1
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Lin J, Shen M, Xiao W, Chen Y, Yu S, Meng Y. Common and rare variants in genetic susceptibility analysis of mature B-cell neoplasm subtypes by whole exome sequencing. Leukemia 2024; 38:2059-2063. [PMID: 38965369 DOI: 10.1038/s41375-024-02332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Affiliation(s)
- Junwei Lin
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Maoting Shen
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Wenjuan Xiao
- Guangzhou Kingmylab Pharmaceutical Research Co. Ltd, Guangzhou, China
| | - Yuxin Chen
- Guangzhou KingMed Diagnostics Group Co. Ltd, Guangzhou, China
| | - Shihui Yu
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
- Guangzhou KingMed Diagnostics Group Co. Ltd, Guangzhou, China
| | - Yuhuan Meng
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China.
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
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2
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Coetzee SG, Hazelett DJ. MotifbreakR v2: extended capability and database integration. ARXIV 2024:arXiv:2407.03441v1. [PMID: 39010878 PMCID: PMC11247919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor suite of software packages and annotations to operate across a diverse array of genomes and motif databases. Initially developed to interrogate the effect of single nucleotide variants (common and rare SNVs) on potential TF binding sites, in motifbreakR v2, we have updated the functionality. New features include the ability to query other types of more complex genetic variants, such as short insertions and deletions (indels). This function allows modeling a more extensive array of variants that may have more significant effects on TF binding. Additionally, while TF binding is based partly on sequence preference, predictions of TF binding based on sequence preference alone can indicate many more potential binding events than observed. Adding information from DNA-binding sequencing datasets lends confidence to motif disruption prediction by demonstrating TF binding in cell lines and tissue types. Therefore, motifbreakR implements querying the ReMap2022 database for evidence that a TF matching the disrupted motif binds over the disrupting variant. Finally, in motifbreakR, in addition to the existing interface, we have implemented an R/Shiny graphical user interface to simplify and enhance access to researchers with different skill sets.
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Affiliation(s)
- Simon G Coetzee
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
| | - Dennis J Hazelett
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
- Cancer Prevention and Control - Samuel Oschin Cancer Center, Cedars-Sinai
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3
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Zhang R, Lu Y, Bian Z, Zhou S, Xu L, Jiang F, Yuan S, Tan X, Chen X, Ding Y, Li X. Sleep, physical activity, and sedentary behaviors in relation to overall cancer and site-specific cancer risk: A prospective cohort study. iScience 2024; 27:109931. [PMID: 38974470 PMCID: PMC11225818 DOI: 10.1016/j.isci.2024.109931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/20/2024] [Accepted: 05/05/2024] [Indexed: 07/09/2024] Open
Abstract
Large prospective studies are required to better elucidate the associations of physical activity, sedentary behaviors (SBs), and sleep with overall cancer and site-specific cancer risk, accounting for the interactions with genetic predisposition. The study included 360,271 individuals in UK Biobank. After a median follow-up of 12.52 years, we found higher total physical activity (TPA) level and higher sleep scores were related to reduced risk of cancer while higher SB level showed a positive association with cancer. Compared with high TPA-healthy sleep group and low SB-healthy sleep group, low TPA-poor sleep group and high SB-poor sleep group had the highest risk for overall cancer, breast cancer, and lung cancer. Adherence to a more active exercise pattern was associated with a lower risk of cancer irrespective of genetic risk. Our study suggests that improving the quality of sleep and developing physical activity habits might yield benefits in mitigating the cancer risk.
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Affiliation(s)
- Rongqi Zhang
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zilong Bian
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyun Zhou
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liying Xu
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fangyuan Jiang
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuai Yuan
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Xiao Tan
- Department of Big Data in Health Science, School of Public Health and Department of Psychiatry Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiangjun Chen
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xue Li
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
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4
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Turk A, Čeh E, Calin GA, Kunej T. Multiple omics levels of chronic lymphocytic leukemia. Cell Death Discov 2024; 10:293. [PMID: 38906881 PMCID: PMC11192936 DOI: 10.1038/s41420-024-02068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative malignancy characterized by the proliferation of functionally mature but incompetent B cells. It is the most prevalent type of leukemia in Western populations, accounting for approximately 25% of new leukemia cases. While recent advances, such as ibrutinib and venetoclax treatment have improved patient outlook, aggressive forms of CLL such as Richter transformation still pose a significant challenge. This discrepancy may be due to the heterogeneity of factors contributing to CLL development at multiple -omics levels. However, information on the omics of CLL is fragmented, hindering multi-omics-based research into potential treatment options. To address this, we aggregated and presented a selection of important aspects of various omics levels of the disease in this review. The purpose of the present literature analysis is to portray examples of CLL studies from different omics levels, including genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, epiproteomics, metabolomics, glycomics and lipidomics, as well as those identified by multi-omics approaches. The review includes the list of 102 CLL-associated genes with relevant genomics information. While single-omics studies yield substantial and useful data, they omit a significant level of complex biological interplay present in the disease. As multi-omics studies integrate several different layers of data, they may be better suited for complex diseases such as CLL and have thus far yielded promising results. Future multi-omics studies may assist clinicians in improved treatment choices based on CLL subtypes as well as allow the identification of novel biomarkers and targets for treatments.
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Grants
- P4-0220 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Dr. Calin is the Felix L. Haas Endowed Professor in Basic Science. Work in G.A.C.’s laboratory is supported by NCI grants 1R01 CA182905-01 and 1R01CA222007-01A1, NIGMS grant 1R01GM122775-01, DoD Idea Award W81XWH-21-1-0030, a Team DOD grant in Gastric Cancer W81XWH-21-1-0715, a Chronic Lymphocytic Leukemia Moonshot Flagship project, a CLL Global Research Foundation 2019 grant, a CLL Global Research Foundation 2020 grant, a CLL Global Research Foundation 2022 grant, The G. Harold & Leila Y. Mathers Foundation, two grants from Torrey Coast Foundation, an Institutional Research Grant and Development Grant associated with the Brain SPORE 2P50CA127001.
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Affiliation(s)
- Aleksander Turk
- Clinical Institute of Genomic Medicine, University Clinical Centre Ljubljana, Ljubljana, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Čeh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - George A Calin
- Department of Translational Molecular Pathology, Division of Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, 77030, USA.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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5
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Quinten E, Sepúlveda-Yáñez JH, Koning MT, Eken JA, Pfeifer D, Nteleah V, De Groen RAL, Saravia DA, Knijnenburg J, Stuivenberg-Bleijswijk HE, Pantic M, Agathangelidis A, Keppler-Hafkemeyer A, Van Bergen CAM, Uribe-Paredes R, Stamatopoulos K, Vermaat JSP, Zirlik K, Navarrete MA, Jumaa H, Veelken H. Autonomous B-cell receptor signaling and genetic aberrations in chronic lymphocytic leukemia-phenotype monoclonal B lymphocytosis in siblings of patients with chronic lymphocytic leukemia. Haematologica 2024; 109:824-834. [PMID: 37439337 PMCID: PMC10905078 DOI: 10.3324/haematol.2022.282542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
Clonal expansion of CD5-expressing B cells, commonly designated as monoclonal B lymphocytosis (MBL), is a precursor condition for chronic lymphocytic leukemia (CLL). The mechanisms driving subclinical MBL B-cell expansion and progression to CLL, occurring in approximately 1% of affected individuals, are unknown. An autonomously signaling B-cell receptor (BCR) is essential for the pathogenesis of CLL. The objectives of this study were functional characterization of the BCR of MBL in siblings of CLL patients and a comparison of genetic variants in MBL-CLL sibling pairs. Screening of peripheral blood by flow cytometry detected 0.2-480 clonal CLL-phenotype cells per microliter (median: 37/μL) in 34 of 191 (17.8%) siblings of CLL patients. Clonal BCR isolated from highly purified CLL-phenotype cells induced robust calcium mobilization in BCR-deficient murine pre-B cells in the absence of external antigen and without experimental crosslinking. This autonomous BCR signal was less intense than the signal originating from the CLL BCR of their CLL siblings. According to genotyping by single nucleotide polymorphism array, whole exome, and targeted panel sequencing, CLL risk alleles were found with high and similar prevalence in CLL patients and MBL siblings, respectively. Likewise, the prevalence of recurrent CLL-associated genetic variants was similar between CLL and matched MBL samples. However, copy number variations and small variants were frequently subclonal in MBL cells, suggesting their acquisition during subclinical clonal expansion. These findings support a stepwise model of CLL pathogenesis, in which autonomous BCR signaling leads to a non-malignant (oligo)clonal expansion of CD5+ B cells, followed by malignant progression to CLL after acquisition of pathogenic genetic variants.
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Affiliation(s)
- Edwin Quinten
- Department of Hematology, Leiden University Medical Center, Leiden
| | - Julieta H Sepúlveda-Yáñez
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands; School of Medicine, Universidad de Magallanes, Punta Arenas, Chile
| | - Marvyn T Koning
- Department of Hematology, Leiden University Medical Center, Leiden
| | - Janneke A Eken
- Department of Hematology, Leiden University Medical Center, Leiden
| | - Dietmar Pfeifer
- Department of Medicine I, University Medical Center Freiburg, Freiburg
| | - Valeri Nteleah
- Department of Hematology, Leiden University Medical Center, Leiden
| | | | | | - Jeroen Knijnenburg
- Department of Clinical Genetics, Leiden University Medical Center, Leiden
| | | | - Milena Pantic
- Department of Medicine I, University Medical Center Freiburg, Freiburg
| | - Andreas Agathangelidis
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | | | - Roberto Uribe-Paredes
- Department of Computer Engineering, Universidad de Magallanes, Punta Arenas, Chile; Centre for Biotechnology and Bioengineering, Santiago, Chile
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm
| | | | - Katja Zirlik
- Department of Medicine I, University Medical Center Freiburg, Freiburg, Germany; Tumor-und Brustzentrum Ostschweiz, Chur
| | | | | | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden.
