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Venney CJ, Mérot C, Normandeau E, Rougeux C, Laporte M, Bernatchez L. Epigenetic and Genetic Differentiation Between Coregonus Species Pairs. Genome Biol Evol 2024; 16:evae013. [PMID: 38271269 PMCID: PMC10849188 DOI: 10.1093/gbe/evae013] [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: 07/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Clément Rougeux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Ministère des Forêts, de la Faune et des Parcs (MFFP), Québec, Québec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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Li Y, Zhan Y, Mao W, Wang B, Dong P, Na R. Interaction between Genetic Risks and Socioeconomic Factors on Thyroid Cancer: Evidence from 0.5 Million UK Biobank Participants. Cancers (Basel) 2023; 15:5028. [PMID: 37894396 PMCID: PMC10605197 DOI: 10.3390/cancers15205028] [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: 08/08/2023] [Revised: 09/21/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND There is a research gap between genetic predisposition, socioeconomic factors, and their interactions on thyroid tumorigenesis. METHODS Individual and genetic data were obtained from UK Biobank. Logistic regression models were used to evaluate the association between genetic risk, socioeconomic factors, and thyroid cancer (TCa). A stratified analysis was conducted to estimate their joint effects. A two-sample Mendelian randomization (MR) analysis was further used to examine the potential causality. RESULTS A total of 502,394 participants were included in this study. Three index loci (rs4449583, rs7726159, and rs7725218) of telomerase reverse transcriptase (TERT) were found to be significantly related to incident TCa. Association analyses showed that high genetic risk, low household income, and high education level were independent risk factors, while unemployment and frequent social connection were suggestive risk factors for TCa. Interaction analyses showed that in participants with low genetic risk, low household income was significantly associated with TCa (odds ratio [OR] = 1.56, 95% confidence interval [CI]: 1.00-2.46). In participants with high genetic risk, those with a high education level (OR = 1.32, 95%CI: 1.06-1.65) and frequent social connection (OR = 1.36, 95%CI: 1.02-1.81) had a significantly increased risk of TCa. However, no causal relationship was observed in the MR analysis. CONCLUSION Interactions exist between genetic risk, household income, education level, and social connection and thyroid cancer.
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Affiliation(s)
- Yu Li
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Yongle Zhan
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wei Mao
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Baoxin Wang
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Pin Dong
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Rong Na
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
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Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW. DNA methylation markers for kidney function and progression of diabetic kidney disease. Nat Commun 2023; 14:2543. [PMID: 37188670 PMCID: PMC10185566 DOI: 10.1038/s41467-023-37837-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Epigenetic markers are potential biomarkers for diabetes and related complications. Using a prospective cohort from the Hong Kong Diabetes Register, we perform two independent epigenome-wide association studies to identify methylation markers associated with baseline estimated glomerular filtration rate (eGFR) and subsequent decline in kidney function (eGFR slope), respectively, in 1,271 type 2 diabetes subjects. Here we show 40 (30 previously unidentified) and eight (all previously unidentified) CpG sites individually reach epigenome-wide significance for baseline eGFR and eGFR slope, respectively. We also develop a multisite analysis method, which selects 64 and 37 CpG sites for baseline eGFR and eGFR slope, respectively. These models are validated in an independent cohort of Native Americans with type 2 diabetes. Our identified CpG sites are near genes enriched for functional roles in kidney diseases, and some show association with renal damage. This study highlights the potential of methylation markers in risk stratification of kidney disease among type 2 diabetes individuals.
