, United States of America
- Lymphoma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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21
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Kumar V, Yi Lo PH, Sawai H, Kato N, Takahashi A, Deng Z, Urabe Y, Mbarek H, Tokunaga K, Tanaka Y, Sugiyama M, Mizokami M, Muroyama R, Tateishi R, Omata M, Koike K, Tanikawa C, Kamatani N, Kubo M, Nakamura Y, Matsuda K. Soluble MICA and a MICA variation as possible prognostic biomarkers for HBV-induced hepatocellular carcinoma. PLoS One 2012; 7:e44743. [PMID: 23024757 PMCID: PMC3443094 DOI: 10.1371/journal.pone.0044743] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/07/2012] [Indexed: 12/13/2022] Open
Abstract
MHC class I polypeptide-related chain A (MICA) molecule is induced in response to viral infection and various types of stress. We recently reported that a single nucleotide polymorphism (SNP) rs2596542 located in the MICA promoter region was significantly associated with the risk for hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) and also with serum levels of soluble MICA (sMICA). In this study, we focused on the possible involvement of MICA in liver carcinogenesis related to hepatitis B virus (HBV) infection and examined correlation between the MICA polymorphism and the serum sMICA levels in HBV-induced HCC patients. The genetic association analysis revealed a nominal association with an SNP rs2596542; a G allele was considered to increase the risk of HBV-induced HCC (P = 0.029 with odds ratio of 1.19). We also found a significant elevation of sMICA in HBV-induced HCC cases. Moreover, a G allele of SNP rs2596542 was significantly associated with increased sMICA levels (P = 0.009). Interestingly, HCC patients with the high serum level of sMICA (>5 pg/ml) exhibited poorer prognosis than those with the low serum level of sMICA (≤5 pg/ml) (P = 0.008). Thus, our results highlight the importance of MICA genetic variations and the significance of sMICA as a predictive biomarker for HBV-induced HCC.
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Affiliation(s)
- Vinod Kumar
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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22
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Tirado CA, Chen W, García R, Kohlman KA, Rao N. Genomic profiling using array comparative genomic hybridization define distinct subtypes of diffuse large B-cell lymphoma: a review of the literature. J Hematol Oncol 2012; 5:54. [PMID: 22967872 PMCID: PMC3479011 DOI: 10.1186/1756-8722-5-54] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 05/31/2012] [Indexed: 11/13/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin Lymphoma comprising of greater than 30% of adult non-Hodgkin Lymphomas. DLBCL represents a diverse set of lymphomas, defined as diffuse proliferation of large B lymphoid cells. Numerous cytogenetic studies including karyotypes and fluorescent in situ hybridization (FISH), as well as morphological, biological, clinical, microarray and sequencing technologies have attempted to categorize DLBCL into morphological variants, molecular and immunophenotypic subgroups, as well as distinct disease entities. Despite such efforts, most lymphoma remains undistinguishable and falls into DLBCL, not otherwise specified (DLBCL-NOS). The advent of microarray-based studies (chromosome, RNA, gene expression, etc) has provided a plethora of high-resolution data that could potentially facilitate the finer classification of DLBCL. This review covers the microarray data currently published for DLBCL. We will focus on these types of data; 1) array based CGH; 2) classical CGH; and 3) gene expression profiling studies. The aims of this review were three-fold: (1) to catalog chromosome loci that are present in at least 20% or more of distinct DLBCL subtypes; a detailed list of gains and losses for different subtypes was generated in a table form to illustrate specific chromosome loci affected in selected subtypes; (2) to determine common and distinct copy number alterations among the different subtypes and based on this information, characteristic and similar chromosome loci for the different subtypes were depicted in two separate chromosome ideograms; and, (3) to list re-classified subtypes and those that remained indistinguishable after review of the microarray data. To the best of our knowledge, this is the first effort to compile and review available literatures on microarray analysis data and their practical utility in classifying DLBCL subtypes. Although conventional cytogenetic methods such as Karyotypes and FISH have played a major role in classification schemes of lymphomas, better classification models are clearly needed to further understanding the biology, disease outcome and therapeutic management of DLBCL. In summary, microarray data reviewed here can provide better subtype specific classifications models for DLBCL.
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Affiliation(s)
- Carlos A Tirado
- Department of Pathology & Laboratory Medicine UCLA - David Geffen UCLA, School of Medicine, Los Angeles, USA.
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