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6
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Tizu M, Calenic B, Hârza M, Cristea BM, Maruntelu I, Caragea AM, Talangescu A, Dima A, Constantinescu AE, Constantinescu I. HLA Gene Polymorphisms in Romanian Patients with Chronic Lymphocytic Leukemia. Genet Res (Camb) 2024; 2024:8852876. [PMID: 38449839 PMCID: PMC10917483 DOI: 10.1155/2024/8852876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/24/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
Materials and Methods This study included 66 patients with CLL, diagnosed between 2020 and 2022, and 100 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQA1/DQB1/DPA1/DPB1, and HLA-DRB1/3/4/5) were investigated using next-generation sequencing technology. Results Several HLA alleles were strongly associated with CLL. The most important finding was that HLA-DRB1∗04:02:01 (p=0.001, OR = 1.05) and HLA-DRB3∗02:01:01 (p=0.009, OR = 1.03) have a predisposing role in CLL development. Moreover, we identified that HLA-A∗24:02:01 0.01 (p=0.01, OR = 0.38), HLA-DQA1∗05:05:01 (p=0.01, OR = 0.56), HLA-DQB1∗03:02:01 (p=0.03, OR = 0.40), and HLA-DRB4∗01:03:01 (p=0.03, OR = 0.54 alleles have protective roles. Correlations between HLA expression and gender showed that women had a higher expression of protective HLA alleles when compared to men. Conclusions Our data are the first to indicate that in Romanian patients with CLL, the HLA-A∗24:02:01 and HLA-DQA1∗05:05:01 alleles have a protective role against CLL development, whereas HLA-DRB1∗04:02:01 and HLA-DRB3∗02:01:01alleles are positively associated with CLL.
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Affiliation(s)
- Maria Tizu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan Calenic
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Mihai Hârza
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan M. Cristea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ion Maruntelu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Andreea M. Caragea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Adriana Talangescu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Alina Dima
- Colentina Clinical Hospital, Rheumatology Department Bucharest, 19-21 Stefan Cel Mare Street, Bucharest 020125, Romania
| | - Alexandra E. Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ileana Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
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7
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Joulia E, Michieletto MF, Agesta A, Peillex C, Girault V, Le Dorze AL, Peroceschi R, Bucciarelli F, Szelechowski M, Chaubet A, Hakim N, Marrocco R, Lhuillier E, Lebeurrier M, Argüello RJ, Saoudi A, El Costa H, Adoue V, Walzer T, Sarry JE, Dejean AS. Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation. J Exp Med 2024; 221:e20230449. [PMID: 38189779 PMCID: PMC10772920 DOI: 10.1084/jem.20230449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
The mechanisms whereby Eomes controls tissue accumulation of T cells and strengthens inflammation remain ill-defined. Here, we show that Eomes deletion in antigen-specific CD4+ T cells is sufficient to protect against central nervous system (CNS) inflammation. While Eomes is dispensable for the initial priming of CD4+ T cells, it is required for long-term maintenance of CNS-infiltrating CD4+ T cells. We reveal that the impact of Eomes on effector CD4+ T cell longevity is associated with sustained expression of multiple genes involved in mitochondrial organization and functions. Accordingly, epigenetic studies demonstrate that Eomes supports mitochondrial function by direct binding to either metabolism-associated genes or mitochondrial transcriptional modulators. Besides, the significance of these findings was confirmed in CD4+ T cells from healthy donors and multiple sclerosis patients. Together, our data reveal a new mechanism by which Eomes promotes severity and chronicity of inflammation via the enhancement of CD4+ T cell mitochondrial functions and resistance to stress-induced cell death.
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Affiliation(s)
- Emeline Joulia
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Michaël F. Michieletto
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arantxa Agesta
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Cindy Peillex
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Virginie Girault
- Suivi Immunologique des Thérapeutiques Innovantes, Pôle de Biologie, Pontchaillou University Hospital, Rennes, France
- UMR1236, University of Rennes, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Bretagne, Rennes, France
| | - Anne-Louise Le Dorze
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Romain Peroceschi
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Florence Bucciarelli
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Marion Szelechowski
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Adeline Chaubet
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Nawad Hakim
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Rémi Marrocco
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Emeline Lhuillier
- GeT-Santé, Plateforme Génome et Transcriptome, GenoToul, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Manuel Lebeurrier
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Rafael J. Argüello
- Aix Marseille University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Abdelhadi Saoudi
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Hicham El Costa
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Veronique Adoue
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, Lyon, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, UMR1037, Institut National de la Santé et de la Recherche Médicale, Toulouse, France
| | - Anne S. Dejean
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
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8
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Nakanishi T, Willett J, Farjoun Y, Allen RJ, Guillen-Guio B, Adra D, Zhou S, Richards JB. Alternative splicing in lung influences COVID-19 severity and respiratory diseases. Nat Commun 2023; 14:6198. [PMID: 37794074 PMCID: PMC10550956 DOI: 10.1038/s41467-023-41912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Alternative splicing generates functional diversity in isoforms, impacting immune response to infection. Here, we evaluate the causal role of alternative splicing in COVID-19 severity and susceptibility by applying two-sample Mendelian randomization to cis-splicing quantitative trait loci and the results from COVID-19 Host Genetics Initiative. We identify that alternative splicing in lung, rather than total expression of OAS1, ATP11A, DPP9 and NPNT, is associated with COVID-19 severity. MUC1 and PMF1 splicing is associated with COVID-19 susceptibility. Colocalization analyses support a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at the ATP11A and DPP9 loci, and with chronic obstructive lung diseases at the NPNT locus. Last, we show that ATP11A, DPP9, NPNT, and MUC1 are highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. These findings clarify the importance of alternative splicing in lung for COVID-19 and respiratory diseases, providing isoform-based targets for drug discovery.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan.
| | - Julian Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Five Prime Sciences Inc, Montréal, QC, Canada
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Darin Adra
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Five Prime Sciences Inc, Montréal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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9
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Cabrera-Serrano AJ, Sánchez-Maldonado JM, ter Horst R, Macauda A, García-Martín P, Benavente Y, Landi S, Clay-Gilmour A, Niazi Y, Espinet B, Rodríguez-Sevilla JJ, Pérez EM, Maffei R, Blanco G, Giaccherini M, Cerhan JR, Marasca R, López-Nevot MÁ, Chen-Liang T, Thomsen H, Gámez I, Campa D, Moreno V, de Sanjosé S, Marcos-Gragera R, García-Álvarez M, Dierssen-Sotos T, Jerez A, Butrym A, Norman AD, Luppi M, Slager SL, Hemminki K, Li Y, Berndt SI, Casabonne D, Alcoceba M, Puiggros A, Netea MG, Försti A, Canzian F, Sainz J. Do GWAS-Identified Risk Variants for Chronic Lymphocytic Leukemia Influence Overall Patient Survival and Disease Progression? Int J Mol Sci 2023; 24:8005. [PMID: 37175717 PMCID: PMC10178669 DOI: 10.3390/ijms24098005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/14/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults worldwide. Although genome-wide association studies (GWAS) have uncovered the germline genetic component underlying CLL susceptibility, the potential use of GWAS-identified risk variants to predict disease progression and patient survival remains unexplored. Here, we evaluated whether 41 GWAS-identified risk variants for CLL could influence overall survival (OS) and disease progression, defined as time to first treatment (TTFT) in a cohort of 1039 CLL cases ascertained through the CRuCIAL consortium. Although this is the largest study assessing the effect of GWAS-identified susceptibility variants for CLL on OS, we only found a weak association of ten single nucleotide polymorphisms (SNPs) with OS (p < 0.05) that did not remain significant after correction for multiple testing. In line with these results, polygenic risk scores (PRSs) built with these SNPs in the CRuCIAL cohort showed a modest association with OS and a low capacity to predict patient survival, with an area under the receiver operating characteristic curve (AUROC) of 0.57. Similarly, seven SNPs were associated with TTFT (p < 0.05); however, these did not reach the multiple testing significance threshold, and the meta-analysis with previous published data did not confirm any of the associations. As expected, PRSs built with these SNPs showed reduced accuracy in prediction of disease progression (AUROC = 0.62). These results suggest that susceptibility variants for CLL do not impact overall survival and disease progression in CLL patients.
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Affiliation(s)
- Antonio José Cabrera-Serrano
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain
| | - José Manuel Sánchez-Maldonado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain
| | - Rob ter Horst
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria;
| | - Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (A.M.); (F.C.)
| | | | - Yolanda Benavente
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (Y.B.); (V.M.); (S.d.S.); (D.C.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Stefano Landi
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (S.L.); (M.G.); (D.C.)
| | - Alyssa Clay-Gilmour
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Greenville, SC 29208, USA;
| | - Yasmeen Niazi
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (Y.N.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (B.E.); (G.B.); (A.P.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | | | - Eva María Pérez
- Hospital Campus de la Salud, PTS, 18016 Granada, Spain; (P.G.-M.); (E.M.P.)
| | - Rossana Maffei
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (R.M.); (R.M.); (M.L.)
| | - Gonzalo Blanco
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (B.E.); (G.B.); (A.P.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Matteo Giaccherini
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (S.L.); (M.G.); (D.C.)
| | - James R. Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (J.R.C.); (A.D.N.)
| | - Roberto Marasca
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (R.M.); (R.M.); (M.L.)
| | | | - Tzu Chen-Liang
- Hematology Department, Morales Meseguer University Hospital, 30008 Murcia, Spain; (T.C.-L.); (I.G.)
| | | | - Irene Gámez
- Hematology Department, Morales Meseguer University Hospital, 30008 Murcia, Spain; (T.C.-L.); (I.G.)
| | - Daniele Campa
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (S.L.); (M.G.); (D.C.)
| | - Víctor Moreno
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (Y.B.); (V.M.); (S.d.S.); (D.C.)
- Cancer Prevention and Control Program, Unit of Biomarkers and Susceptibility, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology, 08907 Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Silvia de Sanjosé
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (Y.B.); (V.M.); (S.d.S.); (D.C.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
| | - Rafael Marcos-Gragera
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
- Epidemiology Unit and Girona Cancer Registry, Oncology Coordination Plan, Department of Health, Autonomous Government of Catalonia, Catalan Institute of Oncology, Girona Biomedical Research Institute (IdiBGi), 17190 Girona, Spain
- Department of Nursing, Universitat de Girona, 17007 Girona, Spain
- Josep Carreras Leukemia Research Institute, 08916 Girona, Spain
| | - María García-Álvarez
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (M.A.)
| | - Trinidad Dierssen-Sotos
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
- Faculty of Medicine, University of Cantabria, 39011 Santander, Spain
| | - Andrés Jerez
- Department of Hematology, Experimental Hematology Unit, Vall d’Hebron Institute of Oncology (VHIO), University Hospital Vall d’Hebron, 08035 Barcelona, Spain;
| | - Aleksandra Butrym
- Department of Cancer Prevention and Therapy, Medical University of Wrocław, 50-556 Wrocław, Poland;
| | - Aaron D. Norman
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (J.R.C.); (A.D.N.)
| | - Mario Luppi
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (R.M.); (R.M.); (M.L.)
| | - Susan L. Slager
- Division of Computational Genomics, Mayo Clinic, Rochester, MN 85054, USA;
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kari Hemminki
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (Y.L.); (M.G.N.)
- Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA;
| | - Delphine Casabonne
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (Y.B.); (V.M.); (S.d.S.); (D.C.)
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
| | - Miguel Alcoceba
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (M.A.)
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (B.E.); (G.B.); (A.P.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (Y.L.); (M.G.N.)
- Department for Immunology & Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Asta Försti
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (Y.N.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (A.M.); (F.C.)
| | - Juan Sainz
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), University of Barcelona, 08908 Barcelona, Spain; (R.M.-G.); (T.D.-S.)
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada (UGR), 18012 Granada, Spain
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10
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Kleinstern G, Slager SL. The inherited genetic contribution and polygenic risk score for risk of CLL and MBL: a narrative review. Leuk Lymphoma 2023; 64:788-798. [PMID: 36576061 PMCID: PMC10121840 DOI: 10.1080/10428194.2022.2157215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a neoplasm of B-cells in the blood and monoclonal B-cell lymphocytosis (MBL) is a precursor state to CLL. This narrative review provides an overview of the genetic studies that identified 43 common variants associated with risk of CLL among individuals of European ancestry. Emerging studies found that ∼50% of these variants are associated with MBL risk. Moreover, the polygenic risk score (PRS) calculated from these CLL variants has been shown to be a robust predictor for both CLL and MBL risk among European ancestry individuals but a weak predictor among African ancestry individuals. By summarizing these genetic studies, we conclude that additional studies are needed in other race/ethnic populations to identify race-specific susceptibility variants, that functional studies are needed to validate the biological mechanisms of the variants, and that the clinical utility of the PRS is limited until preventive strategies for CLL are developed.
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Affiliation(s)
- Geffen Kleinstern
- School of Public Health, University of Haifa, Haifa, Israel
- Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Susan L Slager
- Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
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11
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Wan Mohamad Zamri WN, Mohd Yunus N, Abdul Aziz AA, Zulkipli NN, Sulong S. Perspectives on the Application of Cytogenomic Approaches in Chronic Lymphocytic Leukaemia. Diagnostics (Basel) 2023; 13:964. [PMID: 36900108 PMCID: PMC10001075 DOI: 10.3390/diagnostics13050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a haematological malignancy characterised by the accumulation of monoclonal mature B lymphocytes (positive for CD5+ and CD23+) in peripheral blood, bone marrow, and lymph nodes. Although CLL is reported to be rare in Asian countries compared to Western countries, the disease course is more aggressive in Asian countries than in their Western counterparts. It has been postulated that this is due to genetic variants between populations. Various cytogenomic methods, either of the traditional type (conventional cytogenetics or fluorescence in situ hybridisation (FISH)) or using more advanced technology such as DNA microarrays, next generation sequencing (NGS), or genome wide association studies (GWAS), were used to detect chromosomal aberrations in CLL. Up until now, conventional cytogenetic analysis remained the gold standard in diagnosing chromosomal abnormality in haematological malignancy including CLL, even though it is tedious and time-consuming. In concordance with technological advancement, DNA microarrays are gaining popularity among clinicians as they are faster and better able to accurately diagnose the presence of chromosomal abnormalities. However, every technology has challenges to overcome. In this review, CLL and its genetic abnormalities will be discussed, as well as the application of microarray technology as a diagnostic platform.
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Affiliation(s)
| | - Nazihah Mohd Yunus
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ahmad Aizat Abdul Aziz
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ninie Nadia Zulkipli
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Terengganu 21300, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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12
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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] [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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13
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Kulis M, Martin-Subero JI. Integrative epigenomics in chronic lymphocytic leukaemia: Biological insights and clinical applications. Br J Haematol 2023; 200:280-290. [PMID: 36121003 DOI: 10.1111/bjh.18465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 01/21/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is not only characterised by driver genetic alterations but by extensive epigenetic changes. Over the last decade, epigenomic studies have described the DNA methylome, chromatin accessibility, histone modifications and the three-dimensional (3D) genome architecture of CLL. Beyond its regulatory role, the DNA methylome contains imprints of the cellular origin and proliferative history of CLL cells. These two aspects are strong independent prognostic factors. Integrative analyses of chromatin marks have uncovered novel regulatory elements and altered transcription factor networks as non-genetic means mediating gene deregulation in CLL. Additionally, CLL cells display a disease-specific pattern of 3D genome interactions. From the technological perspective, we are currently witnessing a transition from bulk omics to single-cell analyses. This review aims at summarising the major findings from the epigenomics field as well as providing a prospect of the present and future of single-cell analyses in CLL.
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Affiliation(s)
- Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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14
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Mesini N, Fiorcari S, Atene CG, Maffei R, Potenza L, Luppi M, Marasca R. Role of Notch2 pathway in mature B cell malignancies. Front Oncol 2023; 12:1073672. [PMID: 36686759 PMCID: PMC9846264 DOI: 10.3389/fonc.2022.1073672] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023] Open
Abstract
In recent decades, the Notch pathway has been characterized as a key regulatory signaling of cell-fate decisions evolutionarily conserved in many organisms and different tissues during lifespan. At the same time, many studies suggest a link between alterations of this signaling and tumor genesis or progression. In lymphopoiesis, the Notch pathway plays a fundamental role in the correct differentiation of T and B cells, but its deregulated activity leads to leukemic onset and evolution. Notch and its ligands Delta/Jagged exhibit a pivotal role in the crosstalk between leukemic cells and their environment. This review is focused in particular on Notch2 receptor activity. Members of Notch2 pathway have been reported to be mutated in Chronic Lymphocytic Leukemia (CLL), Splenic Marginal Zone Lymphoma (SMZL) and Nodal Marginal Zone Lymphoma (NMZL). CLL is a B cell malignancy in which leukemic clones establish supportive crosstalk with non-malignant cells of the tumor microenvironment to grow, survive, and resist even the new generation of drugs. SMZL and NMZL are indolent B cell neoplasms distinguished by a distinct pattern of dissemination. In SMZL leukemic cells affect mainly the spleen, bone marrow, and peripheral blood, while NMZL has a leading nodal distribution. Since Notch2 is involved in the commitment of leukemic cells to the marginal zone as a major regulator of B cell physiological differentiation, it is predominantly affected by the molecular lesions found in both SMZL and NMZL. In light of these findings, a better understanding of the Notch receptor family pathogenic role, in particular Notch2, is desirable because it is still incomplete, not only in the physiological development of B lymphocytes but also in leukemia progression and resistance. Several therapeutic strategies capable of interfering with Notch signaling, such as monoclonal antibodies, enzyme or complex inhibitors, are being analyzed. To avoid the unwanted multiple "on target" toxicity encountered during the systemic inhibition of Notch signaling, the study of an appropriate pharmaceutical formulation is a pressing need. This is why, to date, there are still no Notch-targeted therapies approved. An accurate analysis of the Notch pathway could be useful to drive the discovery of new therapeutic targets and the development of more effective therapies.
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Affiliation(s)
- Nicolò Mesini
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Fiorcari
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Claudio Giacinto Atene
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Rossana Maffei
- Hematology Unit, Department of Oncology and Hematology, Azienda-Ospedaliero Universitaria (AOU) of Modena, Modena, Italy
| | - Leonardo Potenza
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy,Hematology Unit, Department of Oncology and Hematology, Azienda-Ospedaliero Universitaria (AOU) of Modena, Modena, Italy
| | - Mario Luppi
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy,Hematology Unit, Department of Oncology and Hematology, Azienda-Ospedaliero Universitaria (AOU) of Modena, Modena, Italy
| | - Roberto Marasca
- Department of Medical and Surgical Sciences, Section of Hematology, University of Modena and Reggio Emilia, Modena, Italy,Hematology Unit, Department of Oncology and Hematology, Azienda-Ospedaliero Universitaria (AOU) of Modena, Modena, Italy,*Correspondence: Roberto Marasca,
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15
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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] [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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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; 2:226-234. [PMID: 39036553 PMCID: PMC11256700 DOI: 10.1016/j.jncc.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/20/2022] [Accepted: 08/07/2022] [Indexed: 11/24/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) contributes to significant cancer burden and mortality globally. In recent years, much insight into the causes of NHL has been gained by evaluating global differences through international collaboration and data pooling. NHL comprises different subtypes that are known to behave differently, exhibit different prognoses, and start in distinct cell types (B-cell, T-cell, and NK-cell, predominantly), and there is increasing evidence that NHL subtypes have different etiologies. Classification of NHL can be complex, with varying subtype frequencies, and is a consideration when evaluating geographic differences. Because of this, international pooling of well-executed epidemiologic studies has conferred power to evaluate NHL by subtype and confidence with minimal misclassification. Given the decreasing burden in some regions while cases rise in Asia, and especially China, this report focuses on a review of the established etiology of NHL from the epidemiologic literature in recent decades, highlighting work from China. Topics covered include demographic patterns and genetic determinants including family history of NHL, as well as infection and immunosuppression, lifestyle, environment, and certain occupational exposures contributing to increased disease risk.
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Affiliation(s)
- Jiajun Luo
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
- Comprehensive Cancer Center, University of Chicago, Chicago, United States of America
| | - Andrew Craver
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
| | - Kendall Bahl
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
| | - Liz Stepniak
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
| | - Kayla Moore
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
| | - Jaime King
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
| | - Yawei Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Briseis Aschebrook-Kilfoy
- Institute for Population and Precision Health, University of Chicago, Chicago, United States of America
- Comprehensive Cancer Center, University of Chicago, Chicago, United States of America
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
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17
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Righolt CH, Zhang G, Gibson SB, Johnston JB, Banerji V, Mahmud SM. Patterns and predictors of referral to the specialized chronic lymphocytic leukemia clinic in Manitoba, Canada. Cancer Epidemiol 2022; 81:102279. [PMID: 36279643 DOI: 10.1016/j.canep.2022.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/26/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Better CLL patient survival has been reported for specialized CLL clinics/hematologists (compared to other CLL patients). It is possible that improved survival is driven by a better prognosis of referred patients. METHODS We used logistic regression to calculate the odds ratios (ORs) and 95 % confidence intervals 95 %CIs) of the association between patient characteristics and CLL referral of all persons diagnosed in 2005-2016 with a pathologically-confirmed CLL or SLL. RESULTS Two-thirds of 1293 patients were referred to the CLL clinic. Referred patients were younger (16 % vs 44 % were 80 +) and in better health (47 % vs 56 % with a chronic diseases) than non-referred patients. Referral increased over time: in 2005-2010, about 60 % of patients were referred; in 2011-2016, this increased to 76 %. Gender did not affect referral (the OR for females is 1.0, 95 %CI 0.8-1.2), but age played a major role; CLL patients diagnosed at age 80 + were less likely to be referred than patients diagnosed < 60, 0.2 (0.1-0.3). CONCLUSION Because referral to Manitoba's specialized CLL clinic is associated with age and the patient's overall health before referral, one should be careful in interpreting differences in outcomes between CLL patients based on referral status alone.