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Affiliation(s)
- Kelly Yichen Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha Day
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies and Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Cadmon King Poo Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Heung Man Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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Kumar A, Kos MZ, Roybal D, Carless MA. A pilot investigation of differential hydroxymethylation levels in patient-derived neural stem cells implicates altered cortical development in bipolar disorder. Front Psychiatry 2023; 14:1077415. [PMID: 37139321 PMCID: PMC10150707 DOI: 10.3389/fpsyt.2023.1077415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Bipolar disorder (BD) is a chronic mental illness characterized by recurrent episodes of mania and depression and associated with social and cognitive disturbances. Environmental factors, such as maternal smoking and childhood trauma, are believed to modulate risk genotypes and contribute to the pathogenesis of BD, suggesting a key role in epigenetic regulation during neurodevelopment. 5-hydroxymethylcytosine (5hmC) is an epigenetic variant of particular interest, as it is highly expressed in the brain and is implicated in neurodevelopment, and psychiatric and neurological disorders. Methods Induced pluripotent stem cells (iPSCs) were generated from the white blood cells of two adolescent patients with bipolar disorder and their same-sex age-matched unaffected siblings (n = 4). Further, iPSCs were differentiated into neuronal stem cells (NSCs) and characterized for purity using immuno-fluorescence. We used reduced representation hydroxymethylation profiling (RRHP) to perform genome-wide 5hmC profiling of iPSCs and NSCs, to model 5hmC changes during neuronal differentiation and assess their impact on BD risk. Functional annotation and enrichment testing of genes harboring differentiated 5hmC loci were performed with the online tool DAVID. Results Approximately 2 million sites were mapped and quantified, with the majority (68.8%) located in genic regions, with elevated 5hmC levels per site observed for 3' UTRs, exons, and 2-kb shorelines of CpG islands. Paired t-tests of normalized 5hmC counts between iPSC and NSC cell lines revealed global hypo-hydroxymethylation in NSCs and enrichment of differentially hydroxymethylated sites within genes associated with plasma membrane (FDR = 9.1 × 10-12) and axon guidance (FDR = 2.1 × 10-6), among other neuronal processes. The most significant difference was observed for a transcription factor binding site for the KCNK9 gene (p = 8.8 × 10-6), encoding a potassium channel protein involved in neuronal activity and migration. Protein-protein-interaction (PPI) networking showed significant connectivity (p = 3.2 × 10-10) between proteins encoded by genes harboring highly differentiated 5hmC sites, with genes involved in axon guidance and ion transmembrane transport forming distinct sub-clusters. Comparison of NSCs of BD cases and unaffected siblings revealed additional patterns of differentiation in hydroxymethylation levels, including sites in genes with functions related to synapse formation and regulation, such as CUX2 (p = 2.4 × 10-5) and DOK-7 (p = 3.6 × 10-3), as well as an enrichment of genes involved in the extracellular matrix (FDR = 1.0 × 10-8). Discussion Together, these preliminary results lend evidence toward a potential role for 5hmC in both early neuronal differentiation and BD risk, with validation and more comprehensive characterization to be achieved through follow-up study.
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Affiliation(s)
- Ashish Kumar
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Mark Z. Kos
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, San Antonio, TX, United States
| | - Donna Roybal
- Traditions Behavioral Health, Larkspur, CA, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Melanie A. Carless
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
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Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines. Genome Med 2022; 14:134. [PMID: 36443794 PMCID: PMC9706884 DOI: 10.1186/s13073-022-01137-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. METHODS In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14 + CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. RESULTS We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. CONCLUSION Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.
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Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
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Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
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9
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Cheung AC, Juran BD, Schlicht EM, McCauley BM, Atkinson EJ, Moore R, Heimbach JK, Watt KD, Wu TT, LaRusso NF, Gores GJ, Sun Z, Lazaridis KN. DNA methylation profile of liver tissue in end-stage cholestatic liver disease. Epigenomics 2022; 14:481-497. [PMID: 35473391 PMCID: PMC9096606 DOI: 10.2217/epi-2021-0343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aims: In this methylome-wide association study of cholestatic liver diseases (primary sclerosing cholangitis and primary biliary cholangitis), the authors aimed to elucidate changes in methylome and pathway enrichment to identify candidate genes. Patients & methods: Reduced representation bisulfite sequencing was performed on liver tissue from 58 patients with primary sclerosing cholangitis (n = 13), primary biliary cholangitis (n = 20), alcoholic liver disease (n = 21) and live liver donors (n = 4). Pathway enrichment and network analysis were used to explore key genes/pathways. Results: Both cholestatic liver diseases were characterized by global hypomethylation, with pathway enrichment demonstrating distinct genes and pathways associated with the methylome. Conclusions: This novel study demonstrated that differential methylation in cholestatic liver disease was associated with unique pathways, suggesting it may drive disease pathogenesis. While DNA is the permanent code that defines each living being, the epigenome comprises sequences attached to DNA that can change with the environment. This means that abnormal changes to the epigenome may lead to disease and that finding and treating these abnormalities may in turn help treat disease. In this study of liver tissue from individuals with two rare liver diseases, primary sclerosing cholangitis and primary biliary cholangitis, the authors found that the epigenome of these two conditions is distinct, suggesting that the epigenome is linked to the development of these conditions and may be the key to treating them. Novel study in rare cholestatic liver diseases (primary sclerosing cholangitis and primary biliary cholangitis) shows unique methylome changes, which may lead to novel treatment opportunities.
