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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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2
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Zang Z, Yin Y, Liu C, Zhu Q, Huang X, Li H, Yang R. IL21R hypomethylation as a biomarker for distinguishing benign and malignant breast tumours. Epigenetics 2024; 19:2352683. [PMID: 38723244 PMCID: PMC11086039 DOI: 10.1080/15592294.2024.2352683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Some benign and malignant breast tumours are similar in pathological morphology, which are difficult to be distinguished in clinical diagnosis. In this study, we intended to explore novel biomarkers for differential diagnosis of benign and malignant breast tumours. Methylation EPIC 850K beadchip and RNA-sequencing were used to analyse 29 tissue samples from patients with early-stage breast cancer (BC) and benign breast tumours for differently methylated and expressed genes. The altered methylation of IL21R was semi-quantitatively validated in an independent study with 566 tissue samples (279 BC vs. 287 benign breast tumours) using mass spectrometry. Binary logistic regression analysis was performed to evaluate the association between IL21R methylation and BC. BC-associated IL21R hypomethylation and overexpression were identified in the discovery round. In the validation round, BC patients presented significant IL21R hypomethylation compared to women with benign breast tumours (ORs ≥1.29 per-10% methylation, p-values ≤ 5.69E-14), and this hypomethylation was even enhanced in BC patients with ER-negative and PR-negative tumours as well as with triple-negative tumours. The methylation of IL21R showed efficient discriminatory power to distinguish benign breast tumours from BC (area under curve (AUC) = 0.88), and especially from ER-negative BC (AUC = 0.95), PR-negative BC (AUC = 0.93) and triple-negative BC (AUC = 0.96). We disclosed significant IL21R hypomethylation in patients with BC compared to women with benign breast tumours, and revealed the somatic change of DNA methylation could be a potential biomarker for molecular pathology of BC.
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Affiliation(s)
- Zishan Zang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifei Yin
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuandong Huang
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Hong Li
- Department of Pathology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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3
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Stanojević D, Li Z, Bakić S, Foo R, Šikić M. Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing. Nat Commun 2024; 15:5580. [PMID: 38961062 PMCID: PMC11222435 DOI: 10.1038/s41467-024-49847-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
DNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most important methylation in mammals is 5-methylcytosine mostly occurring in the context of CpG dinucleotides. Sequencing methods such as whole-genome bisulfite sequencing successfully detect 5-methylcytosine DNA modifications. However, they suffer from the serious drawbacks of short read lengths and might introduce an amplification bias. Here we present Rockfish, a deep learning algorithm that significantly improves read-level 5-methylcytosine detection by using Nanopore sequencing. Rockfish is compared with other methods based on Nanopore sequencing on R9.4.1 and R10.4.1 datasets. There is an increase in the single-base accuracy and the F1 measure of up to 5 percentage points on R.9.4.1 datasets, and up to 0.82 percentage points on R10.4.1 datasets. Moreover, Rockfish shows a high correlation with whole-genome bisulfite sequencing, requires lower read depth, and achieves higher confidence in biologically important regions such as CpG-rich promoters while being computationally efficient. Its superior performance in human and mouse samples highlights its versatility for studying 5-methylcytosine methylation across varied organisms and diseases. Finally, its adaptable architecture ensures compatibility with new versions of pores and chemistry as well as modification types.
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Affiliation(s)
- Dominik Stanojević
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Zhe Li
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sara Bakić
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Roger Foo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mile Šikić
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia.
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4
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Taff CC, McNew SM, Campagna L, Vitousek MN. Corticosterone exposure is associated with long-term changes in DNA methylation, physiology and breeding decisions in a wild bird. Mol Ecol 2024:e17456. [PMID: 38953311 DOI: 10.1111/mec.17456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 06/07/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
When facing challenges, vertebrates activate a hormonal stress response that can dramatically alter behaviour and physiology. Although this response can be costly, conceptual models suggest that it can also recalibrate the stress response system, priming more effective responses to future challenges. Little is known about whether this process occurs in wild animals, particularly in adulthood, and if so, how information about prior experience with stressors is encoded. One potential mechanism is hormonally mediated changes in DNA methylation. We simulated the spikes in corticosterone that accompany a stress response using non-invasive dosing in tree swallows (Tachycineta bicolor) and monitored the phenotypic effects 1 year later. In a subset of individuals, we characterized DNA methylation using reduced representation bisulfite sequencing shortly after treatment and a year later. The year after treatment, experimental females had stronger negative feedback and initiated breeding earlier-traits that are associated with stress resilience and reproductive performance in our population-and higher baseline corticosterone. We also found that natural variation in corticosterone predicted patterns of DNA methylation. Finally, corticosterone treatment influenced methylation on short (1-2 weeks) and long (1 year) time scales; however, these changes did not have clear links to functional regulation of the stress response. Taken together, our results are consistent with corticosterone-induced priming of future stress resilience and support DNA methylation as a potential mechanism, but more work is needed to demonstrate functional consequences. Uncovering the mechanisms linking experience with the response to future challenges has implications for understanding the drivers of stress resilience.
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Affiliation(s)
- Conor C Taff
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Biology, Colby College, Waterville, Maine, USA
| | - Sabrina M McNew
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Leonardo Campagna
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Maren N Vitousek
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
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5
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Çokoğlu SS, Koptekin D, Fidan FR, Somel M. Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise. Evol Appl 2024; 17:e13743. [PMID: 38957308 PMCID: PMC11217591 DOI: 10.1111/eva.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024] Open
Abstract
The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.
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Affiliation(s)
| | - Dilek Koptekin
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
| | | | - Mehmet Somel
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
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Kolli RT, Glenn TC, Bringolf RB, Henderson M, Cummings BS, Kenneke JF. Changes in CpG Methylation of the Vitellogenin 1 Promoter in Adult Male Zebrafish after Exposure to 17α-Ethynylestradiol. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:1547-1556. [PMID: 38785270 DOI: 10.1002/etc.5879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/17/2023] [Accepted: 03/28/2024] [Indexed: 05/25/2024]
Abstract
Numerous pharmaceutical and industrial chemicals are classified as endocrine-disrupting chemicals (EDCs) that interfere with hormonal homeostasis, leading to developmental disorders and other pathologies. The synthetic estrogen 17α-ethynylestradiol (EE2) is used in oral contraceptives and other hormone therapies. EE2 and other estrogens are inadvertently introduced into aquatic environments through municipal wastewater and agricultural effluents. Exposure of male fish to estrogens increases expression of the egg yolk precursor protein vitellogenin (Vtg), which is used as a molecular marker of exposure to estrogenic EDCs. The mechanisms behind Vtg induction are not fully known, and we hypothesized that it is regulated via DNA methylation. Adult zebrafish were exposed to either dimethyl sulfoxide or 20 ng/L EE2 for 14 days. Messenger RNA (mRNA) expression and DNA methylation were assessed in male zebrafish livers at 0, 0.25, 0.5, 1, 4, 7, and 14 days of exposure; and those of females were assessed at 13 days (n ≥ 4/group/time point). To test the persistence of any changes, we included a recovery group that received EE2 for 7 days and did not receive any for the following 7 days, in the total 14-day study. Methylation of DNA at the vtg1 promoter was assessed with targeted gene bisulfite sequencing in livers of adult male and female zebrafish. A significant increase in vtg1 mRNA was observed in the EE2-exposed male fish as early as 6 h. Interestingly, DNA methylation changes were observed at 4 days. Decreases in the overall methylation of the vtg1 promoter in exposed males resulted in levels comparable to those in female controls, suggesting feminization. Importantly, DNA methylation levels in males remained significantly impacted after 7 days post-EE2 removal, unlike mRNA levels. These data identify an epigenetic mark of feminization that may serve as an indicator of not only estrogenic exposure but also previous exposure to EE2. Environ Toxicol Chem 2024;43:1547-1556. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Ramya T Kolli
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
- Student Services Authority, Athens, Georgia, USA
| | - Travis C Glenn
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
- Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - Robert B Bringolf
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | - Matthew Henderson
- Center for Environmental Measurement and Modeling, Office of Research and Development, US Environmental Protection Agency, Athens, Georgia
| | - Brian S Cummings
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
- Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - John F Kenneke
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Athens, Georgia
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Nair VD, Pincas H, Smith GR, Zaslavsky E, Ge Y, Amper MAS, Vasoya M, Chikina M, Sun Y, Raja AN, Mao W, Gay NR, Esser KA, Smith KS, Zhao B, Wiel L, Singh A, Lindholm ME, Amar D, Montgomery S, Snyder MP, Walsh MJ, Sealfon SC. Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures. CELL GENOMICS 2024; 4:100421. [PMID: 38697122 PMCID: PMC11228891 DOI: 10.1016/j.xgen.2023.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 05/04/2024]
Abstract
Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8 weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.
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Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gregory R Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mary Anne S Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mital Vasoya
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Weiguang Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicole R Gay
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Karyn A Esser
- Department of Physiology and Aging, University of Florida, Gainesville, FL 32610, USA
| | - Kevin S Smith
- Departments of Pathology and Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Bingqing Zhao
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Laurens Wiel
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Aditya Singh
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Malene E Lindholm
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - David Amar
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Stephen Montgomery
- Departments of Pathology and Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596845. [PMID: 38895201 PMCID: PMC11185511 DOI: 10.1101/2024.05.31.596845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.
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Yuan B, Qi Y, Zhang X, Hu J, Fan Y, Ji X. The relationship of MITF gene expression and promoter methylation with plumage colour in quail. Br Poult Sci 2024; 65:259-264. [PMID: 38578288 DOI: 10.1080/00071668.2024.2326962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/16/2024] [Indexed: 04/06/2024]
Abstract
1. This study focused on the relationship between MITF mRNA expression and plumage colour in quail and the effect of promoter methylation on the expression of MITF mRNA.2. The CDS region of MITF mRNA was cloned by RT-PCR, followed by DNA sequencing. The RT-qPCR method was used to analyse the expression levels of MITF mRNA in dorsal skin tissue in Korean quail and Beijing white quail. The promoter region of the MITF gene was cloned, and the CpG island was predicted by the CpGplot program. The methylation levels of the CpG island were analysed using BS-PCR technology.3. Quail MITF mRNA contains a 1,476 bp complete ORF, which encodes a 492 amino acid residue protein. The MITF protein has no signal peptide or transmembrane region. The expression of MITF mRNA in dorsal tissue of Korean quail was significantly higher than that in Beijing white quail (p < 0.01). Abundant cis-elements and a 346 bp CpG island were found in the promoter region of the MITF gene. The average methylation level of the CpG island was 22 (22%) in Korean quail, and 46 (30%) in Beijing white quail (p < 0.05).4. The hypermethylation of the MITF gene promoter region in Beijing white quail resulted in a decrease in expression level, which was related to white feather colour.