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MESH Headings
- Aged, 80 and over
- Female
- Humans
- Canada
- Chronic Disease
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Manitoba/epidemiology
- Referral and Consultation/statistics & numerical data
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Affiliation(s)
- Christiaan H Righolt
- Vaccine and Drug Evaluation Centre, Department of Community Health Sciences, University of Manitoba, 337-750 McDermot Avenue, Winnipeg, MB, Canada R3E 0T5
| | - Geng Zhang
- Vaccine and Drug Evaluation Centre, Department of Community Health Sciences, University of Manitoba, 337-750 McDermot Avenue, Winnipeg, MB, Canada R3E 0T5
| | - Spencer B Gibson
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Hematology and Oncology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - James B Johnston
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Hematology and Oncology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Versha Banerji
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department of Hematology and Oncology, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Department Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Salaheddin M Mahmud
- Vaccine and Drug Evaluation Centre, Department of Community Health Sciences, University of Manitoba, 337-750 McDermot Avenue, Winnipeg, MB, Canada R3E 0T5.
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18
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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] [Abstract] [Key Words] [MESH Headings] [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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19
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Role of Polygenic Risk Score in Cancer Precision Medicine of Non-European Populations: A Systematic Review. Curr Oncol 2022; 29:5517-5530. [PMID: 36005174 PMCID: PMC9406904 DOI: 10.3390/curroncol29080436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
The development of new screening methods and diagnostic tests for traits, common diseases, and cancer is linked to the advent of precision genomic medicine, in which health care is individually adjusted based on a person’s lifestyle, environmental influences, and genetic variants. Based on genome-wide association study (GWAS) analysis, rapid and continuing progress in the discovery of relevant single nucleotide polymorphisms (SNPs) for traits or complex diseases has increased interest in the potential application of genetic risk models for routine health practice. The polygenic risk score (PRS) estimates an individual’s genetic risk of a trait or disease, calculated by employing a weighted sum of allele counts combined with non-genetic variables. However, 98.38% of PRS records held in public databases relate to the European population. Therefore, PRSs for multiethnic populations are urgently needed. We performed a systematic review to discuss the role of polygenic risk scores in advancing precision medicine for different cancer types in multiethnic non-European populations.
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20
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Meiotic drive in chronic lymphocytic leukemia compared with other malignant blood disorders. Sci Rep 2022; 12:6138. [PMID: 35413962 PMCID: PMC9005523 DOI: 10.1038/s41598-022-09602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
The heredity of the malignant blood disorders, leukemias, lymphomas and myeloma, has so far been largely unknown. The present study comprises genealogical investigations of one hundred and twelve Scandinavian families with unrelated parents and two or more cases of malignant blood disease. For comparison, one large family with related family members and three hundred and forty-one cases of malignant blood disease from the Faroese population was included. The inheritance is non-Mendelian, a combination of genomic parental imprinting and feto-maternal microchimerism. There is significantly more segregation in maternal than in paternal lines, predominance of mother-daughter combinations in maternal lines, and father-son combinations in paternal lines. Chronic lymphocytic leukemia is the most frequent diagnosis in the family material, and chronic lymphocytic leukemia has a transgenerational segregation that is unique in that inheritance of susceptibility to chronic lymphocytic leukemia is predominant in males of paternal lines. Male offspring with chronic lymphocytic leukemia in paternal lines have a birth-order effect, which is manifest by the fact that there are significantly more male patients late in the sibling line. In addition, there is contravariation in chronic lymphocytic leukemia, i.e. lower occurrence than expected in relation to other diagnoses, interpreted in such a way that chronic lymphocytic leukemia remains isolated in the pedigree in relation to other diagnoses of malignant blood disease. Another non-Mendelian function appears in the form of anticipation, i.e. increased intensity of malignancy down through the generations and a lower age at onset of disease than otherwise seen in cases from the Cancer Registers, in acute lymphoblastic leukemia, for example. It is discussed that this non-Mendelian segregation seems to spread the susceptibility genes depending on the gender of the parents and not equally to all children in the sibling line, with some remaining unaffected by susceptibility i.e. "healthy and unaffected", due to a birth order effect. In addition, anticipation is regarded as a non-Mendelian mechanism that can amplify, «preserve» these vital susceptibility genes in the family. Perhaps this segregation also results in a sorting of the susceptibility, as the percentage of follicular lymphoma and diffuse large B-cell lymphoma is lower in the family material than in an unselected material. Although leukemias, lymphomas and myelomas are potentially fatal diseases, this non-Mendelian distribution and amplification hardly play any quantitative role in the survival of Homo sapiens, because these diseases mostly occur after fertile age.
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21
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Fraschilla I, Amatullah H, Jeffrey KL. One genome, many cell states: epigenetic control of innate immunity. Curr Opin Immunol 2022; 75:102173. [PMID: 35405493 PMCID: PMC9081230 DOI: 10.1016/j.coi.2022.102173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
A hallmark of the innate immune system is its ability to rapidly initiate short-lived or sustained transcriptional programs in a cell-specific and pathogen-specific manner that is dependent on dynamic chromatin states. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental cues also induce changes in chromatin that can either promote tolerance or 'train' innate immune cells for amplified secondary responses. We review chromatin processes that enable innate immune cell differentiation and functional transcriptional responses in naive or experienced cells, in concert with signal transduction and cellular metabolic shifts. We discuss how immune chromatin mechanisms are maladapted in disease and novel therapeutic approaches for cellular reprogramming.
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Affiliation(s)
- Isabella Fraschilla
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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22
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Polygenic risk score and risk of monoclonal B-cell lymphocytosis in caucasians and risk of chronic lymphocytic leukemia (CLL) in African Americans. Leukemia 2022; 36:119-125. [PMID: 34285341 PMCID: PMC8727288 DOI: 10.1038/s41375-021-01344-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022]
Abstract
Monoclonal B-cell lymphocytosis (MBL) is a precursor to CLL. Other than age, sex, and CLL family-history, little is known about factors associated with MBL risk. A polygenic-risk-score (PRS) of 41 CLL-susceptibility variants has been found to be associated with CLL risk among individuals of European-ancestry(EA). Here, we evaluate these variants, the PRS, and environmental factors for MBL risk. We also evaluate these variants and the CLL-PRS among African-American (AA) and EA-CLL cases and controls. Our study included 560 EA MBLs, 869 CLLs (696 EA/173 AA), and 2866 controls (2631 EA/235 AA). We used logistic regression, adjusting for age and sex, to estimate odds ratios (OR) and 95% confidence intervals within each race. We found significant associations with MBL risk among 21 of 41 variants and with the CLL-PRS (OR = 1.86, P = 1.9 × 10-29, c-statistic = 0.72). Little evidence of any association between MBL risk and environmental factors was observed. We observed significant associations of the CLL-PRS with EA-CLL risk (OR = 2.53, P = 4.0 × 10-63, c-statistic = 0.77) and AA-CLL risk (OR = 1.76, P = 5.1 × 10-5, c-statistic = 0.62). Inherited genetic factors and not environmental are associated with MBL risk. In particular, the CLL-PRS is a strong predictor for both risk of MBL and EA-CLL, but less so for AA-CLL supporting the need for further work in this population.
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23
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Okamoto L, Watanabe S, Deno S, Nie X, Maruyama J, Tomita M, Hatano A, Yugi K. Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach. Neurosci Res 2021; 175:82-97. [PMID: 34979163 DOI: 10.1016/j.neures.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 01/13/2023]
Abstract
There have been a number of reports about the transcriptional regulatory networks in schizophrenia. However, most of these studies were based on a specific transcription factor or a single dataset, an approach that is inadequate to understand the diverse etiology and underlying common characteristics of schizophrenia. Here we reconstructed and compared the transcriptional regulatory network for lipid metabolism enzymes using 15 public transcriptome datasets of neural cells from schizophrenia patients. Since many of the well-known schizophrenia-related SNPs are in enhancers, we reconstructed a network including enhancer-dependent regulation and found that 53.3 % of the total number of edges (7,577 pairs) involved regulation via enhancers. By examining multiple datasets, we found common and unique transcriptional modes of regulation. Furthermore, enrichment analysis of SNPs that were connected with genes in the transcriptional regulatory networks by eQTL suggested an association with hematological cell counts and some other traits/diseases, whose relationship to schizophrenia was either not or insufficiently reported in previous studies. Based on these results, we suggest that in future studies on schizophrenia, information on genotype, comorbidities and hematological cell counts should be included, along with the transcriptome, for a more detailed genetic stratification and mechanistic exploration of schizophrenia.
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Affiliation(s)
- Lisa Okamoto
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Soyoka Watanabe
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Senka Deno
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Xiang Nie
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Junichi Maruyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Atsushi Hatano
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Department of Omics and Systems Biology, Niigata University Graduate School of Medical and Dental Sciences, 757 Ichibancho, Asahimachi-dori, Chuo Ward, Niigata City, 951-8510, Japan
| | - Katsuyuki Yugi
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; PRESTO, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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24
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Sud A, Law PJ, Houlston RS. The clinical utility of polygenic risk scores for chronic lymphocytic leukemia. Leukemia 2021; 35:3608-3610. [PMID: 34564698 PMCID: PMC8632671 DOI: 10.1038/s41375-021-01429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
- Department of Haemato-Oncology, The Royal Marsden Hospital NHS Foundation Trust, London, UK.