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Affiliation(s)
- Angela C Cheung
- Division of Gastroenterology, The Ottawa Hospital, Ottawa, ON, K1H 8L6, Canada.,Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Brian D Juran
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Erik M Schlicht
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bryan M McCauley
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Raymond Moore
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Julie K Heimbach
- Division of Transplantation Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Kymberly D Watt
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tsung-Teh Wu
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas F LaRusso
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory J Gores
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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10
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Miller CL. The Epigenetics of Psychosis: A Structured Review with Representative Loci. Biomedicines 2022; 10:561. [PMID: 35327363 PMCID: PMC8945330 DOI: 10.3390/biomedicines10030561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
The evidence for an environmental component in chronic psychotic disorders is strong and research on the epigenetic manifestations of these environmental impacts has commenced in earnest. In reviewing this research, the focus is on three genes as models for differential methylation, MCHR1, AKT1 and TDO2, each of which have been investigated for genetic association with psychotic disorders. Environmental factors associated with psychotic disorders, and which interact with these model genes, are explored in depth. The location of transcription factor motifs relative to key methylation sites is evaluated for predicted gene expression results, and for other sites, evidence is presented for methylation directing alternative splicing. Experimental results from key studies show differential methylation: for MCHR1, in psychosis cases versus controls; for AKT1, as a pre-existing methylation pattern influencing brain activation following acute administration of a psychosis-eliciting environmental stimulus; and for TDO2, in a pattern associated with a developmental factor of risk for psychosis, in all cases the predicted expression impact being highly dependent on location. Methylation induced by smoking, a confounding variable, exhibits an intriguing pattern for all three genes. Finally, how differential methylation meshes with Darwinian principles is examined, in particular as it relates to the "flexible stem" theory of evolution.
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11
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Huang W, Fan L, Tang Y, Chi Y, Li J. A Pan-Cancer Analysis of the Oncogenic Role of Integrin Beta4 (ITGB4) in Human Tumors. Int J Gen Med 2021; 14:9629-9645. [PMID: 34924769 PMCID: PMC8674675 DOI: 10.2147/ijgm.s341076] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Background Integrin beta4 (ITGB4) is a transmembrane receptor that plays a key role in tumorigenesis and tumor development. However, there are no pan-cancer analyses of ITGB4. Methods This study demonstrates the first potential oncogenic roles of ITGB4 across 33 tumors based on the dataset of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Results ITGB4 is highly expressed in many cancers, and distinct correlations exist between ITGB4 expression and the prognosis of tumor patients. We also found that the methylation and genetic alteration level of ITGB4 was associated with some cancer prognosis. Furthermore, we found a reduced phosphorylation of ITGB4 at S1457 in several tumors, such as breast and ovarian cancers. Finally, ITGB4 expression was correlated with cancer-associated fibroblasts in liver hepatocellular carcinoma and prostate adenocarcinoma, and the infiltration level of NK cells and neutrophils was observed in other cancers, such as breast invasive carcinoma and lung adenocarcinoma. Moreover, RNA metabolism and protein processing-associated functions are involved in the functional mechanism of ITGB4. Conclusion Our first pan-cancer study may offer a relatively comprehensive understanding of the oncogenic roles of ITGB4 across different tumors.
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Affiliation(s)
- Wenjie Huang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Li Fan
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Yongmei Tang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Yinxiu Chi
- School of Basic Medicine, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Jingjing Li
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
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12
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Dratwa M, Wysoczańska B, Łacina P, Kubik T, Bogunia-Kubik K. TERT-Regulation and Roles in Cancer Formation. Front Immunol 2020; 11:589929. [PMID: 33329574 PMCID: PMC7717964 DOI: 10.3389/fimmu.2020.589929] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) is a catalytic subunit of telomerase. Telomerase complex plays a key role in cancer formation by telomere dependent or independent mechanisms. Telomere maintenance mechanisms include complex TERT changes such as gene amplifications, TERT structural variants, TERT promoter germline and somatic mutations, TERT epigenetic changes, and alternative lengthening of telomere. All of them are cancer specific at tissue histotype and at single cell level. TERT expression is regulated in tumors via multiple genetic and epigenetic alterations which affect telomerase activity. Telomerase activity via TERT expression has an impact on telomere length and can be a useful marker in diagnosis and prognosis of various cancers and a new therapy approach. In this review we want to highlight the main roles of TERT in different mechanisms of cancer development and regulation.
