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Fialková V, Ďúranová H, Borotová P, Klongová L, Grabacka M, Speváková I. Natural Stilbenes: Their Role in Colorectal Cancer Prevention, DNA Methylation, and Therapy. Nutr Cancer 2024:1-29. [PMID: 38950568 DOI: 10.1080/01635581.2024.2364391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024]
Abstract
The resistance of colorectal cancer (CRC) to conventional therapeutic modalities, such as radiation therapy and chemotherapy, along with the associated side effects, significantly limits effective anticancer strategies. Numerous epigenetic investigations have unveiled that naturally occurring stilbenes can modify or reverse abnormal epigenetic alterations, particularly aberrant DNA methylation status, offering potential avenues for preventing or treating CRC. By modulating the activity of the DNA methylation machinery components, phytochemicals may influence the various stages of CRC carcinogenesis through multiple molecular mechanisms. Several epigenetic studies, especially preclinical research, have highlighted the effective DNA methylation modulatory effects of stilbenes with minimal adverse effects on organisms, particularly in combination therapies for CRC. However, the available preclinical and clinical data regarding the effects of commonly encountered stilbenes against CRC are currently limited. Therefore, additional epigenetic research is warranted to explore the preventive potential of these phytochemicals in CRC development and to validate their therapeutic application in the prevention and treatment of CRC. This review aims to provide an overview of selected bioactive stilbenes as potential chemopreventive agents for CRC with a focus on their modulatory mechanisms of action, especially in targeting alterations in DNA methylation machinery in CRC.
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Affiliation(s)
- Veronika Fialková
- AgroBioTech Research Centre, Slovak University of Agriculture, Nitra, Slovakia
| | - Hana Ďúranová
- AgroBioTech Research Centre, Slovak University of Agriculture, Nitra, Slovakia
| | - Petra Borotová
- AgroBioTech Research Centre, Slovak University of Agriculture, Nitra, Slovakia
| | - Lucia Klongová
- AgroBioTech Research Centre, Slovak University of Agriculture, Nitra, Slovakia
| | - Maja Grabacka
- Department of Biotechnology and General Technology of Foods, Faculty of Food Technology, University of Agriculture, Cracow, Poland
| | - Ivana Speváková
- AgroBioTech Research Centre, Slovak University of Agriculture, Nitra, Slovakia
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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Sawada Y, Minei R, Tabata H, Ikemura T, Wada K, Wada Y, Nagata H, Iwasaki Y. Unsupervised AI reveals insect species-specific genome signatures. PeerJ 2024; 12:e17025. [PMID: 38464746 PMCID: PMC10924456 DOI: 10.7717/peerj.17025] [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: 11/17/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Abstract
Insects are a highly diverse phylogeny and possess a wide variety of traits, including the presence or absence of wings and metamorphosis. These diverse traits are of great interest for studying genome evolution, and numerous comparative genomic studies have examined a wide phylogenetic range of insects. Here, we analyzed 22 insects belonging to a wide phylogenetic range (Endopterygota, Paraneoptera, Polyneoptera, Palaeoptera, and other insects) by using a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions in their genomic fragments (100-kb or 1-Mb sequences), which is an unsupervised machine learning algorithm that can extract species-specific characteristics of the oligonucleotide compositions (genome signatures). The genome signature is of particular interest in terms of the mechanisms and biological significance that have caused the species-specific difference, and can be used as a powerful search needle to explore the various roles of genome sequences other than protein coding, and can be used to unveil mysteries hidden in the genome sequence. Since BLSOM is an unsupervised clustering method, the clustering of sequences was performed based on the oligonucleotide composition alone, without providing information about the species from which each fragment sequence was derived. Therefore, not only the interspecies separation, but also the intraspecies separation can be achieved. Here, we have revealed the specific genomic regions with oligonucleotide compositions distinct from the usual sequences of each insect genome, e.g., Mb-level structures found for a grasshopper Schistocerca americana. One aim of this study was to compare the genome characteristics of insects with those of vertebrates, especially humans, which are phylogenetically distant from insects. Recently, humans seem to be the "model organism" for which a large amount of information has been accumulated using a variety of cutting-edge and high-throughput technologies. Therefore, it is reasonable to use the abundant information from humans to study insect lineages. The specific regions of Mb length with distinct oligonucleotide compositions have also been previously observed in the human genome. These regions were enriched by transcription factor binding motifs (TFBSs) and hypothesized to be involved in the three-dimensional arrangement of chromosomal DNA in interphase nuclei. The present study characterized the species-specific oligonucleotide compositions (i.e., genome signatures) in insect genomes and identified specific genomic regions with distinct oligonucleotide compositions.
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Affiliation(s)
- Yui Sawada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Ryuhei Minei
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Hiromasa Tabata
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Kennosuke Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Yoshiko Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Hiroshi Nagata
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
| | - Yuki Iwasaki
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Tamura-cho, Japan
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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1213-1222. [PMID: 38174900 PMCID: PMC10843815 DOI: 10.1021/acs.langmuir.3c02609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of significant interest because it impacts an organism's response to a nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. A residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Lysine methylation experiments reveal subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX rates become slower overall in the presence of PSNPs. However, some regions of the R2ab protein exhibit faster than average exchange rates in the presence of PSNPs, while others are slower than the average behavior, suggesting conformational changes upon binding. HDX rates and methylation ratios support a recently proposed "adsorbotope" model for PSNPs, wherein adsorbed proteins consist of unfolded anchor points interspersed with partially structured regions. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how R2ab adsorbs onto PSNP surfaces, this research emphasizes the need for advanced methods to comprehend residue-level interactions in the nanoparticle corona.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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Wang Y, Gao X, Yang Z, Yan X, He X, Guo T, Zhao S, Zhao H, Chen ZJ. Deciphering the DNA methylome in women with PCOS diagnosed using the new international evidence-based guidelines. Hum Reprod 2023; 38:ii69-ii79. [PMID: 37982419 DOI: 10.1093/humrep/dead191] [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: 12/26/2022] [Revised: 07/16/2023] [Indexed: 11/21/2023] Open
Abstract
STUDY QUESTION Is there any methylome alteration in women with PCOS who were diagnosed using the new international evidence-based guidelines? SUMMARY ANSWER A total of 264 differentially methylated probes (DMPs) and 53 differentially methylated regions (DMRs) were identified in patients with PCOS and healthy controls. WHAT IS KNOWN ALREADY PCOS is a common endocrine disorder among women of reproductive age and polycystic ovarian morphology (PCOM) is one of the main features of the disease. Owing to the availability of more sensitive ultrasound machines, the traditional diagnosis of PCOM according to the Rotterdam criteria (≥12 antral follicles per ovary) is currently debated as there is a risk of overdiagnosis. The new international evidence-based guidelines set the threshold for PCOM as ≥20 antral follicles per ovary when using endovaginal ultrasound transducers with a frequency bandwidth that includes 8 MHz. However, current DNA methylation studies in PCOS are still based on the Rotterdam criteria. This study aimed to explore aberrant DNA methylation in patients diagnosed with PCOS according to the new evidence-based guidelines. STUDY DESIGN, SIZE, DURATION This cross-sectional case-control study included 34 PCOS cases diagnosed using new international evidence-based guidelines and 36 controls. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 70 women, including 34 PCOS cases and 36 controls, were recruited. DNA extracted from whole blood samples of participants were profiled using array technology. Data quality control, preprocessing, annotation, and statistical analyses were performed. Least absolute shrinkage and selection operator (LASSO) regression were used to build a PCOS diagnosis model with DNA methylation sites. MAIN RESULTS AND THE ROLE OF CHANCE We identified 264 DMPs between PCOS cases and controls, which were mainly located in intergenic regions or gene bodies of the genome, CpG open sea sites, and heterochromatin of functional elements. Pathway enrichment analysis showed that DMPs were significantly enriched in biological processes involved in triglyceride regulation. Three of these DMPs overlapped with the PCOS susceptibility genes thyroid adenoma-associated protein (THADA), aminopeptidase O (AOPEP), and tripartite motif family-like protein 2 (TRIML2). Fifty-three DMRs were identified and their annotated genes were largely enriched in allograft rejection, thyroid hormone production, and peripheral downstream signaling effects. Two DMRs were closely related to the PCOS susceptibility genes, potassium voltage-gated channel subfamily A member 4 (KCNA4) and farnesyl-diphosphate farnesyltransferase 1 (FDFT1). Finally, based on LASSO regression, we built a methylation marker model with high accuracy for PCOS diagnosis (AUC=0.952). LIMITATIONS, REASONS FOR CAUTION The study cohort was single-center and the sample size was relatively limited. Further analyses with a larger number of participants are required. WIDER IMPLICATIONS OF THE FINDINGS This is the first study to identify DNA methylation alterations in women with PCOS diagnosed using the new international evidence-based guideline, and it provided new molecular insight into the application of the new guidelines. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the National Key Research and Development Program of China (2021YFC2700400), Basic Science Center Program of NSFC (31988101), CAMS Innovation Fund for Medical Sciences (2021-I2M-5-001), National Natural Science Foundation of China (32370916, 82071606, 82101707, 82192874, and 31871509), Shandong Provincial Key Research and Development Program (2020ZLYS02), Taishan Scholars Program of Shandong Province (ts20190988), and Fundamental Research Funds of Shandong University. The authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Yuteng Wang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xueying Gao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziyi Yang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xueqi Yan
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xinmiao He
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Ting Guo
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Shigang Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, Albiheyri RS, Zari AT, Bahieldin A, Bellacosa A, Bronner C, Hamiche A. MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. J Exp Clin Cancer Res 2023; 42:301. [PMID: 37957685 PMCID: PMC10644448 DOI: 10.1186/s13046-023-02882-z] [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: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T transitions resulting from spontaneous deamination of 5'-methylcytosine. METHODS Here, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments. RESULTS Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. CONCLUSIONS Our data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions.
