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Ming L, Tang J, Qin F, Qin Y, Wang D, Huang L, Cao Y, Huang Z, Yin Y. Exosome secretion related gene signature predicts chemoresistance in patients with colorectal cancer. Pathol Res Pract 2024; 257:155313. [PMID: 38642509 DOI: 10.1016/j.prp.2024.155313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/14/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a highly heterogeneous malignancy, and patients often have different responses to treatment. In this study, the genetic characteristics related to exosome formation and secretion procedure were used to predict chemoresistance and guide the individualized treatment of patients. METHODS Firstly, seven microarray datasets in Gene Expression Omnibus (GEO) and RNA-Seq dataset from the Cancer Genome Atlas (TCGA) were used to analysis the transcriptome profiles and associated characteristics of CRC patients. Then, a predictive model based on gene features linked to exosome formation and secretion was created and validated using Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) machine learning. Finally, we evaluated the model using chemoresistant/chemosensitive cells and tissues by immunofluorescence (IF), western blot (WB), quantitative real-time PCR (qRT-PCR) and immunocytochemistry (IHC) experiments, and the predictive value of integrated model in the clinical validation cohort were performed by Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) curves analyses. RESULTS We established a risk score signature based on three genes related to exosome secretion in CRC. Better Overall Survival (OS) and greater chemosensitivity were seen in the low-risk group, whereas the high-risk group exhibited chemoresistance and a subpar response to immune checkpoint blockade (ICB) therapy. Higher expression of the model genes EXOC2, EXOC3 and STX4 were observed in chemoresistant cells and specimens. The AUC of 5-year disease-free survival (DFS) was 0.804. Compared with that in the low-risk group, patients' DFS was found to be significantly worse in the high-risk group. CONCLUSIONS In summary, the gene signature related to exosome formation and secretion could reliably predict patients' chemosensitivity and ICB treatment response, which providing new independent biomarkers for the treatment of CRC.
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Affiliation(s)
- Liang Ming
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junhui Tang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Feiyu Qin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Qin
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China
| | - Duo Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liuying Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Diamanti I, Fylaktou A, Verrou E, Vlachaki E, Sinakos M, Katodritou E, Ouranos K, Minti F, Gioula G. HLA variations in patients with diffuse large B-cell lymphoma and association with disease risk and prognosis: a case-control study. Front Genet 2024; 15:1341822. [PMID: 38680423 PMCID: PMC11045888 DOI: 10.3389/fgene.2024.1341822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA) polymorphisms have been associated with the development of various autoimmune diseases, as well as malignant neoplasms. Non-Hodgkin lymphomas (NHLs) are a heterogenous group of lymphoid malignancies in which a genetic substrate has been established and is deemed to play a crucial role in disease pathogenesis. This study aimed to identify whether variations in the HLA gene region were associated with diffuse large B-cell lymphoma (DLBCL) risk and prognosis. Methods We defined HLA class I (HLA-A, HLA-B, HLA-C) and class II (HLA-DRB1, HLA-DQB1) alleles in 60 patients with DLBCL and compared the results to those found by 236 healthy adult donors from the bone marrow bank of Northern Greece. HLA typing was performed by two molecular methods, Sequence - Specific Oligonucleotide HLA typing (SSO) and Sequence - Specific Primer HLA typing (SSP), from white blood cells recovered from peripheral blood. The phenotypic frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 between patients and controls were compared with the 2-sided Fisher's exact test. Results with p-value <0.05 were considered statistically significant. Odds Ratios with 95% Confidence Intervals were calculated to further strengthen the results. The 2-sided Fisher's exact test was also applied to alleles found only in one of the two groups, while the odds ratios together with the confidence intervals were corrected with Haldane-Anscombe method. Results Among the studied HLA polymorphisms, the frequency HLA-C*12 allele was significantly lower in patients with DLBCL compared with control subjects (6.7% vs. 34.7%, OR = 0.16, 95% CI: 0.04-0.44). Frequency of HLA-B*39 was significantly lower in patients with DLBCL compared with controls, but due to the low frequency of this polymorphism in the studied population and small sample size, determinations regarding the significance of this findings were limited. Survival analysis revealed that the presence of HLA-C*12 was not associated with improved or worsened overall and progression-free survival. No statistically significant associations were observed in the phenotypic frequencies of HLA-A, HLA-DQB1, HLA-DRB1 and the rest of HLA-B alleles between the control and DLBCL groups. Discussion Collectively, our results provide valuable insight regarding the role of HLA variations on DLBCL risk. Further studies are required to consolidate our findings and ascertain the clinical implications of these genetic variations on DLBCL management and prognosis.
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Affiliation(s)
- Ioanna Diamanti
- Biochemisty and Microbiology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Asimina Fylaktou
- National Peripheral Histocompatibility Center-Immunology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Evgenia Verrou
- Hematology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Efthimia Vlachaki
- Thalassemia Unit-2nd Department of Internal Medicine, Hippokration General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Manolis Sinakos
- 4th Department of Internal Medicine, Hippokration General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eirini Katodritou
- Hematology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Konstantinos Ouranos
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Fani Minti
- Microbiology Department, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgia Gioula
- Microbiology Department, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Rosenberger A, Crossland RE, Dressel R, Kube D, Wolff D, Wulf G, Bickeböller H, Dickinson A, Holler E. A genome-wide association study on hematopoietic stem cell transplantation reveals novel genomic loci associated with transplant outcomes. Front Immunol 2024; 15:1280876. [PMID: 38384455 PMCID: PMC10879589 DOI: 10.3389/fimmu.2024.1280876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Data on genomic susceptibility for adverse outcomes after hematopoietic stem cell transplantation (HSCT) for recipients are scarce. Methods We performed a genome wide association study (GWAS) to identify genes associated with survival/mortality, relapse, and severe graft-versus-host disease (sGvHD), fitting proportional hazard and subdistributional models to data of n=1,392 recipients of European ancestry from three centres. Results The single nucleotide polymorphism (SNP) rs17154454, intronic to the neuronal growth guidant semaphorin 3C gene (SEMA3C), was genome-wide significantly associated with event-free survival (p=7.0x10-8) and sGvHD (p=7.5x10-8). Further associations were detected for SNPs in the Paxillin gene (PXN) with death without prior relapse or sGvHD, as well as for SNPs of the Plasmacytoma Variant Translocation 1 gene (PVT1, a long non-coding RNA gene), the Melanocortin 5 Receptor (MC5R) gene and the WW Domain Containing Oxidoreductase gene (WWOX), all associated with the occurrence of sGvHD. Functional considerations support the observed associations. Discussion Thus, new genes were identified, potentially influencing the outcome of HSCT.
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Affiliation(s)
- Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Rachel E. Crossland
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Dieter Kube
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Gerald Wulf
- Hematology and Medical Oncology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Anne Dickinson
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ernst Holler
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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Cornish N, Haycock P, Brenner H, Figueiredo JC, Galesloot TE, Grant RC, Johansson M, Mariosa D, McKay J, Pai R, Pellatt AJ, Samadder NJ, Shi J, Thibord F, Trégouët DA, Voegele C, Thirlwell C, Mumford A, Langdon R. Causal relationships between risk of venous thromboembolism and 18 cancers: a bidirectional Mendelian randomization analysis. Int J Epidemiol 2024; 53:dyad170. [PMID: 38124529 PMCID: PMC10859161 DOI: 10.1093/ije/dyad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND People with cancer experience high rates of venous thromboembolism (VTE). Risk of subsequent cancer is also increased in people experiencing their first VTE. The causal mechanisms underlying this association are not completely understood, and it is unknown whether VTE is itself a risk factor for cancer. METHODS We used data from large genome-wide association study meta-analyses to perform bidirectional Mendelian randomization analyses to estimate causal associations between genetic liability to VTE and risk of 18 different cancers. RESULTS We found no conclusive evidence that genetic liability to VTE was causally associated with an increased incidence of cancer, or vice versa. We observed an association between liability to VTE and pancreatic cancer risk [odds ratio for pancreatic cancer: 1.23 (95% confidence interval: 1.08-1.40) per log-odds increase in VTE risk, P = 0.002]. However, sensitivity analyses revealed this association was predominantly driven by a variant proxying non-O blood group, with inadequate evidence to suggest a causal relationship. CONCLUSIONS These findings do not support the hypothesis that genetic liability to VTE is a cause of cancer. Existing observational epidemiological associations between VTE and cancer are therefore more likely to be driven by pathophysiological changes which occur in the setting of active cancer and anti-cancer treatments. Further work is required to explore and synthesize evidence for these mechanisms.
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Affiliation(s)
- Naomi Cornish
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philip Haycock
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert C Grant
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Daniela Mariosa
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Andrew J Pellatt
- Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | | | - Catherine Voegele
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Chrissie Thirlwell
- University of Exeter Medical School, University of Exeter, Exeter, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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Mortlock SA, Asada MC, Soh PXY, Hsu WT, Lee C, Bennett PF, Taylor RM, Khatkar MS, Williamson P. Genomic Analysis of Lymphoma Risk in Bullmastiff Dogs. Vet Sci 2023; 10:703. [PMID: 38133254 PMCID: PMC10747964 DOI: 10.3390/vetsci10120703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Lymphoma is the most common haematological malignancy affecting dogs and has a high incidence in the Bullmastiff breed. The aim of this study was to identify risk loci predisposing this breed to the disease. The average age of lymphoma diagnosis in 55 cases was less than 6 years, similar to the median age of 64 cases from our clinical and pathology databases. When fine-scale population structure was explored using NETVIEW, cases were distributed throughout an extended pedigree. When genotyped cases (n = 49) and dogs from the control group (n = 281) were compared in a genome-wide association analysis of lymphoma risk, the most prominent associated regions were detected on CFA13 and CFA33. The top SNPs in a 5.4 Mb region on CFA13 were significant at a chromosome-wide level, and the region was fine-mapped to ~1.2 Mb (CFA13: 25.2-26.4 Mb; CanFam3.1) with four potential functional candidates, including the MYC proto-oncogene bHLH transcription factor (MYC) and a region syntenic with the human and mouse lncRNA Pvt1 oncogene (PVT1). A 380 Kb associated region at CFA33: 7.7-8.1 Mb contained the coding sequence for SUMO specific peptidase7 (SENP7) and NFK inhibitor zeta (NFKBIZ) genes. These genes have annotations related to cancer, amongst others, and both have functional links to MYC regulation. Genomic signatures identified in lymphoma cases suggest that increased risk contributed by the regions identified by GWAS may complement a complex predisposing genetic background.
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Affiliation(s)
- Sally A. Mortlock
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Monica C. Asada
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Pamela Xing Yi Soh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Wei-Tse Hsu
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Carol Lee
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Peter F. Bennett
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Rosanne M. Taylor
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
| | - Mehar S. Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371, Australia
| | - Peter Williamson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia (M.S.K.)
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Yu J, Fu L, Zhang Z, Ding L, Hong L, Gao F, Jin J, Feng W, Fu J, Hong P, Xu C. Causal relationships between circulating inflammatory cytokines and diffuse large B cell lymphoma: a bidirectional Mendelian randomization study. Clin Exp Med 2023; 23:4585-4595. [PMID: 37910257 DOI: 10.1007/s10238-023-01221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Studies indicated that inflammatory cytokines involved in the occurrence and progression of DLBCL and it is challenging to discern causality from the effects due to the presence of feedback loops. We conducted a bidirectional Mendelian randomization (MR) study to investigate the potential causal relationship between DLBCL and inflammatory cytokines. The genetic variants associated with inflammatory cytokines were obtained from a genome-wide association study (GWAS) involving 8293 European participants, and the data on 1010 individuals with DLBCL were sourced from the FinnGen consortium. The primary method employed in this study was the inverse-variance weighted (IVW) method, with supplementary analyses conducted using the MR-Egger, weighted median, and MR-PRESSO approaches. Based on the IVW method, genetically predicted that increasing level of Monokine induced by interferon gamma (MIG/CXC chemokine ligand 9, CXCL9) [OR: 1.31; 95% CI: 1.05-1.62; P = 0.01] and interferon gamma-induced protein 10(IP-10/CXC chemokine ligand 10, CXCL10) [OR: 1.30; 95% CI: 1.02-1.66; P = 0.03] showed suggestive associations with DLBCL risk. DLBCL may increase the level of macrophage colony-stimulating factor (M-CSF) [OR: 1.12; 95% CI: 1.01-1.2; P = 0.03], tumor necrosis factor beta (TNF-β) [OR: 1.16; 95% CI: 1.02-1.31; P = 0.02] and TNF-related apoptosis-inducing ligand (TRAIL) [OR: 1.07; 95% CI: 1.01-1.13; P = 0.02]. This study presents evidence supporting a causal relationship between inflammation cytokines and DLBCL. Specifically, MIG/CXCL9 and IP-10/CXCL10 were identified as indicators of upstream causes of DLBCL; while, DLBCL itself was found to elevate the levels of M-CSF, TNF-β, and TRAIL. These findings suggest that targeting specific inflammatory factors through regulation and intervention could serve as a potential approach for the treatment and prevention of DLBCL.
