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da Silva Santos R, Pascoalino Pinheiro D, Gustavo Hirth C, Barbosa Bezerra MJ, Joyce de Lima Silva-Fernandes I, Andréa da Silva Oliveira F, Viana de Holanda Barros M, Silveira Ramos E, A. Moura A, Filho ODMM, Pessoa C, Miranda Furtado CL. Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection. Epigenetics 2024; 19:2305081. [PMID: 38245880 PMCID: PMC10802203 DOI: 10.1080/15592294.2024.2305081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Penile squamous cell carcinoma (SCC) is a rare and aggressive tumour mainly related to lifestyle behaviour and human papillomavirus (HPV) infection. Environmentally induced loss of imprinting (LOI) at the H19 differentially methylated region (H19DMR) is associated with many cancers in the early events of tumorigenesis and may be involved in the pathogenesis of penile SCC. We sought to evaluate the DNA methylation pattern at H19DMR and its association with HPV infection in men with penile SCC by bisulfite sequencing (bis-seq). We observed an average methylation of 32.2% ± 11.6% at the H19DMR of penile SCC and did not observe an association between the p16INK4a+ (p = 0.59) and high-risk HPV+ (p = 0.338) markers with methylation level. The average methylation did not change according to HPV positive for p16INK4a+ or hrHPV+ (35.4% ± 10%) and negative for both markers (32.4% ± 10.1%) groups. As the region analysed has a binding site for the CTCF protein, the hypomethylation at the surrounding CpG sites might alter its insulator function. In addition, there was a positive correlation between intense polymorphonuclear cell infiltration and hypomethylation at H19DMR (p = 0.035). Here, we report that hypomethylation at H19DMR in penile SCC might contribute to tumour progression and aggressiveness regardless of HPV infection.
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Affiliation(s)
- Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | | | | | | | - Maisa Viana de Holanda Barros
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Arlindo A. Moura
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Animal Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Odorico de Moraes Manoel Filho
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil
- Graduate Program in Medical Sciences, Universidade de Fortaleza, Fortaleza, Ceará, Brazil
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2
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Dhanasiri AK, Siciliani D, Kortner TM, Krogdahl Å. Epigenetic changes in pyloric caeca of Atlantic salmon fed diets containing increasing levels of lipids and choline. Epigenetics 2024; 19:2305079. [PMID: 38281164 PMCID: PMC10824149 DOI: 10.1080/15592294.2024.2305079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
An earlier study of ours investigating the effect of dietary lipid levels on the choline requirement of Atlantic salmon showed increasing severity of intestinal steatosis with increasing lipid levels. As choline is involved in epigenetic regulation by being the key methyl donor, pyloric caeca samples from the study were analysed for epigenetic effects of dietary lipid and choline levels. The diets varied in lipid levels between 16% and 28%, and choline levels between 1.9 and 2.3 g/kg. The diets were fed for 8 weeks to Atlantic salmon of 25 g of initial weight. Using reduced representation bisulfite sequencing (RRBS), this study revealed that increasing dietary lipid levels induced methylation differences in genes involved in membrane transport and signalling pathways, and in microRNAs important for the regulation of lipid homoeostasis. Increasing choline levels also affected genes involved in fatty acid biosynthesis and transport, lipolysis, and lipogenesis, as well as important immune genes. Our observations confirmed that choline is involved in epigenetic regulation in Atlantic salmon, as has been reported for higher vertebrates. This study showed the need for the inclusion of biomarkers of epigenetic processes in studies that must be conducted to define optimal choline levels in diets for Atlantic salmon.
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Affiliation(s)
- Anusha K.S. Dhanasiri
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Daphne Siciliani
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Trond M. Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
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3
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Opsasnick LA, Zhao W, Schmitz LL, Ratliff SM, Faul JD, Zhou X, Needham BL, Smith JA. Epigenome-wide association study of long-term psychosocial stress in older adults. Epigenetics 2024; 19:2323907. [PMID: 38431869 PMCID: PMC10913704 DOI: 10.1080/15592294.2024.2323907] [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: 11/13/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Long-term psychosocial stress is strongly associated with negative physical and mental health outcomes, as well as adverse health behaviours; however, little is known about the role that stress plays on the epigenome. One proposed mechanism by which stress affects DNA methylation is through health behaviours. We conducted an epigenome-wide association study (EWAS) of cumulative psychosocial stress (n = 2,689) from the Health and Retirement Study (mean age = 70.4 years), assessing DNA methylation (Illumina Infinium HumanMethylationEPIC Beadchip) at 789,656 CpG sites. For identified CpG sites, we conducted a formal mediation analysis to examine whether smoking, alcohol use, physical activity, and body mass index (BMI) mediate the relationship between stress and DNA methylation. Nine CpG sites were associated with psychosocial stress (all p < 9E-07; FDR q < 0.10). Additionally, health behaviours and/or BMI mediated 9.4% to 21.8% of the relationship between stress and methylation at eight of the nine CpGs. Several of the identified CpGs were in or near genes associated with cardiometabolic traits, psychosocial disorders, inflammation, and smoking. These findings support our hypothesis that psychosocial stress is associated with DNA methylation across the epigenome. Furthermore, specific health behaviours mediate only a modest percentage of this relationship, providing evidence that other mechanisms may link stress and DNA methylation.
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Affiliation(s)
- Lauren A. Opsasnick
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lauren L. Schmitz
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Belinda L. Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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4
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Zhao Y, Zhao L, Jin H, Xie Y, Chen L, Zhang W, Dong L, Zhang L, Huang Y, Wan K, Yang Q, Wang S. Plasma methylated GNB4 and Riplet as a novel dual-marker panel for the detection of hepatocellular carcinoma. Epigenetics 2024; 19:2299044. [PMID: 38154055 PMCID: PMC10761049 DOI: 10.1080/15592294.2023.2299044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. We aimed to develop a novel marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC. The differentially methylated CpG sites (DMCs) specific for HCC blood diagnosis were selected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, then validated by the whole genome bisulphite sequencing (WGBS) of 12 paired HCC and paracancerous tissues. The clinical performance of the panel was evaluated using tissue samples [32 HCC, chronic liver disease (CLD), and healthy individuals] and plasma cohorts (173 HCC, 199 CLD, and 98 healthy individuals). The combination of G protein subunit beta 4 (GNB4) and Riplet had the optimal area under the curve (AUC) in seven candidates through TCGA, GEO, and WGBS analyses. In tissue validation, the GNB4 and Riplet showed an AUC of 100% with a sensitivity and specificity of 100% for detecting any-stage HCC. In plasma, it demonstrated a high sensitivity of 84.39% at 91.92% specificity, with an AUC of 92.51% for detecting any-stage HCC. The dual-marker panel had a higher sensitivity of 78.26% for stage I HCC than alpha-fetoprotein (AFP) of 47.83%, and a high sensitivity of 70.27% for detecting a single tumour (size ≤3 cm). In conclusion, we developed a novel dual-marker panel that demonstrates high accuracy in detecting HCC, surpassing the performance of AFP testing.
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Affiliation(s)
- Yanteng Zhao
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lei Zhao
- Plastic maxillofacial surgery, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi, China
| | - Huifang Jin
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Xie
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liyinghui Chen
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lanlan Dong
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Lianglu Zhang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Yue Huang
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Kangkang Wan
- Research and development department, Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei, China
| | - Qiankun Yang
- Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shaochi Wang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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Habeshian TS, Cannavale KL, Slezak JM, Shu YH, Chien GW, Chen X, Shi F, Siegmund KD, Van Den Eeden SK, Huang J, Chao CR. DNA methylation markers for risk of metastasis in a cohort of men with localized prostate cancer. Epigenetics 2024; 19:2308920. [PMID: 38525786 DOI: 10.1080/15592294.2024.2308920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Accurately identifying life-threatening prostate cancer (PCa) at time of diagnosis remains an unsolved problem. We evaluated whether DNA methylation status of selected candidate genes can predict the risk of metastasis beyond clinical risk factors in men with untreated PCa. A nested case-control study was conducted among men diagnosed with localized PCa at Kaiser Permanente California between 01/01/1997-12/31/2006 who did not receive curative treatments. Cases were those who developed metastasis within 10 years from diagnosis. Controls were selected using density sampling. Ninety-eight candidate genes were selected from functional categories of cell cycle control, metastasis/tumour suppressors, cell signalling, cell adhesion/motility/invasion, angiogenesis, and immune function, and 41 from pluripotency genes. Cancer DNA from diagnostic biopsy blocks were extracted and analysed. Associations of methylation status were assessed using CpG site level and principal components-based analysis in conditional logistic regressions. In 215 cases and 404 controls, 27 candidate genes were found to be statistically significant in at least one of the two analytical approaches. The agreement between the methods was 25.9% (7 candidate genes, including 2 pluripotency markers). The DNA methylation status of several candidate genes was significantly associated with risk of metastasis in untreated localized PCa patients. These findings may inform future risk prediction models for PCa metastasis beyond clinical characteristics.