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Affiliation(s)
- Christophe Papin
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Abdulkhaleg Ibrahim
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
- National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan, 99316, Libya
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stéphanie Le Gras
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Isabelle Stoll
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Raed S Albiheyri
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alfonso Bellacosa
- Cancer Biology Program, Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Christian Bronner
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| | - Ali Hamiche
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
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Fogliano C, Motta CM, Acloque H, Avallone B, Carotenuto R. Water contamination by delorazepam induces epigenetic defects in the embryos of the clawed frog Xenopus laevis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165300. [PMID: 37414173 DOI: 10.1016/j.scitotenv.2023.165300] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/23/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
Delorazepam, a derivative of diazepam, is a psychotropic drug belonging to the benzodiazepine class. Used as a nervous-system inhibitor, it treats anxiety, insomnia, and epilepsy, but is also associated with misuse and abuse. Nowadays benzodiazepines are considered emerging pollutants: conventional wastewater treatment plants indeed are unable to eliminate these compounds. Consequently, they persist in the environment and bioaccumulate in non-target aquatic organisms with consequences still not fully clear. To collect more information, we investigated the possible epigenetic activity of delorazepam, at three concentrations (1, 5 and 10 μg/L) using Xenopus laevis embryos as a model. Analyses demonstrated a significant increase in genomic DNA methylation and differential methylation of the promoters of some early developmental genes (otx2, sox3, sox9, pax6, rax1, foxf1, and myod1). Moreover, studies on gene expression highlighted an unbalancing in apoptosis/proliferation pathways and an aberrant expression of DNA-repair genes. Results are alarming considering the growing trend of benzodiazepine concentrations in superficial waters, especially after the peak occurred as a consequence of the pandemic COVID-19, and the fact that benzodiazepine GABA-A receptors are highly conserved and present in all aquatic organisms.
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Affiliation(s)
- Chiara Fogliano
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Chiara Maria Motta
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Bice Avallone
- Department of Biology, University of Naples "Federico II", Naples, Italy.
| | - Rosa Carotenuto
- Department of Biology, University of Naples "Federico II", Naples, Italy
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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.554951. [PMID: 37693402 PMCID: PMC10491123 DOI: 10.1101/2023.08.28.554951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of high interest because it impacts the organism's response to the nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. Ultimately, a residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Through lysine methylation, we observe subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX measurements reveal that certain regions of the R2ab protein undergo faster exchange rates in the presence of PSNPs, suggesting conformational changes upon binding. Both results support a recently proposed "adsorbotope" model, wherein adsorbed proteins consist of unfolded anchor points interspersed with regions of partial structure. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how proteins respond to nanoparticle surfaces, this research emphasizes the need for advanced methods to comprehend these intricate interactions fully at the residue level.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
| | | | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
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Fu S, Debes JD, Boonstra A. DNA methylation markers in the detection of hepatocellular carcinoma. Eur J Cancer 2023; 191:112960. [PMID: 37473464 DOI: 10.1016/j.ejca.2023.112960] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and has a poor prognosis. Epigenetic modification has been shown to be deregulated during HCC development by dramatically impacting the differentiation, proliferation, and function of cells. One important epigenetic modification is DNA methylation during which methyl groups are added to cytosines without changing the DNA sequence itself. Studies found that methylated DNA markers can be specific for detection of HCC. On the basis of these findings, the utility of methylated DNA markers as novel biomarkers for early-stage HCC has been measured in blood, and indeed superior sensitivity and specificity have been found in several studies when compared to current surveillance methods. However, a variety of factors currently limit the immediate application of these exciting biomarkers. In this review, we provide a detailed rationalisation of the approach and basis for the use of methylation biomarkers for HCC detection and summarise recent studies on methylated DNA markers in HCC focusing on the importance of the aetiological cause of liver disease in the mechanisms leading to cancer.
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Affiliation(s)
- Siyu Fu
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - José D Debes
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - André Boonstra
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands.
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Shu J, Yin X, Liu Y, Mi Y, Zhang B, Zhang A, Guo H, Dong J. MBD3 Regulates Male Germ Cell Division and Sperm Fertility in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2654. [PMID: 37514268 PMCID: PMC10384339 DOI: 10.3390/plants12142654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
DNA methylation plays important roles through the methyl-CpG-binding domain (MBD) to realize epigenetic modifications. Thirteen AtMBD proteins have been identified from the Arabidopsis thaliana genome, but the functions of some members are unclear. AtMBD3 was found to be highly expressed in pollen and seeds and it preferably binds methylated CG, CHG, and unmethylated DNA sequences. Then, two mutant alleles at the AtMBD3 locus were obtained in order to further explore its function using CRISPR/Cas9. When compared with 92.17% mature pollen production in the wild type, significantly lower percentages of 84.31% and 78.91% were observed in the mbd3-1 and mbd3-2 mutants, respectively. About 16-21% of pollen from the mbd3 mutants suffered a collapse in reproductive transmission, whereas the other pollen was found to be normal. After pollination, about 16% and 24% of mbd3-1 and mbd3-2 mutant seeds underwent early or late abortion, respectively. Among all the late abortion seeds in mbd3-2 plants, 25% of the abnormal seeds were at the globular stage, 31.25% were at the transition stage, and 43.75% were at the heart stage. A transcriptome analysis of the seeds found 950 upregulated genes and 1128 downregulated genes between wild type and mbd3-2 mutants. Some transcriptional factors involved in embryo development were selected to be expressed, and we found significant differences between wild type and mbd3 mutants, such as WOXs, CUC1, AIB4, and RGL3. Furthermore, we found a gene that is specifically expressed in pollen, named PBL6. PBL6 was found to directly interact with AtMBD3. Our results provide insights into the function of AtMBD3 in plants, especially in sperm fertility.
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Affiliation(s)
- Jia Shu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Yin
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yannan Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingjie Mi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Bin Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Aoyuan Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Hongbo Guo
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
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11
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Ma L, Li C, Yin H, Huang J, Yu S, Zhao J, Tang Y, Yu M, Lin J, Ding L, Cui Q. The Mechanism of DNA Methylation and miRNA in Breast Cancer. Int J Mol Sci 2023; 24:ijms24119360. [PMID: 37298314 DOI: 10.3390/ijms24119360] [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: 04/07/2023] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Breast cancer is the most prevalent cancer in the world. Currently, the main treatments for breast cancer are radiotherapy, chemotherapy, targeted therapy and surgery. The treatment measures for breast cancer depend on the molecular subtype. Thus, the exploration of the underlying molecular mechanisms and therapeutic targets for breast cancer remains a hotspot in research. In breast cancer, a high level of expression of DNMTs is highly correlated with poor prognosis, that is, the abnormal methylation of tumor suppressor genes usually promotes tumorigenesis and progression. MiRNAs, as non-coding RNAs, have been identified to play key roles in breast cancer. The aberrant methylation of miRNAs could lead to drug resistance during the aforementioned treatment. Therefore, the regulation of miRNA methylation might serve as a therapeutic target in breast cancer. In this paper, we reviewed studies on the regulatory mechanisms of miRNA and DNA methylation in breast cancer from the last decade, focusing on the promoter region of tumor suppressor miRNAs methylated by DNMTs and the highly expressed oncogenic miRNAs inhibited by DNMTs or activating TETs.
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Affiliation(s)
- Lingyuan Ma
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Chenyu Li
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Hanlin Yin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Jiashu Huang
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Shenghao Yu
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Jin Zhao
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Yongxu Tang
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Min Yu
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Jie Lin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Lei Ding
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
| | - Qinghua Cui
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China
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Tang FL, Zhang XG, Ke PY, Liu J, Zhang ZJ, Hu DM, Gu J, Zhang H, Guo HK, Zang QW, Huang R, Ma YL, Kwan P. MBD5 regulates NMDA receptor expression and seizures by inhibiting Stat1 transcription. Neurobiol Dis 2023; 181:106103. [PMID: 36997128 DOI: 10.1016/j.nbd.2023.106103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Epilepsy is considered to result from an imbalance between excitation and inhibition of the central nervous system. Pathogenic mutations in the methyl-CpG binding domain protein 5 gene (MBD5) are known to cause epilepsy. However, the function and mechanism of MBD5 in epilepsy remain elusive. Here, we found that MBD5 was mainly localized in the pyramidal cells and granular cells of mouse hippocampus, and its expression was increased in the brain tissues of mouse models of epilepsy. Exogenous overexpression of MBD5 inhibited the transcription of the signal transducer and activator of transcription 1 gene (Stat1), resulting in increased expression of N-methyl-d-aspartate receptor (NMDAR) subunit 1 (GluN1), 2A (GluN2A) and 2B (GluN2B), leading to aggravation of the epileptic behaviour phenotype in mice. The epileptic behavioural phenotype was alleviated by overexpression of STAT1 which reduced the expression of NMDARs, and by the NMDAR antagonist memantine. These results indicate that MBD5 accumulation affects seizures through STAT1-mediated inhibition of NMDAR expression in mice. Collectively, our findings suggest that the MBD5-STAT1-NMDAR pathway may be a new pathway that regulates the epileptic behavioural phenotype and may represent a new treatment target.