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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25
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Else M, Blakemore SJ, Strefford JC, Catovsky D. The association between deaths from infection and mutations of the BRAF, FBXW7, NRAS and XPO1 genes: a report from the LRF CLL4 trial. Leukemia 2021; 35:2563-2569. [PMID: 33580200 PMCID: PMC7880018 DOI: 10.1038/s41375-021-01165-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 11/22/2022]
Abstract
Causes of death, in particular deaths due to infection, have not been widely studied in randomised trials in chronic lymphocytic leukaemia. With long-term follow-up (median 13 years) we examined the cause of death in 600/777 patients in the LRF CLL4 trial. Blood samples, taken at randomisation from 499 patients, were available for identifying gene mutations. Infection was a cause of death in 258 patients (43%). Patients dying of infection were more likely than those who died of other causes to have received ≥2 lines of treatment (194/258 [75%] versus 231/342 [68%], P = 0.04) and to have died in the winter months (149/258 [58%] versus 166/342 [49%], P = 0.03), respectively. In patients with mutation data, the factors significantly associated with death from infection versus all other deaths were 11q deletion (47/162 [29%] versus 40/209 [19%], P = 0.03) and mutations of the BRAF, FBXW7, NRAS and XPO1 genes. Death was caused by an infection in 46/67 assessable patients (69%) who had a mutation of one or more of these four genes versus only 129/333 patients (39%) without any of these mutations (odds ratio: 3.46 [95% CI 1.98-6.07] P < 0.0001). Careful management of infection risk, including prophylaxis against infection, may be important in patients who carry these mutations.
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Affiliation(s)
- Monica Else
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Stuart J Blakemore
- Cancer Genomics, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Jonathan C Strefford
- Cancer Genomics, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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26
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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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27
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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. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 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] [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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28
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Waller RG, Klein RJ, Vijai J, McKay JD, Clay-Gilmour A, Wei X, Madsen MJ, Sborov DW, Curtin K, Slager SL, Offit K, Vachon CM, Lipkin SM, Dumontet C, Camp NJ. Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes. Hum Mol Genet 2021; 30:1142-1153. [PMID: 33751038 PMCID: PMC8188404 DOI: 10.1093/hmg/ddab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/14/2022] Open
Abstract
Inherited genetic risk factors play a role in multiple myeloma (MM), yet considerable missing heritability exists. Rare risk variants at genome-wide association study (GWAS) loci are a new avenue to explore. Pleiotropy between lymphoid neoplasms (LNs) has been suggested in family history and genetic studies, but no studies have interrogated sequencing for pleiotropic genes or rare risk variants. Sequencing genetically enriched cases can help discover rarer variants. We analyzed exome sequencing in familial or early-onset MM cases to identify rare, functionally relevant variants near GWAS loci for a range of LNs. A total of 149 distinct and significant LN GWAS loci have been published. We identified six recurrent, rare, potentially deleterious variants within 5 kb of significant GWAS single nucleotide polymorphisms in 75 MM cases. Mutations were observed in BTNL2, EOMES, TNFRSF13B, IRF8, ACOXL and TSPAN32. All six genes replicated in an independent set of 255 early-onset MM or familial MM or precursor cases. Expansion of our analyses to the full length of these six genes resulted in a list of 39 rare and deleterious variants, seven of which segregated in MM families. Three genes also had significant rare variant burden in 733 sporadic MM cases compared with 935 control individuals: IRF8 (P = 1.0 × 10-6), EOMES (P = 6.0 × 10-6) and BTNL2 (P = 2.1 × 10-3). Together, our results implicate six genes in MM risk, provide support for genetic pleiotropy between LN subtypes and demonstrate the utility of sequencing genetically enriched cases to identify functionally relevant variants near GWAS loci.
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MESH Headings
- Acyl-CoA Oxidase/genetics
- Butyrophilins/genetics
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Hodgkin Disease/genetics
- Hodgkin Disease/pathology
- Humans
- Interferon Regulatory Factors/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphocytes/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Multiple Myeloma/genetics
- Multiple Myeloma/pathology
- Polymorphism, Single Nucleotide/genetics
- Risk Factors
- T-Box Domain Proteins/genetics
- Tetraspanins/genetics
- Transmembrane Activator and CAML Interactor Protein/genetics
- Exome Sequencing
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Affiliation(s)
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY 10029-5674, USA
| | - Joseph Vijai
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - James D McKay
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, 69372 Lyon Cedex 08, France
| | - Alyssa Clay-Gilmour
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaomu Wei
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael J Madsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Douglas W Sborov
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Karen Curtin
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Susan L Slager
- Department of Health Sciences, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Celine M Vachon
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Charles Dumontet
- INSERM 1052, CNRS 5286, University of Lyon, 69361 Lyon Cedex 07, France
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
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29
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Rönkkö R, Hirvonen E, Malila N, Kilpivaara O, Wartiovaara-Kautto U, Pitkäniemi J. Familial aggregation of early-onset haematological malignancies. Br J Haematol 2021; 193:1134-1141. [PMID: 34002362 DOI: 10.1111/bjh.17477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/22/2021] [Indexed: 02/04/2023]
Abstract
Population-based studies on familial aggregation of haematological malignancies (HM) have rarely focused specifically on early-onset HMs. We estimated standardized incidence ratios (SIR) and cumulative risks of relatives with Hodgkin lymphoma (HL), non-Hodgkin lymphomas (NHL), acute lymphoblastic leukaemia/lymphoma (ALL/LBL) and acute myeloid leukaemia (AML) when index persons and relatives were diagnosed with early-onset HM. A total of 8791 patients aged ≤40 years and diagnosed with primary HM in Finland from 1970 to 2012 were identified from the Finnish Cancer Registry and their 75 774 family members were retrieved from the population registry. SIRs for concordant HMs were elevated among first-degree relatives in all of the most common HMs of children and adolescents and young adults (AYA). The risk was highest among siblings with HL (SIR 9·09, 95% confidence interval 5·55-14·04) and AML (8·29, 1·00-29·96). HL also had the highest cumulative risk for siblings at ≤40 years of age (0·92% vs. 0·11% in the population). In conclusion, significantly elevated SIRs indicate a role of shared aetiological factors in some families, which should be noted in the clinical setting when caring for patients with early-onset HMs.
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Affiliation(s)
- Rosa Rönkkö
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland.,Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland.,Department of Hematology, University of Helsinki, Helsinki, Finland
| | - Elli Hirvonen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Nea Malila
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,HUSLAB Laboratory of Genetics, HUS Diagnostic Center (Helsinki University Hospital), Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Department of Hematology, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Janne Pitkäniemi
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland.,Faculty of Social Sciences, Tampere University, Tampere, Finland.,Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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30
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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] [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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31
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Slager SL, Lanasa MC, Marti GE, Achenbach SJ, Camp NJ, Abbasi F, Kay NE, Vachon CM, Cerhan JR, Johnston JB, Call TG, Rabe KG, Kleinstern G, Boddicker NJ, Norman AD, Parikh SA, Leis JF, Banerji V, Brander DM, Glenn M, Ferrajoli A, Curtin K, Braggio E, Shanafelt TD, McMaster ML, Weinberg JB, Hanson CA, Caporaso NE. Natural history of monoclonal B-cell lymphocytosis among relatives in CLL families. Blood 2021; 137:2046-2056. [PMID: 33512457 PMCID: PMC8057266 DOI: 10.1182/blood.2020006322] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/14/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic lymphocytic lymphoma (CLL) has one of the highest familial risks among cancers. Monoclonal B-cell lymphocytosis (MBL), the precursor to CLL, has a higher prevalence (13%-18%) in families with 2 or more members with CLL compared with the general population (5%-12%). Although, the rate of progression to CLL for high-count MBLs (clonal B-cell count ≥500/µL) is ∼1% to 5%/y, no low-count MBLs have been reported to progress to date. We report the incidence and natural history of MBL in relatives from CLL families. In 310 CLL families, we screened 1045 relatives for MBL using highly sensitive flow cytometry and prospectively followed 449 of them. MBL incidence was directly age- and sex-adjusted to the 2010 US population. CLL cumulative incidence was estimated using Kaplan-Meier survival curves. At baseline, the prevalence of MBL was 22% (235/1045 relatives). After a median follow-up of 8.1 years among 449 relatives, 12 individuals progressed to CLL with a 5-year cumulative incidence of 1.8%. When considering just the 139 relatives with low-count MBL, the 5-year cumulative incidence increased to 5.7%. Finally, 264 had no MBL at baseline, of whom 60 individuals subsequently developed MBL (2 high-count and 58 low-count MBLs) with an age- and sex-adjusted incidence of 3.5% after a median of 6 years of follow-up. In a screening cohort of relatives from CLL families, we reported progression from normal-count to low-count MBL to high-count MBL to CLL, demonstrating that low-count MBL precedes progression to CLL. We estimated a 1.1% annual rate of progression from low-count MBL, which is in excess of that in the general population.
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Affiliation(s)
- Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Mark C Lanasa
- Department of Medicine, Duke University, Duke Cancer Institute, Durham, NC
| | - Gerald E Marti
- Lymphoid Malignancies Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sara J Achenbach
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Nicola J Camp
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Fatima Abbasi
- Center for Biologics Research and Evaluation, Food and Drug Administration, Silver Springs, MD
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - James B Johnston
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Timothy G Call
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | - Aaron D Norman
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Sameer A Parikh
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Jose F Leis
- Department of Hematology and Oncology, Mayo Clinic, Phoenix, AZ
| | - Versha Banerji
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Danielle M Brander
- Department of Medicine, Duke University, Duke Cancer Institute, Durham, NC
| | - Martha Glenn
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Alessandra Ferrajoli
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Karen Curtin
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Esteban Braggio
- Department of Hematology and Oncology, Mayo Clinic, Phoenix, AZ
| | - Tait D Shanafelt
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Mary L McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - J Brice Weinberg
- Department of Medicine, Duke University, Duke Cancer Institute, Durham, NC
- Department of Immunology, Duke University Medical Center, Durham, NC
- Durham Veterans Affairs Medical Center, Durham, NC; and
| | - Curtis A Hanson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Besson C, Moore A, Wu W, Vajdic CM, de Sanjose S, Camp NJ, Smedby KE, Shanafelt TD, Morton LM, Brewer JD, Zablotska L, Engels EA, Cerhan JR, Slager SL, Han J, Berndt SI. Common genetic polymorphisms contribute to the association between chronic lymphocytic leukaemia and non-melanoma skin cancer. Int J Epidemiol 2021; 50:1325-1334. [PMID: 33748835 DOI: 10.1093/ije/dyab042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Epidemiological studies have demonstrated a positive association between chronic lymphocytic leukaemia (CLL) and non-melanoma skin cancer (NMSC). We hypothesized that shared genetic risk factors between CLL and NMSC could contribute to the association observed between these diseases. METHODS We examined the association between (i) established NMSC susceptibility loci and CLL risk in a meta-analysis including 3100 CLL cases and 7667 controls and (ii) established CLL loci and NMSC risk in a study of 4242 basal cell carcinoma (BCC) cases, 825 squamous cell carcinoma (SCC) cases and 12802 controls. Polygenic risk scores (PRS) for CLL, BCC and SCC were constructed using established loci. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS Higher CLL-PRS was associated with increased BCC risk (OR4th-quartile-vs-1st-quartile = 1.13, 95% CI: 1.02-1.24, Ptrend = 0.009), even after removing the shared 6p25.3 locus. No association was observed with BCC-PRS and CLL risk (Ptrend = 0.68). These findings support a contributory role for CLL in BCC risk, but not for BCC in CLL risk. Increased CLL risk was observed with higher SCC-PRS (OR4th-quartile-vs-1st-quartile = 1.22, 95% CI: 1.08-1.38, Ptrend = 1.36 × 10-5), which was driven by shared genetic susceptibility at the 6p25.3 locus. CONCLUSION These findings highlight the role of pleiotropy regarding the pathogenesis of CLL and NMSC and shows that a single pleiotropic locus, 6p25.3, drives the observed association between genetic susceptibility to SCC and increased CLL risk. The study also provides evidence that genetic susceptibility for CLL increases BCC risk.