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Affiliation(s)
- Jieni Yu
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Leihua Fu
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Zhijian Zhang
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Lina Ding
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Li Hong
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Feidan Gao
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Jing Jin
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Weiying Feng
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Jiaping Fu
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Pan Hong
- Department of Hematology, Shaoxing People's Hospital, Shaoxing, Zhejiang, People's Republic of China
| | - Chao Xu
- Department of Vascular and Hernia Surgery, Shaoxing People's Hospital, Shaoxing, 312000, Zhejiang, People's Republic of China.
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Wang SS. Epidemiology and etiology of diffuse large B-cell lymphoma. Semin Hematol 2023; 60:255-266. [PMID: 38242772 PMCID: PMC10962251 DOI: 10.1053/j.seminhematol.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024]
Abstract
As the most common non-Hodgkin lymphoma subtype, diffuse large B-cell lymphoma (DLBCL) incidence patterns generally parallel that for NHL overall. Globally, DLBCL accounts for a third of all NHLs, ranging between 20% and 50% by country. Based on United States (U.S.) cancer registry data, age-standardized incidence rate for DLBCL was 7.2 per 100,000. DLBCL incidence rises with age and is generally higher in males than females; in the U.S., incidence is highest among non-Hispanic whites (9.2/100,000). Like NHL incidence, DLBCL incidence rose in the first half of the 20th century but has largely plateaued. However, there is some evidence that incidence rates are rising in areas of historically low rates, such as Asia; there are also estimates for rising DLBCL incidence in the near future due to the changing demographics in developed countries whose aging population is growing. Established risk factors for DLBCL include those that result in severe immune deficiency such as HIV/AIDS, inherited immunodeficiency syndromes, and organ transplant recipients. Factors that lead to chronic immune dysregulations are also established risk factors, and include a number of autoimmune conditions (eg, Sjögren syndrome, systemic lupus erythematosus, rheumatoid arthritis), viral infections (eg, HIV, KSHV/HHV8, HCV, EBV), and obesity. Family history of NHL/DLBCL, personal history of cancer, and multiple genetic susceptibility loci are also well-established risk factors for DLBCL. There is strong evidence for multiple environmental exposures in DLBCL etiology, including exposure to trichloroethylene, benzene, and pesticides and herbicides, with recent associations noted with glyphosate. There is also strong evidence for associations with other viruses, such as HBV. Recent estimates suggest that obesity accounts for nearly a quarter of DLBCLs that develop, but despite recent gains in the understanding of DLBCL etiology, the majority of disease remain unexplained. An understanding of the host and environmental contributions to disease etiology, and concerted efforts to expand our understanding to multiple race/ethnic groups, will be essential for constructing clinically relevant risk prediction models and develop effective strategies for disease prevention.
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Affiliation(s)
- Sophia S Wang
- City of Hope Comprehensive Cancer Center, Duarte, CA.
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8
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Haycock PC, Borges MC, Burrows K, Lemaitre RN, Harrison S, Burgess S, Chang X, Westra J, Khankari NK, Tsilidis KK, Gaunt T, Hemani G, Zheng J, Truong T, O’Mara TA, Spurdle AB, Law MH, Slager SL, Birmann BM, Saberi Hosnijeh F, Mariosa D, Amos CI, Hung RJ, Zheng W, Gunter MJ, Davey Smith G, Relton C, Martin RM. Design and quality control of large-scale two-sample Mendelian randomization studies. Int J Epidemiol 2023; 52:1498-1521. [PMID: 38587501 PMCID: PMC10555669 DOI: 10.1093/ije/dyad018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2023] [Indexed: 03/27/2024] Open
Abstract
Background Mendelian randomization (MR) studies are susceptible to metadata errors (e.g. incorrect specification of the effect allele column) and other analytical issues that can introduce substantial bias into analyses. We developed a quality control (QC) pipeline for the Fatty Acids in Cancer Mendelian Randomization Collaboration (FAMRC) that can be used to identify and correct for such errors. Methods We collated summary association statistics from fatty acid and cancer genome-wide association studies (GWAS) and subjected the collated data to a comprehensive QC pipeline. We identified metadata errors through comparison of study-specific statistics to external reference data sets (the National Human Genome Research Institute-European Bioinformatics Institute GWAS catalogue and 1000 genome super populations) and other analytical issues through comparison of reported to expected genetic effect sizes. Comparisons were based on three sets of genetic variants: (i) GWAS hits for fatty acids, (ii) GWAS hits for cancer and (iii) a 1000 genomes reference set. Results We collated summary data from 6 fatty acid and 54 cancer GWAS. Metadata errors and analytical issues with the potential to introduce substantial bias were identified in seven studies (11.6%). After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls. Conclusions In this large MR collaboration, 11.6% of included studies were affected by a substantial metadata error or analytical issue. By increasing the integrity of collated summary data prior to their analysis, our protocol can be used to increase the reliability of downstream MR analyses. Our pipeline is available to other researchers via the CheckSumStats package (https://github.com/MRCIEU/CheckSumStats).
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Affiliation(s)
- Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Sean Harrison
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat—National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Jason Westra
- Department of Mathematics, Statistics, and Computer Science, Dordt College, Sioux Center, IA, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Truong
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Team “Exposome, Heredity, Cancer and Health”, CESP, Villejuif, France
| | - Tracy A O’Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Daniela Mariosa
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health and University of Toronto, Toronto, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC), Lyon, France
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
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9
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Im C, Sharafeldin N, Yuan Y, Wang Z, Sapkota Y, Lu Z, Spector LG, Howell RM, Arnold MA, Hudson MM, Ness KK, Robison LL, Bhatia S, Armstrong GT, Neglia JP, Yasui Y, Turcotte LM. Polygenic Risk and Chemotherapy-Related Subsequent Malignancies in Childhood Cancer Survivors: A Childhood Cancer Survivor Study and St Jude Lifetime Cohort Study Report. J Clin Oncol 2023; 41:4381-4393. [PMID: 37459583 PMCID: PMC10522108 DOI: 10.1200/jco.23.00428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/18/2023] [Indexed: 08/07/2023] Open
Abstract
PURPOSE Chemotherapeutic exposures are associated with subsequent malignant neoplasm (SMN) risk. The role of genetic susceptibility in chemotherapy-related SMNs should be defined as use of radiation therapy (RT) decreases. PATIENTS AND METHODS SMNs among long-term childhood cancer survivors of European (EUR; N = 9,895) and African (AFR; N = 718) genetic ancestry from the Childhood Cancer Survivor Study and St Jude Lifetime Cohort Study were evaluated. An externally validated 179-variant polygenic risk score (PRS) associated with pleiotropic adult cancer risk from the UK Biobank Study (N > 400,000) was computed for each survivor. SMN cumulative incidence comparing top and bottom PRS quintiles was estimated, along with hazard ratios (HRs) from proportional hazards models. RESULTS A total of 1,594 survivors developed SMNs, with basal cell carcinomas (n = 822), breast cancers (n = 235), and thyroid cancers (n = 221) being the most frequent. Although SMN risk associations with the PRS were extremely modest in RT-exposed EUR survivors (HR, 1.22; P = .048; n = 4,630), the increase in 30-year SMN cumulative incidence and HRs comparing top and bottom PRS quintiles was statistically significant among nonirradiated EUR survivors (n = 4,322) treated with alkylating agents (17% v 6%; HR, 2.46; P < .01), anthracyclines (20% v 8%; HR, 2.86; P < .001), epipodophyllotoxins (23% v 1%; HR, 12.20; P < .001), or platinums (46% v 7%; HR, 8.58; P < .01). This PRS also significantly modified epipodophyllotoxin-related SMN risk among nonirradiated AFR survivors (n = 414; P < .01). Improvements in prediction attributable to the PRS were greatest for epipodophyllotoxin-exposed (AUC, 0.71 v 0.63) and platinum-exposed (AUC,0.68 v 0.58) survivors. CONCLUSION A pleiotropic cancer PRS has strong potential for improving SMN clinical risk stratification among nonirradiated survivors treated with specific chemotherapies. A polygenic risk screening approach may be a valuable complement to an early screening strategy on the basis of treatments and rare cancer-susceptibility mutations.
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Affiliation(s)
- Cindy Im
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Noha Sharafeldin
- Hematology Oncology Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Yan Yuan
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Zhanni Lu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Rebecca M. Howell
- Department of Radiation Physics, University of Texas at MD Anderson Cancer Center, Houston, TX
| | - Michael A. Arnold
- Department of Pathology and Laboratory Medicine, University of Colorado and Children's Hospital Colorado, Anschutz Medical Campus, Aurora, CO
| | - Melissa M. Hudson
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Kirsten K. Ness
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Gregory T. Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Joseph P. Neglia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
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10
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Lu C, Chen Q, Tao H, Xu L, Li J, Wang C, Yu L. The causal effect of inflammatory bowel disease on diffuse large B-cell lymphoma: two-sample Mendelian randomization study. Front Immunol 2023; 14:1171446. [PMID: 37593734 PMCID: PMC10427854 DOI: 10.3389/fimmu.2023.1171446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/13/2023] [Indexed: 08/19/2023] Open
Abstract
Background It has been reported that inflammatory bowel disease (IBD) is associated with an increased risk of malignancies, including lymphoma. A number of large observational studies have been devoted to exploring the causal link between IBD and malignant lymphoma. However, no consensus exists on whether there is a causal relationship between IBD and malignant lymphoma. Methods The summary dataset of the IBD and lymphoma genome-wide association studies (GWAS) was obtained from the OPEN GWAS website. Single-nucleotide polymorphisms (SNPs) were selected as genetic instrumental variants (IVs) for fulling P < 5 × 10-8 and linkage disequilibrium (LD) of r2 = 0.001 in the IBD GWAS. The proxy SNPs with LD of r2 > 0.8 were identified. Palindromic SNPs and outlier SNPs were excluded. The assessments of sensitivity employed the Cochran's Q test, Mendelian randomization (MR)-Egger intercept test, and leave-one-out analysis. Results The MR analysis results proved the causality of IBD on diffuse large B-cell lymphoma (DLBCL). The risk of developing DLBCL is increased by 28.6% in patients with IBD [odds ratio (OR)IVW = 1.286, 95% confidence interval (CI) 1.066-1.552, P = 0.009]. The results of the subgroup analysis showed that Crohn's disease (ORIVW = 1.218, 95% CI 1.030-1.441, P = 0.021) rather than ulcerative colitis (ORIVW = 1.206, 95% CI 0.984-1.478, P = 0.072) had a causal effect on DLBCL. No horizontal and directional pleiotropy was observed in the MR studies. Conclusions The above MR study concluded that IBD itself is causally responsible for DLBCL, especially Crohn's disease. Further investigations are needed to elucidate the mechanism underlying this direct causal link.
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Affiliation(s)
- Chuanyang Lu
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Qiuni Chen
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Hong Tao
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Lei Xu
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Jiaxin Li
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Chunling Wang
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Liang Yu
- Department of Hematology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
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11
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Fu S, Purdue MP, Zhang H, Qin J, Song L, Berndt SI, Yu K. Improve the model of disease subtype heterogeneity by leveraging external summary data. PLoS Comput Biol 2023; 19:e1011236. [PMID: 37437002 DOI: 10.1371/journal.pcbi.1011236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/02/2023] [Indexed: 07/14/2023] Open
Abstract
Researchers are often interested in understanding the disease subtype heterogeneity by testing whether a risk exposure has the same level of effect on different disease subtypes. The polytomous logistic regression (PLR) model provides a flexible tool for such an evaluation. Disease subtype heterogeneity can also be investigated with a case-only study that uses a case-case comparison procedure to directly assess the difference between risk effects on two disease subtypes. Motivated by a large consortium project on the genetic basis of non-Hodgkin lymphoma (NHL) subtypes, we develop PolyGIM, a procedure to fit the PLR model by integrating individual-level data with summary data extracted from multiple studies under different designs. The summary data consist of coefficient estimates from working logistic regression models established by external studies. Examples of the working model include the case-case comparison model and the case-control comparison model, which compares the control group with a subtype group or a broad disease group formed by merging several subtypes. PolyGIM efficiently evaluates risk effects and provides a powerful test for disease subtype heterogeneity in situations when only summary data, instead of individual-level data, is available from external studies due to various informatics and privacy constraints. We investigate the theoretic properties of PolyGIM and use simulation studies to demonstrate its advantages. Using data from eight genome-wide association studies within the NHL consortium, we apply it to study the effect of the polygenic risk score defined by a lymphoid malignancy on the risks of four NHL subtypes. These results show that PolyGIM can be a valuable tool for pooling data from multiple sources for a more coherent evaluation of disease subtype heterogeneity.