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Hu Y, Xu B, He J, Shan H, Zhou G, Wang D, Bai L, Shang H, Nie L, Pan F, Lan HY, Wang Q. Hypermethylation of Smad7 in CD4 + T cells is associated with the disease activity of rheumatoid arthritis. Front Immunol 2023; 14:1104881. [PMID: 36845150 PMCID: PMC9947360 DOI: 10.3389/fimmu.2023.1104881] [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: 12/02/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Background Smad7 is protective in a mouse model of rheumatoid arthritis. Here we investigated whether Smad7-expressing CD4+ T cells and the methylation of Smad7 gene in CD4+ T cells contribute to the disease activity of RA in patients. Methods Peripheral CD4+ T cells were collected from 35 healthy controls and 57 RA patients. Smad7 expression by CD4+ T cells were determined and correlated with the clinical parameters of RA including RA score and serum levels of IL-6, CRP, ESR, DAS28-CRP, DAS28-ESR, Swollen joints and Tender joints. Bisulfite sequencing (BSP-seq) was used to determine the DNA methylation in Smad7 promoter (-1000 to +2000) region in CD4+ T cells. In addition, a DNA methylation inhibitor, 5-Azacytidine (5-AzaC), was added to CD4+ T cells to examine the possible role of Smad7 methylation in CD4+ T cell differentiation and functional activity. Results Compared to the heath controls, Smad7 expression was significantly decreased in CD4+ T cells from RA patients and inversely correlated with the RA activity score and serum levels of IL-6 and CRP. Importantly, loss of Smad7 in CD4+ T cell was associated with the alteration of Th17/Treg balance by increasing Th17 over the Treg population. BSP-seq detected that DNA hypermethylation occurred in the Smad7 promoter region of CD4+ T cells obtained from RA patients. Mechanistically, we found that the DNA hypermethylation in the Smad7 promoter of CD4+ T cells was associated with decreased Smad7 expression in RA patients. This was associated with overreactive DNA methyltransferase (DMNT1) and downregulation of the methyl-CpG binding domain proteins (MBD4). Inhibition of DNA methylation by treating CD4+ T cells from RA patients with 5-AzaC significantly increased Smad7 mRNA expression along with the increased MBD4 but reduced DNMT1 expression, which was associated with the rebalance in the Th17/Treg response. Conclusion DNA hypermethylation at the Smad7 promoter regions may cause a loss of Smad7 in CD4+ T cells of RA patients, which may contribute to the RA activity by disrupting the Th17/Treg balance.
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Affiliation(s)
- Yiping Hu
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, Guangdong, China
| | - Bihua Xu
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, Guangdong, China
| | - Juan He
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, Guangdong, China
| | - Hongying Shan
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, Guangdong, China
| | - Gengmin Zhou
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Deli Wang
- Department of Bone and Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Lu Bai
- Department of Sports Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Hongxi Shang
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Liping Nie
- Department of Clinical Laboratory, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Fan Pan
- Center for Cancer Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China,*Correspondence: Qingwen Wang, ; Hui Yao Lan, ; Fan Pan,
| | - Hui Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China,Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Disease, Department of Pathology, Guangdong Academy of Medical Science, Guangdong Provincial People’s Hospital, Guangzhou, China,*Correspondence: Qingwen Wang, ; Hui Yao Lan, ; Fan Pan,
| | - Qingwen Wang
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, Guangdong, China,*Correspondence: Qingwen Wang, ; Hui Yao Lan, ; Fan Pan,
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14
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Chow CN, Yang CW, Chang WC. Databases and prospects of dynamic gene regulation in eukaryotes: A mini review. Comput Struct Biotechnol J 2023; 21:2147-2159. [PMID: 37013004 PMCID: PMC10066511 DOI: 10.1016/j.csbj.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/18/2023] [Accepted: 03/19/2023] [Indexed: 04/05/2023] Open
Abstract
In eukaryotes, dynamic regulation enables DNA polymerases to catalyze a variety of RNA products in spatial and temporal patterns. Dynamic gene expression is regulated by transcription factors (TFs) and epigenetics (DNA methylation and histone modification). The applications of biochemical technology and high-throughput sequencing enhance the understanding of mechanisms of these regulations and affected genomic regions. To provide a searchable platform for retrieving such metadata, numerous databases have been developed based on the integration of genome-wide maps (e.g., ChIP-seq, whole-genome bisulfite sequencing, RNA-seq, ATAC-seq, DNase-seq, and MNase-seq data) and functionally genomic annotation. In this mini review, we summarize the main functions of TF-related databases and outline the prevalent approaches used in inferring epigenetic regulations, their associated genes, and functions. We review the literature on crosstalk between TF and epigenetic regulation and the properties of non-coding RNA regulation, which are challenging topics that promise to pave the way for advances in database development.
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15
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Ageing Skeletal Muscle: The Ubiquitous Muscle Stem Cell. Subcell Biochem 2023; 102:365-377. [PMID: 36600140 DOI: 10.1007/978-3-031-21410-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 1999, in a review by Beardsley, the potential of adult stem cells, in repair and regeneration was heralded (Beardsley Sci Am 281:30-31, 1999). Since then, the field of regenerative medicine has grown exponentially, with the capability of restoring or regenerating the function of damaged, diseased or aged human tissues being an underpinning motivation. If successful, stem cell therapies offer the potential to treat, for example degenerative diseases. In the subsequent 20 years, extensive progress has been made in the arena of adult stem cells (for a recent review see (Zakrzewski et al. Stem Cell Res Ther 10:68, 2019)). Prior to the growth of the adult stem cell research arena, much focus had been placed on the potential of embryonic stem cells (ESCs). The first research revealing the potential of these cells was published in 1981, when scientists reported the ability of cultured stem cells from murine embryos, to not only self-renew, but to also become all cells of the three germ layers of the developing embryo (Evans and Kaufman Nature 292:154-156, 1981), (Martin Proc Natl Acad Sci U S A 78:7634-7638, 1981). It took almost 20 years, following these discoveries, for this technology to translate to human ESCs, using donated human embryos. In 1998, Thomson et al. reported the creation of the first human embryonic cell line (Thomson et al. Science 282:1145-1147, 1998). However, research utilising human ESCs was hampered by ethical and religious constraints and indeed in 2001 George W. Bush restricted US research funding to human ESCs, which had already been banked. The contentious nature of this arena perhaps facilitated the use of and the research potential for adult stem cells. It is beyond the scope of this review to focus on ESCs, although their potential for enhancing our understanding of human development is huge (for a recent review see (Cyranoski Nature 555:428-430, 2018)). Rather, although ESCs and their epigenetic regulation will be introduced for background understanding, the focus will be on stem cells more generally, the role of epigenetics in stem cell fate, skeletal muscle, skeletal muscle stem cells, the impact of ageing on muscle wasting and the mechanisms underpinning loss, with a focus on epigenetic adaptation.
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Brander SM, White JW, DeCourten BM, Major K, Hutton SJ, Connon RE, Mehinto A. Accounting for transgenerational effects of toxicant exposure in population models alters the predicted long-term population status. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac023. [PMID: 36518876 PMCID: PMC9730329 DOI: 10.1093/eep/dvac023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/12/2022] [Accepted: 11/01/2022] [Indexed: 06/04/2023]
Abstract
Acute environmental stressors such as short-term exposure to pollutants can have lasting effects on organisms, potentially impacting future generations. Parental exposure to toxicants can result in changes to the epigenome (e.g., DNA methylation) that are passed down to subsequent, unexposed generations. However, it is difficult to gauge the cumulative population-scale impacts of epigenetic effects from laboratory experiments alone. Here, we developed a size- and age-structured delay-coordinate population model to evaluate the long-term consequences of epigenetic modifications on population sustainability. The model emulated changes in growth, mortality, and fecundity in the F0, F1, and F2 generations observed in experiments in which larval Menidia beryllina were exposed to environmentally relevant concentrations of bifenthrin (Bif), ethinylestradiol (EE2), levonorgestrel (LV), or trenbolone (TB) in the parent generation (F0) and reared in clean water up to the F2 generation. Our analysis suggests potentially dramatic population-level effects of repeated, chronic exposures of early-life stage fish that are not captured by models not accounting for those effects. Simulated exposures led to substantial declines in population abundance (LV and Bif) or near-extinction (EE2 and TB) with the exact trajectory and timeline of population decline dependent on the combination of F0, F1, and F2 effects produced by each compound. Even acute one-time exposures of each compound led to declines and recovery over multiple years due to lagged epigenetic effects. These results demonstrate the potential for environmentally relevant concentrations of commonly used compounds to impact the population dynamics and sustainability of an ecologically relevant species and model organism.
