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Taylor B, Zhao Y, Perez NB, Potts-Thompson S, Crusto C, Creber RM, Taylor JY. Epigenome-Wide Association Study of Depressive Symptoms in Black Women in the InterGEN Study. Int J Mol Sci 2024; 25:7681. [PMID: 39062924 PMCID: PMC11277114 DOI: 10.3390/ijms25147681] [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: 05/23/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
(1) The prevalence of depression is two times higher in women than men. Black women have an increased risk of depression due to stressors such as low socioeconomic status and perceived discrimination. Depression is likely influenced by both genetic and environmental factors. Psychosocial stressors can influence DNA methylation (DNAm), leading to changes in gene expression and ultimately, depression. The objective of this study was to examine associations between DNAm and depressive symptoms in Black women. (2) This study was a secondary analysis of data from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) Study. Perceived discrimination was assessed using Krieger's Experiences of Discrimination and Waelde's Race-Related Events Scale, and participants were screened for depressive symptoms with the Beck Depression Inventory. Raw data from saliva samples were analyzed using the Illumina Infinium Epic (850 K) BeadChip and then preprocessed in RStudio. (3) Differential methylation analysis identified DNAm sites and regions associated with depressive symptoms. Six DNAm sites had a q-value less than 0.05. Additionally, of the 25 regions identified, 12 were associated with neurological diseases or disorders. (4) These findings suggest that there is a neurological component to depression, which should be considered during treatment.
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Affiliation(s)
- Brittany Taylor
- School of Nursing, Columbia University, New York, NY 10032, USA; (B.T.); (Y.Z.); (S.P.-T.); (R.M.C.)
| | - Yihong Zhao
- School of Nursing, Columbia University, New York, NY 10032, USA; (B.T.); (Y.Z.); (S.P.-T.); (R.M.C.)
| | - Nicole B. Perez
- Rory Meyers College of Nursing, New York University, New York, NY 10010, USA;
| | - Stephanie Potts-Thompson
- School of Nursing, Columbia University, New York, NY 10032, USA; (B.T.); (Y.Z.); (S.P.-T.); (R.M.C.)
| | - Cindy Crusto
- School of Medicine, Yale University, New Haven, CT 06510, USA;
| | - Ruth Masterson Creber
- School of Nursing, Columbia University, New York, NY 10032, USA; (B.T.); (Y.Z.); (S.P.-T.); (R.M.C.)
| | - Jacquelyn Y. Taylor
- School of Nursing, Columbia University, New York, NY 10032, USA; (B.T.); (Y.Z.); (S.P.-T.); (R.M.C.)
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Mohanraj L, Wolf H, Silvey S, Liu J, Toor A, Swift-Scanlan T. DNA Methylation Changes in Autologous Hematopoietic Stem Cell Transplant Patients. Biol Res Nurs 2023; 25:310-325. [PMID: 36321693 PMCID: PMC10236442 DOI: 10.1177/10998004221135628] [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] [Indexed: 11/07/2022]
Abstract
BACKGROUND Blood cancers may be potentially cured with hematopoietic stem cell transplantation (HCT); however, standard pre-assessments for transplant eligibility do not capture all contributing factors for transplant outcomes. Epigenetic biomarkers predict outcomes in various diseases. This pilot study aims to explore epigenetic changes (epigenetic age and differentially methylated genes) in patients before and after autologous HCT, that can serve as potential biomarkers to better predict HCT outcomes. METHODS This study used a prospective longitudinal study design to compare genome wide DNA methylation changes in 36 autologous HCT eligible patients recruited from the Cellular Immunotherapies and Transplant clinic at a designated National Cancer Center. RESULTS Genome-wide DNA methylation, measured by the Illumina Infinium Human Methylation 850K BeadChip, showed a significant difference in DNA methylation patterns post-HCT compared to pre-HCT. Compared to baseline levels of DNA methylation pre-HCT, 3358 CpG sites were hypo-methylated and 3687 were hyper-methylated. Identified differentially methylated positions overlapped with genes involved in hematopoiesis, blood cancers, inflammation and immune responses. Enrichment analyses showed significant alterations in biological processes such as immune response and cell structure organization, however no significant pathways were noted. Though participants had an advanced epigenetic age compared to chronologic age before and after HCT, both epigenetic age and accelerated age decreased post-HCT. CONCLUSION Epigenetic changes, both in epigenetic age and differentially methylated genes were observed in autologous HCT recipients, and should be explored as biomarkers to predict transplant outcomes after autologous HCT in larger, longitudinal studies.