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Affiliation(s)
- B Yuan
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Y Qi
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - X Zhang
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - J Hu
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Y Fan
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Xingyu Ji
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
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10
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Bittel AJ, Chen YW. DNA Methylation in the Adaptive Response to Exercise. Sports Med 2024; 54:1419-1458. [PMID: 38561436 DOI: 10.1007/s40279-024-02011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.
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Affiliation(s)
- Adam J Bittel
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St NW, Washington, DC, 20052, USA
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11
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Salazar M, Joly S, Anglada-Escudé G, Ribas L. Epigenetic and physiological alterations in zebrafish subjected to hypergravity. PLoS One 2024; 19:e0300310. [PMID: 38776274 PMCID: PMC11111069 DOI: 10.1371/journal.pone.0300310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/27/2024] [Indexed: 05/24/2024] Open
Abstract
Gravity is one of the most constant environmental factors across Earth's evolution and all organisms are adapted to it. Consequently, spatial exploration has captured the interest in studying the biological changes that physiological alterations are caused by gravity. In the last two decades, epigenetics has explained how environmental cues can alter gene functions in organisms. Although many studies addressed gravity, the underlying biological and molecular mechanisms that occur in altered gravity for those epigenetics-related mechanisms, are mostly inexistent. The present study addressed the effects of hypergravity on development, behavior, gene expression, and most importantly, on the epigenetic changes in a worldwide animal model, the zebrafish (Danio rerio). To perform hypergravity experiments, a custom-centrifuge simulating the large diameter centrifuge (100 rpm ~ 3 g) was designed and zebrafish embryos were exposed during 5 days post fertilization (dpf). Results showed a significant decrease in survival at 2 dpf but no significance in the hatching rate. Physiological and morphological alterations including fish position, movement frequency, and swimming behavior showed significant changes due to hypergravity. Epigenetic studies showed significant hypermethylation of the genome of the zebrafish larvae subjected to 5 days of hypergravity. Downregulation of the gene expression of three epigenetic-related genes (dnmt1, dnmt3, and tet1), although not significant, was further observed. Taken altogether, gravity alterations affected biological responses including epigenetics in fish, providing a valuable roadmap of the putative hazards of living beyond Earth.
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Affiliation(s)
- Marcela Salazar
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
| | - Silvia Joly
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
| | - Guillem Anglada-Escudé
- Department of Astrophysics, Institut de Ciències de l’Espai—Consejo Superior de Investigaciones Científicas (ICE-CSIC), UAB Campus at Cerdanyola del Vallès, Barcelona, Spain
- Institut d’Estudis Espacials de Catalunya–IEEC/CERCA, Gran Capità, 2–4, Edifici Nexus, Despatx 201, Barcelona, Spain
| | - Laia Ribas
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
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Nadiger N, Veed JK, Chinya Nataraj P, Mukhopadhyay A. DNA methylation and type 2 diabetes: a systematic review. Clin Epigenetics 2024; 16:67. [PMID: 38755631 PMCID: PMC11100087 DOI: 10.1186/s13148-024-01670-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE DNA methylation influences gene expression and function in the pathophysiology of type 2 diabetes mellitus (T2DM). Mapping of T2DM-associated DNA methylation could aid early detection and/or therapeutic treatment options for diabetics. DESIGN A systematic literature search for associations between T2DM and DNA methylation was performed. Prospero registration ID: CRD42020140436. METHODS PubMed and ScienceDirect databases were searched (till October 19, 2023). Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and New Castle Ottawa scale were used for reporting the selection and quality of the studies, respectively. RESULT Thirty-two articles were selected. Four of 130 differentially methylated genes in blood, adipose, liver or pancreatic islets (TXNIP, ABCG1, PPARGC1A, PTPRN2) were reported in > 1 study. TXNIP was hypomethylated in diabetic blood across ethnicities. Gene enrichment analysis of the differentially methylated genes highlighted relevant disease pathways (T2DM, type 1 diabetes and adipocytokine signaling). Three prospective studies reported association of methylation in IGFBP2, MSI2, FTO, TXNIP, SREBF1, PHOSPHO1, SOCS3 and ABCG1 in blood at baseline with incident T2DM/hyperglycemia. Sex-specific differential methylation was reported only for HOOK2 in visceral adipose tissue (female diabetics: hypermethylated, male diabetics: hypomethylated). Gene expression was inversely associated with methylation status in 8 studies, in genes including ABCG1 (blood), S100A4 (adipose tissue), PER2 (pancreatic islets), PDGFA (liver) and PPARGC1A (skeletal muscle). CONCLUSION This review summarizes available evidence for using DNA methylation patterns to unravel T2DM pathophysiology. Further validation studies in diverse populations will set the stage for utilizing this knowledge for identifying early diagnostic markers and novel druggable pathways.
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Affiliation(s)
- Nikhil Nadiger
- Research Scholar, Manipal Academy of Higher Education, Manipal, India
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Jyothisha Kana Veed
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Priyanka Chinya Nataraj
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
- Vedantu, Bangalore, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India.
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13
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Mas-Ponte D, Supek F. Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation. Nucleic Acids Res 2024; 52:4393-4408. [PMID: 38587182 PMCID: PMC11077091 DOI: 10.1093/nar/gkae252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Local mutation rates in human are highly heterogeneous, with known variability at the scale of megabase-sized chromosomal domains, and, on the other extreme, at the scale of oligonucleotides. The intermediate, kilobase-scale heterogeneity in mutation risk is less well characterized. Here, by analyzing thousands of somatic genomes, we studied mutation risk gradients along gene bodies, representing a genomic scale spanning roughly 1-10 kb, hypothesizing that different mutational mechanisms are differently distributed across gene segments. The main heterogeneity concerns several kilobases at the transcription start site and further downstream into 5' ends of gene bodies; these are commonly hypomutated with several mutational signatures, most prominently the ubiquitous C > T changes at CpG dinucleotides. The width and shape of this mutational coldspot at 5' gene ends is variable across genes, and corresponds to variable interval of lowered DNA methylation depending on gene activity level and regulation. Such hypomutated loci, at 5' gene ends or elsewhere, correspond to DNA hypomethylation that can associate with various landmarks, including intragenic enhancers, Polycomb-marked regions, or chromatin loop anchor points. Tissue-specific DNA hypomethylation begets tissue-specific local hypomutation. Of note, direction of mutation risk is inverted for AID/APOBEC3 cytosine deaminase activity, whose signatures are enriched in hypomethylated regions.
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Affiliation(s)
- David Mas-Ponte
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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14
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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15
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024; 17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. RESULTS Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. CONCLUSIONS Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Loic H Steinthal
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Dias
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gladys E Zapata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA.
| | - Alli M Nuotio-Antar
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.
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Melis M, Loi E, Mastinu M, Naciri LC, Zavattari P, Barbarossa IT. Gene Methylation Affects Salivary Levels of the Taste Buds' Trophic Factor, Gustin Protein. Nutrients 2024; 16:1304. [PMID: 38732551 PMCID: PMC11085126 DOI: 10.3390/nu16091304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
The salivary protein, Gustin/carbonic anhydrase VI, has been described as a trophic factor responsible for the growth of taste buds. We found, in a genetically homogeneous population, that the polymorphism rs2274333 (A/G) of the Gustin gene is crucial for the full functionality of the protein and is associated with taste sensitivity. However, other studies have failed to find this evidence. Here, we verified if Gustin gene methylation can affect the salivary levels of the protein, also concerning the polymorphism rs2274333 and PROP bitter responsiveness. The Gustin gene methylation profiling and the quantification of the Gustin salivary levels were determined in sixty-six volunteers genotyped for the polymorphism rs2274333 (A/G) (Ser90Gly in the protein sequence). The fungiform papillae density was also determined. The results confirm our earlier observations by showing that AA genotypes had a greater density of fungiform taste papillae, whereas the GG genotypes showed a lower density. We also found variations in the protein levels in the three genotype groups and an inverse relationship between Gustin gene methylation and the salivary levels of the protein, mostly evident in AA and ST volunteers, i.e., in volunteers who would be carriers of the functional isoform of the protein. These findings could justify the conflicting data in the literature.
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Affiliation(s)
- Melania Melis
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (E.L.); (L.C.N.); (P.Z.); (I.T.B.)
| | - Eleonora Loi
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (E.L.); (L.C.N.); (P.Z.); (I.T.B.)
| | - Mariano Mastinu
- Smell & Taste Clinic, Department of Otorhinolaryngology, Technical University of Dresden, 01307 Dresden, Germany;
| | - Lala Chaimae Naciri
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (E.L.); (L.C.N.); (P.Z.); (I.T.B.)
| | - Patrizia Zavattari
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (E.L.); (L.C.N.); (P.Z.); (I.T.B.)
| | - Iole Tomassini Barbarossa
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (E.L.); (L.C.N.); (P.Z.); (I.T.B.)
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17
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Thomas D, Palczewski M, Kuschman H, Hoffman B, Yang H, Glynn S, Wilson D, Kool E, Montfort W, Chang J, Petenkaya A, Chronis C, Cundari T, Sappa S, Islam K, McVicar D, Fan Y, Chen Q, Meerzaman D, Sierk M. Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome. RESEARCH SQUARE 2024:rs.3.rs-4131804. [PMID: 38645113 PMCID: PMC11030528 DOI: 10.21203/rs.3.rs-4131804/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
DNA methylation at cytosine bases of eukaryotic DNA (5-methylcytosine, 5mC) is a heritable epigenetic mark that can regulate gene expression in health and disease. Enzymes that metabolize 5mC have been well-characterized, yet the discovery of endogenously produced signaling molecules that regulate DNA methyl-modifying machinery have not been described. Herein, we report that the free radical signaling molecule nitric oxide (NO) can directly inhibit the Fe(II)/2-OG-dependent DNA demethylases ten-eleven translocation (TET) and human AlkB homolog 2 (ALKBH2). Physiologic NO concentrations reversibly inhibited TET and ALKBH2 demethylase activity by binding to the mononuclear non-heme iron atom which formed a dinitrosyliron complex (DNIC) preventing cosubstrates (2-OG and O2) from binding. In cancer cells treated with exogenous NO, or cells endogenously synthesizing NO, there was a global increase in 5mC and 5-hydroxymethylcytosine (5hmC) in DNA, the substrates for TET, that could not be attributed to increased DNA methyltransferase activity. 5mC was also elevated in NO-producing cell-line-derived mouse xenograft and patient-derived xenograft tumors. Genome-wide DNA methylome analysis of cells chronically treated with NO (10 days) demonstrated enrichment of 5mC and 5hmC at gene-regulatory loci which correlated to changes in the expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a novel epigenetic role for NO.