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Affiliation(s)
- Susanne M Brander
- *Correspondence address. Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, 2030 SE Marine Science Drive, Newport, OR 97365, USA. Tel: +541-737-5413; E-mail:
| | - J Wilson White
- Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR 97365, USA
| | | | - Kaley Major
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Sara J Hutton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Richard E Connon
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95656, USA
| | - Alvine Mehinto
- Toxicology Department, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
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Xu L, Shi Z, Li H, He J, Chen B, Tao Z, Tian Y, Chen L, Li G, Tao Z, Gu T, Xu W, Lu L. Genome-wide DNA methylation differences between conservation and breeding populations of Shaoxing ducks. Heliyon 2022; 8:e11644. [DOI: 10.1016/j.heliyon.2022.e11644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
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Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
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Aging, Skeletal Muscle, and Epigenetics. Plast Reconstr Surg 2022; 150:27S-33S. [DOI: 10.1097/prs.0000000000009670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Azimi Z, Isa MR, Khan J, Wang SM, Ismail Z. Association of zinc level with DNA methylation and its consequences: A systematic review. Heliyon 2022; 8:e10815. [PMID: 36203899 PMCID: PMC9530842 DOI: 10.1016/j.heliyon.2022.e10815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Objectives Method Results Conclusion
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Affiliation(s)
- Ziauddin Azimi
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh Selangor Malaysia
- Department of Public Health Medicine, Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh Selangor Malaysia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Department of Biochemistry, Faculty of Pharmacy, Kabul University, Jamal Mina, Kabul, Afghanistan
| | - Mohamad Rodi Isa
- Department of Public Health Medicine, Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh Selangor Malaysia
| | - Jesmine Khan
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh Selangor Malaysia
| | - Seok Mui Wang
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Non-Destructive Biomedical and Pharmaceutical Research Center, Smart Manufacturing Research Institute (SMRI), Universiti Teknologi MARA, Puncak Alam Campus, Selangor, Malaysia
| | - Zaliha Ismail
- Department of Public Health Medicine, Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh Selangor Malaysia
- Corresponding author.
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MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer. Genome Biol 2022; 23:206. [PMID: 36180891 PMCID: PMC9523997 DOI: 10.1186/s13059-022-02776-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/25/2022] [Indexed: 11/19/2022] Open
Abstract
Background BRCA1-associated protein 1 (BAP1) is an ubiquitin carboxy-terminal hydrolase, which forms a multi-protein complex with different epigenetic factors, such as ASXL1-3 and FOXK1/2. At the chromatin level, BAP1 catalyzes the removal of mono-ubiquitination on histone H2AK119 in collaboration with other subunits within the complex and functions as a transcriptional activator in mammalian cells. However, the crosstalk between different subunits and how these subunits impact BAP1’s function remains unclear. Results We report the identification of the methyl-CpG-binding domain proteins 5 and 6 (MBD5 and MBD6) that bind to the C-terminal PHD fingers of the large scaffold subunits ASXL1-3 and stabilize the BAP1 complex at the chromatin. We further identify a novel Drosophila protein, the six-banded (SBA), as an ortholog of human MBD5 and MBD6, and demonstrate that the core modules of the BAP1 complex is structurally and functionally conserved from Drosophila (Calypso/ASX/SBA) to human cells (BAP1/ASXL/MBD). Dysfunction of the BAP1 complex induced by the misregulation/mutations in its subunit(s) are frequent in many human cancers. In BAP1-dependent human cancers, such as small cell lung cancer (SCLC), MBD6 tends to be a part of the predominant complex formed. Therefore, depletion of MBD6 leads to a global loss of BAP1 occupancy at the chromatin, resulting in a reduction of BAP1-dependent gene expression and tumor growth in vitro and in vivo. Conclusions We characterize MBD5 and MBD6 as important regulators of the BAP1 complex and maintain its transcriptional landscape, shedding light on the therapeutic potential of targeting MBD5 and MBD6 in BAP1-dependent human cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02776-x.
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Shared and Divergent Epigenetic Mechanisms in Cachexia and Sarcopenia. Cells 2022; 11:cells11152293. [PMID: 35892590 PMCID: PMC9332174 DOI: 10.3390/cells11152293] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
Significant loss of muscle mass may occur in cachexia and sarcopenia, which are major causes of mortality and disability. Cachexia represents a complex multi-organ syndrome associated with cancer and chronic diseases. It is often characterized by body weight loss, inflammation, and muscle and adipose wasting. Progressive muscle loss is also a hallmark of healthy aging, which is emerging worldwide as a main demographic trend. A great challenge for the health care systems is the age-related decline in functionality which threatens the independence and quality of life of elderly people. This biological decline can also be associated with functional muscle loss, known as sarcopenia. Previous studies have shown that microRNAs (miRNAs) play pivotal roles in the development and progression of muscle wasting in both cachexia and sarcopenia. These small non-coding RNAs, often carried in extracellular vesicles, inhibit translation by targeting messenger RNAs, therefore representing potent epigenetic modulators. The molecular mechanisms behind cachexia and sarcopenia, including the expression of specific miRNAs, share common and distinctive trends. The aim of the present review is to compile recent evidence about shared and divergent epigenetic mechanisms, particularly focusing on miRNAs, between cachexia and sarcopenia to understand a facet in the underlying muscle wasting associated with these morbidities and disclose potential therapeutic interventions.
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DNA Hypomethylation May Contribute to Metabolic Recovery of Frozen Wood Frog Brains. EPIGENOMES 2022; 6:epigenomes6030017. [PMID: 35893013 PMCID: PMC9326605 DOI: 10.3390/epigenomes6030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Transcriptional suppression is characteristic of extreme stress responses, speculated to preserve energetic resources in the maintenance of hypometabolism. In recent years, epigenetic regulation has become heavily implicated in stress adaptation of many animals, including supporting freeze tolerance of the wood frog (Rana sylvatica). However, nervous tissues are frequently lacking in these multi-tissue analyses which warrants investigation. The present study examines the role of DNA methylation, a core epigenetic mechanism, in the response of wood frog brains to freezing. We use immunoblot analysis to track the relative expression of DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins and ten-eleven-translocation (TET) demethylases across the freeze-thaw cycle in R. sylvatica brain, including selected comparisons to freeze-associated sub-stresses (anoxia and dehydration). Global methyltransferase activities and 5-hmC content were also assessed. The data show coordinated evidence for DNA hypomethylation in wood frog brains during freeze-recovery through the combined roles of depressed DNMT3A/3L expression driving lowered DNMT activity and increased TET2/3 levels leading to elevated 5-hmC genomic content (p < 0.05). Raised levels of DNMT1 during high dehydration were also noteworthy. The above suggest that alleviation of transcriptionally repressive 5-mC DNA methylation is a necessary component of the wood frog freeze-thaw cycle, potentially facilitating the resumption of a normoxic transcriptional state as frogs thaw and resume normal metabolic activities.
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Iwasaki Y, Ikemura T, Wada K, Wada Y, Abe T. Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands. BMC Genomics 2022; 23:497. [PMID: 35804296 PMCID: PMC9264310 DOI: 10.1186/s12864-022-08664-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data. Results In this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes. Conclusion Function of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08664-9.
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Affiliation(s)
- Yuki Iwasaki
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan.
| | - Kennosuke Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Yoshiko Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Takashi Abe
- Smart Information Systems, Faculty of Engineering, Niigata University, Niigata-ken, 950-2181, Japan.
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Kamrani S, Amirchaghmaghi E, Ghaffari F, Shahhoseini M, Ghaedi K. Altered gene expression of VEGF, IGFs and H19 lncRNA and epigenetic profile of H19-DMR region in endometrial tissues of women with endometriosis. Reprod Health 2022; 19:100. [PMID: 35459174 PMCID: PMC9034598 DOI: 10.1186/s12978-022-01406-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Endometriosis, as chronic estrogen-dependent disease, is defined by the presence of endometrial-like tissue outside the uterus. Proliferation of endometrial tissue and neoangiogenesis are critical factors in development of endometriosis. Hence, vascular endothelial growth factor (VEGF) as well as insulin‐like growth factor 1 and 2 (IGF1, 2) may be involved as inducers of cellular proliferation or neoangiogenesis. Imprinted long noncoding RNA H19 (lncRNA H19) has been suggested to be involved in pathogenesis of endometriosis via regulation of cellular proliferation and differentiation. Epigenetic aberrations appear to play an important role in its pathogenesis. The present study was designed to elucidate VEGF, IGF1, IGF2 and H19 lncRNA genes expression and epigenetic alterations of differentially methylated region (DMR) of H19 (H19-DMR) regulatory region in endometrial tissues of patients with endometriosis, in comparison with control women. Methods In this case–control study, 24 women with and without endometriosis were studied for the relative expression of VEGF, IGF1, IGF2 and H19 lncRNA genes using real-time polymerase chain reaction (PCR) technique. Occupancy of the MeCP2 on DMR region of H19 gene was assessed using chromatin immunoprecipitation (ChIP), followed by real-time PCR. Results Genes expression profile of H19, IGF1 and IGF2 was decreased in eutopic and ectopic endometrial tissues of endometriosis group, compared to the control tissues. Decreased expression of H19 in ectopic samples was significant in comparison with the controls (P < 0.05). Gene expression of VEGF was increased in eutopic tissues of endometriosis group, compared to control group. Whereas its expression level was lower in ectopic lesions versus eutopic and control endometrial samples. ChIP analysis revealed significant and nearly significant hypomethylation of H19-DMR region II in eutopic and ectopic samples, compared to the control group respectively. This epigenetic change was aligned with expression of IGF2. While methylation of H19-DMR region I was not significantly different between the eutopic, ectopic and control endometrial samples. Conclusion These data showed that VEGF, IGF1, IGF2 and H19 lncRNA genes expression and epigenetic alterations of H19 lncRNA have dynamic role in the pathogenesis of endometriosis, specifically in the way that hypomethylation of H19-DMR region II can be involved in IGF2 dysregulation in endometriosis.
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Affiliation(s)
- Sedigheh Kamrani
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave, Azadi Square, Isfahan, Iran
| | - Elham Amirchaghmaghi
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Firouzeh Ghaffari
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, P.O.Box: 19395-4644, Tehran, Iran. .,Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave, Azadi Square, Isfahan, Iran.