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Affiliation(s)
- Talar S Habeshian
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kimberly L Cannavale
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Jeff M Slezak
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Yu-Hsiang Shu
- Biostatistics and Innovations, Biostatistics and Programming, Clinical Affairs, Inari Medical, CA, USA
| | - Gary W Chien
- Department of Urology, Los Angeles Medical Center, Kaiser Permanente Southern California, Los Angeles, CA, USA
| | - XuFeng Chen
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Feng Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kimberly D Siegmund
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, USA
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Chen K, Ou B, Huang Q, Deng D, Xiang Y, Hu F. LncRNA NEAT1 aggravates human microvascular endothelial cell injury by inhibiting the Apelin/Nrf2/HO-1 signalling pathway in type 2 diabetes mellitus with obstructive sleep apnoea. Epigenetics 2024; 19:2293409. [PMID: 38232183 PMCID: PMC10795783 DOI: 10.1080/15592294.2023.2293409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate the progression of type 2 diabetes mellitus complicated with obstructive sleep apnoea (T2DM-OSA). However, the role of the lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in T2DM-OSA remains unknown. This study aimed to reveal the function of NEAT1 in T2DM-OSA and the underlying mechanism. KKAy mice were exposed to intermittent hypoxia (IH) or intermittent normoxia to generate a T2DM-OSA mouse model. HMEC-1 cells were treated with high glucose (HG) and IH to construct a T2DM-OSA cell model. RNA expression was detected by qRT-PCR. The protein expression of Apelin, NF-E2-related factor 2 (Nrf2), haem oxygenase-1 (HO-1), and up-frameshift suppressor 1 (UPF1) was assessed using western blot. Cell injury was evaluated using flow cytometry, enzyme-linked immunosorbent assay, and oxidative stress kit assays. RIP, RNA pull-down, and actinomycin D assays were performed to determine the associations between NEAT1, UPF1, and Apelin. NEAT1 expression was upregulated in the aortic vascular tissues of mice with T2DM exposed to IH and HMEC-1 cells stimulated with HG and IH, whereas Apelin expression was downregulated. The absence of NEAT1 protected HMEC-1 cells from HG- and IH-induced damage. Furthermore, NEAT1 destabilized Apelin mRNA by recruiting UPF1. Apelin overexpression decreased HG- and IH-induced injury to HMEC-1 cells by activating the Nrf2/HO-1 pathway. Moreover, NEAT1 knockdown reduced HG- and IH-induced injury to HMEC-1 cells through Apelin. NEAT1 silencing reduced HMEC-1 cell injury through the Apelin/Nrf2/HO-1 signalling pathway in T2DM-OSA.Abbreviations: LncRNAs, long non-coding RNAs; T2DM, type 2 diabetes mellitus; OSA, obstructive sleep apnoea; NEAT1, nuclear paraspeckle assembly transcript 1; IH, intermittent hypoxia; HMEC-1, human microvascular endothelial cells; HG, high glucose; Nrf2, NF-E2-related factor 2; UPF1, up-frameshift suppressor 1; HO-1, haem oxygenase-1; qRT-PCR, quantitative real-time polymerase chain reaction; ELISA, enzyme-linked immunosorbent assay; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; TNF-α, tumour necrosis factor-α; CCK-8, Cell Counting Kit-8; IL-1β, interleukin-1β; ROS, reactive oxygen species; MDA, malondialdehyde; SOD, superoxide dismutase; RIP, RNA immunoprecipitation; SD, standard deviations; GSH, glutathione; AIS, acute ischaemic stroke; HMGB1, high mobility group box-1 protein; TLR4, toll-like receptor 4.
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Affiliation(s)
- Kai Chen
- Department of Cardiovascular Medicine Six Wards (Cardiovascular and Metabolic Diseases), Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Baiqing Ou
- Department of Cardiovascular Medicine Six Wards (Cardiovascular and Metabolic Diseases), Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Quan Huang
- Department of Cardiovascular Medicine Six Wards (Cardiovascular and Metabolic Diseases), Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Daqing Deng
- Department of Cardiovascular Medicine Six Wards (Cardiovascular and Metabolic Diseases), Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Yi Xiang
- Department of Cardiovascular Medicine Six Wards (Cardiovascular and Metabolic Diseases), Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Fang Hu
- Comprehensive internal medicine of Hunan Provincial People’s Hospital, Changsha, Hunan, China
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Onuzulu CD, Lee S, Basu S, Comte J, Hai Y, Hizon N, Chadha S, Fauni MS, Halayko AJ, Pascoe CD, Jones MJ. Novel DNA methylation changes in mouse lungs associated with chronic smoking. Epigenetics 2024; 19:2322386. [PMID: 38436597 PMCID: PMC10913724 DOI: 10.1080/15592294.2024.2322386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Smoking is a potent cause of asthma exacerbations, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most studies of smoking and DNAm have been done using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is lacking. Here, we identified DNAm patterns in the lungs that are altered by smoking. We used an established mouse model to measure the effects of chronic smoke exposure first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model recapitulates previous DNAm patterns observed in smoking humans, specifically measuring DNAm at a candidate gene responsive to cigarette smoke, Cyp1a1. Finally, we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are associated with nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, to fully understand mechanisms underlying CS-mediated health outcomes.
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Affiliation(s)
- Chinonye Doris Onuzulu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Samantha Lee
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sujata Basu
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeannette Comte
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Yan Hai
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nikho Hizon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shivam Chadha
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maria Shenna Fauni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew J. Halayko
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Christopher D. Pascoe
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Meaghan J. Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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Saito T, Espe M, Vikeså V, Bock C, Thomsen TH, Adam AC, Fernandes JMO, Skjaerven KH. One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic salmon. Epigenetics 2024; 19:2318517. [PMID: 38404006 PMCID: PMC10900267 DOI: 10.1080/15592294.2024.2318517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulphite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.
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Affiliation(s)
- Takaya Saito
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Marit Espe
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Vibeke Vikeså
- Skretting AI, Aquaculture Innovation, Stavanger, Norway
| | - Christoph Bock
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Anne-Catrin Adam
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | | | - Kaja H Skjaerven
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
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Miranda Furtado CL, Hansen M, Kogure GS, Ribeiro VB, Taylor N, Racy Soares M, Ferriani RA, Aston KI, Jenkins T, dos Reis RM. Resistance and aerobic training increases genome-wide DNA methylation in women with polycystic ovary syndrome. Epigenetics 2024; 19:2305082. [PMID: 38245873 PMCID: PMC10802204 DOI: 10.1080/15592294.2024.2305082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Physical activity is a first-line treatment for polycystic ovary syndrome (PCOS). Resistance or aerobic exercise improves metabolic complications, reproductive outcomes, and quality of life in PCOS. DNA methylation reprogramming during exercise may be the major modifier behind these changes. We sought to evaluate genome-wide DNA methylation changes after supervised resistance and aerobic exercise in women with PCOS. Exercises were performed in 56 women with PCOS (resistance, n = 30; aerobic, n = 26), for 16 weeks (wks), three times per week, in 50-minute to one-hour sessions. Anthropometric indices and hormonal and metabolic parameters were measured before and after training. Genome-wide leukocyte DNA methylation was analysed by Infinium Human MethylationEPIC 850K BeadChip microarrays (Illumina). Both resistance and aerobic exercise improved anthropometric indices, metabolic dysfunction, and hyperandrogenism in PCOS after the training programme, but no differences were observed between the two exercises. Resistance and aerobic exercise increased genome-wide DNA methylation, although resistance changed every category in the CpG island context (islands, shores, shelve, and open sea), whereas aerobic exercise altered CpG shores and the open sea. Using a stringent FDR (>40), 6 significantly differentially methylated regions (DMRs) were observed in the resistance exercise cohort and 14 DRMs in the aerobic cohort, all of which were hypermethylated. The increase in genome-wide DNA methylation may be related to the metabolic and hormonal changes observed in PCOS after resistance and aerobic exercise. Since the mammalian genome is hypermethylated globally to prevent genomic instability and ageing, resistance and aerobic exercise may promote health and longevity through environmentally induced epigenetic changes.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza, Fortaleza, Ceará, Brazil
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Megan Hansen
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Gislaine Satyko Kogure
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Victor Barbosa Ribeiro
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Nathanael Taylor
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Murilo Racy Soares
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Kenneth Ivan Aston
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rosana Maria dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
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11
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Liu Y, Koo JS, Zhang H. Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes. Epigenetics 2024; 19:2294515. [PMID: 38118075 PMCID: PMC10761033 DOI: 10.1080/15592294.2023.2294515] [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: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development.Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR.
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Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Ji Sun Koo
- Department of Biology, Boston University, Boston, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
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12
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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [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: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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13
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Chen L, Cheng Y, Zhang G, Zhou Y, Zhang Z, Chen Q, Feng Y. WGBS of embryonic gonads revealed that long non-coding RNAs in the MHM region might be involved in cell autonomous sex identity and female gonadal development in chickens. Epigenetics 2024; 19:2283657. [PMID: 38037805 PMCID: PMC10761181 DOI: 10.1080/15592294.2023.2283657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/01/2023] [Indexed: 12/02/2023] Open
Abstract
DNA methylation plays a key role in sex determination and differentiation in vertebrates. However, there are few studies on DNA methylation involved in chicken gonad development, and most focused on male hypermethylated regions (MHM). It is unclear whether there are specific differentially methylated regions (DMRs) in chicken embryonic gonads regulating sex determination and differentiation. Here, the DNA methylation maps showed that the difference of DNA methylation level between sexes was much higher at embryonic day 10 (E10) than that at embryonic day 6 (E6), and the significant differentially methylated regions at both stages were mainly distributed on the Z chromosome, including MHM1 and MHM2. The results of bisulphite sequencing PCR (BSP) and qRT-PCR showed hypomethylation of female MHM and upregulation of long non-coding RNAs (lncRNAs) whose promoter in the MHM region was consistent with the sequencing results, and similar results were in brain and muscle. In female sex-reversed gonads, the methylation pattern of MHM remained unchanged, and the expression levels of the three candidate lncRNAs were significantly decreased compared with those in females, but were significantly increased compared to males. The fluorescence in situ hybridization (FISH) results also showed that these lncRNAs were highly expressed in female embryonic gonads. The results of methyltransferase inhibitor and dual-luciferase reporter assay suggest that lncRNA expression may be regulated by DNA methylation within their promoters. Therefore, we speculated that MHM may be involved in cell-autonomous sex identity in chickens, and that lncRNAs regulated by MHM may be involved in female sexual differentiation.
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Affiliation(s)
- Ligen Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yu Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Guixin Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zhen Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qianhong Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
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14
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Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
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Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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15
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Reynolds SR, Salas LA, Chen JQ, Christensen BC. Detailed immune profiling in pediatric Crohn's disease using methylation cytometry. Epigenetics 2024; 19:2289786. [PMID: 38090774 PMCID: PMC10761011 DOI: 10.1080/15592294.2023.2289786] [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: 06/21/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation has been extensively utilized to study epigenetic patterns across many diseases as well as to deconvolve blood cell type proportions. This study builds upon previous studies examining methylation patterns in paediatric patients with varying stages of Crohn's disease to extend the immune profiling of these patients using a novel deconvolution approach. Compared with control subjects, we observed significantly decreased levels of CD4 memory and naive, CD8 naive, and natural killer cells and elevated neutrophil levels in Crohn's disease. In addition, Crohn's patients had a significantly elevated neutrophil-to-lymphocyte ratio. Using an epigenome-wide association approach and adjusting for potential confounders, including cell type, we observed 397 differentially methylated CpG (DMC) sites associated with Crohn's disease. The top genetic pathway associated with the DMCs was the regulation of arginine metabolic processes which are involved in the regulation of T cells.