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Affiliation(s)
- Lathika Mohanraj
- Department of Adult Health and Nursing
Systems, VCU School of Nursing, Richmond, VA, USA
| | - Hope Wolf
- Department of Human and Molecular Genetics, VCU School of Medicine, Richmond, VA, USA
| | - Scott Silvey
- Department of Biostatistics, VCU School of Medicine, Richmond, VA, USA
| | - Jinze Liu
- Department of Biostatistics, VCU School of Medicine, Richmond, VA, USA
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, VA, USA
| | - Theresa Swift-Scanlan
- Endowed Professor and Director,
Biobehavioral Research Lab, VCU School of Nursing, Richmond, VA, USA
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Munday RM, Haque R, Jan NJ, Wojcik GL, Marie C, Duchen D, Mentzer AJ, Nayak U, Korpe P, Kirkpatrick BD, Petri WA, Duggal P. Genome-Wide Association Study of Campylobacter -Positive Diarrhea Identifies Genes Involved in Toxin Processing and Inflammatory Response. mBio 2022; 13:e0055622. [PMID: 35420468 PMCID: PMC9239263 DOI: 10.1128/mbio.00556-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Diarrhea is responsible for the deaths of more than 500,000 children each year, many of whom reside in low-to-middle-income countries (LMICs). Additionally, children with multiple diarrheal infections early in life have increased growth stunting and malnutrition and decreased vaccine efficacy. Two bacteria that contribute to the burden of diarrhea are Campylobacter jejuni and Campylobacter coli, both are endemic in Bangladesh. However, not all children that are exposed to these pathogens, including Campylobacter, will experience diarrhea. We hypothesized that host genetics may influence susceptibility to Campylobacter infections and performed a genome-wide association study in 534 children from two independent birth cohorts in Dhaka, Bangladesh. Infants were monitored for diarrhea for the first 2 years of life and only defined as controls if all diarrheal samples in the first year were negative for Campylobacter jejuni/C. coli. Each cohort was analyzed separately under an additive model and adjusted for length-for-age z-scores at birth and 12 months, sex, water treatment, and ancestry. In a fixed effect inverse-variance weighted meta-analysis of these two cohorts, we identified a genome-wide significant region on chromosome 8 in intron 4 of the rho guanine nucleotide exchange factor 10 gene (ARHGEF10). Individuals with the G allele (rs13281104) had a 2-fold lower risk of having a Campylobacter-associated diarrheal episode than individuals with the A allele (OR 0.41, 95% CI 0.29 to 0.58, P = 3.6 × 10-7). This SNP is associated with decreased expression of the neighboring gene, CLN8, which may be involved in the transport of the cytolethal distending toxin produced by Campylobacter. IMPORTANCE Children in low-to-middle-income countries often suffer from multiple enteric infections in their first few years of life, many of which have the potential for long-lasting effects. These children are already likely to be malnourished and underweight, and chronic intestinal disturbances exacerbate these conditions. Despite public health interventions aimed at improving water, sanitation, and hygiene, enteric infections are still a leading cause of death for children under five. Previous work has included transmission dynamics, pathogen characteristics, and evaluation of interventions. Here, we examined the role of host genetic variation in susceptibility to diarrhea-associated Campylobacter infection. In our meta-analysis of two independent birth cohorts from Dhaka, Bangladesh, we found that children carrying a specific genetic variant (rs13281104, in an intron of ARHGEF10) were half as likely to have a diarrhea-associated Campylobacter infection in their first year of life. This protective effect may be achieved by decreasing gene expression and thereby impacting host-pathogen interactions and host immune response.
