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Li Y, Wong KY, Howard AG, Gordon-Larsen P, Highland HM, Graff M, North KE, Downie CG, Avery CL, Yu B, Young KL, Buchanan VL, Kaplan R, Hou L, Joyce BT, Qi Q, Sofer T, Moon JY, Lin DY. Mendelian randomization with incomplete measurements on the exposure in the Hispanic Community Health Study/Study of Latinos. HGG Adv 2024; 5:100245. [PMID: 37817410 PMCID: PMC10628889 DOI: 10.1016/j.xhgg.2023.100245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
Mendelian randomization has been widely used to assess the causal effect of a heritable exposure variable on an outcome of interest, using genetic variants as instrumental variables. In practice, data on the exposure variable can be incomplete due to high cost of measurement and technical limits of detection. In this paper, we propose a valid and efficient method to handle both unmeasured and undetectable values of the exposure variable in one-sample Mendelian randomization analysis with individual-level data. We estimate the causal effect of the exposure variable on the outcome using maximum likelihood estimation and develop an expectation maximization algorithm for the computation of the estimator. Simulation studies show that the proposed method performs well in making inference on the causal effect. We apply our method to the Hispanic Community Health Study/Study of Latinos, a community-based prospective cohort study, and estimate the causal effect of several metabolites on phenotypes of interest.
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Affiliation(s)
- Yilun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kin Yau Wong
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Penny Gordon-Larsen
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina G Downie
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christy L Avery
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dan-Yu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Zheng Y, Musa J, Joyce BT, Wang J, Gursel D, Silas OA, Abdulkareem FB, Imade G, Akanmu A, Wei JJ, Kocherginsky M, Kim KY, Wehbe FH, Achenbach C, Anorlu R, Simon MA, Sagay A, Ogunsola F, Murphy R, Hou L. Global line-1 hypomethylation as novel biomarker for cervical cancer in Nigerian women living with HIV. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e17513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e17513 Background: Nigeria faces a high health burden of cervical cancer (CC), which is worsened by high prevalence of human immunodeficiency virus (HIV) infection. Repetitive elements (RE) are DNA sequences that occur in multiple copies throughout the human genome. HIV infection can lead to RE hypomethylation that causes genome instability, an event often seen in the early phase of tumorigenesis. We aim to examine global RE hypomethylation as a novel epigenetic biomarker for CC among HIV-positive women in Nigeria. Methods: This study involved three groups of women: a) HIV-positive with CC (n=39); b) HIV-positive and cancer-free (n=52); and c) HIV-negative with CC (n=23). We estimated three types of global RE methylation in cervical tissue using genome-wide methylation data: long interspersed nuclear elements (LINE-1), Alu, and human endogenous retrovirus (HERV). We used multiple linear regression adjusting for age, education, parity, employment, cancer stage, body mass index, and sample batch to compare the biomarkers across the HIV/ICC groups and paired t-test to compare 26 pairs of tumor vs. surrounding normal tissues, stratified by HIV status. Receiver operating characteristic curve (ROC) and area under the ROC (AUC) were used to examine the diagnostic value. Results: Among HIV-positive women, all 3 global RE methylation biomarkers were hypomethylated in CC compared to cancer-free (LINE-1: mean difference [MD]=-0.049, p-value=2.9e-8; Alu: MD=-0.011, p-value=2.0e-4; HERV: MD=-0.013, p-value=1.7e-6). Paired analyses showed a larger, more significant MD in HIV-positive stratum than HIV-negative, especially LINE-1 (MD=-0.048 vs. -0.020, p-value=0.004 vs. 0.254). LINE-1 achieved the highest AUC (0.85, 95% CI: 0.76-0.95) in distinguishing tumor tissue from normal tissue among HIV-positive women, followed by HERV (0.82, 95% CI: 0.73-0.92) and Alu (0.60, 95% CI: 0.47-0.72). Conclusions: Global LINE-1 hypomethylation may serve as a novel biomarker for CC screening and early detection for women living with HIV in low- and middle-income countries.