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Affiliation(s)
- Samuel R. Reynolds
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, NH, Lebanon, USA
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, NH, Lebanon, USA
| | - Ji-Qing Chen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, NH, Lebanon, USA
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, NH, Lebanon, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, NH, Lebanon, USA
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16
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Sapozhnikov DM, Szyf M. Genetic confounds of transgenerational epigenetic inheritance in mice. Epigenetics 2024; 19:2318519. [PMID: 38369744 PMCID: PMC10878023 DOI: 10.1080/15592294.2024.2318519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
Transgenerational epigenetic inheritance in mammals remains a controversial phenomenon. A recent study by Takahashi et al. provides evidence for this mode of inheritance in mice by using a CRISPR/Cas9-based epigenetic editing technique to modify DNA methylation levels at specific promoters and then demonstrating the inheritance of the gain in methylation in offspring. In this technical commentary, we argue that the method used in the original study inherently amplifies the likelihood of genetic changes that thereafter lead to the heritability of epigenetic changes. We provide evidence that genetic changes from multiple sources do indeed occur in these experiments and explore several avenues by which these changes could be causal to the apparent inheritance of epigenetic changes. We conclude a genetic basis of inheritance cannot be ruled out and thus transgenerational epigenetic inheritance has not been adequately established by the original study.
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Affiliation(s)
- Daniel M. Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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17
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van Vliet MM, Schoenmakers S, Gribnau J, Steegers-Theunissen RP. The one-carbon metabolism as an underlying pathway for placental DNA methylation - a systematic review. Epigenetics 2024; 19:2318516. [PMID: 38484284 PMCID: PMC10950272 DOI: 10.1080/15592294.2024.2318516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
Epigenetic modifications, including DNA methylation, are proposed mechanisms explaining the impact of parental exposures to foetal development and lifelong health. Micronutrients including folate, choline, and vitamin B12 provide methyl groups for the one-carbon metabolism and subsequent DNA methylation processes. Placental DNA methylation changes in response to one-carbon moieties hold potential targets to improve obstetrical care. We conducted a systematic review on the associations between one-carbon metabolism and human placental DNA methylation. We included 22 studies. Findings from clinical studies with minimal ErasmusAGE quality score 5/10 (n = 15) and in vitro studies (n = 3) are summarized for different one-carbon moieties. Next, results are discussed per study approach: (1) global DNA methylation (n = 9), (2) genome-wide analyses (n = 4), and (3) gene specific (n = 14). Generally, one-carbon moieties were not associated with global methylation, although conflicting outcomes were reported specifically for choline. Using genome-wide approaches, few differentially methylated sites associated with S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), or dietary patterns. Most studies taking a gene-specific approach indicated site-specific relationships depending on studied moiety and genomic region, specifically in genes involved in growth and development including LEP, NR3C1, CRH, and PlGF; however, overlap between studies was low. Therefore, we recommend to further investigate the impact of an optimized one-carbon metabolism on DNA methylation and lifelong health.
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Affiliation(s)
- Marjolein M van Vliet
- Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
- Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Sam Schoenmakers
- Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
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Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
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Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
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El Sharkawy M, Felix JF, Grote V, Voortman T, Jaddoe VWV, Koletzko B, Küpers LK. Animal and plant protein intake during infancy and childhood DNA methylation: a meta-analysis in the NutriPROGRAM consortium. Epigenetics 2024; 19:2299045. [PMID: 38198623 PMCID: PMC10793674 DOI: 10.1080/15592294.2023.2299045] [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: 03/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Higher early-life animal protein intake is associated with a higher childhood obesity risk compared to plant protein intake. Differential DNA methylation may represent an underlying mechanism. METHODS We analysed associations of infant animal and plant protein intakes with DNA methylation in early (2-6 years, N = 579) and late (7̄-12 years, N = 604) childhood in two studies. Study-specific robust linear regression models adjusted for relevant confounders were run, and then meta-analysed using a fixed-effects model. We also performed sex-stratified meta-analyses. Follow-up analyses included pathway analysis and eQTM look-up. RESULTS Infant animal protein intake was not associated with DNA methylation in early childhood, but was associated with late-childhood DNA methylation at cg21300373 (P = 4.27 × 10¯8, MARCHF1) and cg10633363 (P = 1.09 × 10¯7, HOXB9) after FDR correction. Infant plant protein intake was associated with early-childhood DNA methylation at cg25973293 (P = 2.26 × 10-7, C1orf159) and cg15407373 (P = 2.13 × 10-7, MBP) after FDR correction. There was no overlap between the findings from the animal and plant protein analyses. We did not find enriched functional pathways at either time point using CpGs associated with animal and plant protein. These CpGs were not previously associated with childhood gene expression. Sex-stratified meta-analyses showed sex-specific DNA methylation associations for both animal and plant protein intake. CONCLUSION Infant animal protein intake was associated with DNA methylation at two CpGs in late childhood. Infant plant protein intake was associated with DNA methylation in early childhood at two CpGs. A potential mediating role of DNA methylation at these CpGs between infant protein intake and health outcomes requires further investigation.
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Affiliation(s)
- Mohammed El Sharkawy
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
- Munich Medical Research School, Faculty of Medicine, LMU - Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Leanne K. Küpers
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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20
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Morgan D, DeMeo DL, Glass K. Using methylation data to improve transcription factor binding prediction. Epigenetics 2024; 19:2309826. [PMID: 38300850 PMCID: PMC10841018 DOI: 10.1080/15592294.2024.2309826] [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: 08/07/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Modelling the regulatory mechanisms that determine cell fate, response to external perturbation, and disease state depends on measuring many factors, a task made more difficult by the plasticity of the epigenome. Scanning the genome for the sequence patterns defined by Position Weight Matrices (PWM) can be used to estimate transcription factor (TF) binding locations. However, this approach does not incorporate information regarding the epigenetic context necessary for TF binding. CpG methylation is an epigenetic mark influenced by environmental factors that is commonly assayed in human cohort studies. We developed a framework to score inferred TF binding locations using methylation data. We intersected motif locations identified using PWMs with methylation information captured in both whole-genome bisulfite sequencing and Illumina EPIC array data for six cell lines, scored motif locations based on these data, and compared with experimental data characterizing TF binding (ChIP-seq). We found that for most TFs, binding prediction improves using methylation-based scoring compared to standard PWM-scores. We also illustrate that our approach can be generalized to infer TF binding when methylation information is only proximally available, i.e. measured for nearby CpGs that do not directly overlap with a motif location. Overall, our approach provides a framework for inferring context-specific TF binding using methylation data. Importantly, the availability of DNA methylation data in existing patient populations provides an opportunity to use our approach to understand the impact of methylation on gene regulatory processes in the context of human disease.
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Affiliation(s)
- Daniel Morgan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
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21
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Ren J, Chen X, Li J, Zan Y, Wang S, Tan Y, Ding Y. TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy. Epigenetics 2024; 19:2323751. [PMID: 38431880 PMCID: PMC10913696 DOI: 10.1080/15592294.2024.2323751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Methylation modifications play pertinent roles in regulating gene expression and various biological processes. The silencing of the demethylase enzyme TET1 can affect the expressions of key oncogenes or tumour suppressor genes, thus contributing to tumour formation. Nonetheless, how TET1 affects the progression of cervical cancer is yet to be elucidated. In this study, we found that the expression of TET1 was significantly downregulated in cervical cancer tissues. Functionally, TET1 knockdown in cervical cancer cells can promote cell proliferation, migration, invasion, cervical xenograft tumour formation and EMT. On the contrary, its overexpression can reverse the aforementioned processes. Moreover, the autophagy level of cervical cancer cells can be enhanced after TET1 knockdown. Mechanistically, methylated DNA immunoprecipitation (MeDIP)-sequencing and MeDIP quantitative real-time PCR revealed that TET1 mediates the methylation of autophagy promoter regions. These findings suggest that TET1 affects the autophagy of cervical cancer cells by altering the methylation levels of NKRF or HIST1H2AK, but the specific mechanism needs to be investigated further.
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Affiliation(s)
- Ji Ren
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiuying Chen
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Tongren city people’s hospital, Tongren, Guizhou, China
| | - Jing Li
- Gynecology, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxin Zan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shan Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yujie Tan
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Hubei University of Medicine, Shiyan, Hubei, China
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22
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Zheng C, Ma L, Song F, Tian L, Cai W, Li H, Duan Y. Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene. Epigenetics 2024; 19:2333665. [PMID: 38525798 DOI: 10.1080/15592294.2024.2333665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.
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Affiliation(s)
- Caiqing Zheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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23
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Quan J, Song S, Xing L, Liu X, Yue M. DNA methylation variation and growth in the clonal Duchesnea indica is regulated by both past and present lead environments. Epigenetics 2024; 19:2305078. [PMID: 38245907 PMCID: PMC10802196 DOI: 10.1080/15592294.2024.2305078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Studies suggest that clonal plants' ability to select habitats and forage in a heterogeneous environment is influenced by their past environment, with stress legacy potentially playing a crucial role. In this study, we examined parental ramets of Duchesnea indica Focke that were subject to either a control or lead-contaminated environment (past environment), and their newborn offspring were then transplanted into control, homogeneous lead or heterogeneous lead environment (present environment). We analysed how past and present environments affect plant growth and DNA methylation in offspring. The result shown that the DNA methylation loci composition of offspring was affected by the interaction of parental environment and offspring environment, and DNA methylation levels were higher in heterogeneous environments. Moreover, our findings indicate that offspring would thrive in the heterogeneous lead environment if they did not experience lead pollution in the past, their progeny will avoid lead toxicity by reducing underground biomass allocation. However, when the parents experienced lead stress environment, their biomass allocation strategies disappeared, and they prefer to grow in favourable patches to avoid lead-contaminated patches. We concluded that the integration of historical parental exposure to lead-contaminated and current information about their offspring's environment are impacting plant phenotypes. It is possible that the stress legacy from the parents has been transmitted to their offspring ramets, and the stress legacy is at least partly based on heritable epigenetic variation. The phenotypic variation regulated by the stress legacy affects the growth performance, biomass allocation strategy, and even the behaviour of D. indica.
