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Migliaccio G, Morikka J, Del Giudice G, Vaani M, Möbus L, Serra A, Federico A, Greco D. Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages. Comput Struct Biotechnol J 2024; 25:143-152. [PMID: 39257962 PMCID: PMC11385784 DOI: 10.1016/j.csbj.2024.08.018] [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: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024] Open
Abstract
Macrophage plasticity allows the adoption of distinct functional states in response to environmental cues. While unique transcriptomic profiles define these states, focusing solely on transcription neglects potential long-term effects. The investigation of epigenetic changes can be used to understand how temporary stimuli can result in lasting effects. Epigenetic alterations play an important role in the pathophysiology of macrophages, including their trained innate immunity, enabling faster and more efficient inflammatory responses upon subsequent encounters to the same pathogen or insult. In this study, we used a multi-omics approach to elucidate the interplay between gene expression and DNA-methylation, to explore the potential long-term effects of diverse polarizing environments on macrophage activity. We identified a common core set of genes that are differentially methylated regardless of exposure type, indicating a potential common fundamental mechanism for adaptation to various stimuli. Functional analysis revealed that processes requiring rapid responses displayed transcriptomic regulation, whereas functions critical for long-term adaptations exhibited co-regulation at both transcriptomic and epigenetic levels. Our study uncovers a novel set of genes linked to the long-term effects of macrophage polarization. This discovery underscores the potential of epigenetics in elucidating how macrophages establish long-term memory and influence health outcomes.
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Affiliation(s)
- Giorgia Migliaccio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jack Morikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
| | - Giusy Del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Maaret Vaani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lena Möbus
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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2
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Fisher DN, Bechsgaard J, Bilde T. Exploring changes in social spider DNA methylation profiles in all cytosine contexts following infection. Heredity (Edinb) 2024:10.1038/s41437-024-00724-y. [PMID: 39266675 DOI: 10.1038/s41437-024-00724-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024] Open
Abstract
Living at high density and with low genetic diversity are factors that should both increase the susceptibility of organisms to disease. Therefore, group living organisms, especially those that are inbred, should be especially vulnerable to infection and therefore have particular strategies to cope with infection. Phenotypic plasticity, underpinned by epigenetic changes, could allow group living organisms to rapidly respond to infection challenges. To explore the potential role of epigenetic modifications in the immune response to a group-living species with low genetic diversity, we compared the genome-wide DNA methylation profiles of five colonies of social spiders (Stegodyphus dumicola) in their natural habitat in Namibia at the point just before they succumbed to infection to a point at least six months previously where they were presumably healthier. We found increases in genome- and chromosome-wide methylation levels in the CpG, CHG, and CHH contexts, although the genome-wide changes were not clearly different from zero. These changes were most prominent in the CHG context, especially at a narrow region of chromosome 13, hinting at an as-of-yet unsuspected role of this DNA methylation context in phenotypic plasticity. However, there were few clear patterns of differential methylation at the base level, and genes with a known immune function in spiders had mean methylation changes close to zero. Our results suggest that DNA methylation may change with infection at large genomic scales, but that this type of epigenetic change is not necessarily integral to the immune response of social spiders.
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Affiliation(s)
- David N Fisher
- School of Biological Sciences, University of Aberdeen, King's College, Aberdeen, UK.