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Affiliation(s)
| | - Jonah Musa
- University of Jos, Jos, Plateau, Nigeria
| | | | - Jun Wang
- Northwestern University, Chicago, IL
| | - Demirkan Gursel
- Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | | | | | | | - Jian-Jun Wei
- Department of Pathology, Northwestern University, Feinberg Medical School, Chicago, IL
| | | | | | | | - Chad Achenbach
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Melissa A. Simon
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | | | | | - Lifang Hou
- Feinberg School of Medicine, Northwestern University, Chicago, IL
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Joyce BT, Hibler E, Matthews C, Moore R, Eron J, Mayer K, Kitahata M, Saag M, Hou L, Achenbach C. Abstract LB-160: Incidence of non-AIDS-defining cancers over time in the post-ART era. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: In the current era of potent antiretroviral therapy (ART), complications and mortality from HIV/AIDS have declined dramatically. ART increasingly allows persons with HIV-infection (PWH) to live longer, but also increases lifetime risk of age-associated chronic diseases such as cancer. Furthermore, the interplay of HIV, immune dysfunction, ART use, aging, and other traditional chronic disease risk factors is under-studied in the context of specific non-AIDS-defining cancers (NADCs). These cancers represent a public health problem that will grow increasingly urgent as HIV-infected individuals age. Descriptive epidemiology of these cancers (compared to Kaposi's sarcoma [KS] and non-Hodgkin's lymphoma [NHL], the most common AIDS-defining cancers [ADCs]), and its changes with the evolution of ART over time, are necessary to address this issue.
Methods: This study used longitudinally collected data from the Centers for AIDS Research (CFAR) Network of Integrated Clinical Systems (CNICS) which captures clinical, sociodemographic, and behavioral data on over 32,000 PWH in care at eight US treatment sites. We included patients who enrolled in CNICS from 2000 through 2014, were not diagnosed with cancer prior to enrollment, and were followed at a CNICS site for at least 180 days. We used linear regression to calculate cancer type-specific time trends, and poisson regression to calculate incidence densities for all cancers, NADCs, and ADCs. Poisson models were adjusted for: age in 2000 (study baseline), nadir CD4 count, any ART use, and hepatitis C virus co-infection. Age and nadir CD4 were standardized to the population mean prior to Poisson regression.
Results: We observed significant changes over time in the incidence rates of colorectal, oropharyngeal, and prostate cancers as well as KS, NHL, and melanoma. From 2000-2014 we observed increases in the incidence densities of colorectal (10.4 to 38.6 cases per 100,000 person-years), oropharyngeal (10.4 to 29.0), and prostate cancers (10.4 to 87.1). Over the same period, we observed decreases in the incidence densities of KS (251.5 to 68.2 cases per 100,000 person-years) and NHL (250.5 to 126.1). The adjusted all-cancer incidence density decreased from 728.6.3 (per 100,000 person-years) in 2000-1 to 518.1 in 2013-4. For ADCs the adjusted incidence density decreased from 224.2 in 2000-1 to 115.5 in 2013-4, while for NADCs the adjusted incidence density increased from 286.7 in 2000-1 to 358.6 in 2013-4.
Conclusion: Changes in the incidence densities of NADCs from 2000-2014 reflect the increasing efficacy of ART. PWH are living longer, with reduced incidence of AIDS-defining cancers and increased incidence of age-related NADCs such as colorectal and prostate cancer. These findings support the continued need to study cancer among PWH to better understand their unique risk factors, including the potential influence of immune recovery and ART on specific NADC risk.
Citation Format: Brian Thomas Joyce, Elizabeth Hibler, Christopher Matthews, Richard Moore, Joseph Eron, Kenneth Mayer, Mari Kitahata, Michael Saag, Lifang Hou, Chad Achenbach. Incidence of non-AIDS-defining cancers over time in the post-ART era [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-160.