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Musolino E, Pagiatakis C, Serio S, Borgese M, Gamberoni F, Gornati R, Bernardini G, Papait R. The Yin and Yang of epigenetics in the field of nanoparticles. NANOSCALE ADVANCES 2022; 4:979-994. [PMID: 36131763 PMCID: PMC9419747 DOI: 10.1039/d1na00682g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/30/2021] [Indexed: 05/02/2023]
Abstract
Nanoparticles (NPs) have become a very exciting research avenue, with multitudinous applications in various fields, including the biomedical one, whereby they have been gaining considerable interest as drug carriers able to increase bioavailability, therapeutic efficiency and specificity of drugs. Epigenetics, a complex network of molecular mechanisms involved in gene expression regulation, play a key role in mediating the effect of environmental factors on organisms and in the etiology of several diseases (e.g., cancers, neurological disorders and cardiovascular diseases). For many of these diseases, epigenetic therapies have been proposed, whose application is however limited by the toxicity of epigenetic drugs. In this review, we will analyze two aspects of epigenetics in the field of NPs: the first is the role that epigenetics play in mediating nanotoxicity, and the second is the possibility of using NPs for delivery of "epi-drugs" to overcome their limitations. We aim to stimulate discussion among specialists, specifically on the potential contribution of epigenetics to the field of NPs, and to inspire newcomers to this exciting technology.
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Affiliation(s)
- Elettra Musolino
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
| | - Christina Pagiatakis
- Department of Cardiovascular Medicine, Humanitas Research Hospital Rozzano MI Italy
| | - Simone Serio
- Department of Cardiovascular Medicine, Humanitas Research Hospital Rozzano MI Italy
- Department of Biomedical Sciences, Humanitas University Via Rita Levi Montalcini 4 20090 Pieve Emanuele MI Italy
| | - Marina Borgese
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
| | - Federica Gamberoni
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
| | - Rosalba Gornati
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
| | - Giovanni Bernardini
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
| | - Roberto Papait
- Department of and Life Sciences, Insubria University Via Dunant 3 21100 Varese Italy
- Department of Cardiovascular Medicine, Humanitas Research Hospital Rozzano MI Italy
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Li Y, Cheng Z, Fan H, Hao C, Yao W. Epigenetic Changes and Functions in Pneumoconiosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2523066. [PMID: 35096264 PMCID: PMC8794660 DOI: 10.1155/2022/2523066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022]
Abstract
Pneumoconiosis is one of the most common occupational diseases in the world, and specific treatment methods of pneumoconiosis are lacking at present, so it carries great social and economic burdens. Pneumoconiosis, coronavirus disease 2019, and idiopathic pulmonary fibrosis all have similar typical pathological changes-pulmonary fibrosis. Pulmonary fibrosis is a chronic lung disease characterized by excessive deposition of the extracellular matrix and remodeling of the lung tissue structure. Clarifying the pathogenesis of pneumoconiosis plays an important guiding role in its treatment. The occurrence and development of pneumoconiosis are accompanied by epigenetic factors (e.g., DNA methylation and noncoding RNA) changes, which in turn can promote or inhibit the process of pneumoconiosis. Here, we summarize epigenetic changes and functions in the several kinds of evidence classification (epidemiological investigation, in vivo, and in vitro experiments) and main types of cells (macrophages, fibroblasts, and alveolar epithelial cells) to provide some clues for finding specific therapeutic targets for pneumoconiosis and even for pulmonary fibrosis.
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Affiliation(s)
- Yiping Li
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, Henan Province, China
| | - Zhiwei Cheng
- Department of Case Management, The Third Affiliated Hospital of Zhengzhou University, China
| | - Hui Fan
- Ultrasonography Department, The Third Affiliated Hospital of Zhengzhou University, China
| | - Changfu Hao
- Department of Child and Adolecence Health, School of Public Health, Zhengzhou University, Henan, 450001, China
| | - Wu Yao
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, Henan Province, China
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Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
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Woods ML, Weiss A, Sokol AM, Graumann J, Boettger T, Richter AM, Schermuly RT, Dammann RH. Epigenetically silenced apoptosis-associated tyrosine kinase (AATK) facilitates a decreased expression of Cyclin D1 and WEE1, phosphorylates TP53 and reduces cell proliferation in a kinase-dependent manner. Cancer Gene Ther 2022; 29:1975-1987. [PMID: 35902728 PMCID: PMC9750878 DOI: 10.1038/s41417-022-00513-x] [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: 11/25/2021] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 01/25/2023]
Abstract
Silencing of the Apoptosis associated Tyrosine Kinase gene (AATK) has been described in cancer. In our study, we specifically investigated the epigenetic inactivation of AATK in pancreatic adenocarcinoma, lower grade glioma, lung, breast, head, and neck cancer. The resulting loss of AATK correlates with impaired patient survival. Inhibition of DNA methyltransferases (DNMTs) reactivated AATK in glioblastoma and pancreatic cancer. In contrast, epigenetic targeting via the CRISPR/dCas9 system with either EZH2 or DNMT3A inhibited the expression of AATK. Via large-scale kinomic profiling and kinase assays, we demonstrate that AATK acts a Ser/Thr kinase that phosphorylates TP53 at Ser366. Furthermore, whole transcriptome analyses and mass spectrometry associate AATK expression with the GO term 'regulation of cell proliferation'. The kinase activity of AATK in comparison to the kinase-dead mutant mediates a decreased expression of the key cell cycle regulators Cyclin D1 and WEE1. Moreover, growth suppression through AATK relies on its kinase activity. In conclusion, the Ser/Thr kinase AATK represses growth and phosphorylates TP53. Furthermore, expression of AATK was correlated with a better patient survival for different cancer entities. This data suggests that AATK acts as an epigenetically inactivated tumor suppressor gene.
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Affiliation(s)
- Michelle L. Woods
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Astrid Weiss
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Anna M. Sokol
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Johannes Graumann
- grid.418032.c0000 0004 0491 220XScientific Service Group Biomolecular Mass Spectrometry, Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany ,grid.10253.350000 0004 1936 9756Present Address: Institute for Translational Proteomics, Department of Medicine, Philipps-University, 35037 Marburg, Germany
| | - Thomas Boettger
- grid.418032.c0000 0004 0491 220XMax-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Antje M. Richter
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph T. Schermuly
- grid.8664.c0000 0001 2165 8627Department of Internal Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.452624.3German Center for Lung Research (DZL), Giessen, Germany
| | - Reinhard H. Dammann
- grid.8664.c0000 0001 2165 8627Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany ,grid.440517.3German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392 Giessen, Germany
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Lite C, Raja GL, Juliet M, Sridhar VV, Subhashree KD, Kumar P, Chakraborty P, Arockiaraj J. In utero exposure to endocrine-disrupting chemicals, maternal factors and alterations in the epigenetic landscape underlying later-life health effects. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 89:103779. [PMID: 34843942 DOI: 10.1016/j.etap.2021.103779] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Widespread persistence of endocrine-disrupting chemicals (EDCs) in the environment has mandated the need to study their potential effects on an individual's long-term health after both acute and chronic exposure periods. In this review article a particular focus is given on in utero exposure to EDCs in rodent models which resulted in altered epigenetic programming and transgenerational effects in the offspring causing disrupted reproductive and metabolic phenotypes. The literature to date establishes the impact of transgenerational effects of EDCs potentially associated with epigenetic mediated mechanisms. Therefore, this review aims to provide a comprehensive overview of epigenetic programming and it's regulation in mammals, primarily focusing on the epigenetic plasticity and susceptibility to exogenous hormone active chemicals during the early developmental period. Further, we have also in depth discussed the epigenetic alterations associated with the exposure to selected EDCs such as Bisphenol A (BPA), di-2-ethylhexyl phthalate (DEHP) and vinclozlin upon in utero exposure especially in rodent models.
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Affiliation(s)
- Christy Lite
- Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India.
| | - Glancis Luzeena Raja
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulatur, Chennai 603203, Tamil Nadu, India
| | - Melita Juliet
- Department of Oral and Maxillofacial Surgery, SRM Kattankulathur Dental College and Hospital, SRM Institute of Science and Technology, Kattankulatur, Chennai 603203, Tamil Nadu, India
| | - Vasisht Varsh Sridhar
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulatur, Chennai 603203, Tamil Nadu, India
| | - K Divya Subhashree
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulatur, Chennai 603203, Tamil Nadu, India
| | - Praveen Kumar
- Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Paromita Chakraborty
- Environmental Science and Technology Laboratory, Department of Chemical Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamil Nadu, India.
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulatur, Chennai 603203, Tamil Nadu, India.
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Sahabi S, Jafari-Gharabaghlou D, Zarghami N. A new insight into cell biological and biochemical changes through aging. Acta Histochem 2022; 124:151841. [PMID: 34995929 DOI: 10.1016/j.acthis.2021.151841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022]
Abstract
After several years of extensive research, the main cause of aging is yet elusive. There are some theories about aging, such as stem cell aging, senescent cells accumulation, and neuro-endocrine theories. None of them is able to explain all changes that happen in cells and body through aging. By finding out the main cause of aging, it will be much easier to control, prevent and even reverse the aging process. Our cells, regardless of their replicative capacity, get old through aging and they have almost the same epigenetic age. Different cell signaling pathways contribute to aging. The most important one is mTORC1 that becomes hyperactive in cells that undergo aging. Other significant changes with age are lysosome accumulation, impaired autophagy, and mitophagy. Immune system undergoes gradual changes through aging including a shift from lymphoid to myeloid lineage production as well as increased IL-6 and TNF-α which lead to age-related weight loss and meta-inflammation. Additionally, our endocrine system also experiences some changes that should be taken into consideration when looking for the main cause of aging in the human body. In this review, we planned to summarize some of the changes that happen in cells and the body through aging.