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Affiliation(s)
- Jiaxin Quan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Shanshan Song
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Linya Xing
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Xiao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an, China
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24
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Michels KB, Binder AM. Impact of folic acid supplementation on the epigenetic profile in healthy unfortified individuals - a randomized intervention trial. Epigenetics 2024; 19:2293410. [PMID: 38096372 PMCID: PMC10730197 DOI: 10.1080/15592294.2023.2293410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
Folate is an essential mediator in one-carbon metabolism, which provides methyl groups for DNA synthesis and methylation. The availability of active methyl groups can be influenced by the uptake of folic acid. We conducted a randomized intervention trial to test the influence of folic acid supplementation on DNA methylation in an unfortified population in Germany. A total of 16 healthy male volunteers (age range 23-61 y) were randomized to receive either 400 μg (n = 9) or 800 μg (n = 7) folic acid supplements daily for 8 weeks. Infinium Human Methylation 450K BeadChip Microarrays were used to assay site-specific DNA methylation across the genome. Microarray analyses were conducted on PBL DNA. We estimated several epigenetic clocks and mean DNA methylation across all autosomal probes on the array. AgeAccel was estimated as the residual variation in each metric. In virtually all participants, both serum and red blood cell (RBC) folate increased successively throughout the trial period. Participants with a larger increase in RBC folate had a larger increase in DNAmAge AgeAccel (Spearman Rho: 0.56, p-value = 0.03). No notable changes in the methylome resulting from the folic acid supplementation emerged. In this population with adequate folate levels derived from diet, an increase in RBC folate had a modest impact on the epigenetic clock predicting chronologic age.
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Affiliation(s)
- Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Alexandra M. Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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25
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Jeremias G, Muñiz-González AB, Mendes Gonçalves FJ, Martínez-Guitarte JL, Asselman J, Luísa Pereira J. History of exposure to copper influences transgenerational gene expression responses in Daphnia magna. Epigenetics 2024; 19:2296275. [PMID: 38154067 PMCID: PMC10761054 DOI: 10.1080/15592294.2023.2296275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
The establishment of transgenerational effects following chemical exposure is a powerful phenomenon, capable of modulating ecosystem health beyond exposure periods. This study assessed the transgenerational effects occurring due to copper exposure in the invertebrate D. magna at the transcriptional level, while evaluating the role of exposure history on such responses. Thus, daphnids acclimated for several generations in a copper vs. clean medium were then exposed for one generation (F0) to this metal, and monitored for the following non-exposed generations (F1, F2 and F3). Organisms differing in exposure histories showed remarkably different transcriptional profiles at the F0, with naïve organisms being more profoundly affected. These trends were confirmed for F3 treatments, which presented different transcriptional patterns for genes involved in detoxification, oxidative stress, DNA damage repair, circadian clock functioning and epigenetic regulation. Furthermore, regardless of exposure history, a great number of histone modifier genes were always found transcriptionally altered, thus suggesting the involvement of histone modifications in the response of Daphnia to metal exposure. Lastly, remarkably distinct transgenerational transcriptional responses were found between naïve and non-naïve organisms, thereby highlighting the influence of exposure history on gene expression and confirming the capacity of metals to determine transgenerational transcriptional effects across non-exposed generations.
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Affiliation(s)
- Guilherme Jeremias
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ana-Belén Muñiz-González
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | | | - José-Luis Martínez-Guitarte
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Ostend, Belgium
| | - Joana Luísa Pereira
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
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26
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Vidal AC, Sosnowski DW, Marchesoni J, Grenier C, Thorp J, Murphy SK, Johnson SB, Schlief B, Hoyo C. Maternal adverse childhood experiences (ACEs) and offspring imprinted gene DMR methylation at birth. Epigenetics 2024; 19:2293412. [PMID: 38100614 PMCID: PMC10730185 DOI: 10.1080/15592294.2023.2293412] [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: 05/24/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Adverse childhood experiences (ACEs) contribute to numerous negative health outcomes across the life course and across generations. Here, we extend prior work by examining the association of maternal ACEs, and their interaction with financial stress and discrimination, with methylation status within eight differentially methylated regions (DMRs) in imprinted domains in newborns. ACEs, financial stress during pregnancy, and experience of discrimination were self-reported among 232 pregnant women. DNA methylation was assessed at PEG10/SGCE, NNAT, IGF2, H19, PLAGL1, PEG3, MEG3-IG, and DLK1/MEG3 regulatory sequences using pyrosequencing. Using multivariable linear regression models, we found evidence to suggest that financial stress was associated with hypermethylation of MEG3-IG in non-Hispanic White newborns; discrimination was associated with hypermethylation of IGF2 and NNAT in Hispanic newborns, and with hypomethylation of PEG3 in non-Hispanic Black newborns. We also found evidence that maternal ACEs interacted with discrimination to predict offspring PLAGL1 altered DMR methylation, in addition to interactions between maternal ACEs score and discrimination predicting H19 and SGCE/PEG10 altered methylation in non-Hispanic White newborns. However, these interactions were not statistically significant after multiple testing corrections. Findings from this study suggest that maternal ACEs, discrimination, and financial stress are associated with newborn aberrant methylation in imprinted gene regions.
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Affiliation(s)
- Adriana C. Vidal
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David W. Sosnowski
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joddy Marchesoni
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - John Thorp
- Department of Obstetrics and Gynecology, Maternal and Child Health, UNC Gillings School of Public Health, UNC, Chapel Hill, NC, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Sara B. Johnson
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Population, Family & Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Billy Schlief
- Johns Hopkins All Children’s Pediatric Biorepository, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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27
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Doan TNA, Cowley JM, Phillips AL, Briffa JF, Leemaqz SY, Burton RA, Romano T, Wlodek ME, Bianco-Miotto T. Imprinted gene alterations in the kidneys of growth restricted offspring may be mediated by a long non-coding RNA. Epigenetics 2024; 19:2294516. [PMID: 38126131 PMCID: PMC10761017 DOI: 10.1080/15592294.2023.2294516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Altered epigenetic mechanisms have been previously reported in growth restricted offspring whose mothers experienced environmental insults during pregnancy in both human and rodent studies. We previously reported changes in the expression of the DNA methyltransferase Dnmt3a and the imprinted genes Cdkn1c (Cyclin-dependent kinase inhibitor 1C) and Kcnq1 (Potassium voltage-gated channel subfamily Q member 1) in the kidney tissue of growth restricted rats whose mothers had uteroplacental insufficiency induced on day 18 of gestation, at both embryonic day 20 (E20) and postnatal day 1 (PN1). To determine the mechanisms responsible for changes in the expression of these imprinted genes, we investigated DNA methylation of KvDMR1, an imprinting control region (ICR) that includes the promoter of the antisense long non-coding RNA Kcnq1ot1 (Kcnq1 opposite strand/antisense transcript 1). Kcnq1ot1 expression decreased by 51% in growth restricted offspring compared to sham at PN1. Interestingly, there was a negative correlation between Kcnq1ot1 and Kcnq1 in the E20 growth restricted group (Spearman's ρ = 0.014). No correlation was observed between Kcnq1ot1 and Cdkn1c expression in either group at any time point. Additionally, there was a 11.25% decrease in the methylation level at one CpG site within KvDMR1 ICR. This study, together with others in the literature, supports that long non-coding RNAs may mediate changes seen in tissues of growth restricted offspring.
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Affiliation(s)
- Thu N. A. Doan
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - James M. Cowley
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Aaron L. Phillips
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Jessica F. Briffa
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Shalem Y. Leemaqz
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- SAHMRI Women and Kids, South Australian Health & Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Rachel A. Burton
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tania Romano
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Mary E. Wlodek
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tina Bianco-Miotto
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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28
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Andersen A, Milefchik E, Papworth E, Penaluna B, Dawes K, Moody J, Weeks G, Froehlich E, deBlois K, Long JD, Philibert R. ZSCAN25 methylation predicts seizures and severe alcohol withdrawal syndrome. Epigenetics 2024; 19:2298057. [PMID: 38166538 PMCID: PMC10766392 DOI: 10.1080/15592294.2023.2298057] [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: 08/26/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
Currently, clinicians use their judgement and indices such as the Prediction of Alcohol Withdrawal Syndrome Scale (PAWSS) to determine whether patients are admitted to hospitals for consideration of withdrawal syndrome (AWS). However, only a fraction of those admitted will experience severe AWS. Previously, we and others have shown that epigenetic indices, such as the Alcohol T-Score (ATS), can quantify recent alcohol consumption. However, whether these or other alcohol biomarkers, such as carbohydrate deficient transferrin (CDT), could identify those at risk for severe AWS is unknown. To determine this, we first conducted genome-wide DNA methylation analyses of subjects entering and exiting alcohol treatment to identify loci whose methylation quickly reverted as a function of abstinence. We then tested whether methylation at a rapidly reverting locus, cg07375256, or other existing metrics including PAWSS scores, CDT levels, or ATS, could predict outcome in 125 subjects admitted for consideration of AWS. We found that PAWSS did not significantly predict severe AWS nor seizures. However, methylation at cg07375256 (ZSCAN25) and CDT strongly predicted severe AWS with ATS (p < 0.007) and cg07375256 (p < 6 × 10-5) methylation also predicting AWS associated seizures. We conclude that epigenetic methods can predict those likely to experience severe AWS and that the use of these or similar Precision Epigenetic approaches could better guide AWS management.
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Affiliation(s)
- Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily Milefchik
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emma Papworth
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Brandan Penaluna
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Behavioral Diagnostics LLC, Coralville, IA, USA
| | - Joanna Moody
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Gracie Weeks
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ellyse Froehlich
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Kaitlyn deBlois
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Behavioral Diagnostics LLC, Coralville, IA, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
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29
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Mortillo M, Kennedy EG, Hermetz KM, Burt AA, Marsit CJ. Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta. Epigenetics 2024; 19:2326869. [PMID: 38507502 PMCID: PMC10956631 DOI: 10.1080/15592294.2024.2326869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth G. Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen M. Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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30
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Ma S, Pan X, Gan J, Guo X, He J, Hu H, Wang Y, Ning S, Zhi H. DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma. Epigenetics 2024; 19:2318506. [PMID: 38439715 PMCID: PMC10936651 DOI: 10.1080/15592294.2024.2318506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (CpGct) in glioma tissues. We identified eight prognosis-related CpGct to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight CpGct might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient's prognosis.