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Affiliation(s)
- Caroline Besson
- Service d'hématologie et Oncologie, Centre Hospitalier de Versailles, Le Chesnay; Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, 94805, Villejuif, France
| | - Amy Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wenting Wu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, USA
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Tait D Shanafelt
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jerry D Brewer
- Department of Dermatology, Mayo Clinic, Rochester, MN, USA
| | - Lydia Zablotska
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Eric A Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - James R Cerhan
- Service d'hématologie et Oncologie, Centre Hospitalier de Versailles, Le Chesnay; Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, 94805, Villejuif, France
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jiali Han
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Fanfani V, Citi L, Harris AL, Pezzella F, Stracquadanio G. The Landscape of the Heritable Cancer Genome. Cancer Res 2021; 81:2588-2599. [PMID: 33731442 DOI: 10.1158/0008-5472.can-20-3348] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022]
Abstract
Genome-wide association studies (GWAS) have found hundreds of single-nucleotide polymorphisms (SNP) associated with increased risk of cancer. However, the amount of heritable risk explained by SNPs is limited, leaving most of the cancer heritability unexplained. Tumor sequencing projects have shown that causal mutations are enriched in genic regions. We hypothesized that SNPs located in protein coding genes and nearby regulatory regions could explain a significant proportion of the heritable risk of cancer. To perform gene-level heritability analysis, we developed a new method, called Bayesian Gene Heritability Analysis (BAGHERA), to estimate the heritability explained by all genotyped SNPs and by those located in genic regions using GWAS summary statistics. BAGHERA was specifically designed for low heritability traits such as cancer and provides robust heritability estimates under different genetic architectures. BAGHERA-based analysis of 38 cancers reported in the UK Biobank showed that SNPs explain at least 10% of the heritable risk for 14 of them, including late onset malignancies. We then identified 1,146 genes, called cancer heritability genes (CHG), explaining a significant proportion of cancer heritability. CHGs were involved in hallmark processes controlling the transformation from normal to cancerous cells. Importantly, 60 of them also harbored somatic driver mutations, and 27 are tumor suppressors. Our results suggest that germline and somatic mutation information could be exploited to identify subgroups of individuals at higher risk of cancer in the broader population and could prove useful to establish strategies for early detection and cancer surveillance. SIGNIFICANCE: This study describes a new statistical method to identify genes associated with cancer heritability in the broader population, creating a map of the heritable cancer genome with gene-level resolution.See related commentary by Bader, p. 2586.
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Affiliation(s)
- Viola Fanfani
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Luca Citi
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, United Kingdom
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Oncology, The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Francesco Pezzella
- Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Giovanni Stracquadanio
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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Mosquera Orgueira A, Cid López M, Peleteiro Raíndo A, Díaz Arias JÁ, Antelo Rodríguez B, Bao Pérez L, Alonso Vence N, Bendaña López Á, Abuin Blanco A, Melero Valentín P, Ferreiro Ferro R, Aliste Santos C, Fraga Rodríguez MF, González Pérez MS, Pérez Encinas MM, Bello López JL. Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms. Cancers (Basel) 2021; 13:cancers13061340. [PMID: 33809641 PMCID: PMC8001490 DOI: 10.3390/cancers13061340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The global importance of rare variants in tumorigenesis has been addressed by some pan-cancer analysis, revealing significant enrichments in protein-truncating variants affecting genes such as ATM, BRCA1/2, BRIP1, and MSH6. Germline variants can influence treatment response and contribute to the development of treatment-related second neoplasms, especially in childhood leukemia. We aimed to analyze the genomes of patients with B-cell lymphoproliferative disorders for the discovery of genes enriched in rare pathogenic variants. We discovered a significant enrichment for two genes in germline rare and dysfunctional variants. Additionally, we detected rare and likely pathogenic variants associated with disease prognosis and potential druggability, indicating a relevant role of these events in the variability of cancer phenotypes. Abstract There is growing evidence indicating the implication of germline variation in cancer predisposition and prognostication. Here, we describe an analysis of likely disruptive rare variants across the genomes of 726 patients with B-cell lymphoid neoplasms. We discovered a significant enrichment for two genes in rare dysfunctional variants, both of which participate in the regulation of oxidative stress pathways (CHMP6 and GSTA4). Additionally, we detected 1675 likely disrupting variants in genes associated with cancer, of which 44.75% were novel events and 7.88% were protein-truncating variants. Among these, the most frequently affected genes were ATM, BIRC6, CLTCL1A, and TSC2. Homozygous or germline double-hit variants were detected in 28 cases, and coexisting somatic events were observed in 17 patients, some of which affected key lymphoma drivers such as ATM, KMT2D, and MYC. Finally, we observed that variants in six different genes were independently associated with shorter survival in CLL. Our study results support an important role for rare germline variation in the pathogenesis and prognosis of B-cell lymphoid neoplasms.
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Affiliation(s)
- Adrián Mosquera Orgueira
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
- Correspondence: ; Tel.: +34-981-950-191
| | - Miguel Cid López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Andrés Peleteiro Raíndo
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - José Ángel Díaz Arias
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Beatriz Antelo Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Laura Bao Pérez
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Natalia Alonso Vence
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Ángeles Bendaña López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Aitor Abuin Blanco
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Paula Melero Valentín
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Roi Ferreiro Ferro
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Carlos Aliste Santos
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - Máximo Francisco Fraga Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
- Department of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Marta Sonia González Pérez
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
| | - Manuel Mateo Pérez Encinas
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Pathology, SERGAS, 15706 Santiago de Compostela, Spain;
| | - José Luis Bello López
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.C.L.); (A.P.R.); (J.Á.D.A.); (B.A.R.); (N.A.V.); (Á.B.L.); (M.F.F.R.); (M.S.G.P.); (M.M.P.E.); (J.L.B.L.)
- Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Department of Hematology, SERGAS, 15706 Santiago de Compostela, Spain; (L.B.P.); (A.A.B.); (P.M.V.); (R.F.F.)
- Department of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
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Senkevich K, Bandres-Ciga S, Yu E, Liyanage UE, Noyce AJ, Gan-Or Z. No Evidence for a Causal Relationship Between Cancers and Parkinson's Disease. JOURNAL OF PARKINSONS DISEASE 2021; 11:801-809. [PMID: 33646179 DOI: 10.3233/jpd-202474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Epidemiological data suggest that cancer patients have a reduced risk of subsequent Parkinson's disease (PD) development, but the prevalence of PD in melanoma patients is often reported to be increased. Causal relationships between cancers and PD have not been fully explored. OBJECTIVE To study causal relationship between different cancers and PD. METHODS We used GWAS summary statistics of 15 different types of cancers and two-sample Mendelian randomization to study the causal relationship with PD. RESULTS There was no evidence to support a causal relationship between the studied cancers and PD. We also performed reverse analyses between PD and cancers with available full summary statistics (melanoma, breast, prostate, endometrial and keratinocyte cancers) and did not find evidence of causal relationship. CONCLUSION We found no evidence to support a causal relationship between cancers and PD and the previously reported associations could be a result of genetic pleiotropy, shared biology or biases.
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Affiliation(s)
- Konstantin Senkevich
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, QC, Canada.,Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, USA
| | - Eric Yu
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, QC, Canada.,Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Upekha E Liyanage
- Cancer and Population Studies group, Population Health Department, QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital, Queensland, Australia
| | | | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK.,Department of Clinical and Movement Neurosciences, University College London Institute of Neurology, London, UK
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, QC, Canada.,Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada.,Department of Human Genetics, McGill University, Montréal, QC, Canada
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36
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Abstract
Patients with chronic lymphocytic leukemia can be divided into three categories: those who are minimally affected by the problem, often never requiring therapy; those that initially follow an indolent course but subsequently progress and require therapy; and those that from the point of diagnosis exhibit an aggressive disease necessitating treatment. Likewise, such patients pass through three phases: development of the disease, diagnosis, and need for therapy. Finally, the leukemic clones of all patients appear to require continuous input from the exterior, most often through membrane receptors, to allow them to survive and grow. This review is presented according to the temporal course that the disease follows, focusing on those external influences from the tissue microenvironment (TME) that support the time lines as well as those internal influences that are inherited or develop as genetic and epigenetic changes occurring over the time line. Regarding the former, special emphasis is placed on the input provided via the B-cell receptor for antigen and the C-X-C-motif chemokine receptor-4 and the therapeutic agents that block these inputs. Regarding the latter, prominence is laid upon inherited susceptibility genes and the genetic and epigenetic abnormalities that lead to the developmental and progression of the disease.