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Affiliation(s)
| | | | | | | | - Joseph Eron
- 4University of North Carolina Chapel Hill, Chapel Hill, NC
| | | | | | - Michael Saag
- 7University of Alabama-Birmingham, Birmingham, AL
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Gao T, Joyce BT, Liu L, Zheng Y, Dai Q, Zhang Z, Zhang W, Shrubsole MJ, Tao MH, Schwartz J, Baccarelli A, Hou L. DNA methylation of oxidative stress genes and cancer risk in the Normative Aging Study. Am J Cancer Res 2016; 6:553-561. [PMID: 27186424 PMCID: PMC4859680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023] Open
Abstract
Oxidative stress (OS) is a primary mechanism of carcinogenesis, and methylation of genes related to it may play a role in cancer development. In this study, we examined the prospective association between blood DNA methylation of four oxidative stress genes and cancer incidence. Our study population included a total of 582 participants in the Normative Aging Study (NAS) who had blood drawn during 1-4 visits from 1999-2012 (mean follow up 9.0 years). Promoter DNA methylation of CRAT, iNOS, OGG1 and GCR in blood leukocytes was measured using pyrosequencing. We used Cox regression models to examine prospective associations between cancer incidence and both methylation at the baseline visit and methylation rate of changes over time. Baseline OGG1 methylation was associated with higher risk of all-cancer (HR: 1.43, 95% CI: 1.15-1.78) and prostate cancer (HR: 1.52, 95% CI: 1.03-2.25) incidence. Compared with participants remaining cancer-free, those who eventually developed cancer had significantly accelerated CRAT methylation (p = 0.04) and decelerated iNOS methylation (p<0.01) over time prior to cancer diagnosis. Accelerated CRAT methylation was associated with higher all-cancer incidence (HR: 3.88, 95% CI: 1.06-14.30), whereas accelerated iNOS methylation was associated with lower all-cancer incidence (HR: 0.08, 95% CI 0.02-0.38). Our results suggest that methylation and its dynamic change over time in OS-related genes, including OGG1, CRAT and iNOS, may play an important role in carcinogenesis. These results can potentially facilitate the development of early detection biomarkers and new treatments for a variety of cancers.
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Affiliation(s)
- Tao Gao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-ChicagoChicago, IL, USA 60612
| | - Lei Liu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Qi Dai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashville, TN, USA 37232
| | - Zhou Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Wei Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashville, TN, USA 37232
| | - Meng-Hua Tao
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science CenterFort Worth, TX, USA 76107
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public HealthBoston, MA, USA 02115
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard School of Public HealthBoston, MA, USA 02115
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
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5
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Zhang Z, Zheng Y, Zhang X, Liu C, Joyce BT, Kibbe WA, Hou L, Zhang W. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines. Hum Genet 2015; 135:223-32. [PMID: 26714498 DOI: 10.1007/s00439-015-1628-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/17/2015] [Indexed: 01/26/2023]
Abstract
Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits.