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Affiliation(s)
| | - Marianne Palczewski
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences
| | - Hannah Kuschman
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences
| | | | - Hao Yang
- Weinberg College of Arts and Sciences, Northwestern University, Department of Chemistry
| | - Sharon Glynn
- University of Galway, College of Medicine, Nursing and Health Sciences, School of Medicine, D. of Pathology
| | | | - Eric Kool
- Stanford University, Department of Chemistry, School of Humanities and Sciences
| | | | - Jenny Chang
- Houston Methodist, Department of Medicine and Oncology, Weill Cornell Medical College
| | - Aydolun Petenkaya
- University of Illinois Chicago, College of Medicine, Biochemistry and Molecular Genetics
| | - Constantinos Chronis
- University of Illinois Chicago, College of Medicine, Biochemistry and Molecular Genetics
| | | | - Sushma Sappa
- University of Pittsburgh, Department of Chemistry
| | | | - Daniel McVicar
- National Institutes of Health, National Cancer Institute, Center for Cancer Research
| | - Yu Fan
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Qingrong Chen
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Daoud Meerzaman
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Michael Sierk
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
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18
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Wang M, Bissonnette N, Laterrière M, Dudemaine PL, Gagné D, Roy JP, Sirard MA, Ibeagha-Awemu EM. DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits. BMC Biol 2024; 22:65. [PMID: 38486242 PMCID: PMC10941392 DOI: 10.1186/s12915-024-01843-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND DNA methylation has been documented to play vital roles in diseases and biological processes. In bovine, little is known about the regulatory roles of DNA methylation alterations on production and health traits, including mastitis. RESULTS Here, we employed whole-genome DNA methylation sequencing to profile the DNA methylation patterns of milk somatic cells from sixteen cows with naturally occurring Staphylococcus aureus (S. aureus) subclinical mastitis and ten healthy control cows. We observed abundant DNA methylation alterations, including 3,356,456 differentially methylated cytosines and 153,783 differential methylation haplotype blocks (dMHBs). The DNA methylation in regulatory regions, including promoters, first exons and first introns, showed global significant negative correlations with gene expression status. We identified 6435 dMHBs located in the regulatory regions of differentially expressed genes and significantly correlated with their corresponding genes, revealing their potential effects on transcriptional activities. Genes harboring DNA methylation alterations were significantly enriched in multiple immune- and disease-related pathways, suggesting the involvement of DNA methylation in regulating host responses to S. aureus subclinical mastitis. In addition, we found nine discriminant signatures (differentiates cows with S. aureus subclinical mastitis from healthy cows) representing the majority of the DNA methylation variations related to S. aureus subclinical mastitis. Validation of seven dMHBs in 200 cows indicated significant associations with mammary gland health (SCC and SCS) and milk production performance (milk yield). CONCLUSIONS In conclusion, our findings revealed abundant DNA methylation alterations in milk somatic cells that may be involved in regulating mammary gland defense against S. aureus infection. Particularly noteworthy is the identification of seven dMHBs showing significant associations with mammary gland health, underscoring their potential as promising epigenetic biomarkers. Overall, our findings on DNA methylation alterations offer novel insights into the regulatory mechanisms of bovine subclinical mastitis, providing further avenues for the development of effective control measures.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Université de Montréal, St-Hyacinthe, QC, Canada
| | | | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
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19
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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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20
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Cao P, Li H, Wang P, Zhang X, Guo Y, Zhao K, Guo J, Li X, Nashun B. DNA Hypomethylation-Mediated Transcription Dysregulation Participates in Pathogenesis of Polycystic Ovary Syndrome. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00072-5. [PMID: 38403164 DOI: 10.1016/j.ajpath.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a highly heterogeneous and genetically complex endocrine disorder. Although the etiology remains mostly elusive, growing evidence suggested abnormal changes of DNA methylation correlate well with systemic and tissue-specific dysfunctions in PCOS. A dehydroepiandrosterone-induced PCOS-like mouse model was generated, which has a similar metabolic and reproductive phenotype as human patients with PCOS, and was used to experimentally validate the potential role of aberrant DNA methylation in PCOS in this study. Integrated DNA methylation and transcriptome analysis revealed the potential role of genomic DNA hypomethylation in transcription regulation of PCOS and identified several key candidate genes, including BMP4, Adcy7, Tnfaip3, and Fas, which were regulated by aberrant DNA hypomethylation. Moreover, i.p. injection of S-adenosylmethionine increased the overall DNA methylation level of PCOS-like mice and restored expression of the candidate genes to similar levels as the control, alleviating reproductive and metabolic abnormalities in PCOS-like mice. These findings provided direct evidence showing the importance of normal DNA methylation in epigenetic regulation of PCOS and potential targets for diagnosis and treatment of the disease.
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Affiliation(s)
- Pengbo Cao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Inner Mongolia Qilu Pharmaceutical Company, Hohhot, China
| | - Haoran Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Peijun Wang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xinna Zhang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuxuan Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Keyu Zhao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiaojiao Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xihe Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animals, Hohhot, China
| | - Buhe Nashun
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
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21
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Pelland-St-Pierre L, Pham MC, Nguyen AQH, Pasquet R, Taylor SA, Bosson-Rieutort D, Koushik A, Ho V. The Influence of Smoking and Occupational Risk Factors on DNA Methylation in the AHRR and F2RL3 Genes. Cancer Epidemiol Biomarkers Prev 2024; 33:224-233. [PMID: 38051301 DOI: 10.1158/1055-9965.epi-23-0828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND AHRR and F2RL3 hypomethylation has been associated with lung cancer. In this study, we investigated the cross-sectional association between smoking and occupational exposures, and AHRR and F2RL3 methylation. METHODS A case-control study was nested in CARTaGENE to examine the association between AHRR and F2RL3 methylation and lung cancer risk (200 cases; 400 controls). A secondary analysis was conducted using the data collected from this nested study; namely, baseline information on participants' smoking behavior and longest-held job was obtained. A cumulative smoking index summarized information on the number of cigarettes smoked, duration of smoking, and time since cessation. Exposure to 13 occupational agents was estimated using the Canadian Job Exposure Matrix. In baseline blood samples, methylation ratios of 40 CpG sites in the AHRR and F2RL3 genes were measured using Sequenom EpiTYPER. Separate least squares regression models were used to estimate the associations between smoking and occupational exposures, and average AHRR and F2RL3 methylation levels, while adjusting for confounders identified from directed acyclic graphs. RESULTS In both genes, smoking was associated with lower average methylation levels. Occupational exposure to aromatic amines, cadmium, and formaldehyde were associated with lower AHRR methylation while, only benzene was associated with F2RL3 hypomethylation; these associations were stronger among ever smokers. CONCLUSIONS Our findings support that smoking and occupational exposures to some agents are associated with AHRR and F2RL3 hypomethylation. IMPACT Our results inform on mechanisms underlying environmental exposures in lung cancer etiology; future studies should prioritize studying joint exposures.
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Affiliation(s)
- Laura Pelland-St-Pierre
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
- Centre de recherche en santé publique (CReSP), University of Montréal and CIUSSS Centre-Sud, Montréal, Québec, Canada
| | - Michael C Pham
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Alice Quynh Huong Nguyen
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Romain Pasquet
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Sherryl A Taylor
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Delphine Bosson-Rieutort
- Centre de recherche en santé publique (CReSP), University of Montréal and CIUSSS Centre-Sud, Montréal, Québec, Canada
- Department of Health Management, Evaluation and Policy, University of Montreal, Montreal, Quebec, Canada
| | - Anita Koushik
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
| | - Vikki Ho
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Quebec, Canada
- Health Innovation and Evaluation Hub, University of Montreal Hospital Research Centre (CRCHUM), Montreal, Quebec, Canada
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22
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Ghosh K, Zhou JJ, Shao JY, Chen SR, Pan HL. DNA demethylation in the hypothalamus promotes transcription of Agtr1a and Slc12a2 and hypertension development. J Biol Chem 2024; 300:105597. [PMID: 38160798 PMCID: PMC10830874 DOI: 10.1016/j.jbc.2023.105597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Increased expression of angiotensin II AT1A receptor (encoded by Agtr1a) and Na+-K+-Cl- cotransporter-1 (NKCC1, encoded by Slc12a2) in the hypothalamic paraventricular nucleus (PVN) contributes to hypertension development. However, little is known about their transcriptional control in the PVN in hypertension. DNA methylation is a critical epigenetic mechanism that regulates gene expression. Here, we determined whether transcriptional activation of Agtr1a and Slc12a2 results from altered DNA methylation in spontaneously hypertensive rats (SHR). Methylated DNA immunoprecipitation and bisulfite sequencing-PCR showed that CpG methylation at Agtr1a and Slc12a2 promoters in the PVN was progressively diminished in SHR compared with normotensive Wistar-Kyoto rats (WKY). Chromatin immunoprecipitation-quantitative PCR revealed that enrichment of DNA methyltransferases (DNMT1 and DNMT3A) and methyl-CpG binding protein 2, a DNA methylation reader protein, at Agtr1a and Slc12a2 promoters in the PVN was profoundly reduced in SHR compared with WKY. By contrast, the abundance of ten-eleven translocation enzymes (TET1-3) at Agtr1a and Slc12a2 promoters in the PVN was much greater in SHR than in WKY. Furthermore, microinjecting of RG108, a selective DNMT inhibitor, into the PVN of WKY increased arterial blood pressure and correspondingly potentiated Agtr1a and Slc12a2 mRNA levels in the PVN. Conversely, microinjection of C35, a specific TET inhibitor, into the PVN of SHR markedly reduced arterial blood pressure, accompanied by a decrease in Agtr1a and Slc12a2 mRNA levels in the PVN. Collectively, our findings suggest that DNA hypomethylation resulting from the DNMT/TET switch at gene promoters in the PVN promotes transcription of Agtr1a and Slc12a2 and hypertension development.