| | - Jesper Bechsgaard
- Department of Biology, Section for Genetic Ecology and Evolution, Centre for Ecological Genetics, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Department of Biology, Section for Genetic Ecology and Evolution, Centre for Ecological Genetics, Aarhus University, Aarhus, Denmark
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3
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Shaikh M, Doshi G. Epigenetic aging in major depressive disorder: Clocks, mechanisms and therapeutic perspectives. Eur J Pharmacol 2024; 978:176757. [PMID: 38897440 DOI: 10.1016/j.ejphar.2024.176757] [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: 04/16/2024] [Revised: 06/09/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Depression, a chronic mental disorder characterized by persistent sadness, loss of interest, and difficulty in daily tasks, impacts millions globally with varying treatment options. Antidepressants, despite their long half-life and minimal effectiveness, leave half of patients undertreated, highlighting the need for new therapies to enhance well-being. Epigenetics, which studies genetic changes in gene expression or cellular phenotype without altering the underlying Deoxyribonucleic Acid (DNA) sequence, is explored in this article. This article delves into the intricate relationship between epigenetic mechanisms and depression, shedding light on how environmental stressors, early-life adversity, and genetic predispositions shape gene expression patterns associated with depression. We have also discussed Histone Deacetylase (HDAC) inhibitors, which enhance cognitive function and mood regulation in depression. Non-coding RNAs, (ncRNAs) such as Long Non-Coding RNAs (lncRNAs) and micro RNA (miRNAs), are highlighted as potential biomarkers for detecting and monitoring major depressive disorder (MDD). This article also emphasizes the reversible nature of epigenetic modifications and their influence on neuronal growth processes, underscoring the dynamic interplay between genetics, environment, and epigenetics in depression development. It explores the therapeutic potential of targeting epigenetic pathways in treating clinical depression. Additionally, it examines clinical findings related to epigenetic clocks and their role in studying depression and biological aging.
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Affiliation(s)
- Muqtada Shaikh
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, 400 056, India
| | - Gaurav Doshi
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, 400 056, India.
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Min EK, Kim SR, Lee CM, Na KH, Park CH, Oh BC, Jung Y, Hong IS. Identification of memory mechanism in tissue-resident stem cells via ANGPTL4 beyond immune cells upon viral antigen exposure. Mol Ther 2024; 32:3042-3058. [PMID: 38582960 DOI: 10.1016/j.ymthe.2024.04.006] [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: 01/11/2024] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Although memory functions of immune cells characterized by increased resistance to subsequent infections after initial pathogen exposure are well-established, it remains unclear whether non-immune cells, especially tissue-resident stem cells, exhibit similar memory mechanisms. The present study revealed that detrimental effects of initial viral antigen exposure (human papillomavirus [HPV]) on diverse stem cell functions were significantly exacerbated upon subsequent secondary exposure both in vitro and in vivo. Importantly, endometrial stem cells exhibited robust memory functions following consecutive HPV antigen exposures, whereas fully differentiated cells such as fibroblasts and vesicular cells did not show corresponding changes in response to the same antigen exposures. Deficiency of angiopoietin-like 4 (ANGPTL4) achieved through small hairpin RNA knockdown in vitro and knockout (KO) mice in vivo highlighted the critical role of ANGPTL4 in governing memory functions associated with various stem cell processes. This regulation occurred through histone H3 methylation alterations and PI3K/Akt signaling pathways in response to successive HPV antigen exposures. Furthermore, memory functions associated with various stem cell functions that were evident in wild-type mice following consecutive exposures to HPV antigen were not observed in ANGPTL4 KO mice. In summary, our findings strongly support the presence of memory mechanism in non-immune cells, particularly tissue-resident stem cells.
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Affiliation(s)
- Eun-Kyung Min
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Soo-Rim Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Choon-Mi Lee
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Kun-Hee Na
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - Chan Hum Park
- Department of Otolaryngology-Head and Neck Surgery, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon, Republic of Korea
| | - Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Republic of Korea
| | - YunJae Jung
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea.
| | - In-Sun Hong
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea.