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Affiliation(s)
- Sheng Fu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jing Qin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
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12
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Ralli S, Jones SJ, Leach S, Lynch HT, Brooks-Wilson AR. Gene and pathway based burden analyses in familial lymphoid cancer cases: Rare variants in immune pathway genes. PLoS One 2023; 18:e0287602. [PMID: 37379307 DOI: 10.1371/journal.pone.0287602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023] Open
Abstract
Genome-wide association studies have revealed common genetic variants with small effect sizes associated with diverse lymphoid cancers. Family studies have uncovered rare variants with high effect sizes. However, these variants explain only a portion of the heritability of these cancers. Some of the missing heritability may be attributable to rare variants with small effect sizes. We aim to identify rare germline variants associated with familial lymphoid cancers using exome sequencing. One case per family was selected from 39 lymphoid cancer families based on early onset of disease or rarity of subtype. Control data was from Non-Finnish Europeans in gnomAD exomes (N = 56,885) or ExAC (N = 33,370). Gene and pathway-based burden tests for rare variants were performed using TRAPD. Five putatively pathogenic germline variants were found in four genes: INTU, PEX7, EHHADH, and ASXL1. Pathway-based association tests identified the innate and adaptive immune systems, peroxisomal pathway and olfactory receptor pathway as associated with lymphoid cancers in familial cases. Our results suggest that rare inherited defects in the genes involved in immune system and peroxisomal pathway may predispose individuals to lymphoid cancers.
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Affiliation(s)
- Sneha Ralli
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Samantha J Jones
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephen Leach
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Henry T Lynch
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska, United States of America
| | - Angela R Brooks-Wilson
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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13
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Cornish N, Haycock P, Brenner H, Figueiredo JC, Galesloot T, Grant RC, Johansson M, Mariosa D, McKay J, Pai R, Pellatt AJ, Samadder NJ, Shi J, Thibord F, Trégouët DA, Voegele C, Thirlwell C, Mumford A, Langdon R. Causal relationships between risk of venous thromboembolism and 18 cancers: a bidirectional Mendelian randomisation analysis. medRxiv 2023:2023.05.16.23289792. [PMID: 37292802 PMCID: PMC10246038 DOI: 10.1101/2023.05.16.23289792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background People with cancer experience high rates of venous thromboembolism (VTE). Additionally, risk of subsequent cancer is increased in people experiencing their first VTE. The causal mechanisms underlying this association are not completely understood, and it is unknown whether VTE is itself a risk factor for cancer. Methods We used data from large genome-wide association study meta-analyses to perform bi-directional Mendelian randomisation analyses to estimate causal associations between genetically-proxied lifetime risk of VTE and risk of 18 different cancers. Results We found no conclusive evidence that genetically-proxied lifetime risk of VTE was causally associated with an increased incidence of cancer, or vice-versa. We observed an association between VTE and pancreatic cancer risk (odds ratio for pancreatic cancer 1.23 (95% confidence interval 1.08 - 1.40) per log-odds increase in risk of VTE, P = 0.002). However, sensitivity analyses revealed this association was predominantly driven by a variant proxying non-O blood group, with inadequate evidence from Mendelian randomisation to suggest a causal relationship. Conclusions These findings do not support the hypothesis that genetically-proxied lifetime risk of VTE is a cause of cancer. Existing observational epidemiological associations between VTE and cancer are therefore more likely to be driven by pathophysiological changes which occur in the setting of active cancer and anti-cancer treatments. Further work is required to explore and synthesise evidence for these mechanisms.
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Affiliation(s)
- Naomi Cornish
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philip Haycock
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane C. Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles CA
| | - Tessel Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert C Grant
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Daniela Mariosa
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Arizona, Scottsdale, USA
| | - Andrew J Pellatt
- Division of Cancer Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | | | - Catherine Voegele
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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14
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Duns G, Winkle M, Chong L, Ennishi D, Morin RD, Diepstra A, Scott DW, Kluiver JL, Steidl C, van den Berg A. Long non-coding RNAs associated with transcriptomic signatures and treatment outcome in diffuse large B-cell lymphoma. Br J Haematol 2023. [PMID: 37190862 DOI: 10.1111/bjh.18870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lauren Chong
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arjan Diepstra
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joost L Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
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15
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Iyer AR, Gurumurthy A, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rausch D, Gupta J, Hall CN, Runge JS, Weiss M, Rahmat M, Anyoha R, Fulco CP, Ghobrial IM, Engreitz J, Cieslik MP, Ryan RJH. Selective Enhancer Dependencies in MYC -Intact and MYC -Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. bioRxiv 2023:2023.05.02.538892. [PMID: 37205448 PMCID: PMC10187217 DOI: 10.1101/2023.05.02.538892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC -intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer ( BCL6 -SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6 -SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3' enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3' rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene. Key points CRISPR-interference screens identify a conserved germinal center B cell MYC enhancer that is essential for GCB-DLBCL lacking MYC rearrangements. Functional profiling of MYC partner loci reveals principles of MYC enhancer-hijacking activation by non-immunoglobulin rearrangements.
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16
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Rhee J, Birmann BM, De Roos AJ, Epstein MM, Martinez-Maza O, Breen EC, Magpantay LI, Levin LI, Visvanathan K, Hosgood HD, Rohan TE, Smoller SW, Bassig BA, Qi L, Shu XO, Koh WP, Zheng W, Yuan JM, Weinstein SJ, Albanes D, Lan Q, Rothman N, Purdue MP. Circulating immune markers and risks of non-Hodgkin lymphoma subtypes: A pooled analysis. Int J Cancer 2023; 152:865-878. [PMID: 36151863 PMCID: PMC9812887 DOI: 10.1002/ijc.34299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 01/07/2023]
Abstract
Although prediagnostic circulating concentrations of the immune activation markers soluble CD27 (sCD27), sCD30 and chemokine ligand-13 (CXCL13) have been associated with non-Hodgkin lymphoma (NHL) risk, studies have been limited by sample size in associations with NHL subtypes. We pooled data from eight nested case-control studies to investigate subtype-specific relationships for these analytes. Using polytomous regression, we calculated odds ratios (ORs) with 95% confidence intervals (CIs) relating study-specific analyte tertiles to selected subtypes vs controls (n = 3310): chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL; n = 623), diffuse large B cell lymphoma (DLBCL; n = 621), follicular lymphoma (FL; n = 398), marginal zone lymphoma (MZL; n = 138), mantle cell lymphoma (MCL; n = 82) and T cell lymphoma (TCL; n = 92). We observed associations with DLBCL for elevated sCD27 [OR for third vs first tertile (ORT3 ) = 2.2, 95% CI = 1.6-3.1], sCD30 (ORT3 = 2.0, 95% CI = 1.6-2.5) and CXCL13 (ORT3 = 2.3, 95% CI = 1.8-3.0). We also observed associations with sCD27 for CLL/SLL (ORT3 = 3.3, 95% CI = 2.4-4.6), MZL (ORT3 = 7.7, 95% CI = 3.0-20.1) and TCL (ORT3 = 3.4, 95% CI = 1.5-7.7), and between sCD30 and FL (ORT3 = 2.7, 95% CI = 2.0-3.5). In analyses stratified by time from phlebotomy to case diagnosis, the sCD27-TCL and all three DLBCL associations were equivalent across both follow-up periods (<7.5, ≥7.5 years). For other analyte-subtype comparisons, associations were stronger for the follow-up period closer to phlebotomy, particularly for indolent subtypes. In conclusion, we found robust evidence of an association between these immune markers and DLBCL, consistent with hypotheses that mechanisms related to immune activation are important in its pathogenesis. Our other findings, particularly for the rarer subtypes MZL and TCL, require further investigation.
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Affiliation(s)
- Jongeun Rhee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Brenda M. Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Anneclaire J. De Roos
- Department of Environmental and Occupational Health, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Mara M. Epstein
- Department of Medicine and the Meyers Health Care Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Otoniel Martinez-Maza
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA AIDS Institute, Los Angeles, CA, USA
- Department of Obstetrics & Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elizabeth C. Breen
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Larry I. Magpantay
- UCLA AIDS Institute, Los Angeles, CA, USA
- Department of Obstetrics & Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lynn I. Levin
- Statistics and Epidemiology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kala Visvanathan
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - H. Dean Hosgood
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Thomas E. Rohan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sylvia W. Smoller
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bryan A. Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Formerly at the U.S. National Cancer Institute. This author is currently employed by the U.S. Centers for Disease Control and Prevention, National Center for Health Statistics. All work on this study by the author was conducted while employed by the National Cancer Institute
| | - Lihong Qi
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore 117609, Singapore
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie J. Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Abstract
Waldenström macroglobulinemia (WM) is a rare subtype of non-Hodgkin lymphoma characterized by the presence of lymphoplasmacytic lymphoma (LPL) in the bone marrow accompanied by a monoclonal immunoglobulin type M (IgM) in the serum. WM was first described only 80 years ago and became reportable in the US as a malignancy in 1988. Very little systematic research was conducted prior to 2000 to characterize incidence, clinical characteristics, risk factors or diagnostic and prognostic criteria, and there were essentially no WM-specific clinical interventional trials. Since the inaugural meeting of the International Workshop in Waldenström's Macroglobulinemia (IWWM) in 2000, WM has become the focus of a steadily increasing and productive body of research, engaging a growing number of investigators throughout the world. This introductory overview provides summary of the current understanding of the epidemiology of WM/LPL as a backdrop for a series of consensus panel recommendations arising from research presented at the 11th IWWM.
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Affiliation(s)
- Mary L McMaster
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Health and Human Services, Commissioned Corps of the United States Public Health Service, Washington, DC.
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18
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Ochoa S, Hernández-Lemus E. Functional impact of multi-omic interactions in breast cancer subtypes. Front Genet 2023; 13:1078609. [PMID: 36685900 PMCID: PMC9850112 DOI: 10.3389/fgene.2022.1078609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automatically produce network models of the regulatory constraints influencing a biological function. This way, we identified functions significantly enriched on the analyzed omics and described associated features, for each of the four breast cancer molecular subtypes. For instance, we identified functions sustaining over-representation of invasion-related processes in the basal subtype and DNA modification processes in the normal tissue. We found limited overlap on the omics-associated functions between subtypes; however, a startling feature intersection within subtype functions also emerged. The examples presented highlight new, potentially regulatory features, with sound biological reasons to expect a connection with the functions. Multi-omic regulatory networks thus constitute reliable models of the way omics are connected, demonstrating a capability for systematic generation of mechanistic hypothesis.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico,*Correspondence: Enrique Hernández-Lemus,
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19
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Uhl GR. Selecting the appropriate hurdles and endpoints for pentilludin, a novel antiaddiction pharmacotherapeutic targeting the receptor type protein tyrosine phosphatase D. Front Psychiatry 2023; 14:1031283. [PMID: 37139308 PMCID: PMC10149857 DOI: 10.3389/fpsyt.2023.1031283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/30/2023] [Indexed: 05/05/2023] Open
Abstract
Substance use disorders provide challenges for development of effective medications. Use of abused substances is likely initiated, sustained and "quit" by complex brain and pharmacological mechanisms that have both genetic and environmental determinants. Medical utilities of prescribed stimulants and opioids provide complex challenges for prevention: how can we minimize their contribution to substance use disorders while retaining medical benefits for pain, restless leg syndrome, attention deficit hyperactivity disorder, narcolepsy and other indications. Data required to support assessments of reduced abuse liability and resulting regulatory scheduling differs from information required to support licensing of novel prophylactic or therapeutic anti-addiction medications, adding further complexity and challenges. I describe some of these challenges in the context of our current efforts to develop pentilludin as a novel anti-addiction therapeutic for a target that is strongly supported by human and mouse genetic and pharmacologic studies, the receptor type protein tyrosine phosphatase D (PTPRD).