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Affiliation(s)
- Krishna Ghosh
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing-Jing Zhou
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian-Ying Shao
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shao-Rui Chen
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui-Lin Pan
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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23
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Vasileva F, Hristovski R, Font-Lladó R, Georgiev G, Sacot A, López-Ros V, Calleja-González J, Barretina-Ginesta J, López-Bermejo A, Prats-Puig A. Physical Exercise-Induced DNA Methylation in Disease-Related Genes in Healthy Adults-A Systematic Review With Bioinformatic Analysis. J Strength Cond Res 2024; 38:384-393. [PMID: 38088908 DOI: 10.1519/jsc.0000000000004686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
ABSTRACT Vasileva, F, Hristovski, R, Font-Lladó, R, Georgiev, G, Sacot, A, López-Ros, V, Calleja-González, J, Barretina-Ginesta, J, López-Bermejo, A, and Prats-Puig, A. Physical exercise-induced DNA methylation in disease-related genes in healthy adults-A systematic review with bioinformatic analysis. J Strength Cond Res 38(2): 384-393, 2024-This study aimed to systematically review the existing literature regarding physical exercise (PE) and DNA methylation (DNAm) in healthy adults. Specific goals were to (a) identify differently methylated genes (DMGs) after PE intervention, their imprinting status, chromosome and genomic location, function, and related diseases; and (b) to screen for core genes and identify methylation changes of the core genes that can be modified by PE intervention. Our search identified 2,869 articles from which 8 were finally included. We identified 1851 DMGs ( p < 0.05) after PE intervention, although 45 of them were imprinted. Aerobic exercise (AE) seems to induce more DNA hypermethylation rather than hypomethylation, whereas anaerobic exercise (AN) seems to induce more DNA hypomethylation rather than hypermethylation. Aerobic exercise induced highest % of methylation changes on chromosome 6, whereas AN and mixed type (MT) on chromosome 1. Mixed type induced higher % of methylation changes close to transcription start site in comparison to AE and AN. After PE intervention, DMGs were mainly involved in fat metabolism, cell growth, and neuronal differentiation, whereas diseases regulated by those genes were mainly chronic diseases (metabolic, cardiovascular, neurodegenerative). Finally, 19 core genes were identified among DMGs, all related to protein metabolism. In conclusion, our findings may shed some light on the mechanisms explaining PE-induced health benefits such as the potential role that PE-induced DNAm may have in disease prevention and disease treatment.
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Affiliation(s)
- Fidanka Vasileva
- University School of Health and Sport, University of Girona, Girona, Spain
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
| | - Robert Hristovski
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Raquel Font-Lladó
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Culture and Education, Institute of Educational Research, University of Girona, Girona, Spain
| | - Georgi Georgiev
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Arnau Sacot
- University School of Health and Sport, University of Girona, Girona, Spain
- Basquet Girona, Girona, Spain
| | - Víctor López-Ros
- University School of Health and Sport, University of Girona, Girona, Spain
- Chair of Sport and Physical Education-Centre of Olympic Studies, University of Girona, Girona, Spain
| | - Julio Calleja-González
- Department of Physical Education and Sport, Faculty of Education and Sport, University of the Basque Country, Vitoria, Spain
| | | | - Abel López-Bermejo
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
- Pediatric Endocrinology, Dr. Josep Girona Hospital, Girona, Spain
- Department of Medical Sciences, University of Girona, Girona, Spain; and
| | - Anna Prats-Puig
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Clinical Anatomy, Embryology and Neuroscience, Department of Medical Sciences, University of Girona, Girona, Spain
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24
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Yu ST, Zhao R, Sun XQ, Hou MX, Cao YM, Zhang J, Chen YJ, Wang KK, Zhang Y, Li JT, Wang Q. DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp ( Cyprinus carpio). Int J Mol Sci 2024; 25:1635. [PMID: 38338913 PMCID: PMC10855618 DOI: 10.3390/ijms25031635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
DNA methylation and chromatin accessibility play important roles in gene expression, but their function in subgenome expression dominance remains largely unknown. We conducted comprehensive analyses of the transcriptome, DNA methylation, and chromatin accessibility in liver and muscle tissues of allotetraploid common carp, aiming to reveal the function of epigenetic modifications in subgenome expression dominance. A noteworthy overlap in differential expressed genes (DEGs) as well as their functions was observed across the two subgenomes. In the promoter and gene body, the DNA methylation level of the B subgenome was significantly different than that of the A subgenome. Nevertheless, differences in DNA methylation did not align with changes in homoeologous biased expression across liver and muscle tissues. Moreover, the B subgenome exhibited a higher prevalence of open chromatin regions and greater chromatin accessibility, in comparison to the A subgenome. The expression levels of genes located proximally to open chromatin regions were significantly higher than others. Genes with higher chromatin accessibility in the B subgenome exhibited significantly elevated expression levels compared to the A subgenome. Contrastingly, genes without accessibility exhibited similar expression levels in both subgenomes. This study contributes to understanding the regulation of subgenome expression dominance in allotetraploid common carp.
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Affiliation(s)
- Shuang-Ting Yu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ming-Xi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yi-Ming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ying-Jie Chen
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Kai-Kuo Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
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25
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551059. [PMID: 38328142 PMCID: PMC10849524 DOI: 10.1101/2023.07.30.551059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression data suggest a role for epigenetic modification of DNA in gene regulation in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. Taken together, our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C. Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Loic H. Steinthal
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Michelle Dias
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Hari K. Yalamanchili
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Gladys E. Zapata
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Nitesh R. Mehta
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Nicolas L. Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
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26
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Sha Q, Fu Z, Escobar Galvis ML, Madaj Z, Underwood MD, Steiner JA, Dwork A, Simpson N, Galfalvy H, Rozoklija G, Achtyes ED, Mann JJ, Brundin L. Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls. Mol Psychiatry 2024; 29:134-145. [PMID: 37938766 PMCID: PMC11078738 DOI: 10.1038/s41380-023-02311-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Suicide rates have increased steadily world-wide over the past two decades, constituting a serious public health crisis that creates a significant burden to affected families and the society as a whole. Suicidal behavior involves a multi-factorial etiology, including psychological, social and biological factors. Since the molecular neural mechanisms of suicide remain vastly uncharacterized, we examined transcriptional- and methylation profiles of postmortem brain tissue from subjects who died from suicide as well as their neurotypical healthy controls. We analyzed temporal pole tissue from 61 subjects, largely free from antidepressant and antipsychotic medication, using RNA-sequencing and DNA-methylation profiling using an array that targets over 850,000 CpG sites. Expression of NPAS4, a key regulator of inflammation and neuroprotection, was significantly downregulated in the suicide decedent group. Moreover, we identified a total of 40 differentially methylated regions in the suicide decedent group, mapping to seven genes with inflammatory function. There was a significant association between NPAS4 DNA methylation and NPAS4 expression in the control group that was absent in the suicide decedent group, confirming its dysregulation. NPAS4 expression was significantly associated with the expression of multiple inflammatory factors in the brain tissue. Overall, gene sets and pathways closely linked to inflammation were significantly upregulated, while specific pathways linked to neuronal development were suppressed in the suicide decedent group. Excitotoxicity as well as suppressed oligodendrocyte function were also implicated in the suicide decedents. In summary, we have identified central nervous system inflammatory mechanisms that may be active during suicidal behavior, along with oligodendrocyte dysfunction and altered glutamate neurotransmission. In these processes, NPAS4 might be a master regulator, warranting further studies to validate its role as a potential biomarker or therapeutic target in suicidality.
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Affiliation(s)
- Qiong Sha
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhen Fu
- Bioinformatics & Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Zach Madaj
- Bioinformatics & Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Mark D Underwood
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Jennifer A Steiner
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Andrew Dwork
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Norman Simpson
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Hanga Galfalvy
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Mental Health Data Science, New York State Psychiatric Institute, New York, NY, USA
| | - Gorazd Rozoklija
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Eric D Achtyes
- Pine Rest Christian Mental Health Services, Grand Rapids, MI, USA
- Department of Psychiatry, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - J John Mann
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Lena Brundin
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA.
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27
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Arbel-Groissman M, Menuhin-Gruman I, Yehezkeli H, Naki D, Bergman S, Udi Y, Tuller T. The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA. Methods Mol Biol 2024; 2760:371-392. [PMID: 38468099 DOI: 10.1007/978-1-0716-3658-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Genetic engineering has revolutionized our ability to manipulate DNA and engineer organisms for various applications. However, this approach can lead to genomic instability, which can result in unwanted effects such as toxicity, mutagenesis, and reduced productivity. To overcome these challenges, smart design of synthetic DNA has emerged as a promising solution. By taking into consideration the intricate relationships between gene expression and cellular metabolism, researchers can design synthetic constructs that minimize metabolic stress on the host cell, reduce mutagenesis, and increase protein yield. In this chapter, we summarize the main challenges of genomic instability in genetic engineering and address the dangers of unknowingly incorporating genomically unstable sequences in synthetic DNA. We also demonstrate the instability of those sequences by the fact that they are selected against conserved sequences in nature. We highlight the benefits of using ESO, a tool for the rational design of DNA for avoiding genetically unstable sequences, and also summarize the main principles and working parameters of the software that allow maximizing its benefits and impact.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hader Yehezkeli
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Yarin Udi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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28
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Venney CJ, Anastasiadi D, Wellenreuther M, Bernatchez L. The Evolutionary Complexities of DNA Methylation in Animals: From Plasticity to Genetic Evolution. Genome Biol Evol 2023; 15:evad216. [PMID: 38015807 PMCID: PMC10701099 DOI: 10.1093/gbe/evad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of DNA methylation in plastic responses to environmental change and evolutionary dynamics is increasingly recognized. Here, we provide a Perspective piece on the diverse roles of DNA methylation on broad evolutionary timescales, including (i) short-term transient acclimation, (ii) stable phenotypic evolution, and (iii) genomic evolution. We show that epigenetic responses vary along a continuum, ranging from short-term acclimatory responses in variable environments within a generation to long-term modifications in populations and species. DNA methylation thus unlocks additional potential for organisms to rapidly acclimate to their environment over short timeframes. If these changes affect fitness, they can circumvent the need for adaptive changes at the genome level. However, methylation has a complex reciprocal relationship with genetic variation as it can be genetically controlled, yet it can also induce point mutations and contribute to genomic evolution. When habitats remain constant over many generations, or populations are separated across habitats, initially plastic phenotypes can become hardwired through epigenetically facilitated mutagenesis. It remains unclear under what circumstances plasticity contributes to evolutionary outcomes, and when plastic changes will become permanently encoded into genotype. We highlight how studies investigating the evolution of epigenetic plasticity need to carefully consider how plasticity in methylation state could evolve among different evolutionary scenarios, the possible phenotypic outcomes, its effects on genomic evolution, and the proximate energetic and ultimate fitness costs of methylation. We argue that accumulating evidence suggests that DNA methylation can contribute toward evolution on various timescales, spanning a continuum from acclimatory plasticity to genomic evolution.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
| | - Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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30
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Sharma S, Bhonde R. Applicability of mesenchymal stem cell-derived exosomes as a cell-free miRNA therapy and epigenetic modifiers for diabetes. Epigenomics 2023; 15:1323-1336. [PMID: 38018455 DOI: 10.2217/epi-2023-0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Given that exosome nanovesicles constitute various growth factors, miRNAs and lncRNAs, they have implications for epigenetic modifications. Few studies have shown that exosomes from mesenchymal stem cells (MSCs) exhibit therapeutic effects on diabetic complications by substituting miRNAs and regulating histone modifications. Therefore, reversing epigenetic aberrations in diabetes may provide new insight into its treatment. This review discusses the impact of DNA and histone methylations on the development of diabetes and its complications. Further, we talk about miRNAs dysregulated in diabetic conditions and the possibility of utilizing mesenchymal stem cell (MSC) exosomes for the development of miRNA cell-free therapy and epigenetic modifiers in reversing diabetic-induced epigenetic alterations.