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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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Flynn A, Waszak SM, Weischenfeldt J. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Mol Syst Biol 2024; 20:1006-1024. [PMID: 39026103 PMCID: PMC11369196 DOI: 10.1038/s44320-024-00054-5] [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: 12/07/2023] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
Somatic hypermutation in cancer has gained momentum with the increased use of tumour mutation burden as a biomarker for immune checkpoint inhibitors. Spontaneous deamination of 5-methylcytosine to thymine at CpG dinucleotides is one of the most ubiquitous endogenous mutational processes in normal and cancer cells. Here, we performed a systematic investigation of somatic CpG hypermutation at a pan-cancer level. We studied 30,191 cancer patients and 103 cancer types and developed an algorithm to identify somatic CpG hypermutation. Across cancer types, we observed the highest prevalence in paediatric leukaemia (3.5%), paediatric high-grade glioma (1.7%), and colorectal cancer (1%). We discovered germline variants and somatic mutations in the mismatch repair complex MutSα (MSH2-MSH6) as genetic drivers of somatic CpG hypermutation in cancer, which frequently converged on CpG sites and TP53 driver mutations. We further observe an association between somatic CpG hypermutation and response to immune checkpoint inhibitors. Overall, our study identified novel cancer types that display somatic CpG hypermutation, strong association with MutSα-deficiency, and potential utility in cancer immunotherapy.
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Affiliation(s)
- Aidan Flynn
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian M Waszak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Copenhagen, Denmark.
- Department of Urology, Charité University Hospital, Berlin, Germany.
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7
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Chen T, Mahdadi S, Vidal M, Desbène-Finck S. Non-nucleoside inhibitors of DNMT1 and DNMT3 for targeted cancer therapy. Pharmacol Res 2024; 207:107328. [PMID: 39079576 DOI: 10.1016/j.phrs.2024.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
DNA methylation can deactivate tumor suppressor genes thus causing cancers. Two DNA methylation inhibitors have been approved by the Food and Drug Administration (FDA) and have entered clinical use. However, these inhibitors are nucleoside analogues that can be incorporated into DNA or RNA and induce significant side effects. DNMT1 and DNMT3 are key enzymes involved in DNA methylation. In the acute myeloid leukemia model, a non-nucleoside DNMT1-specific inhibitor has shown lower toxicity and improved pharmacokinetics compared to traditional nucleoside drugs. DNMT3 is also implicated in certain specific cancers. Thus, developing non-nucleoside inhibitors for DNMT1 or DNMT3 can help in understanding their roles in carcinogenesis and provide targeted treatment options in certain cancers. Although no non-nucleoside inhibitors have yet entered clinical trials, in this review, we focus on DNMT1 or DNMT3 selective inhibitors. For DNMT1 selective inhibitors, we have compiled information on the repurposed drugs, derivative compounds and selective inhibitors identified through virtual screening. Additionally, we have outlined potential targets for DNMT1, including protein-protein complex, RNA mimics and aptamers. Compared to DNMT1, research on DNMT3-specific inhibitors has been less extensive. In this context, our exploration has identified a limited number of molecular inhibitors, and we have proposed specific long non-coding RNAs (lncRNAs) as potential contributors to the selective inhibition of DNMT3. This collective effort aims to offer valuable insights into the development of non-nucleoside inhibitors that selectively target DNMT1 or DNMT3.