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Affiliation(s)
- George R. Uhl
- Departments of Neurology and Pharmacology, University of Maryland School of Medicine, Neurology Service, VA Maryland Healthcare System, Baltimore, MD, United States
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- *Correspondence: George R. Uhl
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20
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Sara DM, Minelli C, Broccia G, Vineis P, Cocco P. COVID-19 and non-Hodgkin's lymphoma: A common susceptibility pattern? PLoS One 2023; 18:e0277588. [PMID: 36928185 PMCID: PMC10019614 DOI: 10.1371/journal.pone.0277588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
OBJECTIVE To explore the link between COVID-19 incidence, socio-economic covariates, and NHL incidence. DESIGN Ecological study design. SETTING Sardinia, Italy. PARTICIPANTS We used official reports on the total cases of COVID-19 in 2020, published data on NHL incidence, and socio-economic indicators by administrative unit, covering the whole regional population. MAIN OUTCOMES AND MEASURES We used multivariable regression analysis to explore the association between the natural logarithm (ln) of the 2020 cumulative incidence of COVID-19 and the ln-transformed NHL incidence in 1974-2003, weighing by population size and adjusting by socioeconomic deprivation and other covariates. RESULTS The cumulative incidence of COVID-19 increased in relation to past incidence of NHL (p < 0.001), socioeconomic deprivation (p = 0.006), and proportion of elderly residents (p < 0.001) and decreased with urban residency (p = 0.001). Several sensitivity analyses confirmed the finding of an association between COVID-19 and NHL. CONCLUSION This ecological study found an ecological association between NHL and COVID-19. If further investigation would confirm our findings, shared susceptibility factors should be investigated among the plausible underlying mechanisms.
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Affiliation(s)
- De Matteis Sara
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Giorgio Broccia
- Private Consultant, Former director of the Department of Haematology and Bone Marrow Transplants, Hospital A. Businco, Cagliari, Italy
| | - Paolo Vineis
- Faculty of Medicine, School of Public Health, Imperial College, London, United Kingdom
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Health, University of Manchester, Manchester, United Kingdom
- * E-mail:
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21
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Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diepstra A, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia 2022; 36:2835-2844. [PMID: 36273105 PMCID: PMC10337695 DOI: 10.1038/s41375-022-01711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10-8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10-9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10-8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA.
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexandra Nieters
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Caroline Besson
- Centre Hospitalier de Versailles, Le Chesnay, France
- Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Joshua Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York, 11794, NY, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Lisa A Cannon-Albright
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, USA
| | - Brian C H Chiu
- Department of Public Health Sciences University of Chicago, Chicago, IL, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Jacqueline Clavel
- CRESS, UMR1153, INSERM, Villejuif, France
- Université de Paris-Cité, Villejuif, France
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Science, Health Services Research & Primary Care, University of Manchester, Manchester, United Kingdom
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - David V Conti
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Delphine Casabonne
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher K Edlund
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari, Italy
| | - Hervé Ghesquières
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre Benite, France
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphoma Immuno-Biology, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Sally Glaser
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford Cancer Institute, Stanford, CA, USA
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher A Haiman
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Henri Mondor Hospital and University Paris Est, Créteil, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Aalin Izhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | - Laurence N Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yinfei Kong
- Information Systems and Decision Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW, Australia
| | - Annette Lake
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | | | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marc Maynadie
- INSERM U1231, EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Jebsen Center for Genetic epidemiology, NTNU, Trondheim, Norway
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Genetics, Stanford University Medical School, Stanford, CA, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence, Italy
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Thierry J Molina
- Department of Pathology, APHP, Necker and Robert Debré, Université Paris Cité, Institut Imagine, INSERM U1163, Paris, France
| | - Alain Monnereau
- CRESS, UMR1153, INSERM, Villejuif, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux, Cedex, France
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kenan Onel
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, New York, NY, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kristin A Rand
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas W Sborov
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tait D Shanafelt
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Alexandra Smith
- Department of Health Sciences, University of York, York, United Kingdom
| | - Kevin W Song
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lei Song
- Center for Cancer Research, National Cancer Institute, Frederick, MA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, VC, 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Deborah Stephens
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heather J Sutherland
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hervé Tilly
- Centre Henri Becquerel, Université de Rouen, Rouen, France
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Jenny Turner
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, NSW, Australia
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Claire M Vajdic
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anke Van Den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Human Genetics Foundation, Turin, Italy
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, NSW, Australia
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
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22
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García-Sancha N, Corchado-Cobos R, Gómez-Vecino A, Jiménez-Navas A, Pérez-Baena MJ, Blanco-Gómez A, Holgado-Madruga M, Mao JH, Cañueto J, Castillo-Lluva S, Mendiburu-Eliçabe M, Pérez-Losada J. Evolutionary Origins of Metabolic Reprogramming in Cancer. Int J Mol Sci 2022; 23:ijms232012063. [PMID: 36292921 PMCID: PMC9603151 DOI: 10.3390/ijms232012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.
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Affiliation(s)
- Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Cañueto
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007 Salamanca, Spain
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
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23
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Corpas M, Megy K, Metastasio A, Lehmann E. Implementation of individualised polygenic risk score analysis: a test case of a family of four. BMC Med Genomics 2022; 15:207. [PMID: 36192731 PMCID: PMC9531350 DOI: 10.1186/s12920-022-01331-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Background Polygenic risk scores (PRS) have been widely applied in research studies, showing how population groups can be stratified into risk categories for many common conditions. As healthcare systems consider applying PRS to keep their populations healthy, little work has been carried out demonstrating their implementation at an individual level. Case presentation We performed a systematic curation of PRS sources from established data repositories, selecting 15 phenotypes, comprising an excess of 37 million SNPs related to cancer, cardiovascular, metabolic and autoimmune diseases. We tested selected phenotypes using whole genome sequencing data for a family of four related individuals. Individual risk scores were given percentile values based upon reference distributions among 1000 Genomes Iberians, Europeans, or all samples. Over 96 billion allele effects were calculated in order to obtain the PRS for each of the individuals analysed here. Conclusions Our results highlight the need for further standardisation in the way PRS are developed and shared, the importance of individual risk assessment rather than the assumption of inherited averages, and the challenges currently posed when translating PRS into risk metrics.
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Affiliation(s)
- Manuel Corpas
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK. .,Institute of Continuing Education, University of Cambridge, Cambridge, UK. .,Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja, Madrid, Spain.
| | - Karyn Megy
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK.,Department of Haematology, University of Cambridge & NHS Blood and Transplant, Cambridge, UK
| | - Antonio Metastasio
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK.,Camden and Islington NHS Foundation Trust, London, UK
| | - Edmund Lehmann
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
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24
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Koutsi MA, Pouliou M, Champezou L, Vatsellas G, Giannopoulou A, Piperi C, Agelopoulos M. Typical Enhancers, Super-Enhancers, and Cancers. Cancers (Basel) 2022; 14:4375. [PMID: 36139535 PMCID: PMC9496678 DOI: 10.3390/cancers14184375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The cancer genome has been exhaustively studied upon the advent of Next-Generation Sequencing technologies. Coding and non-coding sequences have been defined as hotspots of genomic variations that affect the naïve gene expression programs established in normal cells, thus working as endogenous drivers of carcinogenesis. In this review, we comprehensively summarize fundamental aspects of gene expression regulation, with emphasis on the impact of sequence and structural variations mapped across non-coding cis-acting elements of genes encoding for tumor-related transcription factors. Chromatin architecture, epigenome reprogramming, transcriptional enhancers and Super-enhancers, oncogene regulation, cutting-edge technologies, and pharmacological treatment are substantially highlighted. Abstract Non-coding segments of the human genome are enriched in cis-regulatory modules that constitute functional elements, such as transcriptional enhancers and Super-enhancers. A hallmark of cancer pathogenesis is the dramatic dysregulation of the “archetype” gene expression profiles of normal human cells. Genomic variations can promote such deficiencies when occurring across enhancers and Super-enhancers, since they affect their mechanistic principles, their functional capacity and specificity, and the epigenomic features of the chromatin microenvironment across which these regulatory elements reside. Here, we comprehensively describe: fundamental mechanisms of gene expression dysregulation in cancers that involve genomic abnormalities within enhancers’ and Super-enhancers’ (SEs) sequences, which alter the expression of oncogenic transcription factors (TFs); cutting-edge technologies applied for the analysis of variation-enriched hotspots of the cancer genome; and pharmacological approaches for the treatment of Super-enhancers’ aberrant function. Finally, we provide an intratumor meta-analysis, which highlights that genomic variations in transcription-factor-driven tumors are accompanied overexpression of genes, a portion of which encodes for additional cancer-related transcription factors.
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25
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Paszkiewicz-Kozik E, Kluska A, Piątkowska M, Bałabas A, Żeber-Lubecka N, Karczmarski J, Goryca K, Kulecka M, Wojciechowska-Lampka E, Osiadacz W, Romejko-Jarosińska J, Świerkowska M, Paziewska A, Ambrożkiewicz F, Walewski J, Mikula M, Ostrowski J. Genetic associations with lymphomas in Polish patients: A pooled-DNA genome-wide association analysis. Int J Immunogenet 2022; 49:353-363. [PMID: 36036752 DOI: 10.1111/iji.12596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
Several single nucleotide polymorphisms (SNPs) associated with susceptibility to Hodgkin lymphoma (HL) and diffuse large B-cell lymphoma (DLBCL) have been identified. The aim of this study was to identify susceptibility loci for HL and DLBCL in Polish patients. Altogether, DLBCL (n = 218 and HL patients (n = 224) and healthy individuals (n = 1181) were recruited. Lymphoma diagnosis was based on standard criteria. Genome-wide association study (GWAS) was performed using pooled-DNA samples on llumina Infinium Omni2.5 Exome-8 v1.3, and selected loci were replicated by TaqMan SNP genotyping of individuals. GWAS detected thirteen and seven SNPs associated with DLBCL and HL, respectively. In the replication study, six and seven SNPs reached significance after correction for multiple testing in the DLBCL and HL cohorts, respectively. One and four SNPs associated with DLBCL and HL, respectively, were localized within, and two SNPs-near the major histocompatibility complex (MHC) region. In conclusion, the majority of loci associated with HL and DLBCL aetiology in previous studies have potential roles in immune function. Our pooled-DNA GWAS enabled the identification of several susceptibility loci for DLBCL and HL in the Polish population; some of them were mapped within or adjacent to the MHC, and other associated SNPs were located outside the MHC.
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Affiliation(s)
- Ewa Paszkiewicz-Kozik
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Elżbieta Wojciechowska-Lampka
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Włodzimierz Osiadacz
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Joanna Romejko-Jarosińska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Monika Świerkowska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
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26
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Luo J, Craver A, Bahl K, Stepniak L, Moore K, King J, Zhang Y, Aschebrook-Kilfoy B. Etiology of non-Hodgkin lymphoma: A review from epidemiologic studies. Journal of the National Cancer Center 2022. [DOI: 10.1016/j.jncc.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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27
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Ye X, Maglione PJ, Wehr C, Li X, Wang Y, Abolhassani H, Deripapa E, Liu D, Borte S, Du L, Wan H, Plötner A, Giannoula Y, Ko HM, Hou Y, Zhu S, Grossman JK, Sander B, Grimbacher B, Hammarström L, Fedorova A, Rosenzweig S, Shcherbina A, Wu K, Warnatz K, Cunningham-Rundles C, Pan-Hammarström Q. Genomic characterization of lymphomas in patients with inborn errors of immunity. Blood Adv 2022:bloodadvances. [PMID: 35687490 DOI: 10.1182/bloodadvances.2021006654] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Inborn errors of immunity-associated lymphomas are characterized by distinct clinical features and genetic signatures. Both germline and somatic alterations contribute to lymphomagenesis in patients with inborn errors of immunity.
Patients with inborn errors of immunity (IEI) have a higher risk of developing cancer, especially lymphoma. However, the molecular basis for IEI-related lymphoma is complex and remains elusive. Here, we perform an in-depth analysis of lymphoma genomes derived from 23 IEI patients. We identified and validated disease-causing or -associated germline mutations in 14 of 23 patients involving ATM, BACH2, BLM, CD70, G6PD, NBN, PIK3CD, PTEN, and TNFRSF13B. Furthermore, we profiled somatic mutations in the lymphoma genome and identified 8 genes that were mutated at a significantly higher level in IEI-associated diffuse large B-cell lymphomas (DLBCLs) than in non-IEI DLBCLs, such as BRCA2, NCOR1, KLF2, FAS, CCND3, and BRWD3. The latter, BRWD3, is furthermore preferentially mutated in tumors of a subgroup of activated phosphoinositide 3-kinase δ syndrome patients. We also identified 5 genomic mutational signatures, including 2 DNA repair deficiency-related signatures, in IEI-associated lymphomas and a strikingly high number of inter- and intrachromosomal structural variants in the tumor genome of a Bloom syndrome patient. In summary, our comprehensive genomic characterization of lymphomas derived from patients with rare genetic disorders expands our understanding of lymphomagenesis and provides new insights for targeted therapy.