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MESH Headings
- Disease Progression
- Humans
- Immunotherapy
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Mutation
- PAX5 Transcription Factor/metabolism
- Receptors, Antigen, B-Cell
- Signal Transduction
- Tumor Microenvironment
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Affiliation(s)
- Nicholas Chiorazzi
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Shih-Shih Chen
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Kanti R Rai
- The Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York 11549, USA
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37
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Lin WY, Fordham SE, Sunter N, Elstob C, Rahman T, Willmore E, Shepherd C, Strathdee G, Mainou-Fowler T, Piddock R, Mearns H, Barrow T, Houlston RS, Marr H, Wallis J, Summerfield G, Marshall S, Pettitt A, Pepper C, Fegan C, Forconi F, Dyer MJS, Jayne S, Sellors A, Schuh A, Robbe P, Oscier D, Bailey J, Rais S, Bentley A, Cawkwell L, Evans P, Hillmen P, Pratt G, Allsup DJ, Allan JM. Genome-wide association study identifies risk loci for progressive chronic lymphocytic leukemia. Nat Commun 2021; 12:665. [PMID: 33510140 PMCID: PMC7843618 DOI: 10.1038/s41467-020-20822-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/16/2020] [Indexed: 02/05/2023] Open
Abstract
Prognostication in patients with chronic lymphocytic leukemia (CLL) is challenging due to heterogeneity in clinical course. We hypothesize that constitutional genetic variation affects disease progression and could aid prognostication. Pooling data from seven studies incorporating 842 cases identifies two genomic locations associated with time from diagnosis to treatment, including 10q26.13 (rs736456, hazard ratio (HR) = 1.78, 95% confidence interval (CI) = 1.47-2.15; P = 2.71 × 10-9) and 6p (rs3778076, HR = 1.99, 95% CI = 1.55-2.55; P = 5.08 × 10-8), which are particularly powerful prognostic markers in patients with early stage CLL otherwise characterized by low-risk features. Expression quantitative trait loci analysis identifies putative functional genes implicated in modulating B-cell receptor or innate immune responses, key pathways in CLL pathogenesis. In this work we identify rs736456 and rs3778076 as prognostic in CLL, demonstrating that disease progression is determined by constitutional genetic variation as well as known somatic drivers.
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Affiliation(s)
- Wei-Yu Lin
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah E Fordham
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Nicola Sunter
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Claire Elstob
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Thahira Rahman
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elaine Willmore
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Colin Shepherd
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Gordon Strathdee
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Tryfonia Mainou-Fowler
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Piddock
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah Mearns
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Timothy Barrow
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Helen Marr
- Department of Haematology, Freeman Hospital, Newcastle upon Tyne, UK
| | - Jonathan Wallis
- Department of Haematology, Freeman Hospital, Newcastle upon Tyne, UK
| | | | | | | | | | - Christopher Fegan
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Francesco Forconi
- Cancer Sciences Unit, Cancer Research UK and NIHR Experimental Cancer Medicine Centres, University of Southampton, Southampton, UK
| | - Martin J S Dyer
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Sandrine Jayne
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - April Sellors
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | | | | | | | - James Bailey
- Hull University Teaching Hospital NHS Trust, Hull, UK
| | - Syed Rais
- Hull University Teaching Hospital NHS Trust, Hull, UK
| | - Alison Bentley
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Hull, UK
| | | | - Paul Evans
- Haematological Malignancy Diagnostic Service Laboratory, St James' Institute of Oncology, Leeds, UK
| | - Peter Hillmen
- Section of Experimental Haematology, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Guy Pratt
- University of Birmingham, Birmingham, UK
| | - David J Allsup
- Hull University Teaching Hospital NHS Trust, Hull, UK.
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Hull, UK.
| | - James M Allan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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Barrow TM, Wong Doo N, Milne RL, Giles GG, Willmore E, Strathdee G, Byun HM. Analysis of retrotransposon subfamily DNA methylation reveals novel early epigenetic changes in chronic lymphocytic leukemia. Haematologica 2021; 106:98-110. [PMID: 31919093 PMCID: PMC7776340 DOI: 10.3324/haematol.2019.228478] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/07/2020] [Indexed: 11/30/2022] Open
Abstract
Retrotransposons such as LINE-1 and Alu comprise >25% of the human genome. While global hypomethylation of these elements has been widely reported in solid tumours, their epigenetic dysregulation is yet to be characterised in chronic lymphocytic leukemia (CLL), and there has been scant consideration of their evolutionary history that mediates sensitivity to hypomethylation. Here, we developed an approach for locus- and evolutionary subfamily-specific analysis of retrotransposons using the Illumina Infinium Human Methylation 450K microarray platform, which we applied to publicly-available datasets from CLL and other haematological malignancies. We identified 9,797 microarray probes mapping to 117 LINE-1 subfamilies and 13,130 mapping to 37 Alu subfamilies. Of these, 10,782 were differentially methylated (PFDR<0.05) in CLL patients (n=139) compared with healthy individuals (n=14), with enrichment at enhancers (P=0.002). Differential methylation was associated with evolutionary age of LINE-1 (r2=0.31, P=0.003) and Alu (r2=0.74, P=0.002) elements, with greater hypomethylation of older subfamilies (L1M, AluJ). Locus-specific hypomethylation was associated with differential expression of proximal genes, including DCLK2, HK1, ILRUN, TANK, TBCD, TNFRSF1B and TXNRD2, with higher expression of DCLK2 and TNFRSF1B associated with reduced patient survival. Hypomethylation at nine loci was highly frequent in CLL (>90% patients) but not observed in healthy individuals or other leukaemias, and was detectable in blood samples taken prior to CLL diagnosis in 9 of 82 individuals from the Melbourne Collaborative Cohort Study. Our results demonstrate differential methylation of retrotransposons in CLL by their evolutionary heritage that modulates expression of proximal genes.
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Affiliation(s)
- Timothy M Barrow
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Nicole Wong Doo
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Elaine Willmore
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gordon Strathdee
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hyang-Min Byun
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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39
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Chong AHW, Mitchell RE, Hemani G, Davey Smith G, Yolken RH, Richmond RC, Paternoster L. Genetic Analyses of Common Infections in the Avon Longitudinal Study of Parents and Children Cohort. Front Immunol 2021; 12:727457. [PMID: 34804013 PMCID: PMC8599591 DOI: 10.3389/fimmu.2021.727457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
The burden of infections on an individual and public health is profound. Many observational studies have shown a link between infections and the pathogenesis of disease; however a greater understanding of the role of host genetics is essential. Children from the longitudinal birth cohort, the Avon Longitudinal Study of Parents and Children, had 14 antibodies measured in plasma at age 7: Alpha-casein protein, beta-casein protein, cytomegalovirus, Epstein-Barr virus, feline herpes virus, Helicobacter pylori, herpes simplex virus 1, influenza virus subtype H1N1, influenza virus subtype H3N2, measles virus, Saccharomyces cerevisiae, Theiler's virus, Toxoplasma gondii, and SAG1 protein domain, a surface antigen of Toxoplasma gondii measured for greater precision. We performed genome-wide association analyses of antibody levels against these 14 infections (N = 357 - 5010) and identified three genome-wide signals (P < 5×10-8), two associated with measles virus antibodies and one with Toxoplasma gondii antibodies. In an association analysis focused on the human leukocyte antigen (HLA) region of the genome, we further detected 15 HLA alleles at a two-digit resolution and 23 HLA alleles at a four-digit resolution associated with five antibodies, with eight HLA alleles associated with Epstein-Barr virus antibodies showing strong evidence of replication in UK Biobank. We discuss how our findings from antibody levels complement other studies using self-reported phenotypes in understanding the architecture of host genetics related to infections.
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Affiliation(s)
- Amanda H W Chong
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Ruth E Mitchell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Robert H Yolken
- Stanley Division of Developmental Neurovirology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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40
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Tracking the Genetic Susceptibility Background of B-Cell Non-Hodgkin's Lymphomas from Genome-Wide Association Studies. Int J Mol Sci 2020; 22:ijms22010122. [PMID: 33374413 PMCID: PMC7795678 DOI: 10.3390/ijms22010122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
B-cell non-Hodgkin’s lymphoma (NHL) risk associations had been mainly attributed to family history of the disease, inflammation, and immune components including human leukocyte antigen (HLA) genetic variations. Nevertheless, a broad range of genome-wide association studies (GWAS) have shed light into the identification of several genetic variants presumptively associated with B-cell NHL etiologies, survival or shared genetic risk with other diseases. The present review aims to overview HLA structure and diversity and summarize the evidence of genetic variations, by GWAS, on five NHL subtypes (diffuse large B-cell lymphoma DLBCL, follicular lymphoma FL, chronic lymphocytic leukemia CLL, marginal zone lymphoma MZL, and primary central nervous system lymphoma PCNSL). Evidence indicates that the HLA zygosity status in B-cell NHL might promote immune escape and that genome-wide significance variants can give biological insight but also potential therapeutic markers such as WEE1 in DLBCL. However, additional studies are needed, especially for non-DLBCL, to replicate the associations found to date.
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41
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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] [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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42
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Antimicrobial use before chronic lymphocytic leukemia: a retrospective cohort study. Leukemia 2020; 35:747-751. [PMID: 32684631 DOI: 10.1038/s41375-020-0980-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 11/08/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is accompanied by increased risk of potentially fatal infections. While this can mostly be attributed to disease-related immune dysfunction, it is not known if CLL patients are also constitutionally susceptible to infections. We linked nation-wide Danish registers to explore this possibility, approximating infection susceptibility by use of antimicrobials. We assessed the incidence of antimicrobials among CLL patients and matched controls from the general population for up to 22 years before index diagnosis, and among children and grandchildren of CLL patients and their matched controls. Our analyses showed that for CLL patients overall antimicrobial use began to increase gradually six years before leukemia diagnosis. Before this time point, CLL patients had used significantly more macrolides (relative risk = 1.15; 95% confidence interval 1.10-1.20), antimycotics (1.18; 1.08-1.30), and antivirals (1.62; 1.45-1.81) than controls for up to 22 years before diagnosis. The same pattern of increased use was found among CLL patients' children and grandchildren. Our study suggests that CLL diagnosis is preceded by decades of increased susceptibility to infections. The duration of this time window is compatible with causal roles of immune dysfunction and/or certain infections in CLL pathogenesis, possibly mediating the association between constitutional infection susceptibility and CLL risk.