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Affiliation(s)
- Shuangyue Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Gan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaxin Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaheng He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoyu Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuncong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Li F, Wang F, Wang L, Wang J, Wei S, Meng J, Li Y, Feng L, Jiang P. m6A reader YTHDC2 mediates NCOA4 mRNA stability affecting ferritinophagy to alleviate secondary injury after intracerebral haemorrhage. Epigenetics 2024; 19:2326868. [PMID: 38465865 PMCID: PMC10936596 DOI: 10.1080/15592294.2024.2326868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/01/2024] [Indexed: 03/12/2024] Open
Abstract
Oxidative stress and neuronal dysfunction caused by intracerebral haemorrhage (ICH) can lead to secondary injury. The m6A modification has been implicated in the progression of ICH. This study aimed to investigate the role of the m6A reader YTHDC2 in ICH-induced secondary injury. ICH models were established in rats using autologous blood injection, and neuronal cell models were induced with Hemin. Experiments were conducted to overexpress YTH domain containing 2 (YTHDC2) and examine its effects on neuronal dysfunction, brain injury, and neuronal ferritinophagy. RIP-qPCR and METTL3 silencing were performed to investigate the regulation of YTHDC2 on nuclear receptor coactivator 4 (NCOA4). Finally, NCOA4 overexpression was used to validate the regulatory mechanism of YTHDC2 in ICH. The study found that YTHDC2 expression was significantly downregulated in the brain tissues of ICH rats. However, YTHDC2 overexpression improved neuronal dysfunction and reduced brain water content and neuronal death after ICH. Additionally, it reduced levels of ROS, NCOA4, PTGS2, and ATG5 in the brain tissues of ICH rats, while increasing levels of FTH and FTL. YTHDC2 overexpression also decreased levels of MDA and Fe2+ in the serum, while promoting GSH synthesis. In neuronal cells, YTHDC2 overexpression alleviated Hemin-induced injury, which was reversed by Erastin. Mechanistically, YTHDC2-mediated m6A modification destabilized NCOA4 mRNA, thereby reducing ferritinophagy and alleviating secondary injury after ICH. However, the effects of YTHDC2 were counteracted by NCOA4 overexpression. Overall, YTHDC2 plays a protective role in ICH-induced secondary injury by regulating NCOA4-mediated ferritinophagy.
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Affiliation(s)
- Fengfeng Li
- Department of Neurosurgery, Tengzhou Central People’s Hospital, Jining Medical University, Tengzhou, China
| | - Fang Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Lei Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Jianhua Wang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Shanshan Wei
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Junjun Meng
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Yanan Li
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
| | - Lei Feng
- Department of Neurosurgery, Jining First People’s Hospital, Shandong First Medical University, Jining, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining, China
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Khatib H, Townsend J, Konkel MA, Conidi G, Hasselkus JA. Calling the question: what is mammalian transgenerational epigenetic inheritance? Epigenetics 2024; 19:2333586. [PMID: 38525788 DOI: 10.1080/15592294.2024.2333586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
While transgenerational epigenetic inheritance has been extensively documented in plants, nematodes, and fruit flies, its existence in mammals remains controversial. Several factors have contributed to this debate, including the lack of a clear distinction between intergenerational and transgenerational epigenetic inheritance (TEI), the inconsistency of some studies, the potential confounding effects of in-utero vs. epigenetic factors, and, most importantly, the biological challenge of epigenetic reprogramming. Two waves of epigenetic reprogramming occur: in the primordial germ cells and the developing embryo after fertilization, characterized by global erasure of DNA methylation and remodelling of histone modifications. Consequently, TEI can only occur if specific genetic regions evade this reprogramming and persist through embryonic development. These challenges have revived the long-standing debate about the possibility of inheriting acquired traits, which has been strongly contested since the Lamarckian and Darwinian eras. As a result, coupled with the absence of universally accepted criteria for transgenerational epigenetic studies, a vast body of literature has emerged claiming evidence of TEI. Therefore, the goal of this study is to advocate for establishing fundamental criteria that must be met for a study to qualify as evidence of TEI. We identified five criteria based on the consensus of studies that critically evaluated TEI. To assess whether published original research papers adhere to these criteria, we examined 80 studies that either claimed or were cited as supporting TEI. The findings of this analysis underscore the widespread confusion in this field and highlight the urgent need for a unified scientific consensus on TEI requirements.
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Affiliation(s)
- Hasan Khatib
- The Department of Animal and Dairy Sciences, The University of Wisconsin, Madison, WI, USA
| | - Jessica Townsend
- The Department of Animal and Dairy Sciences, The University of Wisconsin, Madison, WI, USA
| | - Melissa A Konkel
- The Department of Animal and Dairy Sciences, The University of Wisconsin, Madison, WI, USA
| | - Gabi Conidi
- The Department of Animal and Dairy Sciences, The University of Wisconsin, Madison, WI, USA
| | - Julia A Hasselkus
- The Department of Animal and Dairy Sciences, The University of Wisconsin, Madison, WI, USA
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Xue Y, Zhao G, Song L, Qiao L, Huang C, Wang K, Wang T. The signature of cancer methylation markers in maternal plasma: Factors influencing the development and application of cancer liquid biopsy assay. Gene 2024; 906:148261. [PMID: 38342253 DOI: 10.1016/j.gene.2024.148261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND DNA methylation is highly correlated with cancer and embryo development, and plasma-based methylation markers have been widely used for cancer early detection. However, whether the commonly used cancer methylation markers cause "false positives" in the plasma of pregnant women has not been comprehensively evaluated. METHODS We conducted a case-control study from February 2021 to March 2023, which included 138 pregnant women and 44 control women. Plasma cell-free DNA (cfDNA) was isolated and bisulfite-converted, and then the methylation levels of eight methylated markers related to gastrointestinal cancer (SEPT9, SDC2, C9orf50, KCNQ5, CLIP4, TFPI2, ELMO1 and ZNF582) and three markers related to lung cancer (SHOX2, RASSF1A and PTGER4) were analyzed. RESULTS When comparing the plasma of pregnant women to that of control women, SEPT9, CLIP4, ZNF582, SHOX2, RASSF1A and PTGER showed significantly higher levels of methylation (p < 0.05). These positive signals originate from the placenta/fetus rather than the mother. We found no discernible difference in DNA methylation levels between fetal cfDNA fractions of < 10 % and ≥ 10 % in pregnant women (p > 0.05), while CLIP4 and PTGER4 showed high methylation levels in the assisted fertilization group compared to the natural fertilization group (p < 0.05). CONCLUSION Our study shows that cancer and fetus/placenta exhibit similar DNA methylation patterns, and some gastrointestinal cancer and lung cancer-related methylation markers also show positives in maternal plasma. This is an important consideration in the design and application of plasma-based cancer liquid biopsy assays.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Guodong Zhao
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship Fuyang District, Hangzhou, Zhejiang 311400, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Lishuang Song
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Chao Huang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Kai Wang
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
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Kumar G, Gurao A, Vasisth R, Chitkara M, Singh R, Ranganatha Sriranga K, Shivanand Dige M, Mukesh M, Singh P, Singh Kataria R. Genome-wide 5'-C-phosphate-G-3' methylation patterns reveal the effect of heat stress on the altered semen quality in Bubalus bubalis. Gene 2024; 906:148233. [PMID: 38331117 DOI: 10.1016/j.gene.2024.148233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Semen production and quality are closely correlated with different environmental factors in bovines, particularly for the buffalo (Bubalus bubalis) bulls reared under tropical and sub-tropical conditions. Factors including DNA methylation patterns, an intricate process in sperm cells, have an impact on the production of quality semen in buffalo bulls under abiotic stress conditions. The present study was conducted to identify DNA methylome signatures for semen quality in Murrah buffalo bulls, acclaimed as a major dairy breed globally, under summer heat stress. Based on semen quality parameters that significantly varied between the two groups over the seasons, the breeding bulls were classified into seasonally affected (SA = 6) and seasonally non-affected (SNA = 6) categories. DNA was isolated from purified sperm cells and sequenced using the RRBS (Reduced Representation Bisulfite Sequencing) technique for genome-wide methylome data generation. During the hot summer months, the physiological parameters such as scrotal surface temperature, rectal temperature, and respiration rate for both the SA and SNA bulls were significantly higher in the afternoon than in the morning. Whereas, the global CpG% of SA bulls was positively correlated with the afternoon's scrotal surface and rectal temperature. The RRBS results conveyed differentially methylated cytosines in the promoter region of the genes encoding the channels responsible for Ca2+ exchange, NPTN, Ca2+ activated chloride channels, ANO1, and a few structure-related units such as septins (SEPT4 and SEPT6), SPATA, etc. Additionally, the hypermethylated set of genes in SA was significantly enriched for pathways such as the FOXO signaling pathway and oocyte meiosis. The methylation patterns suggest promoter methylation in the genes regulating the sperm structure as well as surface transporters, which could contribute to the reduced semen quality in the Murrah buffalo bulls during the season-related heat stress.
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Affiliation(s)
- Gautam Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Ankita Gurao
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Rashi Vasisth
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Meenakshi Chitkara
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Ravinder Singh
- ICAR-National Dairy Research Institute, Karnal (Haryana), India
| | | | | | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Pawan Singh
- ICAR-National Dairy Research Institute, Karnal (Haryana), India
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35
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Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O. Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis. Sci Total Environ 2024; 923:170949. [PMID: 38365020 DOI: 10.1016/j.scitotenv.2024.170949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
The herbicide linuron can cause endocrine disrupting effects in Xenopus tropicalis frogs, including offspring that were never exposed to the contaminant. The mechanisms by which these effects are transmitted across generations need to be further investigated. Here, we examined transgenerational alterations of brain and testis DNA methylation profiles paternally inherited from grandfathers developmentally exposed to an environmentally relevant concentration of linuron. Reduced representation bisulfite sequencing (RRBS) revealed numerous differentially methylated regions (DMRs) in brain (3060 DMRs) and testis (2551 DMRs) of the adult male F2 generation. Key genes in the brain involved in somatotropic (igfbp4) and thyrotropic signaling (dio1 and tg) were differentially methylated and correlated with phenotypical alterations in body size, weight, hind limb length and plasma glucose levels, indicating that these methylation changes could be potential mediators of the transgenerational effects of linuron. Testis DMRs were found in genes essential for spermatogenesis, meiosis and germ cell development (piwil1, spo11 and tdrd9) and their methylation levels were correlated with the number of germ cells nests per seminiferous tubule, an endpoint of disrupted spermatogenesis. DMRs were also identified in several genes central for the machinery that regulates the epigenetic landscape including DNA methylation (dnmt3a and mbd2) and histone acetylation (hdac8, ep300, elp3, kat5 and kat14), which may at least partly drive the linuron-induced transgenerational effects. The results from this genome-wide DNA methylation profiling contribute to better understanding of potential transgenerational epigenetic inheritance mechanisms in amphibians.