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28
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Dreyling M, André M, Gökbuget N, Tilly H, Jerkeman M, Gribben J, Ferreri A, Morel P, Stilgenbauer S, Fox C, Maria Ribera J, Zweegman S, Aurer I, Bödör C, Burkhardt B, Buske C, Dollores Caballero M, Campo E, Chapuy B, Davies A, de Leval L, Doorduijn J, Federico M, Gaulard P, Gay F, Ghia P, Grønbæk K, Goldschmidt H, Kersten MJ, Kiesewetter B, Landman-Parker J, Le Gouill S, Lenz G, Leppä S, Lopez-Guillermo A, Macintyre E, Mantega MVM, Moreau P, Moreno C, Nadel B, Okosun J, Owen R, Pospisilova S, Pott C, Robak T, Spina M, Stamatopoulos K, Stary J, Tarte K, Tedeschi A, Thieblemont C, Trappe RU, Trümper LH, Salles G. The EHA Research Roadmap: Malignant Lymphoid Diseases. Hemasphere 2022; 6:e726. [PMID: 35620592 PMCID: PMC9126526 DOI: 10.1097/hs9.0000000000000726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Marc André
- Université Catholique de Louvain, CHU UcL Namur, Yvoir, Belgium
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Hervé Tilly
- INSERM U1245, Department of Hematology, Centre Henri Becquerel and Université de Rouen, France
| | | | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Andrés Ferreri
- Lymphoma Unit, Department of Onco-hematology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Pierre Morel
- Service Hematologie Clinique Therapie Cellulaire, CHU Amiens Picardie, Amiens, France
| | - Stephan Stilgenbauer
- Comprehensive Cancer Center Ulm (CCCU), Sektion CLL Klinik für Innere Medizin III, Universität Ulm, Germany
| | - Christopher Fox
- School of Medicine, University of Nottingham, United Kingdom
| | - José Maria Ribera
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Sonja Zweegman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, the Netherlands
| | - Igor Aurer
- University Hospital Centre Zagreb and Medical School, University of Zagreb, Croatia
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Birgit Burkhardt
- Experimentelle und Translationale päd. Hämatologie u Onkologie, Leitung der Bereiche Lymphome und Stammzelltransplantation, Universitätsklinikum Münster (UKM), Klinik für Kinder- und Jugendmedizin, Pädiatrische Hämatologie und Onkologie, Munich, Germany
| | - Christian Buske
- Institute of Experimental Cancer Research, CCC Ulm, University Hospital Ulm, Germany
| | - Maria Dollores Caballero
- Clinical and Transplant Unit, University Hospital of Salamanca, Spain
- Department of Medicine at the University of Salamanca, Spain
- El Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Bjoern Chapuy
- Department of Hematology, Oncology and Tumor Immunology, Charité, University Medical Center Berlin, Campus Benjamin Franklin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Andrew Davies
- Southampton NCRI/UK Experimental Cancer Medicines Centre, Faculty of Medicine, University of Southampton, United Kingdom
| | - Laurence de Leval
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Jeanette Doorduijn
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Philippe Gaulard
- Département de Pathologie, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - Francesca Gay
- Clinical Trial Unit, Division of Hematology 1, AOU Città Della Salute e Della Scienza, University of Torino, Italy
| | - Paolo Ghia
- Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Hartmut Goldschmidt
- University Hospital Heidelberg, Internal Medicine V and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Marie-Jose Kersten
- Department of Hematology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam and LYMMCARE, Amsterdam, the Netherlands
| | - Barbara Kiesewetter
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Austria
| | - Judith Landman-Parker
- Pediatric Hematology Oncology, Sorbonne Université APHP/hôpital A Trousseau, Paris, France
| | - Steven Le Gouill
- Service d’Hématologie, Clinique du Centre Hospitalier Universitaire (CHU) de Nantes, France
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Germany
| | - Sirpa Leppä
- University of Helsinki and Helsinki University Hospital Comprehensive Cancer Centre, Helsinki, Finland
| | | | - Elizabeth Macintyre
- Onco-hematology, Université de Paris and Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, France
| | | | - Philippe Moreau
- Hematology Department, University Hospital Hotel-Dieu, Nantes, France
| | - Carol Moreno
- Hospital de la Santa Creu I Sant Pau, Autonomous University of Barcelona, Spain
| | - Bertrand Nadel
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Roger Owen
- St James’s Institute of Oncology, Leeds, United Kingdom
| | - Sarka Pospisilova
- Department of Internal Medicine—Hematology and Oncology and Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Christiane Pott
- Klinisch-experimentelle Hämatologie, Medizinische Klinik II, Hämatologie und Internistische Onkologie, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Germany
| | | | - Michelle Spina
- Division of Medical Oncology and Immune-related Tumors, National Cancer Institute, Aviano, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Jan Stary
- Department of Pediatric Hematology and Oncology 2nd Faculty of Medicine, Charles University Prague University Hospital, Prague, Czech Republic
| | - Karin Tarte
- Immunology and Cell Therapy Lab at Rennes University Hospital, Rennes, France
| | | | - Catherine Thieblemont
- Department of Hemato-Oncology, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Ralf Ulrich Trappe
- Department of Internal Medicine II: Haematology and Oncology, DIAKO Hospital Bremen, Germany
| | - Lorenz H. Trümper
- Hematology and Medical Oncology, University Medicine Goettingen, Germany
| | - Gilles Salles
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, New York, NY, USA
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Wang SS, Vajdic CM, Linet MS, Slager SL, Voutsinas J, Nieters A, Casabonne D, Cerhan JR, Cozen W, Alarcón G, Martínez-Maza O, Brown EE, Bracci PM, Turner J, Hjalgrim H, Bhatti P, Zhang Y, Birmann BM, Flowers CR, Paltiel O, Holly EA, Kane E, Weisenburger DD, Maynadié M, Cocco P, Foretova L, Breen EC, Lan Q, Brooks-Wilson A, De Roos AJ, Smith MT, Roman E, Boffetta P, Kricker A, Zheng T, Skibola CF, Clavel J, Monnereau A, Chanock SJ, Rothman N, Benavente Y, Hartge P, Smedby KE. B-Cell NHL Subtype Risk Associated with Autoimmune Conditions and PRS. Cancer Epidemiol Biomarkers Prev 2022; 31:1103-1110. [PMID: 35244686 PMCID: PMC9081255 DOI: 10.1158/1055-9965.epi-21-0875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/02/2021] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND A previous International Lymphoma Epidemiology (InterLymph) Consortium evaluation of joint associations between five immune gene variants and autoimmune conditions reported interactions between B-cell response-mediated autoimmune conditions and the rs1800629 genotype on risk of B-cell non-Hodgkin lymphoma (NHL) subtypes. Here, we extend that evaluation using NHL subtype-specific polygenic risk scores (PRS) constructed from loci identified in genome-wide association studies of three common B-cell NHL subtypes. METHODS In a pooled analysis of NHL cases and controls of Caucasian descent from 14 participating InterLymph studies, we evaluated joint associations between B-cell-mediated autoimmune conditions and tertile (T) of PRS for risk of diffuse large B-cell lymphoma (DLBCL; n = 1,914), follicular lymphoma (n = 1,733), and marginal zone lymphoma (MZL; n = 407), using unconditional logistic regression. RESULTS We demonstrated a positive association of DLBCL PRS with DLBCL risk [T2 vs. T1: OR = 1.24; 95% confidence interval (CI), 1.08-1.43; T3 vs. T1: OR = 1.81; 95% CI, 1.59-2.07; P-trend (Ptrend) < 0.0001]. DLBCL risk also increased with increasing PRS tertile among those with an autoimmune condition, being highest for those with a B-cell-mediated autoimmune condition and a T3 PRS [OR = 6.46 vs. no autoimmune condition and a T1 PRS, Ptrend < 0.0001, P-interaction (Pinteraction) = 0.49]. Follicular lymphoma and MZL risk demonstrated no evidence of joint associations or significant Pinteraction. CONCLUSIONS Our results suggest that PRS constructed from currently known subtype-specific loci may not necessarily capture biological pathways shared with autoimmune conditions. IMPACT Targeted genetic (PRS) screening among population subsets with autoimmune conditions may offer opportunities for identifying those at highest risk for (and early detection from) DLBCL.
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Affiliation(s)
- Sophia S. Wang
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Monrovia, California
| | - Claire M. Vajdic
- Centre for Big Data Research in Health, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martha S. Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Susan L. Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jenna Voutsinas
- Division of Health Analytics, Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Monrovia, California
| | - Alexandra Nieters
- The Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Delphine Casabonne
- Unit of Infections and Cancer, Epidemiology, Public Health, Cancer Prevention and Palliative Care Program – Epibell, IDIBELL, Institut Català d’ Oncologia/IDIBELL, Barcelona, Spain
- The Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - James R. Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, California
| | - Graciela Alarcón
- Division of Clinical Immunology and Rheumatology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Otoniel Martínez-Maza
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
| | - Elizabeth E. Brown
- Department of Pathology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
- O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jennifer Turner
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, New South Wales, Australia
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Parveen Bhatti
- British Columbia Cancer Research Center, Vancouver, British Columbia, Canada
| | - Yawei Zhang
- Department of Cancer Prevention and Control at the National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Brenda M. Birmann
- Channing Division of Network Medicine, Department of Medicine Research, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Ora Paltiel
- Department of Hematology, The Hebrew University-Hadassah Braun School of Public Health and Community Medicine, Hadassah University Medical Center, Jerusalem, Israel
| | - Elizabeth A. Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | | | - Marc Maynadié
- Registry of Hematological Malignancies of Cote d'Or, INSERM U1231, Burgundy University and University Hospital, Dijon, France (Maynadie)
| | - Pierluigi Cocco
- Occupational Health Section, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Elizabeth Crabb Breen
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Angela Brooks-Wilson
- Department of Biomedical Physiology and Kinesiology, Faculty of Science, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Anneclaire J. De Roos
- Department of Environmental and Occupational Health, Dornsife School of Public Health, Drexel University, Philadelphia, Pennsylvania
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Tongzhang Zheng
- Department of Epidemiology, School of Public Health, Brown University, Providence, Rhode Island
| | | | - Jacqueline Clavel
- Centre of Research in Epidemiology and Statistics (CRESS), UMR1153, INSERM, Université de Paris, Paris, France
| | - Alain Monnereau
- Centre of Research in Epidemiology and Statistics (CRESS), UMR1153, INSERM, Université de Paris, Paris, France
- Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, University of Bordeaux, Inserm, Team EPICENE, UMR 1219, Paris, France
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Yolanda Benavente
- Unit of Infections and Cancer, Epidemiology, Public Health, Cancer Prevention and Palliative Care Program – Epibell, IDIBELL, Institut Català d’ Oncologia/IDIBELL, Barcelona, Spain
- The Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Karin E. Smedby
- Division of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Park JH, Jin EH, Hong JH, Lee SI, Sung JK. The association between polymorphism of the long noncoding RNA, Plasmacytoma variant translocation 1, and the risk of gastric cancer. Medicine (Baltimore) 2021; 100:e27773. [PMID: 35049170 PMCID: PMC9191314 DOI: 10.1097/md.0000000000027773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Genetic polymorphisms of plasmacytoma variant translocation 1 can affect various tumors including gastro-intestinal, sexual hormone sensitive cancers and lymphoma. Accumulated evidence have shown that plasmacytoma variant translocation 1 acts as an oncogene and tumor suppressor in various cancers. In fact, the rs13255292 and rs2608053 single nucleotide polymorphisms of plasmacytoma variant translocation 1are known to affect lymphoma; however, their effects on gastric cancer are primarily unknown. In this study, we evaluated the association between these plasmacytoma variant translocation 1 polymorphisms and the risk of gastric cancer.In the present study, 462 patients diagnosed with gastric cancer and 377 cancer-free controls were enrolled. The TaqMan genotyping assay was used to analyze the association between rs13255292 and rs2608053 single nucleotide polymorphisms and the risk of gastric cancer.The rs2608053 dominant model (CT + TT) was associated with a decreased risk of gastric cancer in T3 + T4 (odds ratio [OR] = 0.61, confidence interval (CI) = 0.41 - 0.92, P = .019), and stage III Gastric cancer subgroups (OR = 0.59, 95% CI = 0.38 - 0.91, P = .017) compared to the CC genotype. When stratified analysis by sex was carried out, the rs13255292 dominant model (CT + TT) had a significant association with an increased risk of gastric cancer in the female negative lymph node metastasis gastric cancer subgroup, compared to the CC genotype (OR = 1.96, 95% CI = 1.16 - 3.30, P = .012). The recessive model (TT) of rs13255292 was associated with an increased risk of gastric cancer in the male T3 + T4 gastric cancer subgroups compared to the CC + CT genotype (OR = 3.82, 95% CI = 1.02 - 14.33, P = .047). The dominant model (CT + TT) of rs2608053 was related to a decreased risk of gastric cancer in male T3 + T4 (OR = 0.57, 95% CI = 0.33 - 0.98, P = .042) and stage III gastric cancer subgroups (OR = 0.49, 95% CI = 0.27 - 0.89, P = .020) compared to the CC genotype.The rs13255292 and rs2608053 single nucleotide polymorphisms in plasmacytoma variant translocation 1 may contribute to susceptibility of gastric cancer. Further studies with more subjects and different ethnic groups are needed to validate our results.