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Affiliation(s)
- Rebecca M. Munday
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ning-Jiun Jan
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Chelsea Marie
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alexander J. Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, UK
| | - Uma Nayak
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Poonum Korpe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Beth D. Kirkpatrick
- University of Vermont College of Medicine and Vaccine Testing Center, Burlington, Vermont, USA
| | - William A. Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Jin YM, Ye Y, Bao WQ, Tong Y, Ni SB, Liu JP, Zhao B. CACNA1B facilitates breast cancer cell growth and migration by regulating cyclin D1 and EMT: the implication of CACNA1B in breast cancer. J Recept Signal Transduct Res 2020; 42:1-8. [PMID: 33100116 DOI: 10.1080/10799893.2020.1837871] [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] [Indexed: 01/21/2023]
Abstract
PURPOSE This study mainly aimed to explore the influences of Calcium Voltage-Gated Channel Subunit Alpha1 B (CACNA1B) on the development of breast cancer and the related mechanism. MATERIALS AND METHODS The information of patients with breast cancer from TCGA database was used for analyses of CACNA1B expression and its prognostic value. Loss- and gain- of functions of CACNA1B were conducted in MCF7 and Bcap-37 cells, respectively. CCK-8, colony formation and transwell assays were applied for evaluating the cell viability and motility. Western blot was used for protein expression detection. RESULTS We revealed that highly expressed CACNA1B in breast cancer tissues was related to poor prognosis according to the data gained from TCGA database. The outcomes of functional assays showed that depletion of CACNA1B restrained MCF7 cell growth, invasion and migration and high-expression of CACNA1B fortified the growth, invasion and migration in Bcap-37 cells. Finally, we manifested that silencing CACNA1B obviously raised the protein expression level of E-cadherin and reduced the protein levels of Cyclin D1, N-cadherin and Snail in MCF7 cells, whilst, over-expression of CACNA1B reduced the level of E-cadherin and increased the expression of Cyclin D1, N-cadherin and Snail in Bcap-37 cells. CONCLUSIONS These results identified CACNA1B as a forwarder of the growth, invasion and migration in breast cancer cells.
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Affiliation(s)
- Yong-Mei Jin
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai, P.R. China
| | - Ying Ye
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, P.R. China
| | - Wen-Qing Bao
- Gallbladder Diseases Center, East Hospital of Tongji University, Shanghai, China
| | - Yang Tong
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai, P.R. China
| | - Shu-Bin Ni
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai, P.R. China
| | - Jian-Ping Liu
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai, P.R. China
| | - Bin Zhao
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai, P.R. China
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Tremblay BL, Guénard F, Lamarche B, Pérusse L, Vohl MC. Integrative Network Analysis of Multi-Omics Data in the Link between Plasma Carotenoid Concentrations and Lipid Profile. Lifestyle Genom 2019; 13:11-19. [PMID: 31770753 DOI: 10.1159/000503828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/24/2019] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Carotenoids, which are a reliable biomarker of fruit and vegetable consumption, are positively associated with the lipid profile. Circulating carotenoid concentrations may interact with several omics profiles including genome, transcriptome, and epigenome. Few studies have used multi-omics approaches, and they rarely include environmental factors, such as diet. OBJECTIVE The objective of this observational study was to examine the potential role of multi-omics data in the interconnection between diet, represented by total carotenoids, and lipid profile using weighted gene correlation network analysis (WGCNA). METHODS Blood leukocyte DNA methylation levels of 472,245 CpG sites and whole blood gene expression levels of 18,160 transcripts were tested for associations with total carotenoid concentrations using regressions in 48 healthy subjects. WGCNA was used to identify co-omics modules and hub genes related to the lipid profile. RESULTS Among genes associated with total carotenoid concentrations, a total of 236 genes were identified at both DNA methylation and gene expression levels. Using WGCNA, six modules, consisting of groups of highly correlated genes represented by colors, were identified and linked to the lipid profile. Probes clustered in the turquoise and green modules correlated with plasma lipid concentrations. A total of 28 hub genes were identified. CONCLUSIONS Genome-wide DNA methylation and gene expression levels were both associated with plasma total carotenoid concentrations. Several hub genes, mostly involved in lipid metabolism and inflammatory response with several genetic variants associated with plasma lipid concentrations, came out of the integrative analysis. This provides a comprehensive understanding of the interactive molecular system between carotenoids, omics, and plasma lipid profile.
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Affiliation(s)
- Bénédicte L Tremblay
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Benoît Lamarche
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,School of Nutrition, Laval University, Quebec City, Québec, Canada
| | - Louis Pérusse
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada.,Department of Kinesiology, Laval University, Quebec City, Québec, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, Québec, Canada, .,School of Nutrition, Laval University, Quebec City, Québec, Canada,
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Li H, Yu S, Wang R, Sun Z, Zhou X, Zheng L, Yin Z, Sun Y. Polymorphism of CONNEXIN37 gene is a risk factor for ischemic stroke in Han Chinese population. Lipids Health Dis 2018; 17:72. [PMID: 29631604 PMCID: PMC5891898 DOI: 10.1186/s12944-018-0727-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/28/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Stroke has a high fatality and disability rate, and is one of the main burdens to human health. It is thus very important to identify biomarkers for the development of effective approaches for the prevention and treatment of stroke. Connexin37 is an anti-inflammatory cytokine and is involved in chronic inflammation and atherosclerosis. Recent studies have found that CONNEXIN37 gene variations are associated with atherosclerosis diseases, such as coronary heart disease and stroke, but its association with stroke in distinct human populations remains to be determined. We report here the analysis of the association of the single nucleotide polymorphisms (SNPs) of CONNEXIN37 with ischemic stroke in Han Chinese population. METHODS Two SNPs of CONNEXIN37 gene were analyzed in 385 ischemic stroke patients and 362 hypertension control patients using ligase detection reaction (LDR) method. RESULTS Logistic regression analysis demonstrated that, AG and GG genotypes of SNP rs1764390 and CC genotype of rs1764391 of CONNEXIN37 were associated with an increased risk of ischemic stroke, and that G allele of rs1764390 is a risk factor for ischemic stroke. Further, we found that SNP rs1764390 and SNP rs1764391 in CONNEXIN37 were associated with ischemic stroke under additive/dominant model, and recessive/dominant model, respectively. CONCLUSION Our results indicate that CONNEXIN37 gene polymorphism is an ischemic stroke risk factor in Northern Han Chinese.