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Affiliation(s)
- Mauricio Roza
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | | | - Sofie Svanholm
- Department of Environmental Toxicology, Uppsala University, Uppsala, Sweden
| | - Cecilia Berg
- Department of Environmental Toxicology, Uppsala University, Uppsala, Sweden
| | - Oskar Karlsson
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden.
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Shen H, Chen Y, Xu M, Zhou J, Huang C, Wang Z, Shao Y, Zhang H, Lu Y, Li S, Fu Z. Cellular senescence gene TACC3 associated with colorectal cancer risk via genetic and DNA methylated alteration. Arch Toxicol 2024; 98:1499-1513. [PMID: 38480537 DOI: 10.1007/s00204-024-03702-9] [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: 11/19/2023] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
Cell senescence genes play a vital role in the pathogenesis of colorectal cancer, a process that may involve the triggering of genetic variations and reversible phenotypes caused by epigenetic modifications. However, the specific regulatory mechanisms remain unclear. Using CellAge and The Cancer Genome Atlas databases and in-house RNA-seq data, DNA methylation-modified cellular senescence genes (DMCSGs) were validated by Support Vector Machine and correlation analyses. In 1150 cases and 1342 controls, we identified colorectal cancer risk variants in DMCSGs. The regulatory effects of gene, variant, and DNA methylation were explored through dual-luciferase and 5-azacytidine treatment experiments, complemented by multiple database analyses. Biological functions of key gene were evaluated via cell proliferation assays, SA-β-gal staining, senescence marker detection, and immune infiltration analyses. The genetic variant rs4558926 in the downstream of TACC3 was significantly associated with colorectal cancer risk (OR = 1.35, P = 3.22 × 10-4). TACC3 mRNA expression increased due to rs4558926 C > G and decreased DNA methylation levels. The CpG sites in the TACC3 promoter region were regulated by rs4558926. TACC3 knockdown decreased proliferation and senescence in colorectal cancer cells. In addition, subjects with high-TACC3 expression presented an immunosuppressive microenvironment. These findings provide insights into the involvement of genetic variants of cellular senescence genes in the development and progression of colorectal cancer.
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Affiliation(s)
- Hengyang Shen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Menghuan Xu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jieyu Zhou
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Shao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuwei Li
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
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Walia Y, de Bock CE, Huang Y. The landscape of alterations affecting epigenetic regulators in T-cell acute lymphoblastic leukemia: Roles in leukemogenesis and therapeutic opportunities. Int J Cancer 2024; 154:1522-1536. [PMID: 38155420 DOI: 10.1002/ijc.34819] [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: 07/26/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy accounting for 10%-15% of pediatric and 20%-25% of adult ALL cases. Epigenetic irregularities in T-ALL include alterations in both DNA methylation and the post-translational modifications on histones which together play a critical role in the initiation and development of T-ALL. Characterizing the oncogenic mutations that result in these epigenetic changes combined with the reversibility of epigenetic modifications represents an opportunity for the development of epigenetic therapies. Oncogenic mutations and deregulated expression of DNA methyltransferases (DNMTs), Ten-Eleven Translocation dioxygenases (TETs), Histone acetyltransferases (HATs) and members of Polycomb Repressor Complex 2 (PRC2) have all been identified in T-ALL. This review focuses on the current understanding of how these mutations lead to epigenetic changes in T-ALL, their association with disease pathogenesis and the current efforts to exploit these clinically through the development of epigenetic therapies in T-ALL treatment.
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Affiliation(s)
- Yashna Walia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yizhou Huang
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
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38
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Ingram SJ, Vazquez AY, Klump KL, Hyde LW, Burt SA, Clark SL. Associations of depression and anxiety symptoms in childhood and adolescence with epigenetic aging. J Affect Disord 2024; 352:250-258. [PMID: 38360371 DOI: 10.1016/j.jad.2024.02.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Childhood anxiety and depression symptoms are potential risk factors for accelerated biological aging. In child and adolescent twins, we tested whether these symptoms were associated with DNA methylation (DNAm) aging, a measure of biological aging. METHODS 276 twins (135 pairs, 6 singletons) had DNAm assayed from saliva in middle childhood (mean = 7.8 years). Residuals of five different DNAm age estimates regressed on chronological age were used to indicate accelerated aging. Anxiety and depression symptoms were assessed in middle childhood and early adolescence using the Child Behavior Checklist. Mixed effect regression was used to examine potential relationships between anxiety or depression symptoms, and accelerated DNAm age. MZ twin difference analysis was then utilized to determine if associations were environmentally-driven or due to genetic or shared-environment confounding. RESULTS Anxiety and depression symptoms were not associated with accelerated DNAm aging in middle childhood. In early adolescence, only the Wu clock was significant and indicated that each one symptom increase in anxiety symptoms had an associated age acceleration of 0.03 years (~0.4 months; p = 0.019). MZ twin difference analysis revealed non-significant within-pair effects, suggesting genetic and shared environmental influences. LIMITATIONS Sample is predominantly male and white. Generalizability to other populations may be limited. CONCLUSION Accelerated DNAm aging of the Wu clock in middle childhood is associated with anxiety, but not depression, symptoms in early adolescence. Further, this association may be the result of shared genetic and environmental influences. Accelerated DNAm aging may serve as an early risk factor or predictor of later anxiety symptoms.
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Affiliation(s)
- Sarah J Ingram
- Interdisciplinary Graduate Program in Genetics, Department of Psychiatry & Behavioral Sciences, Texas A&M University, United States of America
| | - Alexandra Y Vazquez
- Department of Psychology, Michigan State University, United States of America
| | - Kelly L Klump
- Department of Psychology, Michigan State University, United States of America
| | - Luke W Hyde
- Department of Psychology, University of Michigan, United States of America
| | - S Alexandra Burt
- Department of Psychology, Michigan State University, United States of America
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, United States of America.
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Bashi MA, Ad'hiah AH. Molecular landscape of the interleukin-40 encoding gene, C17orf99, in patients with acute myeloid leukemia. Gene 2024; 904:148214. [PMID: 38286266 DOI: 10.1016/j.gene.2024.148214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Acute myeloid leukemia (AML) is a malignant hematological disorder in which aberrant cytokine signaling and inflammation play a role in disease initiation and progression. Interleukin-40 (IL-40) is a novel cytokine encoded by the chromosome 17 open reading frame 99 (C17orf99) gene. This cytokine is involved in mediating inflammation but its biological significance in the pathogenesis of AML has not been investigated. In this case-control and observational study, mRNA expression and DNA methylation of the C17orf99 gene were evaluated in the peripheral blood of AML patients. In addition, the polymorphism of two novel intergenic variants of the C17orf99 gene, rs2004339 A/G and rs2310998 G/A, were explored using a real-time polymerase chain reaction assay. The study was conducted on 131 patients with AML and 106 controls and gene expression and DNA methylation were expressed as fold-change (2-ΔΔCt). Results revealed that mRNA expression of the C17orf99 gene was down-regulated in AML patients, particularly in females, while up-regulated expression was found in patients with hypoalbuminemia. For DNA methylation, it was up-regulated in AML patients, particularly in females, AML M5 subtype, and CD4-negative and CD14-positive peripheral blood cells. The mutant A allele and the corresponding homozygous AA genotype of rs2004339 was significantly associated with an increased risk of AML. The AA genotype was also associated with significantly up-regulated C17orf99 mRNA expression and DNA methylation of compared to the wild-type GG genotype. In conclusions, C17orf99 mRNA expression showed down-regulated levels in the peripheral blood of AML patients, while DNA methylation was up-regulated. The intergenic variant rs2004339 was associated with susceptibility to AML and had an effect on mRNA expression and DNA methylation.
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Affiliation(s)
- Mustafa A Bashi
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Ali H Ad'hiah
- Tropical-Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
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40
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Lv L, Chen Q, Lu J, Zhao Q, Wang H, Li J, Yuan K, Dong Z. Potential regulatory role of epigenetic modifications in aging-related heart failure. Int J Cardiol 2024; 401:131858. [PMID: 38360101 DOI: 10.1016/j.ijcard.2024.131858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/27/2023] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Heart failure (HF) is a serious clinical syndrome and a serious development or advanced stage of various heart diseases. Aging is an independent factor that causes pathological damage in cardiomyopathy and participates in the occurrence of HF at the molecular level by affecting mechanisms such as telomere shortening and mitochondrial dysfunction. Epigenetic changes have a significant impact on the aging process, and there is increasing evidence that genetic and epigenetic changes are key features of aging and aging-related diseases. Epigenetic modifications can affect genetic information by changing the chromatin state without changing the DNA sequence. Most of the genetic loci that are highly associated with cardiovascular diseases (CVD) are located in non-coding regions of the genome; therefore, the epigenetic mechanism of CVD has attracted much attention. In this review, we focus on the molecular mechanisms of HF during aging and epigenetic modifications mediating aging-related HF, emphasizing that epigenetic mechanisms play an important role in the pathogenesis of aging-related CVD and can be used as potential diagnostic and prognostic biomarkers, as well as therapeutic targets.