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Affiliation(s)
- Jae Ho Park
- Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Eun-Heui Jin
- Translational Immunology Institute, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jang Hee Hong
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
- Clinical Trials Center, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Sang-Il Lee
- Department of Surgery, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jae Kyu Sung
- Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
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Abstract
BACKGROUND Genetic factors play a crucial role in the glioma risk and prognosis of glioma patients. To explore the role of plasmacytoma variant translocation 1 (PVT1) polymorphism in the susceptibility and survival of glioma in the Chinese Han population, we conducted a case-control study. METHODS The three single-nucleotide polymorphisms (SNPs) in PVT1 were genotyped using Agena MassARRAY from 575 patients with glioma and 500 healthy controls. We used the χ2 test to analyze the differences in distribution of allele and genotype between the cases and controls. Odds ratio and 95% confidence interval (CI) were calculated by logistic regression analysis to evaluate the association SNPs with glioma risk. The effects of polymorphisms and clinical features on survival of glioma patients were evaluated using the log-rank test, Kaplan-Meier and Cox regression analysis. RESULTS We found that rs13255292 was associated with a decreased risk of glioma in the recessive model in overall or male; and rs4410871 was significantly associated with an increased the risk of glioma in age ≤40 years old or female. Moreover, the extent of resection and chemotherapy were found to be key prognostic factors in survival of glioma patients. However, the gender, age, tumor grade, radiotherapy and PVT1 polymorphisms have no effect on prognosis of glioma patients. CONCLUSIONS Our results indicated that PVT1 polymorphisms (rs13255292 and rs4410871) were associated with glioma susceptibility, but have no effect on prognosis of glioma patients. Further studies with large samples are required to confirm the results.
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Affiliation(s)
| | | | | | | | - Ya Gao
- Department of Pediatric Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Moore A, Machiela MJ, Machado M, Wang SS, Kane E, Slager SL, Zhou W, Carrington M, Lan Q, Milne RL, Birmann BM, Adami HO, Albanes D, Arslan AA, Becker N, Benavente Y, Bisanzi S, Boffetta P, Bracci PM, Brennan P, Brooks-Wilson AR, Canzian F, Caporaso N, Clavel J, Cocco P, Conde L, Cox DG, Cozen W, Curtin K, De Vivo I, de Sanjose S, Foretova L, Gapstur SM, Ghesquières H, Giles GG, Glenn M, Glimelius B, Gao C, Habermann TM, Hjalgrim H, Jackson RD, Liebow M, Link BK, Maynadie M, McKay J, Melbye M, Miligi L, Molina TJ, Monnereau A, Nieters A, North KE, Offit K, Patel AV, Piro S, Ravichandran V, Riboli E, Salles G, Severson RK, Skibola CF, Smedby KE, Southey MC, Spinelli JJ, Staines A, Stewart C, Teras LR, Tinker LF, Travis RC, Vajdic CM, Vermeulen RCH, Vijai J, Weiderpass E, Weinstein S, Doo NW, Zhang Y, Zheng T, Chanock SJ, Rothman N, Cerhan JR, Dean M, Camp NJ, Yeager M, Berndt SI. Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes. J Transl Genet Genom 2021; 5:200-217. [PMID: 34622145 PMCID: PMC8494431 DOI: 10.20517/jtgg.2021.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AIM Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk. METHODS We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction of the autosome containing runs of homozygosity (FROH); (2) calculating an inbreeding coefficient derived from the correlation among uniting gametes (F3); and (3) examining specific autosomal regions containing ROH. For each, we calculated beta coefficients and standard errors using logistic regression and combined estimates across studies using random-effects meta-analysis. RESULTS We discovered positive associations between FROH and CLL (β = 21.1, SE = 4.41, P = 1.6 × 10-6) and FL (β = 11.4, SE = 5.82, P = 0.02) but not DLBCL (P = 1.0) or MZL (P = 0.91). For F3, we observed an association with CLL (β = 27.5, SE = 6.51, P = 2.4 × 10-5). We did not find evidence of associations with specific ROH, suggesting that the associations observed with FROH and F3 for CLL and FL risk were not driven by a single region of homozygosity. CONCLUSION Our findings support the role of recessive genetic variation in the etiology of CLL and FL; additional research is needed to identify the specific loci associated with NHL risk.
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Affiliation(s)
- Amy Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Moara Machado
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA 91010, USA
| | - Eleanor Kane
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
- Ragon Institute of MGH, Cambridge, MA 02139, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17176, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo 0315, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY 10016, USA
- Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Comprehensive Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Simonetta Bisanzi
- Regional Cancer Prevention Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94118, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jacqueline Clavel
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon 69008, France
| | - 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
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Immaculata De Vivo
- 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 T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Silvia de Sanjose
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 656 53, Czech Republic
| | - Susan M Gapstur
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Hervè Ghesquières
- Department of Hematology, Centre Léon Bérard, Lyon 69008, France
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75105, Sweden
| | - Chi Gao
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH 43210, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Marc Maynadie
- U1231, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - 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
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Thierry J Molina
- Department of Pathology, AP-HP, Necker Enfants Malades, Université Paris Descartes, EA 7324, Sorbonne Paris Cité 75015, France
| | - Alain Monnereau
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
- Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, Bordeaux Cedex 33076, France
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg 79108, Germany
| | - 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
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Sara Piro
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gilles Salles
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
- Department of Hematology, Hospices Civils de Lyon, Pierre Benite Cedex 69495, France
- Department of Hematology, Université Lyon-1, Pierre Benite Cedex 69495, France
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm 17176, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin 9, Ireland
| | - Carolyn Stewart
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98117, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, New South Wales 2139, Australia
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI 02903, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cao P, Li G, Xiang J. Genome instability and lymphoma. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2021; 46:552-557. [PMID: 34148893 PMCID: PMC10930211 DOI: 10.11817/j.issn.1672-7347.2021.190427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Indexed: 11/03/2022]
Abstract
Lymphoma is one of the most common malignant tumor of the hematologic system. The genome instability is not only an important molecular basis for the development of lymphoma, but also has important value in the diagnosis and prognosis of lymphoma. There are 2 types of genome instability: Microsatellite instability (MSI/MIN) at gene level and chromosomal instability at chromosome level. Through the study on genes associated with lymphoma, the unstable genes associated with lymphoma could be found, meanwhile the mechanism of its occurrence and development of lymphoma could be explored, and the important basis of molecular biology could also be provided in the field of current hot lymphoma precision medical research.
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Affiliation(s)
- Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008.
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China.
| | - Guiyuan Li
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China.
| | - Juanjuan Xiang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China
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Labreche K, Daniau M, Sud A, Law PJ, Royer-Perron L, Holroyd A, Broderick P, Went M, Benazra M, Ahle G, Soubeyran P, Taillandier L, Chinot OL, Casasnovas O, Bay JO, Jardin F, Oberic L, Fabbro M, Damaj G, Brion A, Mokhtari K, Philippe C, Sanson M, Houillier C, Soussain C, Hoang-Xuan K, Houlston RS, Alentorn A. A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a LOC Network study. Neuro Oncol 2021; 21:1039-1048. [PMID: 31102405 DOI: 10.1093/neuonc/noz088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a rare form of extra-nodal non-Hodgkin lymphoma. PCNSL is a distinct subtype of non-Hodgkin lymphoma, with over 95% of tumors belonging to the diffuse large B-cell lymphoma (DLBCL) group. We have conducted a genome-wide association study (GWAS) on immunocompetent patients to address the possibility that common genetic variants influence the risk of developing PCNSL. METHODS We performed a meta-analysis of 2 new GWASs of PCNSL totaling 475 cases and 1134 controls of European ancestry. To increase genomic resolution, we imputed >10 million single nucleotide polymorphisms using the 1000 Genomes Project combined with UK10K as reference. In addition we performed a transcription factor binding disruption analysis and investigated the patterns of local chromatin by Capture Hi-C data. RESULTS We identified independent risk loci at 3p22.1 (rs41289586, ANO10, P = 2.17 × 10-8) and 6p25.3 near EXOC2 (rs116446171, P = 1.95 x 10-13). In contrast, the lack of an association between rs41289586 and DLBCL suggests distinct germline predisposition to PCNSL and DLBCL. We found looping chromatin interactions between noncoding regions at 6p25.3 (rs11646171) with the IRF4 promoter and at 8q24.21 (rs13254990) with the MYC promoter, both genes with strong relevance to B-cell tumorigenesis. CONCLUSION To our knowledge this is the first study providing insight into the genetic predisposition to PCNSL. Our findings represent an important step in defining the contribution of common genetic variation to the risk of developing PCNSL.
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Affiliation(s)
- Karim Labreche
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK.,(i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Mailys Daniau
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Louis Royer-Perron
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Molly Went
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Marion Benazra
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Guido Ahle
- Department of Neurology, Colmar Civil Hospitals, Colmar Cedex, France
| | - Pierre Soubeyran
- Department of Medical Oncology, Bergnoié Institute, Bordeaux, France.,Inserm Research Unit U1218, Bordeaux, France
| | - Luc Taillandier
- Neuro-oncology Department, Nancy University Hospital and The Center of Research in Automatic Control of Nancy, Joint Research Unit 7039, National Center for Scientific Research, SBS BEAM Department, Nancy University, Vandoeuvre-lès-Nancy, France
| | - Olivier L Chinot
- Department of Pathology and Neuropathology, Timone Hospital, Aix-Marseille University (AMU), Public Assistance-Hospitals of Marseille, Marseille, France.,AMU Research Center in Oncology Biology and Oncopharmacology, Marseille, France
| | | | - Jacques-Olivier Bay
- Department of Hematology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fabrice Jardin
- Department of Hematology, Henri Becquerel Cancer Center, Rouen, France and Inserm U1245, Henri Becquerel Cancer Center, Institute of Research and Innovation in Biomedicine, University of Normandy, Rouen, France
| | - Lucie Oberic
- Department of Hematology, University Cancer Institute of Toulouse-Oncopole, Toulouse, France
| | | | - Gandhi Damaj
- Department of Hematology, University Hospital of Caen, Caen, France
| | - Annie Brion
- Department of Hematology, Regional and University Hospitals Besançon, Besançon, France
| | - Karima Mokhtari
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Raymond Escourolle Department of Neuropathology, Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | | | - Marc Sanson
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | - Caroline Houillier
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Carole Soussain
- Department of Hematology, René Huguenin Hospital, Curie Institute, Saint-Cloud, France
| | - Khê Hoang-Xuan
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Agusti Alentorn
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
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Abstract
Large B-cell lymphomas, with an estimated 150,000 new cases annually worldwide, represent almost 30% of all cases of non-Hodgkin’s lymphoma. Patients typically present with progressive lymphadenopathy, extranodal disease, or both and require therapy. Despite the advanced stage at presentation in the majority of patients, more than 60% can be cured with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) immunochemotherapy (Fig. 1A). Patients with treatment failure after R-CHOP often have a poor outcome — in particular, those with disease that is refractory to frontline or subsequent therapies — although some patients can have a durable remission and be cured after secondary therapies. Over the past two decades, improved insights into large B-cell lymphomas, in terms of epidemiology, prognostic factors, and biologic heterogeneity, have led to a refinement of disease classification and the development of new therapeutic approaches.