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Affiliation(s)
- Zhou Zhang
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,Institute for Public Health and Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Xu Zhang
- Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Cong Liu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Warren A Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA. .,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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Liu C, Xu J, Chen Y, Guo X, Zheng Y, Wang Q, Chen Y, Ni Y, Zhu Y, Joyce BT, Baccarelli A, Deng F, Zhang W, Hou L. Characterization of genome-wide H3K27ac profiles reveals a distinct PM2.5-associated histone modification signature. Environ Health 2015; 14:65. [PMID: 26276146 PMCID: PMC4537530 DOI: 10.1186/s12940-015-0052-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/31/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Current studies of environmental health suggest a link between air pollution components, such as particulate matter (PM), and various diseases. However, the specific genes and regulatory mechanisms implicated in PM-induced diseases remain largely unknown. Epigenetic systems such as covalent modification of histones in chromatin may mediate environmental factors in gene regulation. Investigating the relationships between PM exposure and histone modification status may help understand the mechanisms underlying environment-associated health conditions. METHODS In this study, we obtained genome-wide profiles of H3K27ac (histone 3 lysine 27 acetylation), known to be an active gene regulatory histone modification marker, in blood samples collected from four Chinese individuals exposed to high or low PM2.5 (particles with diameters up to 2.5 μm). RESULTS The genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) data indicated a comprehensive differential H3K27ac landscape across the individual genomes, which was associated with high PM2.5. Moreover, a substantial number of these PM2.5-associated differential H3K27ac markers were in genes involved in immune cell activation, potentially linking these epigenetic changes with air pollution-induced immune and inflammatory responses. CONCLUSIONS Our study provides the first genome-wide characterization of H3K27ac profiles in individuals subjected to different exposure levels of PM2.5. Future systematic investigations of the relationships between air pollutants and histone modifications in large population samples are warranted to elucidate the contributions of histone modifications to environment-associated diseases.
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Affiliation(s)
- Cong Liu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
| | - Junhui Xu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Yahong Chen
- Respiratory Department, Peking University Third Hospital, Beijing, China.
| | - Xinbiao Guo
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Yinan Zheng
- Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Qianfei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yiyong Chen
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Yang Ni
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Yidan Zhu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA.
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
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Joyce BT, Gao T, Liu L, Zheng Y, Liu S, Zhang W, Penedo F, Dai Q, Schwartz J, Baccarelli AA, Hou L. Longitudinal Study of DNA Methylation of Inflammatory Genes and Cancer Risk. Cancer Epidemiol Biomarkers Prev 2015; 24:1531-8. [PMID: 26265203 DOI: 10.1158/1055-9965.epi-15-0198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/06/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Chronic inflammation plays a key role in cancer etiology. DNA methylation modification, one of the epigenetic mechanisms regulating gene expression, is considered a hallmark of cancer. Human and animal models have identified numerous links between DNA methylation and inflammatory biomarkers. Our objective was to prospectively and longitudinally examine associations between methylation of four inflammatory genes and cancer risk. METHODS We included 795 Normative Aging Study participants with blood drawn one to four times from 1999 to 2012 (median follow-up, 10.6 years). Promoter DNA methylation of IL6, ICAM-1, IFN, and TLR2 in blood leukocytes was measured using pyrosequencing at multiple CpG sites and averaged by gene for data analysis. We used Cox regression models to examine prospective associations of baseline and time-dependent methylation with cancer risk and compared mean methylation differences over time between cancer cases and cancer-free participants. RESULTS Baseline IFN hypermethylation was associated with all-cancer (HR, 1.49; P = 0.04) and prostate cancer incidence (HR, 1.69; P = 0.02). Baseline ICAM-1 and IL6 hypermethylation were associated with prostate cancer incidence (HR, 1.43; P = 0.02; HR, 0.70; P = 0.03, respectively). In our time-dependent analyses, IFN hypermethylation was associated with all-cancer (HR, 1.79; P = 0.007) and prostate cancer (HR, 1.57; P = 0.03) incidence; and ICAM-1 and IL6 hypermethylation were associated with prostate cancer incidence (HR, 1.39; P = 0.02; HR, 0.69; P = 0.03, respectively). We detected significant ICAM-1 hypermethylation in cancer cases (P = 0.0003) 10 to 13 years prediagnosis. CONCLUSION Hypermethylation of IFN and ICAM-1 may play important roles in early carcinogenesis, particularly that of prostate cancer. IMPACT These methylation changes could inform the development of early detection biomarkers and potential treatments of inflammation-related carcinogenesis.
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Affiliation(s)
- Brian Thomas Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-Chicago, Chicago, Illinois.
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lei Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yinan Zheng
- Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Siran Liu
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Frank Penedo
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Qi Dai
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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