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Coronel-Hernández J, Pérez-Yépez EA, Delgado-Waldo I, Contreras-Romero C, Jacobo-Herrera N, Cantú-De León D, Pérez-Plasencia C. Aberrant Metabolism as Inductor of Epigenetic Changes in Breast Cancer: Therapeutic Opportunities. Front Oncol 2021; 11:676562. [PMID: 34692471 PMCID: PMC8531643 DOI: 10.3389/fonc.2021.676562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
Aberrant metabolism is arising interest in the scientific community not only because of the role it plays in the development and establishment of the tumor mass but also the possibility of drug poisoning of key enzymes overexpressed in tumor cells. Moreover, tumor metabolism provides key molecules to maintain the epigenetic changes that are also an undisputed characteristic of each tumor type. This metabolic change includes the Warburg effect and alterations in key pathways involved in glutaminolysis, pentose phosphate, and unsaturated fatty acid biosynthesis. Modifications in all these pathways have consequences that impact genetics and epigenetics processes such as DNA methylation patterns, histone post-translational modifications, triggering oncogenes activation, and loss in tumor suppressor gene expression to lead the tumor establishment. In this review, we describe the metabolic rearrangement and its association with epigenetic regulation in breast cancer, as well as its implication in biological processes involved in cancer progression. A better understanding of these processes could help to find new targets for the diagnosis, prognosis, and treatment of this human health problem.
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Affiliation(s)
| | - Eloy Andrés Pérez-Yépez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico.,Cátedra-CONACYT, Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico City, Mexico
| | | | | | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán, Mexico City, Mexico
| | - David Cantú-De León
- Unidad de Investigación en Cáncer, Instituto Nacional de Cancerología , Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico.,Laboratorio de Genómica Funcional, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
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33
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Gowri V, Monteiro A. Inheritance of Acquired Traits in Insects and Other Animals and the Epigenetic Mechanisms That Break the Weismann Barrier. J Dev Biol 2021; 9:41. [PMID: 34698204 PMCID: PMC8544363 DOI: 10.3390/jdb9040041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
The credibility of the Weismann barrier has come into question. Several studies in various animal systems, from mice to worms, have shown that novel environmental stimuli can generate an altered developmental or behavioral trait that can be transmitted to offspring of the following generation. Recently, insects have become ideal models to study the inheritance of acquired traits. This is because insects can be reared in high numbers at low cost, they have short generation times and produce abundant offspring. Numerous studies have shown that an insect can modify its phenotype in response to a novel stimulus to aid its survival, and also that this modified phenotypic trait can be inherited by its offspring. Epigenetic mechanisms are likely at play but, most studies do not address the mechanisms that underlie the inheritance of acquired traits in insects. Here we first review general epigenetic mechanisms such as DNA methylation, histone acetylation and small noncoding RNAs that have been implicated in the transmission of acquired traits in animals, then we focus on the few insect studies in which these mechanisms have been investigated.
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Affiliation(s)
- V. Gowri
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
- Science Division, Yale-NUS College, Singapore 138609, Singapore
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34
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Vernaz G, Malinsky M, Svardal H, Du M, Tyers AM, Santos ME, Durbin R, Genner MJ, Turner GF, Miska EA. Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes. Nat Commun 2021; 12:5870. [PMID: 34620871 PMCID: PMC8497601 DOI: 10.1038/s41467-021-26166-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.
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Affiliation(s)
- Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Hannes Svardal
- Wellcome Sanger Institute, Cambridge, UK
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Mingliu Du
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Alexandra M Tyers
- School of Natural Sciences, Sciences, Bangor University, Bangor, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - George F Turner
- School of Natural Sciences, Sciences, Bangor University, Bangor, UK
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
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35
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Williamson SM, Ingelson-Filpula WA, Hadj-Moussa H, Storey KB. Epigenetic underpinnings of freeze avoidance in the goldenrod gall moth, Epiblema scudderiana. JOURNAL OF INSECT PHYSIOLOGY 2021; 134:104298. [PMID: 34411584 DOI: 10.1016/j.jinsphys.2021.104298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/13/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The goldenrod gall moth (Epiblema scudderiana) is a cold hardy insect that survives subzero temperatures during the winter by supercooling bodily fluids to approximately -40 °C, allowing the insect to remain unfrozen despite the freezing temperatures. This is characterized by a drastic increase of cryoprotectant glycerol along with widespread downregulation of non-essential genes and processes to conserve cellular energy. This study examined the role of epigenetic enzymes in regulating this freeze-avoidant process across a range of freezing temperatures experienced in nature. Cold and subzero temperature exposure in E. scudderiana resulted in upregulation of select DNA methyltransferase (DNMT) enzymes with concurrent decreases in DNMT activity and no change in activity of the Ten-Eleven Translocation (TET) demethylation enzyme activities. Levels of histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity decreased during cold exposures. The increase in DNMT expression and concurrent decrease in HAT activity suggests a role for DNA methylation to assist with transcriptional suppression. These findings propose that epigenetic regulation of genes and histones underpin the winter survival strategies of this insect.
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Affiliation(s)
- Sam M Williamson
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - W Aline Ingelson-Filpula
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Hanane Hadj-Moussa
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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36
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Turner DC, Gorski PP, Seaborne RA, Viggars M, Murphy M, Jarvis JC, Martin NR, Stewart CE, Sharples AP. Mechanical loading of bioengineered skeletal muscle in vitro recapitulates gene expression signatures of resistance exercise in vivo. J Cell Physiol 2021; 236:6534-6547. [PMID: 33586196 PMCID: PMC8653897 DOI: 10.1002/jcp.30328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/17/2021] [Accepted: 02/03/2021] [Indexed: 11/10/2022]
Abstract
Understanding the role of mechanical loading and exercise in skeletal muscle (SkM) is paramount for delineating the molecular mechanisms that govern changes in muscle mass. However, it is unknown whether loading of bioengineered SkM in vitro adequately recapitulates the molecular responses observed after resistance exercise (RE) in vivo. To address this, the transcriptional and epigenetic (DNA methylation) responses were compared after mechanical loading in bioengineered SkM in vitro and after RE in vivo. Specifically, genes known to be upregulated/hypomethylated after RE in humans were analyzed. Ninety-three percent of these genes demonstrated similar changes in gene expression post-loading in the bioengineered muscle when compared to acute RE in humans. Furthermore, similar differences in gene expression were observed between loaded bioengineered SkM and after programmed RT in rat SkM tissue. Hypomethylation occurred for only one of the genes analysed (GRIK2) post-loading in bioengineered SkM. To further validate these findings, DNA methylation and mRNA expression of known hypomethylated and upregulated genes post-acute RE in humans were also analyzed at 0.5, 3, and 24 h post-loading in bioengineered muscle. The largest changes in gene expression occurred at 3 h, whereby 82% and 91% of genes responded similarly when compared to human and rodent SkM respectively. DNA methylation of only a small proportion of genes analyzed (TRAF1, MSN, and CTTN) significantly increased post-loading in bioengineered SkM alone. Overall, mechanical loading of bioengineered SkM in vitro recapitulates the gene expression profile of human and rodent SkM after RE in vivo. Although some genes demonstrated differential DNA methylation post-loading in bioengineered SkM, such changes across the majority of genes analyzed did not closely mimic the epigenetic response to acute-RE in humans.
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Affiliation(s)
- Daniel C. Turner
- Institute for Science and Technology in Medicine (ISTM), School of Pharmacy and BioengineeringKeele UniversityStaffordshireUK
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Exercise Metabolism and Adaptation Research Group (EMARG), Research Institute for Sport and Exercise Sciences (RISES)Liverpool John Moores UniversityLiverpoolUK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical BiosciencesKing's College LondonLondonUK
| | - Piotr P. Gorski
- Institute for Science and Technology in Medicine (ISTM), School of Pharmacy and BioengineeringKeele UniversityStaffordshireUK
- Institute for Physical PerformanceNorwegian School of Sport Sciences (NiH)OsloNorway
| | - Robert A. Seaborne
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Exercise Metabolism and Adaptation Research Group (EMARG), Research Institute for Sport and Exercise Sciences (RISES)Liverpool John Moores UniversityLiverpoolUK
- Center for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Mark Viggars
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Exercise Metabolism and Adaptation Research Group (EMARG), Research Institute for Sport and Exercise Sciences (RISES)Liverpool John Moores UniversityLiverpoolUK
| | - Mark Murphy
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Jonathan C. Jarvis
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Exercise Metabolism and Adaptation Research Group (EMARG), Research Institute for Sport and Exercise Sciences (RISES)Liverpool John Moores UniversityLiverpoolUK
| | - Neil R.W. Martin
- School of Sport, Exercise and Health SciencesLoughborough UniversityLoughboroughUK
| | - Claire E. Stewart
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Exercise Metabolism and Adaptation Research Group (EMARG), Research Institute for Sport and Exercise Sciences (RISES)Liverpool John Moores UniversityLiverpoolUK
| | - Adam P. Sharples
- Institute for Physical PerformanceNorwegian School of Sport Sciences (NiH)OsloNorway
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37
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Renn SC, Hurd PL. Epigenetic Regulation and Environmental Sex Determination in Cichlid Fishes. Sex Dev 2021; 15:93-107. [PMID: 34433170 PMCID: PMC8440468 DOI: 10.1159/000517197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Studying environmental sex determination (ESD) in cichlids provides a phylogenetic and comparative approach to understand the evolution of the underlying mechanisms, their impact on the evolution of the overlying systems, and the neuroethology of life history strategies. Natural selection normally favors parents who invest equally in the development of male and female offspring, but evolution may favor deviations from this 50:50 ratio when environmental conditions produce an advantage for doing so. Many species of cichlids demonstrate ESD in response to water chemistry (temperature, pH, and oxygen concentration). The relative strengths of and the exact interactions between these factors vary between congeners, demonstrating genetic variation in sensitivity. The presence of sizable proportions of the less common sex towards the environmental extremes in most species strongly suggests the presence of some genetic sex-determining loci acting in parallel with the ESD factors. Sex determination and differentiation in these species does not seem to result in the organization of a final and irreversible sexual fate, so much as a life-long ongoing battle between competing male- and female-determining genetic and hormonal networks governed by epigenetic factors. We discuss what is and is not known about the epigenetic mechanism behind the differentiation of both gonads and sex differences in the brain. Beyond the well-studied tilapia species, the 2 best-studied dwarf cichlid systems showing ESD are the South American genus Apistogramma and the West African genus Pelvicachromis. Both species demonstrate male morphs with alternative reproductive tactics. We discuss the further neuroethology opportunities such systems provide to the study of epigenetics of alternative life history strategies and other behavioral variation.