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43
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Delineation of clinical and biological factors associated with cutaneous squamous cell carcinoma among patients with chronic lymphocytic leukemia. J Am Acad Dermatol 2020; 83:1581-1589. [PMID: 32682027 DOI: 10.1016/j.jaad.2020.06.1024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The incidence of cutaneous squamous cell carcinoma (SCC) in patients with chronic lymphocytic leukemia (CLL) is significantly higher compared with age- and sex-matched controls. OBJECTIVE To evaluate the association of factors associated with SCC risk. METHODS Clinical CLL and SCC data were obtained from Mayo Clinic CLL Resource and self-reported questionnaires among patients with newly diagnosed CLL. We computed the CLL International Prognostic Index (CLL-IPI) from CLL prognostic factors, and a polygenic risk score from SCC susceptibility variants. We used Cox regression to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS Among 1269 patients with CLL, the median follow-up was 7 years, and SCC subsequently developed in 124 patients. Significant associations with SCC risk were history of skin cancer (HR=4.80; 95% CI: 3.37-6.83), CLL-IPI (HR=1.42; 95% CI: 1.13-1.80), and polygenic risk score (HR=2.58; 95% CI: 1.50-4.43). In a multivariable model, these factors were independent predictors (C statistic = 0.69; 95% CI: 0.62-0.76). T-cell immunosuppressive treatments were also associated with SCC risk (HR=2.29; 95% CI: 1.47-3.55; adjusted for age, sex, and prior SCC). LIMITATIONS The sample size decreases when combining all risk factors in a single model. CONCLUSION SCC risk includes history of skin cancer, an aggressive disease at time of CLL diagnosis, receiving T-cell immunosuppressive treatments, and high polygenic risk score. Future studies should develop prediction models that include these factors to improved screening guidelines.
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44
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Zhang YD, Hurson AN, Zhang H, Choudhury PP, Easton DF, Milne RL, Simard J, Hall P, Michailidou K, Dennis J, Schmidt MK, Chang-Claude J, Gharahkhani P, Whiteman D, Campbell PT, Hoffmeister M, Jenkins M, Peters U, Hsu L, Gruber SB, Casey G, Schmit SL, O'Mara TA, Spurdle AB, Thompson DJ, Tomlinson I, De Vivo I, Landi MT, Law MH, Iles MM, Demenais F, Kumar R, MacGregor S, Bishop DT, Ward SV, Bondy ML, Houlston R, Wiencke JK, Melin B, Barnholtz-Sloan J, Kinnersley B, Wrensch MR, Amos CI, Hung RJ, Brennan P, McKay J, Caporaso NE, Berndt SI, Birmann BM, Camp NJ, Kraft P, Rothman N, Slager SL, Berchuck A, Pharoah PDP, Sellers TA, Gayther SA, Pearce CL, Goode EL, Schildkraut JM, Moysich KB, Amundadottir LT, Jacobs EJ, Klein AP, Petersen GM, Risch HA, Stolzenberg-Solomon RZ, Wolpin BM, Li D, Eeles RA, Haiman CA, Kote-Jarai Z, Schumacher FR, Al Olama AA, Purdue MP, Scelo G, Dalgaard MD, Greene MH, Grotmol T, Kanetsky PA, McGlynn KA, Nathanson KL, Turnbull C, Wiklund F, Chanock SJ, Chatterjee N, Garcia-Closas M. Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers. Nat Commun 2020; 11:3353. [PMID: 32620889 PMCID: PMC7335068 DOI: 10.1038/s41467-020-16483-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 05/04/2020] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.
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Affiliation(s)
- Yan Dora Zhang
- Department of Statistics and Actuarial Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Amber N Hurson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Parichoy Pal Choudhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Québec City, QC, Canada
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institution, Tampa, FL, USA
| | - Tracy A O'Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Deborah J Thompson
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Florence Demenais
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), 75006, Paris, France
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - D Timothy Bishop
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Sarah V Ward
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - John K Wiencke
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Beatrice Melin
- Department of Radiation Sciences Oncology, Umeå University, Umeå, Sweden
| | - Jill Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sonja I Berndt
- 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
| | - Nicola J Camp
- Division of Hematology and Hematological Malignancies, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Susan L Slager
- Division of Biomedical Statistics & Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Medical Center, Durham, NC, USA
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institution, Tampa, FL, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Celeste L Pearce
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ellen L Goode
- Division of Epidemiology, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | | | - Kirsten B Moysich
- Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gloria M Petersen
- Division of Epidemiology, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donghui Li
- Division of Cancer Medicine, GI Medical Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ali Amin Al Olama
- Strangeways Research Laboratory, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marlene D Dalgaard
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Genetics and Epidemiology, National Cancer Institute, Rockville, MD, USA
| | | | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institution, Tampa, FL, USA
| | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Katherine L Nathanson
- Division of Translational Health and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Mangaonkar AA, Patnaik MM. Hereditary Predisposition to Hematopoietic Neoplasms: When Bloodline Matters for Blood Cancers. Mayo Clin Proc 2020; 95:1482-1498. [PMID: 32571604 DOI: 10.1016/j.mayocp.2019.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/23/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
With the advent of precision genomics, hereditary predisposition to hematopoietic neoplasms- collectively known as hereditary predisposition syndromes (HPS)-are being increasingly recognized in clinical practice. Familial clustering was first observed in patients with leukemia, which led to the identification of several germline variants, such as RUNX1, CEBPA, GATA2, ANKRD26, DDX41, and ETV6, among others, now established as HPS, with tendency to develop myeloid neoplasms. However, evidence for hereditary predisposition is also apparent in lymphoid and plasma--cell neoplasms, with recent discoveries of germline variants in genes such as IKZF1, SH2B3, PAX5 (familial acute lymphoblastic leukemia), and KDM1A/LSD1 (familial multiple myeloma). Specific inherited bone marrow failure syndromes-such as GATA2 haploinsufficiency syndromes, short telomere syndromes, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, severe congenital neutropenia, and familial thrombocytopenias-also have an increased predisposition to develop myeloid neoplasms, whereas inherited immune deficiency syndromes, such as ataxia-telangiectasia, Bloom syndrome, Wiskott Aldrich syndrome, and Bruton agammaglobulinemia, are associated with an increased risk for lymphoid neoplasms. Timely recognition of HPS is critical to ensure safe choice of donors and/or conditioning-regimen intensity for allogeneic hematopoietic stem-cell transplantation and to enable direction of appropriate genomics-driven personalized therapies. The purpose of this review is to provide a comprehensive overview of HPS and serve as a useful reference for clinicians to recognize relevant signs and symptoms among patients to enable timely screening and referrals to pursue germline assessment. In addition, we also discuss our institutional approach toward identification of HPS and offer a stepwise diagnostic and management algorithm.
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Affiliation(s)
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN.
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Nadeu F, Diaz-Navarro A, Delgado J, Puente XS, Campo E. Genomic and Epigenomic Alterations in Chronic Lymphocytic Leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:149-177. [PMID: 31977296 DOI: 10.1146/annurev-pathmechdis-012419-032810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chronic lymphocytic leukemia is a common disease in Western countries and has heterogeneous clinical behavior. The relevance of the genetic basis of the disease has come to the forefront recently, with genome-wide studies that have provided a comprehensive view of structural variants, somatic mutations, and different layers of epigenetic changes. The mutational landscape is characterized by relatively common copy number alterations, a few mutated genes occurring in 10-15% of cases, and a large number of genes mutated in a small number of cases. The epigenomic profile has revealed a marked reprogramming of regulatory regions in tumor cells compared with normal B cells. All of these alterations are differentially distributed in clinical and biological subsets of the disease, indicating that they may underlie the heterogeneous evolution of the disease. These global studies are revealing the molecular complexity of chronic lymphocytic leukemia and provide new perspectives that have helped to understand its pathogenic mechanisms and improve the clinical management of patients.
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; ,
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematology Department, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
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Kulyté A, Lundbäck V, Lindgren CM, Luan J, Lotta LA, Langenberg C, Arner P, Strawbridge RJ, Dahlman I. Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort. Mol Metab 2020; 34:85-96. [PMID: 32180562 PMCID: PMC7021539 DOI: 10.1016/j.molmet.2020.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Lipolysis, hydrolysis of triglycerides to fatty acids in adipocytes, is tightly regulated, poorly understood, and, if perturbed, can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of lipolysis and elucidate their molecular mechanisms. METHODS Adipocytes from abdominal subcutaneous adipose tissue biopsies were isolated and were incubated without (spontaneous lipolysis) or with a catecholamine (stimulated lipolysis) to analyze lipolysis. DNA was extracted and genome-wide genotyping and imputation conducted. After quality control, 939 samples with genetic and lipolysis data were available. Genome-wide association studies of spontaneous and stimulated lipolysis were conducted. Subsequent in vitro gene expression analyses were used to identify candidate genes and explore their regulation of adipose tissue biology. RESULTS One locus on chromosome 19 demonstrated genome-wide significance with spontaneous lipolysis. 60 loci showed suggestive associations with spontaneous or stimulated lipolysis, of which many influenced both traits. In the chromosome 19 locus, only HIF3A was expressed in the adipocytes and displayed genotype-dependent gene expression. HIF3A knockdown in vitro increased lipolysis and the expression of key lipolysis-regulating genes. CONCLUSIONS In conclusion, we identified a genetic regulator of spontaneous lipolysis and provided evidence of HIF3A as a novel key regulator of lipolysis in subcutaneous adipocytes as the mechanism through which the locus influences adipose tissue biology.
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Affiliation(s)
- Agné Kulyté
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Veroniqa Lundbäck
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Cecilia M Lindgren
- Big Data Institute at the Li Ka Shing Center for Health Information and Discovery, University of Oxford, Oxford, UK; Wellcome Center for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Center, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Luca A Lotta
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Peter Arner
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK; Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden; Health Data Research UK, UK
| | - Ingrid Dahlman
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden.
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48
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Meacham PJ, Williams AM, Strawderman M, Baran AM, Archibald WJ, Wallace DS, Tschernia NP, Burack WR, Barr PM, Zent CS. Additional B-cell malignancies in patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL). Leuk Lymphoma 2020; 61:1636-1644. [PMID: 32175786 DOI: 10.1080/10428194.2020.1737690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Family and migration studies suggest a genetic risk of developing chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL). We hypothesized that CLL patients have an increased risk of additional clonally unrelated B-cell malignancies. To test this, we studied 467 CLL patients (2743 person-years (PYs)) at a single institution over 17 years. The incidence rate (IR) of any additional B-cell lymphoid malignancy was 10.9 per 1000 PYs (n = 30, 6.4%). Eighteen (4%) patients had a clonally unrelated B-cell malignancy (IR = 6.6 per 1000 PYs). Standardized incidence ratios (SIRs) were used to compare the incidence of additional clonally unrelated B-cell malignancies in CLL patients to the age- and sex-matched expected rates in the USA generated from the Surveillance, Epidemiology, and End Results (SEER) database. For the subset of 13 patients having data for comparison in the SEER database, the SIR was 5.41 (95% CI = 2.9, 9.3) which is supportive of our hypothesis.
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Affiliation(s)
| | | | | | | | | | | | | | - Walter Richard Burack
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: https:/doi.org/10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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50
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: 10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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