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Affiliation(s)
- Laurie H Sehn
- From the BC Cancer Centre for Lymphoid Cancer and the University of British Columbia, Vancouver, Canada (L.H.S.); and the Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York (G.S.)
| | - Gilles Salles
- From the BC Cancer Centre for Lymphoid Cancer and the University of British Columbia, Vancouver, Canada (L.H.S.); and the Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York (G.S.)
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38
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Graff RE, Cavazos TB, Thai KK, Kachuri L, Rashkin SR, Hoffman JD, Alexeeff SE, Blatchins M, Meyers TJ, Leong L, Tai CG, Emami NC, Corley DA, Kushi LH, Ziv E, Van Den Eeden SK, Jorgenson E, Hoffmann TJ, Habel LA, Witte JS, Sakoda LC. Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts. Nat Commun 2021; 12:970. [PMID: 33579919 PMCID: PMC7880989 DOI: 10.1038/s41467-021-21288-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
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Affiliation(s)
- Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA. .,Department of Health System Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA.
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Hernández-Verdin I, Labreche K, Benazra M, Mokhtari K, Hoang-Xuan K, Alentorn A. Tracking the Genetic Susceptibility Background of B-Cell Non-Hodgkin's Lymphomas from Genome-Wide Association Studies. Int J Mol Sci 2020; 22:E122. [PMID: 33374413 DOI: 10.3390/ijms22010122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Garcin LM, Gelot A, Gomez RR, Gusto G, Boutron-Ruault MC, Kvaskoff M, Severi G, Besson C. Pigmentary traits, sun exposure, and risk of non-Hodgkin's lymphoma/chronic lymphocytic leukemia: A study within the French E3N prospective cohort. Cancer Med 2020; 10:297-304. [PMID: 33219744 PMCID: PMC7826467 DOI: 10.1002/cam4.3586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022] Open
Abstract
To investigate whether risk factors for keratinocyte carcinomas (KCs), namely pigmentary traits and sun exposure, are associated with risk of non‐Hodgkin's lymphomas (NHL) and chronic lymphocytic leukemia (CLL). E3N is a prospective cohort of French women aged 40–65 years at inclusion in 1990. Cancer data were collected at baseline and updated every 2–3 years. Hazard Ratios (HRs) and 95% confidence intervals (CIs) for associations between pigmentary traits and sun exposure, and risk of CLL/NHL were estimated using Cox models. With a median follow‐up of 24 years, 622 incident cases of CLL/NHL were ascertained among the 92,097 included women. The presence of nevi was associated with CLL/NHL risk: HR for “many or very many nevi” relative to “no nevi”: 1.56 [1.15; 2.11]. Such association with number of nevi appears to be mostly limited to risk of CLL: HR for “many or very many nevi”: 3.00 [1.38; 6.52]; versus 1.32 [0.94; 1.84] for NHL. Women whose skin was highly sensitive to sunburn also had a higher risk of CLL: HR = 1.96 [1.21; 3.18], while no increase in risk of NHL was observed. Skin or hair color, number of freckles, and average daily ultraviolet (UV) dose during spring and summer in location of residence at birth or at inclusion (kJ/m2) were not associated with CLL/NHL risk. Some pigmentary traits (presence of nevi and skin sensitivity), but not sun exposure, were associated with CLL/NHL. These observations suggest that CLL may share some constitutional risk factors with keratinocyte cancers.
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Affiliation(s)
- Louis-Marie Garcin
- Department of Medical Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France.,Hematology-Oncology Department, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Amandine Gelot
- CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Roselyn-Rima Gomez
- CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Gaëlle Gusto
- CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France.,Gustave Roussy, Villejuif, France
| | | | - Marina Kvaskoff
- CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Gianluca Severi
- CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France.,Gustave Roussy, Villejuif, France.,Departement of Statistics, Computer Science and Applications (DISIA), University of Florence, Florence, Italy
| | - Caroline Besson
- Hematology-Oncology Department, Centre Hospitalier de Versailles, Le Chesnay, France.,CESP, Université Paris-Saclay, Univ. Paris-Sud, UVSQ, INSERM, Villejuif, France
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Ricci M, Compagna R, Amato B, Kenanoglu S, Veselenyiova D, Kurti D, Baglivo M, Basha SH, Serrani R, Miggiano GAD, Aquilanti B, Matera G, Marceddu G, Velluti V, Gagliardi L, Dundar M, Krajcovic J, Bertelli M. Mutations in the ARAP3 Gene in Three Families with Primary Lymphedema Negative for Mutations in Known Lymphedema-Associated Genes. Int J Genomics 2020; 2020:3781791. [PMID: 32908855 DOI: 10.1155/2020/3781791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/07/2020] [Accepted: 08/01/2020] [Indexed: 11/18/2022] Open
Abstract
Background ARAP3 is a small GTPase-activating protein regulator, which has important functions in lymphatic vessel organogenesis and modulation of cell adhesion and migration. Mutations in the ARAP3 gene are associated with impaired lymphatic vessel formation. Objective The aim of our study was to determine the genotypes of lymphedema patients in relation to variants in the ARAP3 gene in order to explore its role in the development of lymphedema. Methods and Results We applied next-generation sequencing to DNA samples of a cohort of 246 Italian patients with lymphatic malformations. When we tested probands for known lymphedema genes, 235 out of 246 were negative. Retrospectively, we tested the DNA of these 235 patients for new candidate lymphedema-associated genes, including ARAP3. Three out of 235 probands proved to carry rare missense heterozygous variants in ARAP3. In the case of two families, other family members were also tested and proved negative for the ARAP3 variant, besides being unaffected by lymphedema. According to in silico analysis, alterations due to these variants have a significant impact on the overall structure and stability of the resulting proteins. Conclusions Based on our results, we propose that variants in ARAP3 could be included in genetic testing for lymphedema.
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Baecklund F, Ekberg S, Rosenquist R, Askling J, Eloranta S, Smedby KE. Concordance in survival among first-degree relatives diagnosed with indolent lymphoid malignancies including chronic lymphocytic leukemia. Eur J Haematol 2020; 105:779-785. [PMID: 32871627 PMCID: PMC7702025 DOI: 10.1111/ejh.13510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022]
Abstract
Objectives To investigate concordance in survival time among first‐degree relatives with lymphoid malignancies. Methods By linkage of national Swedish registers, we identified 66 430 patients diagnosed with a lymphoid malignancy 1958‐2016 with information on first‐degree relationships and follow‐up until 2017. Among these, we identified pairs of first‐degree relatives with any (N = 3326) or a similar (N = 690) lymphoid malignancy subtype. We defined survival in the first‐degree relative as good, expected, or poor based on tertiles of deviance residuals from a multivariable Cox regression model. Next, we used Cox regression to estimate hazard ratios (HR) of death with 95% confidence intervals (CI) among patients, using the survival of their first‐degree relative as exposure and adjusting for confounders. Results There was no concordance in survival among first‐degree relatives with any lymphoid malignancy (HRgood = 1.00 (reference), HRExpected = 1.02, 95% CI: 0.89‐1.17, HRPoor = 1.12, 95% CI: 0.98‐1.27, Ptrend = .08). Among first‐degree relatives with indolent lymphoma, including chronic lymphocytic leukemia, those with a first‐degree relative to an expected or poor survival had worse outcome compared to those with a first‐degree relative with good survival (HRExpected = 1.44, 95% CI: 0.82‐2.53, HRPoor = 1.79, 95% CI: 1.07‐3.00, Ptrend = .03). Conclusion Our results support a role of inherited factors in the outcome of indolent lymphoma, including chronic lymphocytic leukemia.
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Affiliation(s)
- Fredrik Baecklund
- Department of Medicine Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden.,Pediatric Oncology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Ekberg
- Department of Medicine Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Askling
- Department of Medicine Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden.,Rheumatology, Theme Inflammation & Infection, Karolinska University Hospital, Stockholm, Sweden
| | - Sandra Eloranta
- Department of Medicine Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden.,Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
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Kachuri L, Beane Freeman LE, Spinelli JJ, Blair A, Pahwa M, Koutros S, Hoar Zahm S, Cantor KP, Weisenburger DD, Pahwa P, Dosman JA, McLaughlin JR, Demers PA, Harris SA. Insecticide use and risk of non-Hodgkin lymphoma subtypes: A subset meta-analysis of the North American Pooled Project. Int J Cancer 2020; 147:3370-3383. [PMID: 32574374 PMCID: PMC7689728 DOI: 10.1002/ijc.33164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
Abstract
Insecticide use has been linked to increased risk of non-Hodgkin lymphoma (NHL), however, findings of epidemiologic studies have been inconsistent, particularly for NHL subtypes. We analyzed 1690 NHL cases and 5131 controls in the North American Pooled Project (NAPP) to investigate self-reported insecticide use and risk of NHL overall and by subtypes: follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL) and small lymphocytic lymphoma (SLL). Odds ratios (OR) and 95% confidence intervals for each insecticide were estimated using logistic regression. Subtype-specific associations were evaluated using ASSET (Association analysis for SubSETs). Increased risks of multiple NHL subtypes were observed for lindane (OR = 1.60, 1.20-2.10: FL, DLCBL, SLL), chlordane (OR = 1.59, 1.17-2.16: FL, SLL) and DDT (OR = 1.36, 1.06-1.73: DLBCL, SLL). Positive trends were observed, within the subsets with identified associations, for increasing categories of exposure duration for lindane (Ptrend = 1.7 × 10-4 ), chlordane (Ptrend = 1.0 × 10-3 ) and DDT (Ptrend = 4.2 × 10-3 ), however, the exposure-response relationship was nonlinear. Ever use of pyrethrum was associated with an increased risk of FL (OR = 3.65, 1.45-9.15), and the relationship with duration of use appeared monotonic (OR for >10 years: OR = 5.38, 1.75-16.53; Ptrend = 3.6 × 10-3 ). Our analysis identified several novel associations between insecticide use and specific NHL subtypes, suggesting possible etiologic heterogeneity in the context of pesticide exposure.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aaron Blair
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Manisha Pahwa
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Shelia Hoar Zahm
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth P Cantor
- Division of Cancer Epidemiology and Genetics, U.S. National Cancer Institute, Bethesda, Maryland, USA
| | | | - Punam Pahwa
- Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - James A Dosman
- Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John R McLaughlin
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Paul A Demers
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada.,Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Population Health and Prevention, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Shelley A Harris
- Occupational Cancer Research Centre, Cancer Care Ontario, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Population Health and Prevention, Cancer Care Ontario, Toronto, Ontario, Canada
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Yang R, Shao T, Long M, Shi Y, Liu Q, Yang L, Zhan M. Long noncoding RNA PVT1 promotes tumor growth and predicts poor prognosis in patients with diffuse large B-cell lymphoma. Cancer Commun (Lond) 2020; 40:551-555. [PMID: 32725807 PMCID: PMC7571398 DOI: 10.1002/cac2.12073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ruifeng Yang
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, P. R. China
| | - Tingting Shao
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P. R. China
| | - Manmei Long
- Department of Pathology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, P. R. China
| | - Yongheng Shi
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Linhua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Ming Zhan
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, P. R. China
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Lee MJ, Koff JL, Switchenko JM, Jhaney CI, Harkins RA, Patel SP, Dave SS, Flowers CR. Genome-defined African ancestry is associated with distinct mutations and worse survival in patients with diffuse large B-cell lymphoma. Cancer 2020; 126:3493-3503. [PMID: 32469082 DOI: 10.1002/cncr.32866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/17/2020] [Accepted: 03/04/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Significant racial differences have been observed in the incidence and clinical outcomes of diffuse large B-cell lymphoma (DLBCL) in the United States, but to the authors' knowledge it remains unclear whether genomic differences contribute to these disparities. METHODS To understand the influences of genetic ancestry on tumor genomic alterations, the authors estimated the genetic ancestry of 1001 previously described patients with DLBCL using unsupervised model-based Admixture global ancestry analysis applied to exome sequencing data and examined the mutational profile of 150 DLBCL driver genes in tumors obtained from this cohort. RESULTS Global ancestry prediction identified 619 patients with >90% European ancestry, 81 patients with >90% African ancestry, and 50 patients with >90% Asian ancestry. Compared with patients with DLBCL with European ancestry, patients with African ancestry were aged >10 years younger at the time of diagnosis and were more likely to present with B symptoms, elevated serum lactate dehydrogenase, extranodal disease, and advanced stage disease. Patients with African ancestry demonstrated worse overall survival compared with patients with European ancestry (median, 4.9 years vs 8.8 years; P = .04). Recurrent mutations of MLL2 (KMT2D), HIST1H1E, MYD88, BCL2, and PIM1 were found across all ancestry groups, suggesting shared mechanisms underlying tumor biology. The authors also identified 6 DLBCL driver genes that were more commonly mutated in patients with African ancestry compared with patients with European ancestry: ATM (21.0% vs 7.75%; P < .001), MGA (19.7% vs 5.33%; P < .001), SETD2 (17.3% vs 5.17%; P < .001), TET2 (12.3% vs 5.82%; P = .029), MLL3 (KMT2C) (11.1% vs 4.36%; P = .013), and DNMT3A (11.1% vs 4.52%; P = .016). CONCLUSIONS Distinct prevalence and patterns of mutation highlight an important difference in the mutational landscapes of DLBCL arising in different ancestry groups. To the authors' knowledge, the results of the current study provide the first-ever characterization of genetic alterations among patients with African descent who are diagnosed with DLBCL.