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Affiliation(s)
- Ting Chen
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Syrine Mahdadi
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Michel Vidal
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France; Toxicology, Cochin Hospital, HUPC, APHP, Paris 75014, France
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8
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Negi CK, Bláhová L, Phan A, Bajard L, Blaha L. Triphenyl Phosphate Alters Methyltransferase Expression and Induces Genome-Wide Aberrant DNA Methylation in Zebrafish Larvae. Chem Res Toxicol 2024. [PMID: 39205618 DOI: 10.1021/acs.chemrestox.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Emerging environmental contaminants, organophosphate flame retardants (OPFRs), pose significant threats to ecosystems and human health. Despite numerous studies reporting the toxic effects of OPFRs, research on their epigenetic alterations remains limited. In this study, we investigated the effects of exposure to 2-ethylhexyl diphenyl phosphate (EHDPP), tricresyl phosphate (TMPP), and triphenyl phosphate (TPHP) on DNA methylation patterns during zebrafish embryonic development. We assessed general toxicity and morphological changes, measured global DNA methylation and hydroxymethylation levels, and evaluated DNA methyltransferase (DNMT) enzyme activity, as well as mRNA expression of DNMTs and ten-eleven translocation (TET) methylcytosine dioxygenase genes. Additionally, we analyzed genome-wide methylation patterns in zebrafish larvae using reduced-representation bisulfite sequencing. Our morphological assessment revealed no general toxicity, but a statistically significant yet subtle decrease in body length following exposure to TMPP and EHDPP, along with a reduction in head height after TPHP exposure, was observed. Eye diameter and head width were unaffected by any of the OPFRs. There were no significant changes in global DNA methylation levels in any exposure group, and TMPP showed no clear effect on DNMT expression. However, EHDPP significantly decreased only DNMT1 expression, while TPHP exposure reduced the expression of several DNMT orthologues and TETs in zebrafish larvae, leading to genome-wide aberrant DNA methylation. Differential methylation occurred primarily in introns (43%) and intergenic regions (37%), with 9% and 10% occurring in exons and promoter regions, respectively. Pathway enrichment analysis of differentially methylated region-associated genes indicated that TPHP exposure enhanced several biological and molecular functions corresponding to metabolism and neurological development. KEGG enrichment analysis further revealed TPHP-mediated potential effects on several signaling pathways including TGFβ, cytokine, and insulin signaling. This study identifies specific changes in DNA methylation in zebrafish larvae after TPHP exposure and brings novel insights into the epigenetic mode of action of TPHP.
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Affiliation(s)
- Chander K Negi
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lucie Bláhová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Audrey Phan
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lola Bajard
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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9
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Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5496-5508. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
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Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
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Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T. In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart. Mamm Genome 2024:10.1007/s00335-024-10057-0. [PMID: 39143382 DOI: 10.1007/s00335-024-10057-0] [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: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
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Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Justyna Rybińska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
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11
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Raynal F, Sengupta K, Plewczynski D, Aliaga B, Pancaldi V. Global chromatin reorganization and regulation of genes of specific evolutionary age in differentiation and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564438. [PMID: 39149250 PMCID: PMC11326123 DOI: 10.1101/2023.10.30.564438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Oncogenesis is accompanied by chromatin organization alterations and reactivation of unicellular phenotypes at the metabolic and transcriptional level. The mechanisms connecting these two observations are unexplored, despite its relevance in cancer biology. Assigning evolutionary ages to genes in the context of 3D chromatin structure, we characterize the epigenomic landscape, expression regulation and spatial organization of genes according to their evolutionary ages. We describe topological changes across differentiation and find some of the patterns, involving Polycomb repression and RNA Pol II pausing, being reversed during oncogenesis. Going beyond the evidence of non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions of old, intermediate and young genes, mediated by respectively RNA Polymerase II, Polycomb and the lamina. Our results are in line and expand recent findings implicating loss of Polycomb repression and activation of embryonal and early evolutionary programs in cancer.