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Affiliation(s)
- Shikha Sharma
- Institute For Stem Cell Science & Regenerative Medicine, Bangalore, 560065, India
| | - Ramesh Bhonde
- Dr D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, India
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31
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Ripley DM, Garner T, Hook SA, Veríssimo A, Grunow B, Moritz T, Clayton P, Shiels HA, Stevens A. Warming during embryogenesis induces a lasting transcriptomic signature in fishes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:165954. [PMID: 37536606 DOI: 10.1016/j.scitotenv.2023.165954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/24/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023]
Abstract
Exposure to elevated temperatures during embryogenesis can influence the plasticity of tissues in later life. Despite these long-term changes in plasticity, few differentially expressed genes are ever identified, suggesting that the developmental programming of later life plasticity may occur through the modulation of other aspects of transcriptomic architecture, such as gene network organisation. Here, we use network modelling approaches to demonstrate that warm temperatures during embryonic development (developmental warming) have consistent effects in later life on the organisation of transcriptomic networks across four diverse species of fishes: Scyliorhinus canicula, Danio rerio, Dicentrarchus labrax, and Gasterosteus aculeatus. The transcriptomes of developmentally warmed fishes are characterised by an increased entropy of their pairwise gene interaction networks, implying a less structured, more 'random' set of gene interactions. We also show that, in zebrafish subject to developmental warming, the entropy of an individual gene within a network is associated with that gene's probability of expression change during temperature acclimation in later life. However, this association is absent in animals reared under 'control' conditions. Thus, the thermal environment experienced during embryogenesis can alter transcriptomic organisation in later life, and these changes may influence an individual's responsiveness to future temperature challenges.
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Affiliation(s)
- Daniel M Ripley
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.
| | - Terence Garner
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Samantha A Hook
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Ana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Bianka Grunow
- Fish Growth Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Timo Moritz
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany; Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Peter Clayton
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Holly A Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Adam Stevens
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.
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32
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Kumar S, Seem K, Kumar S, Singh A, Krishnan SG, Mohapatra T. DNA methylome analysis provides insights into gene regulatory mechanism for better performance of rice under fluctuating environmental conditions: epigenomics of adaptive plasticity. PLANTA 2023; 259:4. [PMID: 37993704 DOI: 10.1007/s00425-023-04272-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
MAIN CONCLUSION Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Archana Singh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Sehovic E, Zellers SM, Youssef MK, Heikkinen A, Kaprio J, Ollikainen M. DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study. Clin Epigenetics 2023; 15:181. [PMID: 37950287 PMCID: PMC10638786 DOI: 10.1186/s13148-023-01594-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic characterisation of pubertal timing and development could lead to important insights. Blood DNA methylation, reacting to both genotype and environment, has been associated with puberty; however, such studies are relatively scarce. We investigated peripheral blood DNA methylation profiles (using Illumina 450 K and EPIC platforms) of 1539 young adult Finnish twins associated with pubertal development scale (PDS) at ages 12 and 14 as well as pubertal age (PA). RESULTS Fixed effect meta-analysis of the two platforms on 347,521 CpGs in common identified 58 CpG sites associated (p < 1 × 10-5) with either PDS or PA. All four CpGs associated with PA and 45 CpGs associated with PDS were sex-specific. Thirteen CpGs had a high heritability (h2: 0.51-0.98), while one CpG site (mapped to GET4) had a high shared environmental component accounting for 68% of the overall variance in methylation at the site. Utilising twin discordance analysis, we found 6 CpG sites (5 associated with PDS and 1 with PA) that had an environmentally driven association with puberty. Furthermore, genes with PDS- or PA-associated CpGs were consistently linked to various developmental processes and diseases such as breast, prostate and ovarian cancer, while methylation quantitative trait loci of associated CpG sites were enriched in immune pathways developing during puberty. CONCLUSIONS By identifying puberty-associated DNA methylation sites and examining the effects of sex, environment and genetics, we shed light on the intricate interplay between environment and genetics in the context of puberty. Through our comprehensive analysis, we not only deepen the understanding of the significance of both genetic and environmental factors in the complex processes of puberty and its timing, but also gain insights into potential links with disease risks.
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Affiliation(s)
- Emir Sehovic
- Department of Life Sciences and Systems Biology, University of Turin, 10100, Turin, Italy
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy
| | - Stephanie M Zellers
- Institute for Molecular Medicine Finland, University of Helsinki, 00290, Helsinki, Finland
| | - Markus K Youssef
- Laboratory for Topology and Neuroscience, Brain Mind Institute, EPFL, 1015, Lausanne, Switzerland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, University of Helsinki, 00290, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, 00290, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
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Naya-Català F, Belenguer A, Montero D, Torrecillas S, Soriano B, Calduch-Giner J, Llorens C, Fontanillas R, Sarih S, Zamorano MJ, Izquierdo M, Pérez-Sánchez J. Broodstock nutritional programming differentially affects the hepatic transcriptome and genome-wide DNA methylome of farmed gilthead sea bream (Sparus aurata) depending on genetic background. BMC Genomics 2023; 24:670. [PMID: 37936076 PMCID: PMC10631108 DOI: 10.1186/s12864-023-09759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Broodstock nutritional programming improves the offspring utilization of plant-based diets in gilthead sea bream through changes in hepatic metabolism. Attention was initially focused on fatty acid desaturases, but it can involve a wide range of processes that remain largely unexplored. How all this can be driven by a different genetic background is hardly underlined, and the present study aimed to assess how broodstock nutrition affects differentially the transcriptome and genome-wide DNA methylome of reference and genetically selected fish within the PROGENSA® selection program. RESULTS After the stimulus phase with a low fish oil diet, two offspring subsets of each genetic background received a control or a FUTURE-based diet. This highlighted a different hepatic transcriptome (RNA-seq) and genome-wide DNA methylation (MBD-seq) pattern depending on the genetic background. The number of differentially expressed transcripts following the challenge phase varied from 323 in reference fish to 2,009 in genetically selected fish. The number of discriminant transcripts, and associated enriched functions, were also markedly higher in selected fish. Moreover, correlation analysis depicted a hyper-methylated and down-regulated gene expression state in selected fish with the FUTURE diet, whereas the opposite pattern appeared in reference fish. After filtering for highly represented functions in selected fish, 115 epigenetic markers were retrieved in this group. Among them, lipid metabolism genes (23) were the most reactive following ordering by fold-change in expression, rendering a final list of 10 top markers with a key role on hepatic lipogenesis and fatty acid metabolism (cd36, pitpna, cidea, fasn, g6pd, lipt1, scd1a, acsbg2, acsl14, acsbg2). CONCLUSIONS Gene expression profiles and methylation signatures were dependent on genetic background in our experimental model. Such assumption affected the magnitude, but also the type and direction of change. Thus, the resulting epigenetic clock of reference fish might depict an older phenotype with a lower methylation for the epigenetically responsive genes with a negative methylation-expression pattern. Therefore, epigenetic markers will be specific of each genetic lineage, serving the broodstock programming in our selected fish to prevent and mitigate later in life the risk of hepatic steatosis through changes in hepatic lipogenesis and fatty acid metabolism.
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Affiliation(s)
- F Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de La Sal (IATS, CSIC), 12595, Castellón, Spain
| | - A Belenguer
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de La Sal (IATS, CSIC), 12595, Castellón, Spain
| | - D Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Ctra. Taliarte S/N, 35214, Telde, Las Palmas, Canary Islands, Spain
| | - S Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Ctra. Taliarte S/N, 35214, Telde, Las Palmas, Canary Islands, Spain
| | - B Soriano
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de La Sal (IATS, CSIC), 12595, Castellón, Spain
- Biotechvana, Parc Científic Universitat de València, 46980, Paterna, Spain
| | - J Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de La Sal (IATS, CSIC), 12595, Castellón, Spain
| | - C Llorens
- Biotechvana, Parc Científic Universitat de València, 46980, Paterna, Spain
| | - R Fontanillas
- Skretting Aquaculture Research Centre, Stavanger, Norway
| | - S Sarih
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Ctra. Taliarte S/N, 35214, Telde, Las Palmas, Canary Islands, Spain
| | - M J Zamorano
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Ctra. Taliarte S/N, 35214, Telde, Las Palmas, Canary Islands, Spain
| | - M Izquierdo
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Ctra. Taliarte S/N, 35214, Telde, Las Palmas, Canary Islands, Spain
| | - J Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de La Sal (IATS, CSIC), 12595, Castellón, Spain.
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Valdivieso A, Caballero-Huertas M, Moraleda-Prados J, Piferrer F, Ribas L. Exploring the Effects of Rearing Densities on Epigenetic Modifications in the Zebrafish Gonads. Int J Mol Sci 2023; 24:16002. [PMID: 37958987 PMCID: PMC10647740 DOI: 10.3390/ijms242116002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries.