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Affiliation(s)
| | - Peter L Hurd
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, CA
- Department of Psychology, University of Alberta, Edmonton, AB, CA
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38
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Xu H, Li S, Liu YS. Roles and Mechanisms of DNA Methylation in Vascular Aging and Related Diseases. Front Cell Dev Biol 2021; 9:699374. [PMID: 34262910 PMCID: PMC8273304 DOI: 10.3389/fcell.2021.699374] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Vascular aging is a pivotal risk factor promoting vascular dysfunction, the development and progression of vascular aging-related diseases. The structure and function of endothelial cells (ECs), vascular smooth muscle cells (VSMCs), fibroblasts, and macrophages are disrupted during the aging process, causing vascular cell senescence as well as vascular dysfunction. DNA methylation, an epigenetic mechanism, involves the alteration of gene transcription without changing the DNA sequence. It is a dynamically reversible process modulated by methyltransferases and demethyltransferases. Emerging evidence reveals that DNA methylation is implicated in the vascular aging process and plays a central role in regulating vascular aging-related diseases. In this review, we seek to clarify the mechanisms of DNA methylation in modulating ECs, VSMCs, fibroblasts, and macrophages functions and primarily focus on the connection between DNA methylation and vascular aging-related diseases. Therefore, we represent many vascular aging-related genes which are modulated by DNA methylation. Besides, we concentrate on the potential clinical application of DNA methylation to serve as a reliable diagnostic tool and DNA methylation-based therapeutic drugs for vascular aging-related diseases.
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Affiliation(s)
- Hui Xu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - Shuang Li
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
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39
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Parveen N, Dhawan S. DNA Methylation Patterning and the Regulation of Beta Cell Homeostasis. Front Endocrinol (Lausanne) 2021; 12:651258. [PMID: 34025578 PMCID: PMC8137853 DOI: 10.3389/fendo.2021.651258] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic beta cells play a central role in regulating glucose homeostasis by secreting the hormone insulin. Failure of beta cells due to reduced function and mass and the resulting insulin insufficiency can drive the dysregulation of glycemic control, causing diabetes. Epigenetic regulation by DNA methylation is central to shaping the gene expression patterns that define the fully functional beta cell phenotype and regulate beta cell growth. Establishment of stage-specific DNA methylation guides beta cell differentiation during fetal development, while faithful restoration of these signatures during DNA replication ensures the maintenance of beta cell identity and function in postnatal life. Lineage-specific transcription factor networks interact with methylated DNA at specific genomic regions to enhance the regulatory specificity and ensure the stability of gene expression patterns. Recent genome-wide DNA methylation profiling studies comparing islets from diabetic and non-diabetic human subjects demonstrate the perturbation of beta cell DNA methylation patterns, corresponding to the dysregulation of gene expression associated with mature beta cell state in diabetes. This article will discuss the molecular underpinnings of shaping the islet DNA methylation landscape, its mechanistic role in the specification and maintenance of the functional beta cell phenotype, and its dysregulation in diabetes. We will also review recent advances in utilizing beta cell specific DNA methylation patterns for the development of biomarkers for diabetes, and targeting DNA methylation to develop translational approaches for supplementing the functional beta cell mass deficit in diabetes.
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Affiliation(s)
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, United States
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40
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Hou Y, Hu J, Zhou L, Liu L, Chen K, Yang X. Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis. Front Oncol 2021; 11:647253. [PMID: 33869043 PMCID: PMC8047072 DOI: 10.3389/fonc.2021.647253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/12/2021] [Indexed: 12/27/2022] Open
Abstract
Prostate adenocarcinoma (PRAD) is the most pervasive carcinoma diagnosed in men with over 170,000 new cases every year in the United States and is the second leading cause of death from cancer in men despite its indolent clinical course. Prostate-specific antigen testing, which is the most commonly used non-invasive diagnostic method for PRAD, has improved early detection rates in the past decade, but its effectiveness for monitoring disease progression and predicting prognosis is controversial. To identify novel biomarkers for these purposes, we carried out weighted gene co-expression network analysis of the top 10,000 variant genes in PRAD from The Cancer Genome Atlas in order to identify gene modules associated with clinical outcomes. Methylation and copy number variation analysis were performed to screen aberrantly expressed genes, and the Kaplan–Meier survival and gene set enrichment analyses were conducted to evaluate the prognostic value and potential mechanisms of the identified genes. Cyclin E2 (CCNE2), rhophilin Rho GTPase-binding protein (RHPN1), enhancer of zeste homolog 2 (EZH2), tonsoku-like DNA repair protein (TONSL), epoxide hydrolase 2 (EPHX2), fibromodulin (FMOD), and solute carrier family 7 member (SLC7A4) were identified as potential prognostic indicators and possible therapeutic targets as well. These findings can improve diagnosis and disease monitoring to achieve better clinical outcomes in PRAD.
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Affiliation(s)
- Yaxin Hou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Junyi Hu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Lijie Zhou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Lilong Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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41
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Katsura Y, Ikemura T, Kajitani R, Toyoda A, Itoh T, Ogata M, Miura I, Wada K, Wada Y, Satta Y. Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency. Life Sci Alliance 2021; 4:4/5/e202000905. [PMID: 33712508 PMCID: PMC7994367 DOI: 10.26508/lsa.202000905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/30/2022] Open
Abstract
Genome sequencing of a unique frog (Glandirana rugosa) having XY/ZW systems within the species and comparative genomics with other six frogs were performed using a batch-learning self-organizing map, which is unsupervised AI for oligonucleotide compositions, to clarify its genome characteristics. The Japanese wrinkled frog (Glandirana rugosa) is unique in having both XX-XY and ZZ-ZW types of sex chromosomes within the species. The genome sequencing and comparative genomics with other frogs should be important to understand mechanisms of turnover of sex chromosomes within one species or during a short period. In this study, we analyzed the newly sequenced genome of G. rugosa using a batch-learning self-organizing map which is unsupervised artificial intelligence for oligonucleotide compositions. To clarify genome characteristics of G. rugosa, we compared its short oligonucleotide compositions in all 1-Mb genomic fragments with those of other six frog species (Pyxicephalus adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, Xenopus laevis, and Xenopus tropicalis). In G. rugosa, we found an Mb-level large size of repeat sequences having a high identity with the W chromosome of the African bullfrog (P. adspersus). Our study concluded that G. rugosa has unique genome characteristics with a high CG frequency, and its genome is assumed to heterochromatinize a large size of genome via methylataion of CG.
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Affiliation(s)
- Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama-shi, Japan .,Amphibian Research Center, Hiroshima University, Hiroshima-shi, Japan.,Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University For Advanced Studies (SOKENDAI), Shonankokuraimura, Hayama-machi, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Rei Kajitani
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo-to, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima-shi, Japan
| | - Takehiko Itoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo-to, Japan
| | | | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Hiroshima-shi, Japan
| | - Kennosuke Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Yoshiko Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University For Advanced Studies (SOKENDAI), Shonankokuraimura, Hayama-machi, Japan
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42
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Maasar MF, Turner DC, Gorski PP, Seaborne RA, Strauss JA, Shepherd SO, Cocks M, Pillon NJ, Zierath JR, Hulton AT, Drust B, Sharples AP. The Comparative Methylome and Transcriptome After Change of Direction Compared to Straight Line Running Exercise in Human Skeletal Muscle. Front Physiol 2021; 12:619447. [PMID: 33679435 PMCID: PMC7933519 DOI: 10.3389/fphys.2021.619447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
The methylome and transcriptome signatures following exercise that are physiologically and metabolically relevant to sporting contexts such as team sports or health prescription scenarios (e.g., high intensity interval training/HIIT) has not been investigated. To explore this, we performed two different sport/exercise relevant high-intensity running protocols in five male sport team members using a repeated measures design of: (1) change of direction (COD) versus; (2) straight line (ST) running exercise with a wash-out period of at least 2 weeks between trials. Skeletal muscle biopsies collected from the vastus lateralis 30 min and 24 h post exercise, were assayed using 850K methylation arrays and a comparative analysis with recent (subject-unmatched) sprint and acute aerobic exercise meta-analysis transcriptomes was performed. Despite COD and ST exercise being matched for classically defined intensity measures (speed × distance and number of accelerations/decelerations), COD exercise elicited greater movement (GPS-Playerload), physiological (HR), metabolic (lactate) as well as central and peripheral (differential RPE) exertion measures compared with ST exercise, suggesting COD exercise evoked a higher exercise intensity. The exercise response alone across both conditions evoked extensive alterations in the methylome 30 min and 24 h post exercise, particularly in MAPK, AMPK and axon guidance pathways. COD evoked a considerably greater hypomethylated signature across the genome compared with ST exercise, particularly at 30 min post exercise, enriched in: Protein binding, MAPK, AMPK, insulin, and axon guidance pathways. Comparative methylome analysis with sprint running transcriptomes identified considerable overlap, with 49% of genes that were altered at the expression level also differentially methylated after COD exercise. After differential methylated region analysis, we observed that VEGFA and its downstream nuclear transcription factor, NR4A1 had enriched hypomethylation within their promoter regions. VEGFA and NR4A1 were also significantly upregulated in the sprint transcriptome and meta-analysis of exercise transcriptomes. We also confirmed increased gene expression of VEGFA, and considerably larger increases in the expression of canonical metabolic genes PPARGC1A (that encodes PGC1-α) and NR4A3 in COD vs. ST exercise. Overall, we demonstrate that increased physiological/metabolic load via COD exercise in human skeletal muscle evokes considerable epigenetic modifications that are associated with changes in expression of genes responsible for adaptation to exercise.