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Affiliation(s)
- Marta Dratwa
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Barbara Wysoczańska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Tomasz Kubik
- Department of Computer Engineering, Faculty of Electronics, Wrocław University of Science and Technology, Wroclaw, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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13
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Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Genome Med 2020; 12:81. [PMID: 32977850 PMCID: PMC7519528 DOI: 10.1186/s13073-020-00779-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. RESULTS We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. CONCLUSION Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.
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Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Lourdes Ortiz-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Elena López-Isac
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Alfredo Guillén-Del-Castillo
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
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14
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Rider CF, Carlsten C. Air pollution and DNA methylation: effects of exposure in humans. Clin Epigenetics 2019; 11:131. [PMID: 31481107 PMCID: PMC6724236 DOI: 10.1186/s13148-019-0713-2] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Air pollution exposure is estimated to contribute to approximately seven million early deaths every year worldwide and more than 3% of disability-adjusted life years lost. Air pollution has numerous harmful effects on health and contributes to the development and morbidity of cardiovascular disease, metabolic disorders, and a number of lung pathologies, including asthma and chronic obstructive pulmonary disease (COPD). Emerging data indicate that air pollution exposure modulates the epigenetic mark, DNA methylation (DNAm), and that these changes might in turn influence inflammation, disease development, and exacerbation risk. Several traffic-related air pollution (TRAP) components, including particulate matter (PM), black carbon (BC), ozone (O3), nitrogen oxides (NOx), and polyaromatic hydrocarbons (PAHs), have been associated with changes in DNAm; typically lowering DNAm after exposure. Effects of air pollution on DNAm have been observed across the human lifespan, but it is not yet clear whether early life developmental sensitivity or the accumulation of exposures have the most significant effects on health. Air pollution exposure-associated DNAm patterns are often correlated with long-term negative respiratory health outcomes, including the development of lung diseases, a focus in this review. Recently, interventions such as exercise and B vitamins have been proposed to reduce the impact of air pollution on DNAm and health. Ultimately, improved knowledge of how exposure-induced change in DNAm impacts health, both acutely and chronically, may enable preventative and remedial strategies to reduce morbidity in polluted environments.
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Affiliation(s)
- Christopher F Rider
- Respiratory Medicine, Faculty of Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease (COERD), University of British Columbia, Vancouver, British Columbia, Canada. .,Diamond Health Care Centre 7252, 2775 Laurel Street, Vancouver, BC, V5Z 1 M9, Canada.
| | - Chris Carlsten
- Respiratory Medicine, Faculty of Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease (COERD), University of British Columbia, Vancouver, British Columbia, Canada.,Diamond Health Care Centre 7252, 2775 Laurel Street, Vancouver, BC, V5Z 1 M9, Canada.,Institute for Heart and Lung Health, University of British Columbia, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Abstract
Increasing numbers of studies implicate abnormal DNA methylation in cancer and many non-malignant diseases. This is consistent with numerous findings about differentiation-associated changes in DNA methylation at promoters, enhancers, gene bodies, and sites that control higher-order chromatin structure. Abnormal increases or decreases in DNA methylation contribute to or are markers for cancer formation and tumour progression. Aberrant DNA methylation is also associated with neurological diseases, immunological diseases, atherosclerosis, and osteoporosis. In this review, I discuss DNA hypermethylation in disease and its interrelationships with normal development as well as proposed mechanisms for the origin of and pathogenic consequences of disease-associated hypermethylation. Disease-linked DNA hypermethylation can help drive oncogenesis partly by its effects on cancer stem cells and by the CpG island methylator phenotype (CIMP); atherosclerosis by disease-related cell transdifferentiation; autoimmune and neurological diseases through abnormal perturbations of cell memory; and diverse age-associated diseases by age-related accumulation of epigenetic alterations.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center and Tulane Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA
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