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Affiliation(s)
- Lin Lv
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - QiuYu Chen
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Lu
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Zhao
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - HongYan Wang
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - JiaHao Li
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - KeYing Yuan
- Department of Pharmacy, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - ZengXiang Dong
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, First Affiliated Hospital of Harbin Medical University, Harbin, China; NHC Key Laboratory of Cell Transplantation, First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Marra PS, Seki T, Nishizawa Y, Chang G, Yamanishi K, Nishiguchi T, Shibata K, Braun P, Shinozaki G. Genome-wide DNA methylation analysis in female veterans with military sexual trauma and comorbid PTSD/MDD. J Affect Disord 2024; 351:624-630. [PMID: 38309478 DOI: 10.1016/j.jad.2024.01.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Military sexual trauma (MST) is a prevalent issue within the U.S. military. Victims are more likely to develop comorbid diseases such as posttraumatic stress disorder (PTSD) and major depressive disorder (MDD). Nonetheless, not everyone who suffers from MST develops PTSD and/or MDD. DNA methylation, which can regulate gene expression, might give us insight into the molecular mechanisms behind this discrepancy. Therefore, we sought to identify genomic loci and enriched biological pathways that differ between patients with and without MST, PTSD, and MDD. METHODS Saliva samples were collected from 113 female veterans. Following DNA extraction and processing, DNA methylation levels were measured through the Infinium HumanMethylationEPIC BeadChip array. We used limma and bump hunting methods to generate the differentially methylated positions and differentially methylated regions (DMRs), respectively. Concurrently, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome to find enriched pathways. RESULTS A DMR close to the transcription start site of ZFP57 was differentially methylated between subjects with and without PTSD, replicating previous findings and emphasizing the potential role of ZFP57 in PTSD susceptibility. In the pathway analyses, none survived multiple correction, although top GO terms included some potentially relevant to MST, PTSD, and MDD etiology. CONCLUSION We conducted one of the first DNA methylation analyses investigating MST along with PTSD and MDD. In addition, we found one DMR near ZFP57 to be associated with PTSD. The replication of this finding indicates further investigation of ZFP57 in PTSD may be warranted.
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Affiliation(s)
- Pedro S Marra
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Tomoteru Seki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Yoshitaka Nishizawa
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Gloria Chang
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; Developmental Psychology Graduate Program, Department of Psychological Sciences, University of Missouri, Columbia, MO, USA
| | - Kyosuke Yamanishi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Hyogo Medical University, Nishinomiya, Hyogo, Japan
| | - Tsuyoshi Nishiguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Kazuki Shibata
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Sumitomo Pharma Co. Ltd, Osaka, Osaka, Japan
| | - Patricia Braun
- Department of Biology, Clarke University, Dubuque, IA, USA
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
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Moulton C, Murri A, Benotti G, Fantini C, Duranti G, Ceci R, Grazioli E, Cerulli C, Sgrò P, Rossi C, Magno S, Di Luigi L, Caporossi D, Parisi A, Dimauro I. The impact of physical activity on promoter-specific methylation of genes involved in the redox-status and disease progression: A longitudinal study on post-surgery female breast cancer patients undergoing medical treatment. Redox Biol 2024; 70:103033. [PMID: 38211440 PMCID: PMC10821067 DOI: 10.1016/j.redox.2024.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Most anticancer treatments act on oxidative-stress pathways by producing reactive oxygen species (ROS) to kill cancer cells, commonly resulting in consequential drug-induced systemic cytotoxicity. Physical activity (PA) has arisen as an integrative cancer therapy, having positive health effects, including in redox-homeostasis. Here, we investigated the impact of an online supervised PA program on promoter-specific DNA methylation, and corresponding gene expression/activity, in 3 antioxidants- (SOD1, SOD2, and CAT) and 3 breast cancer (BC)-related genes (BRCA1, L3MBTL1 and RASSF1A) in a population-based sample of women diagnosed with primary BC, undergoing medical treatment. We further examined mechanisms involved in methylating and demethylating pathways, predicted biological pathways and interactions of exercise-modulated molecules, and the functional relevance of modulated antioxidant markers on parameters related to aerobic capacity/endurance, physical fatigue and quality of life (QoL). PA maintained levels of SOD activity in blood plasma, and at the cellular level significantly increased SOD2 mRNA (≈+77 %), contrary to their depletion due to medical treatment. This change was inversely correlated with DNA methylation in SOD2 promoter (≈-20 %). Similarly, we found a significant effect of PA only on L3MBTL1 promoter methylation (≈-25 %), which was inversely correlated with its mRNA (≈+43 %). Finally, PA increased TET1 mRNA levels (≈+15 %) and decreased expression of DNMT3B mRNA (≈-28 %). Our results suggest that PA-modulated DNA methylation affects several signalling pathways/biological activities involved in the cellular oxidative stress response, chromatin organization/regulation, antioxidant activity and DNA/protein binding. These changes may positively impact clinical outcomes and improve the response to cancer treatment in post-surgery BC patients.
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Affiliation(s)
- Chantalle Moulton
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Arianna Murri
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Gianmarco Benotti
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Cristina Fantini
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Guglielmo Duranti
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Roberta Ceci
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Elisa Grazioli
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Claudia Cerulli
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Paolo Sgrò
- Unit of Endocrinology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Cristina Rossi
- Center for Integrative Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Italy
| | - Stefano Magno
- Center for Integrative Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Italy
| | - Luigi Di Luigi
- Unit of Endocrinology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Attilio Parisi
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy.
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Gissi DB, Rossi R, Lenzi J, Tarsitano A, Gabusi A, Balbi T, Montebugnoli L, Marchetti C, Foschini MP, Morandi L. Thirteen-gene DNA methylation analysis of oral brushing samples: A potential surveillance tool for periodic monitoring of treated patients with oral cancer. Head Neck 2024; 46:728-739. [PMID: 38169119 DOI: 10.1002/hed.27621] [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: 05/29/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND We evaluated the prognostic role of 13-gene DNA methylation analysis by oral brushing repeatedly performed during the follow-up of patients surgically treated for oral cancer. METHODS This is a nested case-control study including 61 patients for a total of 64 outcomes (2/61 patients experienced multiple relapses). Samples were collected at baseline (4-10 months after OSCC resection) and repeatedly every 4-10 months until relapse or death. DNA methylation scores were classified as persistently positive, persistently negative, or mixed. RESULTS Twenty cases who had persistently positive scores and 30 cases with mixed scores had, respectively, an almost 42-fold (p < 0.001) and 32-fold (p = 0.006) higher likelihood of relapse, compared to 14 patients with persistently negative scores. The last score before reoccurrence was positive in 18/19 secondary events. CONCLUSIONS The 13-gene DNA methylation analysis may be considered for the surveillance of patients treated for oral carcinoma.
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Affiliation(s)
- Davide B Gissi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Roberto Rossi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Jacopo Lenzi
- Section of Hygiene, Department of Biomedical and Neuromotor Sciences, Public Health and Medical Statistics, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Maxillofacial Surgery Unit, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, Section of Maxillo-Facial Surgery at Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Andrea Gabusi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Tiziana Balbi
- IRCCS azienda ospedaliero universitaria di Bologna, Unit of Anatomic Pathology S. Orsola Hospital, Bologna, Italy
| | - Lucio Montebugnoli
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Claudio Marchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Maxillofacial Surgery Unit, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, Section of Maxillo-Facial Surgery at Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Maria Pia Foschini
- Department of Biomedical and Neuromotor Sciences, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Luca Morandi
- Functional and Molecular Neuroimaging Unit, Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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Meyer B, Stirzaker C, Ramkomuth S, Harvey K, Chan B, Lee CS, Karim R, Deng N, Avery-Kiejda KA, Scott RJ, Lakhani S, Fox S, Robbins E, Shin JS, Beith J, Gill A, Sioson L, Chan C, Krishnaswamy M, Cooper C, Warrier S, Mak C, Rasko JE, Bailey CG, Swarbrick A, Clark SJ, O'Toole S, Pidsley R. Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma. J Pathol 2024; 262:480-494. [PMID: 38300122 DOI: 10.1002/path.6250] [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: 07/25/2023] [Revised: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Phyllodes tumours (PTs) are rare fibroepithelial lesions of the breast that are classified as benign, borderline, or malignant. As little is known about the molecular underpinnings of PTs, current diagnosis relies on histological examination. However, accurate classification is often difficult, particularly for distinguishing borderline from malignant PTs. Furthermore, PTs can be misdiagnosed as other tumour types with shared histological features, such as fibroadenoma and metaplastic breast cancers. As DNA methylation is a recognised hallmark of many cancers, we hypothesised that DNA methylation could provide novel biomarkers for diagnosis and tumour stratification in PTs, whilst also allowing insight into the molecular aetiology of this otherwise understudied tumour. We generated whole-genome methylation data using the Illumina EPIC microarray in a novel PT cohort (n = 33) and curated methylation microarray data from published datasets including PTs and other potentially histopathologically similar tumours (total n = 817 samples). Analyses revealed that PTs have a unique methylome compared to normal breast tissue and to potentially histopathologically similar tumours (metaplastic breast cancer, fibroadenoma and sarcomas), with PT-specific methylation changes enriched in gene sets involved in KRAS signalling and epithelial-mesenchymal transition. Next, we identified 53 differentially methylated regions (DMRs) (false discovery rate < 0.05) that specifically delineated malignant from non-malignant PTs. The top DMR in both discovery and validation cohorts was hypermethylation at the HSD17B8 CpG island promoter. Matched PT single-cell expression data showed that HSD17B8 had minimal expression in fibroblast (putative tumour) cells. Finally, we created a methylation classifier to distinguish PTs from metaplastic breast cancer samples, where we revealed a likely misdiagnosis for two TCGA metaplastic breast cancer samples. In conclusion, DNA methylation alterations are associated with PT histopathology and hold the potential to improve our understanding of PT molecular aetiology, diagnostics, and risk stratification. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Braydon Meyer
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Sonny Ramkomuth
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Kate Harvey
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Belinda Chan
- Department of Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Cheok Soon Lee
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Department of Anatomical Pathology and Molecular Pathology Laboratory, Liverpool Hospital, Liverpool, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, New South Wales, Australia
| | - Rooshdiya Karim
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Niantao Deng
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
| | - Rodney J Scott
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Sunil Lakhani
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Stephen Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Robbins
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Joo-Shik Shin
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Jane Beith
- Psycho-Oncology Co-Operative Group (PoCoG), University of Sydney, Sydney, New South Wales, Australia
- Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Anthony Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
| | - Loretta Sioson
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
| | - Charles Chan
- NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
- Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Mrudula Krishnaswamy
- NSW Health Pathology, Department of Anatomical Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
- Concord Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Caroline Cooper
- Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Sanjay Warrier
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical Program, The University of Sydney, Sydney, New South Wales, Australia
- Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Cindy Mak
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
- Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - John Ej Rasko
- Faculty of Medicine, The University of Queensland, St Lucia, Queensland, Australia
- Department of Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia
| | - Charles G Bailey
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, Sydney, New South Wales, Australia
- Cancer and Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, New South Wales, Australia
| | - Alexander Swarbrick
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandra O'Toole
- Tumour Progression Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Qi H, Lim QL, Kinoshita K, Nakajima N, Inoue-Murayama M. A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models. Mol Ecol Resour 2024; 24:e13928. [PMID: 38234258 DOI: 10.1111/1755-0998.13928] [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: 05/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.