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Affiliation(s)
- Alejandro Valdivieso
- IHPE, Université de Montpellier, CNRS, IFREMER, Université de Perpignan Via Domitia, 34090 Montpellier, France
| | - Marta Caballero-Huertas
- CIRAD, UMR ISEM, 34398 Montpellier, France;
- ISEM, Université de Montpellier, CIRAD, CNRS, IRD, EPHE, 34090 Montpellier, France
| | - Javier Moraleda-Prados
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
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Qiao R, Zhu Q, Di F, Liu C, Song Y, Zhang J, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Hypomethylation of DYRK4 in peripheral blood is associated with increased lung cancer risk. Mol Carcinog 2023; 62:1745-1754. [PMID: 37530470 DOI: 10.1002/mc.23612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. It is urgent to identify new biomarkers for the early detection of LC. DNA methylation in peripheral blood has been reported to be associated with cancers. We conducted two independent case-control studies and a nested case-control study (168 LC cases and 167 controls in study Ⅰ, 677 LC cases and 833 controls in study Ⅱ, 147 precancers and 21 controls in the nested case-control study). The methylation levels of DYRK4 CpG sites were measured using mass spectrometry and their correlations with LC were analyzed by logistic regression and nonparametric tests. Bonferroni correction was used for the multiple comparisons. LC-related decreased DYRK4 methylation was discovered in Study I and validated in Study II (the odds ratios [ORs] for the lowest vs. highest quartile of all three DYRK4 CpG sites ranged from 1.64 to 2.09, all p < 0.001). Combining the two studies, hypomethylation of DYRK4 was observed in stage I cases (ORs per -10% methylation ranged from 1.16 to 1.38, all p < 5.9E-04), and could be enhanced by male gender (ORs ranged from 1.77 to 4.17 via interquartile analyses, all p < 0.017). Hypomethylation of DYRK4_A_CpG_2 was significantly correlated with tumor size, length, and stage (p = 0.034, 0.002, and 0.002, respectively) in LC cases. Our study disclosed the association between DYRK4 hypomethylation in peripheral blood and LC, suggesting the feasibility of blood-based DNA methylation as new biomarker for LC detection.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Jin Zhang
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
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37
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Katoh I, Tsukinoki K, Hata RI, Kurata SI. ΔNp63 silencing, DNA methylation shifts, and epithelial-mesenchymal transition resulted from TAp63 genome editing in squamous cell carcinoma. Neoplasia 2023; 45:100938. [PMID: 37778252 PMCID: PMC10544079 DOI: 10.1016/j.neo.2023.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
TP63 (p63) is strongly expressed in lower-grade carcinomas of the head and neck, skin, breast, and urothelium to maintain a well-differentiated phenotype. TP63 has two transcription start sites at exons 1 and 3' that produce TAp63 and ΔNp63 isoforms, respectively. The major protein, ΔNp63α, epigenetically activates genes essential for epidermal/craniofacial differentiation, including ΔNp63 itself. To examine the specific role of weakly expressed TAp63, we disrupted exon 1 using CRISPR-Cas9 homology-directed repair in a head and neck squamous cell carcinoma (SCC) line. Surprisingly, TAp63 knockout cells having either monoallelic GFP cassette insertion paired with a frameshift deletion allele or biallelic GFP cassette insertion exhibited ΔNp63 silencing. Loss of keratinocyte-specific gene expression, switching of intermediate filament genes from KRT(s) to VIM, and suppression of cell-cell and cell-matrix adhesion components indicated the core events of epithelial-mesenchymal transition. Many of the positively and negatively affected genes, including ΔNp63, displayed local DNA methylation changes. Furthermore, ΔNp63 expression was partially rescued by transfection of the TAp63 knockout cells with TAp63α and application of DNA methyltransferase inhibitor zebularine. These results suggest that TAp63, a minor part of the TP63 gene, may be involved in the auto-activation mechanism of ΔNp63 by which the keratinocyte-specific epigenome is maintained in SCC.
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Affiliation(s)
- Iyoko Katoh
- Faculty of Dentistry, Kanagawa Dental University, 82 Inaoka-cho, Yokosuka, Kanagawa 238-8580, Japan.
| | - Keiichi Tsukinoki
- Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University, 82 Inaoka-cho, Yokosuka, Kanagawa 238-8580, Japan
| | - Ryu-Ichiro Hata
- Faculty of Dentistry, Kanagawa Dental University, 82 Inaoka-cho, Yokosuka, Kanagawa 238-8580, Japan
| | - Shun-Ichi Kurata
- Faculty of Dentistry, Kanagawa Dental University, 82 Inaoka-cho, Yokosuka, Kanagawa 238-8580, Japan
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38
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Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14:6902. [PMID: 37903791 PMCID: PMC10616205 DOI: 10.1038/s41467-023-42558-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.
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Affiliation(s)
- Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Yael Kalma
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Ilana Gross Carmel
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Betsaida S Melo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ron Flohr
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Maya Fridrikh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Foad Azem
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Hadar Amir
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Ivan Marazzi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT); Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalit Ben-Yosef
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel.
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel.
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Ehlinger JV, Goodrich JM, Dolinoy DC, Watkins DJ, Cantoral A, Mercado-García A, Téllez-Rojo MM, Peterson KE. Associations between blood leukocyte DNA methylation and sustained attention in mid-to-late childhood. Epigenomics 2023; 15:965-981. [PMID: 37942546 PMCID: PMC10718163 DOI: 10.2217/epi-2023-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Aims: To identify associations between DNA methylation (DNAm) across the epigenome and symptoms related to attention-deficit/hyperactivity disorder in a population of Hispanic children. Materials & methods: Among 517 participants in the ELEMENT study aged 9-18 years, we conducted an epigenome-wide association study examining associations between blood leukocyte DNAm and performance on the Conners' continuous performance test (CPT3). Results: DNAm at loci in or near ZNF814, ELF4 and OR6K6 and functional enrichment for gene pathways pertaining to ferroptosis, inflammation, immune response and neurotransmission were significantly related to CPT3 scores. Conclusion: DNAm was associated with CPT3 performance. Further analysis is warranted to understand how these genes and enriched pathways contribute to attention-deficit/hyperactivity disorder.
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Affiliation(s)
- Jessa V Ehlinger
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah J Watkins
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
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Kim S, Xu Z, Forno E, Qin Y, Park HJ, Yue M, Yan Q, Manni ML, Acosta-Pérez E, Canino G, Chen W, Celedón JC. Cis- and trans-eQTM analysis reveals novel epigenetic and transcriptomic immune markers of atopic asthma in airway epithelium. J Allergy Clin Immunol 2023; 152:887-898. [PMID: 37271320 PMCID: PMC10592527 DOI: 10.1016/j.jaci.2023.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/03/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Expression quantitative trait methylation (eQTM) analyses uncover associations between DNA methylation markers and gene expression. Most eQTM analyses of complex diseases have focused on cis-eQTM pairs (within 1 megabase). OBJECTIVES This study sought to identify cis- and trans-methylation markers associated with gene expression in airway epithelium from youth with and without atopic asthma. METHODS In this study, the investigators conducted both cis- and trans-eQTM analyses in nasal (airway) epithelial samples from 158 Puerto Rican youth with atopic asthma and 100 control subjects without atopy or asthma. The investigators then attempted to replicate their findings in nasal epithelial samples from 2 studies of children, while also examining whether their results in nasal epithelium overlap with those from an eQTM analysis in white blood cells from the Puerto Rican subjects. RESULTS This study identified 9,108 cis-eQTM pairs and 2,131,500 trans-eQTM pairs. Trans-associations were significantly enriched for transcription factor and microRNA target genes. Furthermore, significant cytosine-phosphate-guanine sites (CpGs) were differentially methylated in atopic asthma and significant genes were enriched for genes differentially expressed in atopic asthma. In this study, 50.7% to 62.6% of cis- and trans-eQTM pairs identified in Puerto Rican youth were replicated in 2 smaller cohorts at false discovery rate-adjusted P < .1. Replicated genes in the trans-eQTM analysis included biologically plausible asthma-susceptibility genes (eg, HDC, NLRP3, ITGAE, CDH26, and CST1) and are enriched in immune pathways. CONCLUSIONS Studying both cis- and trans-epigenetic regulation of airway epithelial gene expression can identify potential causal and regulatory pathways or networks for childhood asthma. Trans-eQTM CpGs may regulate gene expression in airway epithelium through effects on transcription factor and microRNA target genes.
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Affiliation(s)
- Soyeon Kim
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Zhongli Xu
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University, New York, NY
| | - Michelle L Manni
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa.
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Budeus B, Unger K, Hess J, Sentek H, Klein D. Comparative computational analysis to distinguish mesenchymal stem cells from fibroblasts. Front Immunol 2023; 14:1270493. [PMID: 37822926 PMCID: PMC10562561 DOI: 10.3389/fimmu.2023.1270493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Mesenchymal stem cells (MSCs) are considered to be the most promising stem cell type for cell-based therapies in regenerative medicine. Based on their potential to home to diseased body sites following a therapeutically application, these cells could (i) differentiate then into organ-specific cell types to locally restore injured cells or, most prominently, (ii) foster tissue regeneration including immune modulations more indirectly by secretion of protective growth factors and cytokines. As tissue-resident stem cells of mesenchymal origin, these cells are morphologically and even molecularly- at least concerning the classical marker genes- indistinguishable from similar lineage cells, particularly fibroblasts. Methods Here we used microarray-based gene expression and global DNA methylation analyses as well as accompanying computational tools in order to specify differences between MSCs and fibroblasts, to further unravel potential identity genes and to highlight MSC signaling pathways with regard to their trophic and immunosuppressive action. Results We identified 1352 differentially expressed genes, of which in the MSCs there is a strong signature for e.g., KRAS signaling, known to play essential role in stemness maintenance, regulation of coagulation and complement being decisive for resolving inflammatory processes, as well as of wound healing particularly important for their regenerative capacity. Genes upregulated in fibroblasts addressed predominately transcription and biosynthetic processes and mapped morphological features of the tissue. Concerning the cellular identity, we specified the already known HOX code for MSCs, established a potential HOX code for fibroblasts, and linked certain HOX genes to functional cell-type-specific properties. Accompanied methylation profiles revealed numerous regions, especially in HOX genes, being differentially methylated, which might provide additional biomarker potential. Discussion Conclusively, transcriptomic together with epigenetic signatures can be successfully be used for the definition (cellular identity) of MSCs versus fibroblasts as well as for the determination of the superior functional properties of MSCs, such as their immunomodulatory potential.