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Affiliation(s)
- Mohd-Firdaus Maasar
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Daniel C Turner
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Institute for Science and Technology in Medicine, School of Pharmacy and Bioengineering, Keele University, Staffordshire, United Kingdom
| | - Piotr P Gorski
- Institute for Science and Technology in Medicine, School of Pharmacy and Bioengineering, Keele University, Staffordshire, United Kingdom.,Institute for Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Robert A Seaborne
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Juliette A Strauss
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Sam O Shepherd
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Matt Cocks
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Andrew T Hulton
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Barry Drust
- School of Sport, Exercise and Rehabilitation Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adam P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
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43
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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44
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Use of DNA methylation profiling in translational oncology. Semin Cancer Biol 2020; 83:523-535. [PMID: 33352265 DOI: 10.1016/j.semcancer.2020.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
DNA methylation is a highly regulated process that has a critical role in human development and homeostatic control of the cell. The number of genes affected by anomalous DNA methylation in cancer-associated pathways is swiftly accelerating and with the advancement of molecular technologies, new layers of complexity are opening up and refining our strategies to combat cancer. DNA methylation profiling is an essential facet to understanding malignant transformation and is becoming an increasingly important tool for cancer diagnosis, prognosis and therapy monitoring. In this review, the role of DNA methylation in normal cellular function is discussed, as well as how epigenetic aberrations override normal cellular cues that lead to tumor initiation and propagation. The review also focuses on the latest advancements in DNA methylation profiling as a biomarker for early cancer detection, predicting patient clinical outcomes and responses to treatment and provides new insights into epigenetic-based therapy in clinical oncology.
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45
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Li XJ, Liu LQ, Dong H, Yang JJ, Wang WW, Zhang Q, Wang CL, Zhou J, Chen HQ. Comparative genome-wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs. Anim Genet 2020; 52:78-89. [PMID: 33301219 DOI: 10.1111/age.13029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 12/11/2022]
Abstract
DNA methylation was one of the earliest discovered epigenetic modifications in vertebrates, and is an important epigenetic mechanism involved in the expression of genes in many biological processes, including muscle growth and development. Its effects on economically important traits are evidenced in reported differences in meat quality traits between Chinese indigenous pig breeds (Wannanhua pig) and Western commercial pig breeds (Yorkshire pig), and this presents a unique model for analyzing the effects of DNA methylation on these traits. In the present study, a whole genome DNA methylation analysis was performed on the two breeds using methylated DNA immunoprecipitation. GO functional enrichment and pathway enrichment analyses identified differentially methylated genes primarily associated with fatty acid metabolism, biological processes of muscle development and signaling pathways related to muscle development and pork quality. Differentially methylated genes were verified by sodium pyrosequencing, and the results were consistent with the sequencing results. The results of the integrative analysis between DNA methylation and gene expression revealed that the DNA methylation levels showed a significantly negative correlation with gene expression levels around the transcription start site of genes. In total, 41 genes were both differentially expressed and methylated; these genes were related to fat metabolism, lipid metabolism and skeletal muscle development. This study could help further explore the molecular mechanisms and phenotypic differences in pig growth and development among different breeds.
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Affiliation(s)
- X-J Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - L-Q Liu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - H Dong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J-J Yang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - W-W Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Q Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - C-L Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - H-Q Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
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46
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Kong FC, Ma CL, Zhong MK. Epigenetic Effects Mediated by Antiepileptic Drugs and their Potential Application. Curr Neuropharmacol 2020; 18:153-166. [PMID: 31660836 PMCID: PMC7324883 DOI: 10.2174/1570159x17666191010094849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/01/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
An epigenetic effect mainly refers to a heritable modulation in gene expression in the short term but does not involve alterations in the DNA itself. Epigenetic molecular mechanisms include DNA methylation, histone modification, and untranslated RNA regulation. Antiepileptic drugs have drawn attention to biological and translational medicine because their impact on epigenetic mechanisms will lead to the identification of novel biomarkers and possible therapeutic strategies for the prevention and treatment of various diseases ranging from neuropsychological disorders to cancers and other chronic conditions. However, these transcriptional and posttranscriptional alterations can also result in adverse reactions and toxicity in vitro and in vivo. Hence, in this review, we focus on recent findings showing epigenetic processes mediated by antiepileptic drugs to elucidate their application in medical experiments and shed light on epigenetic research for medicinal purposes.
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Affiliation(s)
- Fan-Cheng Kong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Chun-Lai Ma
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming-Kang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
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47
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Bohnsack JP, Pandey SC. Histone modifications, DNA methylation, and the epigenetic code of alcohol use disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:1-62. [PMID: 33461661 DOI: 10.1016/bs.irn.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality. Despite AUD's substantial contributions to lost economic productivity and quality of life, there are only a limited number of approved drugs for treatment of AUD in the United States. This chapter will update progress made on the epigenetic basis of AUD, with particular focus on histone post-translational modifications and DNA methylation and how these two epigenetic mechanisms interact to contribute to neuroadaptive processes leading to initiation, maintenance and progression of AUD pathophysiology. We will also evaluate epigenetic therapeutic strategies that have arisen from preclinical models of AUD and epigenetic biomarkers that have been discovered in human populations with AUD.
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Affiliation(s)
- John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.
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48
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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49
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Fitz-James MH, Tong P, Pidoux AL, Ozadam H, Yang L, White SA, Dekker J, Allshire RC. Large domains of heterochromatin direct the formation of short mitotic chromosome loops. eLife 2020; 9:e57212. [PMID: 32915140 PMCID: PMC7515631 DOI: 10.7554/elife.57212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
During mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold. Condensin complexes are involved in chromatin compaction, but the contribution of other chromatin proteins, DNA sequence and histone modifications is less understood. A large region of fission yeast DNA inserted into a mouse chromosome was previously observed to adopt a mitotic organisation distinct from that of surrounding mouse DNA. Here, we show that a similar distinct structure is common to a large subset of insertion events in both mouse and human cells and is coincident with the presence of high levels of heterochromatic H3 lysine nine trimethylation (H3K9me3). Hi-C and microscopy indicate that the heterochromatinised fission yeast DNA is organised into smaller chromatin loops than flanking euchromatic mouse chromatin. We conclude that heterochromatin alters chromatin loop size, thus contributing to the distinct appearance of heterochromatin on mitotic chromosomes.
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Affiliation(s)
- Maximilian H Fitz-James
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Pin Tong
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Liyan Yang
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Sharon A White
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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50
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Maimaitiyiming Y, Wang QQ, Hsu CH, Naranmandura H. Arsenic induced epigenetic changes and relevance to treatment of acute promyelocytic leukemia and beyond. Toxicol Appl Pharmacol 2020; 406:115212. [PMID: 32882258 DOI: 10.1016/j.taap.2020.115212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Epigenetic alterations regulate gene expression without changes in the DNA sequence. It is well-demonstrated that aberrant epigenetic changes contribute to the leukemogenesis of acute promyelocytic leukemia (APL). Arsenic trioxide (ATO) is one of the most common drugs used in the frontline treatment of APL that act through targeting and destabilizing the PML/RARα oncofusion protein. ATO together with all-trans retinoic acid (ATRA) lead to durable remission of more than 90% non-high-risk APL patients, turning APL treatment into a paradigm of oncoprotein targeted cure. Although relapse and drug resistance in APL are yet to be resolved in the clinic, epigenetic machineries might hold the key to address this issue. Further, ATO also showed promising anticancer activities against a variety of malignancies, but its application is particularly restricted due to limited understanding of the mechanism. Thus, a thorough understanding of epigenetic mechanism behind anti-leukemic effects of ATO would benefit the development of ATO-based anticancer strategy. Role of ATRA on APL associated epigenetic alterations has been extensively studied and reviewed. Recently, accumulating evidence suggest that ATO also induces some epigenetic changes that might favor APL eradication. In this article, we comprehensively discuss arsenic induced epigenetic changes and its relevance in APL treatment and beyond, so as to provide novel insights into overcoming arsenic resistance in APL and promote application of this drug to other malignancies.
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Affiliation(s)
- Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Qian Wang
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China.
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