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Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Qi Luan Lim
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Chen HS, Wang F, Chen JG. Epigenetic mechanisms in depression: Implications for pathogenesis and treatment. Curr Opin Neurobiol 2024; 85:102854. [PMID: 38401316 DOI: 10.1016/j.conb.2024.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
The risk of depression is influenced by both genetic and environmental factors. It has been suggested that epigenetic mechanisms may mediate the risk of depression following exposure to adverse life events. Epigenetics encompasses stable alterations in gene expression that are controlled through transcriptional, post-transcriptional, translational, or post-translational processes, including DNA modifications, chromatin remodeling, histone modifications, RNA modifications, and non-coding RNA (ncRNA) regulation, without any changes in the DNA sequence. In this review, we explore recent research advancements in the realm of epigenetics concerning depression. Furthermore, we evaluate the potential of epigenetic changes as diagnostic and therapeutic biomarkers for depression.
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Affiliation(s)
- Hong-Sheng Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China
| | - Fang Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China
| | - Jian-Guo Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China.
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Woo PYM, Lee JWY, Lam SW, Pu JKS, Chan DTM, Mak CHK, Ho JMK, Wong ST, Po YC, Lee MWY, Chan KY, Poon WS. Radiotherapy-induced glioblastoma: distinct differences in overall survival, tumor location, pMGMT methylation and primary tumor epidemiology in Hong Kong chinese patients. Br J Neurosurg 2024; 38:385-392. [PMID: 33576706 DOI: 10.1080/02688697.2021.1881445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Radiotherapy-induced glioblastomas (RIGB) are a well-known late and rare complication of brain irradiation. Yet the clinical, radiological and molecular characteristics of these tumors are not well characterized. METHODS This was a retrospective multicentre study that analysed adult patients with newly diagnosed glioblastoma over a 10-year period. Patients with RIGB were identified according to Cahan's criteria for radiation-induced tumors. A case-control analysis was performed to compare known prognostic factors for overall survival (OS) with an independent cohort of IDH-1 wildtype de novo glioblastomas treated with standard temozolomide chemoradiotherapy. Survival analysis was performed by Cox proportional hazards regression. RESULTS A total of 590 adult patients were diagnosed with glioblastoma. 19 patients (3%) had RIGB. The mean age of patients upon diagnosis was 48 years ± 15. The mean latency duration from radiotherapy to RIGB was 14 years ± 8. The mean total dose was 58Gy ± 10. One-third of patients (37%, 7/19) had nasopharyngeal cancer and a fifth (21%, 4/19) had primary intracranial germinoma. Compared to a cohort of 146 de novo glioblastoma patients, RIGB patients had a shorter median OS of 4.8 months versus 19.2 months (p-value: <.001). Over a third of RIGBs involved the cerebellum (37%, 7/19) and was higher than the control group (4%, 6/146; p-value: <.001). A fifth of RIGBs (21%, 3/19) were pMGMT methylated which was significantly fewer than the control group (49%, 71/146; p-value: .01). For RIGB patients (32%, 6/19) treated with re-irradiation, the one-year survival rate was 67% and only 8% for those without such treatment (p-value: .007). CONCLUSION The propensity for RIGBs to develop in the cerebellum and to be pMGMT unmethylated may contribute to their poorer prognosis. When possible re-irradiation may offer a survival benefit. Nasopharyngeal cancer and germinomas accounted for the majority of original malignancies reflecting their prevalence among Southern Chinese.
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Affiliation(s)
- Peter Y M Woo
- Department of Neurosurgery, Kwong Wah Hospital, Hong Kong, Hong Kong
| | - Jennifer W Y Lee
- Department of Neurosurgery, Kwong Wah Hospital, Hong Kong, Hong Kong
| | - Sandy W Lam
- Department of Neurosurgery, Kwong Wah Hospital, Hong Kong, Hong Kong
| | - Jenny K S Pu
- Division of Neurosurgery, Department of Surgery, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Danny T M Chan
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Shatin, Hong Kong
| | - Calvin H K Mak
- Department of Neurosurgery, Queen Elizabeth Hospital, Hong Kong, Hong Kong
| | - Jason M K Ho
- Department of Neurosurgery, Tuen Mun Hospital, Hong Kong, Hong Kong
| | - Sui-To Wong
- Department of Neurosurgery, Tuen Mun Hospital, Hong Kong, Hong Kong
| | - Yin-Chung Po
- Department of Neurosurgery, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Michael W Y Lee
- Department of Neurosurgery, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong
| | - Kwong-Yau Chan
- Department of Neurosurgery, Kwong Wah Hospital, Hong Kong, Hong Kong
| | - Wai-Sang Poon
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Shatin, Hong Kong
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Slowly M, Domingo-Relloso A, Santella RM, Haack K, Fallin DM, Terry MB, Rhoades DA, Herreros-Martinez M, Garcia-Esquinas E, Cole SA, Tellez-Plaza M, Navas-Acien A, Wu HC. Blood DNA methylation and liver cancer in American Indians: evidence from the Strong Heart Study. Cancer Causes Control 2024; 35:661-669. [PMID: 38010586 PMCID: PMC10960679 DOI: 10.1007/s10552-023-01822-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE Liver cancer incidence among American Indians/Alaska Natives has risen over the past 20 years. Peripheral blood DNA methylation may be associated with liver cancer and could be used as a biomarker for cancer risk. We evaluated the association of blood DNA methylation with risk of liver cancer. METHODS We conducted a prospective cohort study in 2324 American Indians, between age 45 and 75 years, from Arizona, Oklahoma, North Dakota and South Dakota who participated in the Strong Heart Study between 1989 and 1991. Liver cancer deaths (n = 21) were ascertained using death certificates obtained through 2017. The mean follow-up duration (SD) for non-cases was 25.1 (5.6) years and for cases, 11.0 (8.8) years. DNA methylation was assessed from blood samples collected at baseline using MethylationEPIC BeadChip 850 K arrays. We used Cox regression models adjusted for age, sex, center, body mass index, low-density lipoprotein cholesterol, smoking, alcohol consumption, and immune cell proportions to examine the associations. RESULTS We identified 9 CpG sites associated with liver cancer. cg16057201 annotated to MRFAP1) was hypermethylated among cases vs. non-cases (hazard ratio (HR) for one standard deviation increase in methylation was 1.25 (95% CI 1.14, 1.37). The other eight CpGs were hypomethylated and the corresponding HRs (95% CI) ranged from 0.58 (0.44, 0.75) for cg04967787 (annotated to PPRC1) to 0.77 (0.67, 0.88) for cg08550308. We also assessed 7 differentially methylated CpG sites associated with liver cancer in previous studies. The adjusted HR for cg15079934 (annotated to LPS1) was 1.93 (95% CI 1.10, 3.39). CONCLUSIONS Blood DNA methylation may be associated with liver cancer mortality and may be altered during the development of liver cancer.
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Affiliation(s)
- Monique Slowly
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Daniele M Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Dorothy A Rhoades
- Department of Medicine, Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK, USA
| | | | - Esther Garcia-Esquinas
- Universidad Autónoma de Madrid, Madrid, Spain
- CIBERESP (CIBER of Epidemiology and Public Health), Madrid, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Hui-Chen Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
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Aroke EN, Srinivasasainagendra V, Kottae P, Quinn TL, Wiggins AM, Hobson J, Kinnie K, Stoudmire T, Tiwari HK, Goodin BR. The Pace of Biological Aging Predicts Nonspecific Chronic Low Back Pain Severity. J Pain 2024; 25:974-983. [PMID: 37907115 PMCID: PMC10960701 DOI: 10.1016/j.jpain.2023.10.018] [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] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/15/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
This study aimed to determine if and how the pace of biological aging was associated with nonspecific chronic low back pain (cLBP) and compare what measure of epigenetic age acceleration most strongly predicts cLBP outcomes. We used the Dunedin Pace of Aging from the Epigenome (DunedinPACE), Horvath's, Hannum's, and PhenoAge clocks to determine the pace of biological aging in 69 cLBP, and 49 pain-free controls (PFCs) adults, ages 18 to 85 years. On average, participants with cLBP had higher DunedinPACE (P < .001) but lower Horvath (P = .04) and Hannum (P = .02) accelerated epigenetic age than PFCs. There was no significant difference in PhenoAge acceleration between the cLBP and PFC groups (P = .97). DunedinPACE had the largest effect size (Cohen's d = .78) on group differences. In univariate regressions, a unit increase in DunedinPACE score was associated with 265.98 times higher odds of cLBP than the PFC group (P < .001). After controlling for sex, race, and body mass index (BMI), the odds ratio of cLBP to PFC group was 149.62 (P < .001). Furthermore, among participants with cLBP, DunedinPACE scores positively correlated with pain severity (rs = .385, P = .001) and interference (rs = .338, P = .005). Epigenetic age acceleration from Horvath, Hannum, and PhenoAge clocks were not significant predictors of cLBP. The odds of a faster pace of biological aging are higher among adults with cLBP, and this was associated with greater pain severity and disability. Future interventions to slow the pace of biological aging may improve cLBP outcomes. PERSPECTIVE: Accelerated epigenetic aging is common among adults with nonspecific cLBP. Higher DunedinPACE scores positively correlate with pain severity and interference, and better predict cLBP than other DNA methylation clocks. Interventions to slow the pace of biological aging may be viable targets for improving pain outcomes.
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Affiliation(s)
- Edwin N. Aroke
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pooja Kottae
- Department of Computer Science, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tammie L. Quinn
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Asia M. Wiggins
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joanna Hobson
- Department of Psychology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kiari Kinnie
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tonya Stoudmire
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Burel R. Goodin
- Department of Anesthesiology, School of Medicine, Washington University, St Louis, USA
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