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Affiliation(s)
- Bettina Budeus
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Hanna Sentek
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Eachus H, Oberski L, Paveley J, Bacila I, Ashton JP, Esposito U, Seifuddin F, Pirooznia M, Elhaik E, Placzek M, Krone NP, Cunliffe VT. Glucocorticoid receptor regulates protein chaperone, circadian clock and affective disorder genes in the zebrafish brain. Dis Model Mech 2023; 16:dmm050141. [PMID: 37525888 PMCID: PMC10565112 DOI: 10.1242/dmm.050141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023] Open
Abstract
Glucocorticoid resistance is commonly observed in depression, and has been linked to reduced expression and/or function of the glucocorticoid receptor (NR3C1 in human, hereafter referred to as GR). Previous studies have shown that GR-mutant zebrafish exhibit behavioural abnormalities that are indicative of an affective disorder, suggesting that GR plays a role in brain function. We compared the brain methylomes and brain transcriptomes of adult wild-type and GR-mutant zebrafish, and identified 249 differentially methylated regions (DMRs) that are regulated by GR. These include a cluster of CpG sites within the first intron of fkbp5, the gene encoding the glucocorticoid-inducible heat shock protein co-chaperone Fkbp5. RNA-sequencing analysis revealed that genes associated with chaperone-mediated protein folding, the regulation of circadian rhythm and the regulation of metabolism are particularly sensitive to loss of GR function. In addition, we identified subsets of genes exhibiting GR-regulated transcription that are known to regulate behaviour, and are linked to unipolar depression and anxiety. Taken together, our results identify key biological processes and novel molecular mechanisms through which the GR is likely to mediate responses to stress in the adult zebrafish brain, and they provide further support for the zebrafish GR mutant as a model for the study of affective disorders.
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Affiliation(s)
- Helen Eachus
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Lara Oberski
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Jack Paveley
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Irina Bacila
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - John-Paul Ashton
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Umberto Esposito
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Building 12, 12 South Drive, Bethesda, MD 20892, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Building 12, 12 South Drive, Bethesda, MD 20892, USA
| | - Eran Elhaik
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Nils P. Krone
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Vincent T. Cunliffe
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Thompson D, Odufuwa AE, Brissette CA, Watt JA. Transcriptome and methylome of the supraoptic nucleus provides insights into the age-dependent loss of neuronal plasticity. Front Aging Neurosci 2023; 15:1223273. [PMID: 37711995 PMCID: PMC10498476 DOI: 10.3389/fnagi.2023.1223273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023] Open
Abstract
The age-dependent loss of neuronal plasticity is a well-known phenomenon that is poorly understood. The loss of this capacity for axonal regeneration is emphasized following traumatic brain injury, which is a major cause of disability and death among adults in the US. We have previously shown the intrinsic capacity of magnocellular neurons within the supraoptic nucleus to undergo axonal regeneration following unilateral axotomization in an age-dependent manner. The aim of this research was to determine the age-dependent molecular mechanisms that may underlie this phenomenon. As such, we characterized the transcriptome and DNA methylome of the supraoptic nucleus in uninjured 35-day old rats and 125-day old rats. Our data indicates the downregulation of a large number of axonogenesis related transcripts in 125-day old rats compared to 35-day old rats. Specifically, several semaphorin and ephrin genes were downregulated, as well as growth factors including FGF's, insulin-like growth factors (IGFs), and brain-derived neurotrophic factor (BDNF). Differential methylation analysis indicates enrichment of biological processes involved in axonogenesis and axon guidance. Conversely, we observed a robust and specific upregulation of MHCI related transcripts. This may involve the activator protein 1 (AP-1) transcription factor complex as motif analysis of differentially methylated regions indicate enrichment of AP-1 binding sites in hypomethylated regions. Together, our data suggests a loss of pro-regenerative capabilities with age which would prevent axonal growth and appropriate innervation following injury.
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Affiliation(s)
| | | | | | - John A. Watt
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, United States
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Zhou Y, Huang X, Wang L, Luo Y. The Expression Characteristics and Function of the RECQ Family in Pan-Cancer. Biomedicines 2023; 11:2318. [PMID: 37626815 PMCID: PMC10452384 DOI: 10.3390/biomedicines11082318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/31/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The genes of the RECQ DNA helicase family play a part in preserving the stability of the genome and controlling different disease mechanisms. However, the expression features of RECQs in relation to pan-cancer, their correlation with the immune microenvironment of tumors, and the landscape of prognostic power are still undisclosed. METHODS Various sequence and clinical data extracted from 33 cancers were utilized to generate a comprehensive overview of RECQs in the landscape. Afterward, we discovered variations in gene expression, potential enrichment of functions, genetic alterations, and analysis related to the immune response in tumors. Additionally, we explored the clinical characteristics and diagnostic significance of RECQs. And the important association of RECQL4 with liver hepatocellular carcinoma (LIHC) was investigated. RESULTS RECQs exhibited extensive mutations in different types of cancers. The expression of RECQ may be influenced by an oncogenic mutation in certain types of cancer, resulting in the observed genomic and epigenetic changes in diverse tumor formations. Furthermore, RECQs originating from tumors exhibited a significant association with the immune microenvironment of the tumor, indicating their potential as promising targets for therapy. Patient prognosis was significantly associated with the majority of genes in the RECQ family. In LIHC, RECQL4 eventually emerged as a separate prognostic determinant. CONCLUSIONS To summarize, RECQs are essential for the regulation of the immune system in tumors, and RECQL4 serves as a prognostic indicator in LIHC. The results of our study offer fresh perspectives on RECQs from a bioinformatics perspective and emphasize the importance of RECQs in the diagnosis and treatment of cancer.
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Affiliation(s)
- Yuanyuan Zhou
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; (Y.Z.); (L.W.)
| | - Xucheng Huang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China;
| | - Liya Wang
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; (Y.Z.); (L.W.)
| | - Yujia Luo
- Department of NICU, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
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Ferreira RS, Assis RIF, Racca F, Bontempi AC, da Silva RA, Wiench M, Andia DC. Analyzes In Silico Indicate the lncRNAs MIR31HG and LINC00939 as Possible Epigenetic Inhibitors of the Osteogenic Differentiation in PDLCs. Genes (Basel) 2023; 14:1649. [PMID: 37628700 PMCID: PMC10454380 DOI: 10.3390/genes14081649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7) and Distal-Less Homeobox 4 (DLX4) osteoblastic transcription factors (TFs), in human periodontal ligament mesenchymal cells (PDLCs) with low (l-PDLCs) and high (h-PDLCs) osteogenic potential. Chromatin accessibility (ATAC-seq), genome DNA methylation (Methylome), and RNA sequencing (RNA-seq) assays were performed in l- and h-PDLCs, cultured at 10 days in non-induced (DMEM) and osteogenic (OM) medium in vitro. Data were processed in HOMER, Genome Studio, and edgeR programs, and metadata was analyzed by online bioinformatics tools and in R and Python environments. ATAC-seq analyses showed the TFs genomic regions are more accessible in l-PDLCs than in h-PDLCs. In Methylome analyses, the TFs presented similar average methylation intensities (AMIs), without differently methylated probes (DMPs) between l- and h-PDLCs; in addition, there were no differences in the expression profiles of TFs signaling pathways. Interestingly, we identified the long non-coding RNAs (lncRNAs), MIR31HG and LINC00939, as upregulated in l-PDLCs, in both DMEM and OM. In the following analysis, the web-based prediction tool LncRRIsearch predicted RNA:RNA base-pairing interactions between SP7, DLX4, MIR31HG, and LINC00939 transcripts. The machine learning program TriplexFPP predicted DNA:RNA triplex-forming potential for the SP7 DNA site and for one of the LINC00939 transcripts (ENST00000502479). PCR data confirmed the upregulation of MIR31HG and LINC00939 transcripts in l-PDLCs (× h-PDLCs) in both DMEM and OM (p < 0.05); conversely, SP7 and DLX4 were downregulated, confirming those results observed in the RNA-Seq analysis. Together, these results indicate the lncRNAs MIR31HG and LINC00939 as possible epigenetic inhibitors of the osteogenic differentiation in PDLCs by (post)transcriptional and translational repression of the SP7 and DLX4 TFs.
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Affiliation(s)
- Rogério S. Ferreira
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
| | - Rahyza I. F. Assis
- Department of Clinical Dentistry, Federal University of Espírito Santo, Vitória 29043-910, ES, Brazil
| | - Francesca Racca
- Periodontology Department, The Ohio State University College of Dentistry, Columbus, OH 43210-1267, USA;
| | - Ana Carolina Bontempi
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
| | - Rodrigo A. da Silva
- Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, SP, Brazil;
| | - Malgorzata Wiench
- School of Dentistry, Institute of Clinical Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B5 7EG, UK
| | - Denise C. Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
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Sarwar MS, Ramirez CN, Dina Kuo HC, Chou P, Wu R, Sargsyan D, Yang Y, Shannar A, Mary Peter R, Yin R, Wang Y, Su X, Kong AN. The environmental carcinogen benzo[a]pyrene regulates epigenetic reprogramming and metabolic rewiring in a two-stage mouse skin carcinogenesis model. Carcinogenesis 2023; 44:436-449. [PMID: 37100755 PMCID: PMC10414144 DOI: 10.1093/carcin/bgad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Non-melanoma skin cancer (NMSC) is the most common cancer in the world. Environmental exposure to carcinogens is one of the major causes of NMSC initiation and progression. In the current study, we utilized a two-stage skin carcinogenesis mouse model generated by sequential exposure to cancer-initiating agent benzo[a]pyrene (BaP) and promoting agent 12-O-tetradecanoylphorbol-13-acetate (TPA), to study epigenetic, transcriptomic and metabolic changes at different stages during the development of NMSC. BaP/TPA caused significant alterations in DNA methylation and gene expression profiles in skin carcinogenesis, as evidenced by DNA-seq and RNA-seq analysis. Correlation analysis between differentially expressed genes and differentially methylated regions found that the mRNA expression of oncogenes leucine rich repeat LGI family member 2 (Lgi2), kallikrein-related peptidase 13 (Klk13) and SRY-Box transcription factor (Sox5) are correlated with the promoter CpG methylation status, indicating BaP/TPA regulates these oncogenes through regulating their promoter methylation at different stages of NMSC. Pathway analysis identified that the modulation of macrophage-stimulating protein-recepteur d'origine nantais and high-mobility group box 1 signaling pathways, superpathway of melatonin degradation, melatonin degradation 1, sirtuin signaling and actin cytoskeleton signaling pathways are associated with the development of NMSC. The metabolomic study showed BaP/TPA regulated cancer-associated metabolisms like pyrimidine and amino acid metabolisms/metabolites and epigenetic-associated metabolites, such as S-adenosylmethionine, methionine and 5-methylcytosine, indicating a critical role in carcinogen-mediated metabolic reprogramming and its consequences on cancer development. Altogether, this study provides novel insights integrating methylomic, transcriptomic and metabolic-signaling pathways that could benefit future skin cancer treatment and interception studies.