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Affiliation(s)
- Michelle J Lee
- Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Medicine, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Jean L Koff
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Jeffrey M Switchenko
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - C Ileen Jhaney
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | | | - Sharvil P Patel
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Sandeep S Dave
- Center for Genomic and Computational Biology, Duke Cancer Institute, Duke University, Durham, North Carolina, USA
| | - Christopher R Flowers
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA.,Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Zou H, Wu LX, Tan L, Shang FF, Zhou HH. Significance of Single-Nucleotide Variants in Long Intergenic Non-protein Coding RNAs. Front Cell Dev Biol 2020; 8:347. [PMID: 32523949 PMCID: PMC7261909 DOI: 10.3389/fcell.2020.00347] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/15/2022] Open
Abstract
Single-nucleotide variants (SNVs) are the most common genetic variants and universally present in the human genome. Genome-wide association studies (GWASs) have identified a great number of disease or trait-associated variants, many of which are located in non-coding regions. Long intergenic non-protein coding RNAs (lincRNAs) are the major subtype of long non-coding RNAs; lincRNAs play crucial roles in various disorders and cellular models via multiple mechanisms. With rapid growth in the number of the identified lincRNAs and genetic variants, there is great demand for an investigation of SNVs in lincRNAs. Hence, in this article, we mainly summarize the significant role of SNVs within human lincRNA regions. Some pivotal variants may serve as risk factors for the development of various disorders, especially cancer. They may also act as important regulatory signatures involved in the modulation of lincRNAs in a tissue- or disorder-specific manner. An increasing number of researches indicate that lincRNA variants would potentially provide additional options for genetic testing and disease risk assessment in the personalized medicine era.
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Affiliation(s)
- Hecun Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lan-Xiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lihong Tan
- Chongqing Medical and Pharmaceutical College, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Fei-Fei Shang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong-Hao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
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Kleinstern G, Camp NJ, Berndt SI, Birmann BM, Nieters A, Bracci PM, McKay JD, Ghesquières H, Lan Q, Hjalgrim H, Benavente Y, Monnereau A, Wang SS, Zhang Y, Purdue MP, Zeleniuch-Jacquotte A, Giles GG, Vermeulen R, Cocco P, Albanes D, Teras LR, Brooks-Wilson AR, Vajdic CM, Kane E, Caporaso NE, Smedby KE, Salles G, Vijai J, Chanock SJ, Skibola CF, Rothman N, Slager SL, Cerhan JR. Lipid Trait Variants and the Risk of Non-Hodgkin Lymphoma Subtypes: A Mendelian Randomization Study. Cancer Epidemiol Biomarkers Prev 2020; 29:1074-1078. [PMID: 32108027 PMCID: PMC7196490 DOI: 10.1158/1055-9965.epi-19-0803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Lipid traits have been inconsistently linked to risk of non-Hodgkin lymphoma (NHL). We examined the association of genetically predicted lipid traits with risk of diffuse large B-cell lymphoma (DLBCL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and marginal zone lymphoma (MZL) using Mendelian randomization (MR) analysis. METHODS Genome-wide association study data from the InterLymph Consortium were available for 2,661 DLBCLs, 2,179 CLLs, 2,142 FLs, 824 MZLs, and 6,221 controls. SNPs associated (P < 5 × 10-8) with high-density lipoprotein (HDL, n = 164), low-density lipoprotein (LDL, n = 137), total cholesterol (TC, n = 161), and triglycerides (TG, n = 123) were used as instrumental variables (IV), explaining 14.6%, 27.7%, 16.8%, and 12.8% of phenotypic variation, respectively. Associations between each lipid trait and NHL subtype were calculated using the MR inverse variance-weighted method, estimating odds ratios (OR) per standard deviation and 95% confidence intervals (CI). RESULTS HDL was positively associated with DLBCL (OR = 1.14; 95% CI, 1.00-1.30) and MZL (OR = 1.09; 95% CI, 1.01-1.18), while TG was inversely associated with MZL risk (OR = 0.90; 95% CI, 0.83-0.99), all at nominal significance (P < 0.05). A positive trend was observed for HDL with FL risk (OR = 1.08; 95% CI, 0.99-1.19; P = 0.087). No associations were noteworthy after adjusting for multiple testing. CONCLUSIONS We did not find evidence of a clear or strong association of these lipid traits with the most common NHL subtypes. While these IVs have been previously linked to other cancers, our findings do not support any causal associations with these NHL subtypes. IMPACT Our results suggest that prior reported inverse associations of lipid traits are not likely to be causal and could represent reverse causality or confounding.
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MESH Headings
- Causality
- Cholesterol/blood
- Cholesterol/metabolism
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lipid Metabolism/genetics
- Lipoproteins, HDL/blood
- Lipoproteins, HDL/metabolism
- Lipoproteins, LDL/blood
- Lipoproteins, LDL/metabolism
- Lymphoma, B-Cell, Marginal Zone/blood
- Lymphoma, B-Cell, Marginal Zone/epidemiology
- Lymphoma, B-Cell, Marginal Zone/genetics
- Lymphoma, B-Cell, Marginal Zone/metabolism
- Lymphoma, Follicular/blood
- Lymphoma, Follicular/epidemiology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/metabolism
- Lymphoma, Large B-Cell, Diffuse/blood
- Lymphoma, Large B-Cell, Diffuse/epidemiology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mendelian Randomization Analysis
- Odds Ratio
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci
- Risk Factors
- Triglycerides/blood
- Triglycerides/metabolism
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Affiliation(s)
| | - Nicola J Camp
- Department of Internal Medicine, Huntsman Cancer Institute and University of Utah School of Medicine, Salt Lake City, Utah
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Alexandra Nieters
- Institute for Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Hervé Ghesquières
- Department of Hematology, Centre Hospitalier Lyon Sud, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Yolanda Benavente
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Unit of Molecular and Genetic Epidemiology in Infections and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Alain Monnereau
- Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, France
| | - Sophia S Wang
- City of Hope Beckman Research Institute, Duarte, California
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health and Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, Monash University, Melbourne, Victoria, Australia
| | - Roel Vermeulen
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Pierluigi Cocco
- Department of Medical Sciences and Public Health, Occupational Health Section, University of Cagliari, Monserrato, Italy
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | | | - Angela R Brooks-Wilson
- BC Cancer, Vancouver, and Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Eleanor Kane
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, Heslington, York, United Kingdom
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Karin E Smedby
- Karolinska Institutet, Division of Clinical Epidemiology, Department of Medicine Solna, Stockholm, Sweden
| | - Gilles Salles
- Department of Hematology, Centre Hospitalier Lyon Sud, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | | | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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48
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Ghetti M, Vannini I, Storlazzi CT, Martinelli G, Simonetti G. Linear and circular PVT1 in hematological malignancies and immune response: two faces of the same coin. Mol Cancer 2020; 19:69. [PMID: 32228602 PMCID: PMC7104523 DOI: 10.1186/s12943-020-01187-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Non coding RNAs (ncRNAs) have emerged as regulators of human carcinogenesis by affecting the expression of key tumor suppressor genes and oncogenes. They are divided into short and long ncRNAs, according to their length. Circular RNAs (circRNAs) are included in the second group and were recently discovered as being originated by back-splicing, joining either single or multiple exons, or exons with retained introns. The human Plasmacytoma Variant Translocation 1 (PVT1) gene maps on the long arm of chromosome 8 (8q24) and encodes for 52 ncRNAs variants, including 26 linear and 26 circular isoforms, and 6 microRNAs. PVT1 genomic locus is 54 Kb downstream to MYC and several interactions have been described among these two genes, including a feedback regulatory mechanism. MYC-independent functions of PVT1/circPVT1 have been also reported, especially in the regulation of immune responses. We here review and discuss the role of both PVT1 and circPVT1 in the hematopoietic system. No information is currently available concerning their transforming ability in hematopoietic cells. However, present literature supports their cooperation with a more aggressive and/or undifferentiated cell phenotype, thus contributing to cancer progression. PVT1/circPVT1 upregulation through genomic amplification or rearrangements and/or increased transcription, provides a proliferative advantage to malignant cells in acute myeloid leukemia, acute promyelocytic leukemia, Burkitt lymphoma, multiple myeloma (linear PVT1) and acute lymphoblastic leukemia (circPVT1). In addition, PVT1 and circPVT1 regulate immune responses: the overexpression of the linear form in myeloid derived suppressor cells induced immune tolerance in preclinical tumor models and circPVT1 showed immunosuppressive properties in myeloid and lymphoid cell subsets. Overall, these recent data on PVT1 and circPVT1 functions in hematological malignancies and immune responses reflect two faces of the same coin: involvement in cancer progression by promoting a more aggressive phenotype of malignant cells and negative regulation of the immune system as a novel potential therapy-resistance mechanism.
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Affiliation(s)
- Martina Ghetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Ivan Vannini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | | | - Giovanni Martinelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
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49
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Wu D, Zhao J, Ma H, Wang MC. Integrating transcriptome-wide association study and copy number variation study identifies candidate genes and pathways for diffuse non-Hodgkin's lymphoma. Cancer Genet 2020; 243:7-10. [PMID: 32179489 DOI: 10.1016/j.cancergen.2020.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/10/2020] [Accepted: 02/20/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND The genetic basis of diffuse non-Hodgkin's lymphoma (DNHL) is largely unknown now. We conducted a large-scale transcriptome-wide association study (TWAS) of DNHL to identify novel candidates for DNHL. METHODS The GWAS summary data of DNHL was obtained from the UKBiobank, involving 685 cases and 451,579 controls. TWAS of DNHL was performed using tissue-specific gene expression weights generated from the Genotype-Tissue Expression (GTEx) data. The DNHLTWAS results were further validated by a previous published copy number alterations (CNA) study of DNHL. Gene ontology (GO) and pathway enrichment analysis of identified candidate genes were conducted by the DAVID 6.8. RESULTS We identified 214 genes with TWAS P value < 0.05 for DNHL, such as MRPL19 (PTWAS = 0.0010), CRCP (PTWAS = 0.0010) and SEMA3C (PTWAS = 0.0010). After further comparing the 214 genes with copy number variations of DNHL patients, we found 1 overlapped gene, BCL10 (PTWAS = 0.0100). We also detected 6 common GO terms shared between gene set enrichment analysis results of TWAS and CNAs, such as cytosol (PTWAS = 0.0003, PCNAs = 4.99 × 10-7) and membrane (PTWAS = 0.0048, PCNAs = 0.0046). The pathway enrichment analysis of TWAS and CNAs detected 3 common pathways, including HIF-1 signaling pathway (PTWAS = 0.0195, PCNAs = 1.96 × 10-5), mTOR signaling pathway (PTWAS = 0.0242, PCNAs = 6.75 × 10-5) and adipocytokine signaling pathway (PTWAS = 0.0392, PCNAs = 0.0103). CONCLUSIONS Our study identified multiple DNHL associated genes and pathways, providing novel useful information for the pathogenetic studies of DNHL.
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Affiliation(s)
- Di Wu
- Department of hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China
| | - Jing Zhao
- Department of hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China
| | - Hong Ma
- Department of hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China
| | - Meng-Chang Wang
- Department of hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China.
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50
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Liang B, Ding H, Huang L, Luo H, Zhu X. GWAS in cancer: progress and challenges. Mol Genet Genomics 2020; 295:537-561. [PMID: 32048005 DOI: 10.1007/s00438-020-01647-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
Abstract
The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.
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Affiliation(s)
- Baiqiang Liang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China
| | - Hongrong Ding
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China
| | - Lianfang Huang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Haiqing Luo
- Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China. .,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China. .,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China.
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