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Affiliation(s)
- Hong Li
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Shasha Yu
- Department of Cardiology, the First Hospital of China Medical University, 155 North Nanjing Street, Shenyang, 110001, China
| | - Rui Wang
- Department of Cardiology, the First Hospital of China Medical University, 155 North Nanjing Street, Shenyang, 110001, China
| | - Zhaoqing Sun
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xinghu Zhou
- Department of Cardiology, the First Hospital of China Medical University, 155 North Nanjing Street, Shenyang, 110001, China
| | - Liqiang Zheng
- Department of Clinical Epidemiology, Library, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Zhihua Yin
- Epidemiology Department of China Medical University, Shenyang, 110122, China
| | - Yingxian Sun
- Department of Cardiology, the First Hospital of China Medical University, 155 North Nanjing Street, Shenyang, 110001, China.
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de Toro-Martín J, Guénard F, Rudkowska I, Lemieux S, Couture P, Vohl MC. A common variant in ARHGEF10 alters delta-6 desaturase activity and influence susceptibility to hypertriglyceridemia. J Clin Lipidol 2017; 12:311-320.e3. [PMID: 29246731 DOI: 10.1016/j.jacl.2017.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/05/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Numbers of single nucleotide polymorphisms (SNPs) associated with fatty acid desaturase activities have been previously identified within the FADS1-FADS2 gene cluster, which encodes delta-5 (D5D) and delta-6 (D6D) desaturases, respectively. OBJECTIVE We aimed at further characterizing the genetic variability associated with D5D and D6D activities on a genome-wide scale. METHODS We conducted a genome-wide association study of D5D and D6D activities in a cohort of 141 individuals from the greater Quebec City metropolitan area using the Illumina HumanOmni5-Quad BeadChip. Estimates of D5D and D6D activities were computed using product-to-precursor fatty acid ratios, arachidonic acid (AA)/dihomo-gamma-linolenic acid (DGLA) for D5D, and DGLA/linoleic acid (LA) for D6D. Levels of fatty acids were measured by gas chromatography in plasma phospholipids. RESULTS We identified 24 previously reported SNPs associated with fatty acid levels and desaturase activities as significantly associated with D5D activity within the FADS1-FADS2 gene cluster (lead SNP rs174566/A>G). Furthermore, we identified 5 novel loci potentially associated with D5D activity at chromosomes 1, 6, 4, 8 and 19. A novel SNP associated with D6D activity and mapped to the ARHGEF10 locus (rs2280885/A>G) was identified, with carriers of the rare allele showing a significant increase in D6D activity and plasma triglyceride levels. After multiple testing correction by permutation, only rs174566 and rs2280885 remained significantly associated to D5D and D6D activity estimates, respectively. CONCLUSIONS These results confirm previous genetic associations within the FADS1-FADS2 gene cluster with D5D activity. A novel genetic variation associated with higher D6D activity within the ARHGEF10 gene is potentially altering plasma triglyceride levels.
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Affiliation(s)
- Juan de Toro-Martín
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC, Canada; School of Nutrition, Laval University, Quebec City, QC, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC, Canada; School of Nutrition, Laval University, Quebec City, QC, Canada
| | - Iwona Rudkowska
- Endocrinology and Nephrology unit, Centre de recherche du CHU de Québec, Laval University, Quebec City, QC, Canada
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC, Canada; School of Nutrition, Laval University, Quebec City, QC, Canada
| | - Patrick Couture
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC, Canada; Endocrinology and Nephrology unit, Centre de recherche du CHU de Québec, Laval University, Quebec City, QC, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC, Canada; School of Nutrition, Laval University, Quebec City, QC, Canada.
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