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Affiliation(s)
- Md. Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christina N Ramirez
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pochung Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuqing Yang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ahmad Shannar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rebecca Mary Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Chen X, Dong L, Chen L, Wang Y, Du J, Ma L, Yan X, Huang J, Liao M, Chen X, Liu D, Li J, Zhang B, Teng W, Yuan K, Sun D, Gao Q, Zeng Y. Epigenome-wide development and validation of a prognostic methylation score in intrahepatic cholangiocarcinoma based on machine learning strategies. Hepatobiliary Surg Nutr 2023; 12:478-494. [PMID: 37601000 PMCID: PMC10432305 DOI: 10.21037/hbsn-21-424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/23/2022] [Indexed: 08/22/2023]
Abstract
Background Clinical parameter-based nomograms and staging systems provide limited information for the prediction of survival in intrahepatic cholangiocarcinoma (ICC) patients. In this study, we developed a methylation signature that precisely predicts overall survival (OS) after surgery. Methods An epigenome-wide study of DNA methylation based on whole-genome bisulfite sequencing (WGBS) was conducted for two independent cohorts (discovery cohort, n=164; validation cohort, n=170) from three hepatobiliary centers in China. By referring to differentially methylated regions (DMRs), we proposed the concept of prognostically methylated regions (PMRs), which were composed of consecutive prognostically methylated CpGs (PMCs). Using machine learning strategies (Random Forest and the least absolute shrinkage and selector regression), a prognostic methylation score (PMS) was constructed based on 14 PMRs in the discovery cohort and confirmed in the validation cohort. Results The C-indices of the PMS for predicting OS in the discovery and validation cohorts were 0.79 and 0.74, respectively. In the whole cohort, the PMS was an independent predictor of OS [hazard ratio (HR) =8.12; 95% confidence interval (CI): 5.48-12.04; P<0.001], and the C-index (0.78) of the PMS was significantly higher than that of the Johns Hopkins University School of Medicine (JHUSM) nomogram (0.69, P<0.001), the Eastern Hepatobiliary Surgery Hospital (EHBSH) nomogram (0.67, P<0.001), American Joint Committee on Cancer (AJCC) tumor-node-metastasis (TNM) staging system (0.61, P<0.001), and MEGNA prognostic score (0.60, P<0.001). The patients in quartile 4 of PMS could benefit from adjuvant therapy (AT) (HR =0.54; 95% CI: 0.32-0.91; log-rank P=0.043), whereas those in the quartiles 1-3 could not. However, other nomograms and staging system failed to do so. Further analyses of potential mechanisms showed that the PMS was associated with tumor biological behaviors, pathway activation, and immune microenvironment. Conclusions The PMS could improve the prognostic accuracy and identify patients who would benefit from AT for ICC patients, and might facilitate decisions in treatment of ICC patients.
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Affiliation(s)
- Xing Chen
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Liangqing Dong
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lu Chen
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yuan Wang
- The Fifth Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- Department of Research and Development, Jiangsu Gaomei Genomics, Nanjing, China
| | - Jinpeng Du
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Lijie Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaokai Yan
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiwei Huang
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Mingheng Liao
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiangzheng Chen
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Dongming Liu
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jin Li
- Department of Research and Development, Jiangsu Gaomei Genomics, Nanjing, China
| | - Bo Zhang
- The Fifth Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Wen Teng
- The Fifth Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Deqiang Sun
- The Fifth Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- Department of Research and Development, Jiangsu Gaomei Genomics, Nanjing, China
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, Laboratory of Liver Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
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Kim JE, Jo MJ, Cho E, Ahn SY, Kwon YJ, Gim JA, Ko GJ. The Effect of DNA Methylation in the Development and Progression of Chronic Kidney Disease in the General Population: An Epigenome-Wide Association Study Using the Korean Genome and Epidemiology Study Database. Genes (Basel) 2023; 14:1489. [PMID: 37510393 PMCID: PMC10379047 DOI: 10.3390/genes14071489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Although knowledge of the genetic factors influencing kidney disease is increasing, epigenetic profiles, which are associated with chronic kidney disease (CKD), have not been fully elucidated. We sought to identify the DNA methylation status of CpG sites associated with reduced kidney function and examine whether the identified CpG sites are associated with CKD development. METHOD We analyzed DNA methylation patterns of 440 participants in the Korean Genome and Epidemiology Study (KoGES) with estimated glomerular filtration rates (eGFRs) ≥ 60 mL/min/1.73 m2 at baseline. CKD development was defined as a decrease in the eGFR of <60 at any time during an 8-year follow-up period ("CKD prediction" analysis). In addition, among the 440 participants, 49 participants who underwent a second methylation profiling were assessed for an association between a decline in kidney function and changes in the degree of methylation of CpG sites during the 8 years ("kidney function slope" analysis). RESULTS In the CKD prediction analysis, methylation profiles of a total of 403,129 CpG sites were evaluated at baseline in 440 participants, and increased and decreased methylation of 268 and 189 CpG sites, respectively, were significantly correlated with the development of CKD in multivariable logistic regression. During kidney function slope analysis using follow-up methylation profiles of 49 participants, the percent methylation changes in 913 CpG sites showed a linear relationship with the percent change in eGFR during 8 years. During functional enrichment analyses for significant CpG sites found in the CKD prediction and kidney function slope analyses, we found that those CpG sites represented MAPK, PI3K/Akt, and Rap1 pathways. In addition, three CpG sites from three genes, NPHS2, CHCHD4, and AHR, were found to be significant in the CKD prediction analysis and related to a decline in kidney function. CONCLUSION It is suggested that DNA methylation on specific genes is associated with the development of CKD and the deterioration of kidney function.
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Affiliation(s)
- Ji-Eun Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Min-Jee Jo
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Eunjung Cho
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Shin-Young Ahn
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Young-Joo Kwon
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Jeong-An Gim
- Medical Science Research Center, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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Jensen D, Chen J, Turner JA, Stephen JM, Wang YP, Wilson TW, Calhoun VD, Liu J. Epigenetic associations with adolescent grey matter maturation and cognitive development. Front Genet 2023; 14:1222619. [PMID: 37529779 PMCID: PMC10390095 DOI: 10.3389/fgene.2023.1222619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Introduction: Adolescence, a critical phase of human neurodevelopment, is marked by a tremendous reorganization of the brain and accompanied by improved cognitive performance. This development is driven in part by gene expression, which in turn is partly regulated by DNA methylation (DNAm). Methods: We collected brain imaging, cognitive assessments, and DNAm in a longitudinal cohort of approximately 200 typically developing participants, aged 9-14. This data, from three time points roughly 1 year apart, was used to explore the relationships between seven cytosine-phosphate-guanine (CpG) sites in genes highly expressed in brain tissues (GRIN2D, GABRB3, KCNC1, SLC12A9, CHD5, STXBP5, and NFASC), seven networks of grey matter (GM) volume change, and scores from seven cognitive tests. Results: The demethylation of the CpGs as well as the rates of change in DNAm were significantly related to improvements in total, crystalized, and fluid cognition scores, executive function, episodic memory, and processing speed, as well as several networks of GM volume increases and decreases that highlight typical patterns of brain maturation. Discussion: Our study provides a first look at the DNAm of genes involved in myelination, excitatory and inhibitory receptors, and connectivity, how they are related to the large-scale changes occurring in the brain structure as well as cognition during adolescence.
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Affiliation(s)
- Dawn Jensen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Jessica A. Turner
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Wexnar Medical Center, Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, United States
| | | | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, United States
| | - Tony W. Wilson
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE, United States
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
- The Mind Research Network, Albuquerque, NM, United States
- Psychology Department and Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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50
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Mas-Parés B, Xargay-Torrent S, Gómez-Vilarrubla A, Carreras-Badosa G, Prats-Puig A, De Zegher F, Ibáñez L, Bassols J, López-Bermejo A. Gestational Weight Gain Relates to DNA Methylation in Umbilical Cord, Which, In Turn, Associates with Offspring Obesity-Related Parameters. Nutrients 2023; 15:3175. [PMID: 37513594 PMCID: PMC10386148 DOI: 10.3390/nu15143175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Excessive gestational weight gain (GWG) has a negative impact on offspring's health. Epigenetic modifications mediate these associations by causing changes in gene expression. We studied the association between GWG and DNA methylation in umbilical cord tissue; and determined whether the DNA methylation and the expression of corresponding annotated genes were associated with obesity-related parameters in offspring at 6 years of age. The methylated CpG sites (CpGs) associated with GWG were identified in umbilical cord tissue by genome-wide DNA methylation (n = 24). Twelve top CpGs were validated in a wider sample by pyrosequencing (n = 87), and the expression of their 5 annotated genes (SETD8, TMEM214, SLIT3, RPTOR, and HOXC8) was assessed by RT-PCR. Pyrosequencing results validated the association of SETD8, SLIT3, and RPTOR methylation with GWG and showed that higher levels of SETD8 and RPTOR methylation and lower levels of SLIT3 methylation relate to a higher risk of obesity in the offspring. The association of SETD8 and SLIT3 gene expression with offspring outcomes paralleled the association of methylation levels in opposite directions. Epigenetic changes in the umbilical cord tissue could explain, in part, the relationship between GWG and offspring obesity risk and be early biomarkers for the prevention of overweight and obesity in childhood.
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Affiliation(s)
- Berta Mas-Parés
- Pediatric Endocrinology Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
| | - Sílvia Xargay-Torrent
- Pediatric Endocrinology Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
| | - Ariadna Gómez-Vilarrubla
- Materno-Fetal Metabolic Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
| | - Gemma Carreras-Badosa
- Pediatric Endocrinology Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
| | - Anna Prats-Puig
- University School of Health and Sport (EUSES), University of Girona, 17190 Salt, Spain
| | - Francis De Zegher
- Department of Development & Regeneration, University of Leuven, 3000 Leuven, Belgium
| | - Lourdes Ibáñez
- Endocrinology Department, Research Institute Sant Joan de Déu, University of Barcelona, 08950 Esplugues, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, 28029 Madrid, Spain
| | - Judit Bassols
- Materno-Fetal Metabolic Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
| | - Abel López-Bermejo
- Pediatric Endocrinology Research Group, (Girona Biomedical Research Institute) IDIBGI, 17190 Salt, Spain
- Department of Pediatrics, Dr. Josep Trueta Hospital, 17007 Girona, Spain
- Department of Medical Sciences, University of Girona, 17003 Girona, Spain
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