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Affiliation(s)
- Flavien Raynal
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Benoît Aliaga
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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12
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Chen F, Zhang Y, Shen L, Creighton CJ. The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival. Nat Commun 2024; 15:6775. [PMID: 39117669 PMCID: PMC11310301 DOI: 10.1038/s41467-024-51276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations also have expression associations with patient survival, including BCOR, TERT, RCOR2, and PDLIM4. DNA methylation changes in recurrent or progressive tumors compared to the initial tumor within the same patient can predict survival in pediatric and adult cancers. Our comprehensive and pan-histology genomic analyses reveal mechanisms of noncoding alterations impacting cancer genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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13
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Li JA, He Y, Yang B, Mokrani A, Li Y, Tan C, Li Q, Liu S. Whole-genome DNA methylation profiling revealed epigenetic regulation of NF-κB signaling pathway involved in response to Vibrio alginolyticus infection in the Pacific oyster, Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109705. [PMID: 38885801 DOI: 10.1016/j.fsi.2024.109705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
DNA methylation, an essential epigenetic alteration, is tightly linked to a variety of biological processes, such as immune response. To identify the epigenetic regulatory mechanism in Pacific oyster (Crassostrea gigas), whole-genome bisulfite sequencing (WGBS) was conducted on C. gigas at 0 h, 6 h, and 48 h after infection with Vibrio alginolyticus. At 6 h and 48 h, a total of 11,502 and 14,196 differentially methylated regions (DMRs) were identified (p<0.05, FDR<0.001) compared to 0 h, respectively. Gene ontology (GO) analysis showed that differentially methylated genes (DMGs) were significantly enriched in various biological pathways including immunity, cytoskeleton, epigenetic modification, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that transcription machinery (ko03021) is one of the most important pathways. Integrated transcriptome and methylome analyses allowed the identification of 167 and 379 DMG-related DEGs at 6 h and 48 h, respectively. These genes were significantly enriched in immune-related pathways, including nuclear factor kappa B (NF-κB) signaling pathway (ko04064) and tumor necrosis factor (TNF) signaling pathway (ko04668). Interestingly, it's observed that the NF-κB pathway could be activated jointly by TNF Receptor Associated Factor 2 (TRAF2) and Baculoviral IAP Repeat Containing 3 (BIRC3, the homolog of human BIRC2) which were regulated by DNA methylation in response to the challenge posed by V. alginolyticus infection. Through this study, we provided insightful information about the epigenetic regulation of immunity-related genes in the C. gigas, which will be valuable for the understanding of the innate immune system modulation and defense mechanism against bacterial infection in invertebrates.
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Affiliation(s)
- Jian-An Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Yameng He
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Ben Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Ahmed Mokrani
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Yin Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Chao Tan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan National Laboratory, Qingdao, 266237, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan National Laboratory, Qingdao, 266237, China.
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14
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Kumar Kore R, Shirbhate E, Singh V, Mishra A, Veerasamy R, Rajak H. New Investigational Drug's Targeting Various Molecular Pathways for Treatment of Cervical Cancer: Current Status and Future Prospects. Cancer Invest 2024; 42:627-642. [PMID: 38966000 DOI: 10.1080/07357907.2024.2373841] [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: 04/28/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Currently, cervical cancer (CC) is the fourth recorded widespread cancer among women globally. There are still many cases of metastatic or recurring disease discovered, despite the incidence and fatality rates declining due to screening identification and innovative treatment approaches. Palliative chemotherapy continues to be the standard of care for patients who are not contenders for curative therapies like surgery and radiotherapy. This article seeks to provide a thorough and current summary of therapies that have been looked into for the management of CC. The authors emphasize the ongoing trials while reviewing the findings of clinical research. Agents that use biological mechanisms to target different molecular pathways such as epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), mammalian target of rapamycin (mTOR), poly ADP-ribosepolymerase (PARP), and epigenetic biological mechanisms epitomize and offer intriguing research prospects.
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Affiliation(s)
- Rakesh Kumar Kore
- Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | - Ekta Shirbhate
- Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | - Vaibhav Singh
- Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | - Achal Mishra
- Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | | | - Harish Rajak
- Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
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15
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Bozdemir N, Kablan T, Altintas MO, Sukur G, Cinar O, Uysal F. Altered DNA methylation and Dnmt expression in obese uterus may cause implantation failure. J Mol Histol 2024; 55:427-436. [PMID: 38850446 DOI: 10.1007/s10735-024-10212-6] [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: 10/28/2023] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Obesity is defined by increased adipose tissue volume and has become a major risk factor for reproduction. Recent studies have revealed a substantial link between obesity and epigenetics. The epigenome is dynamically regulated mainly by DNA methylation. DNA methylation, which is controlled by DNA methyltransferases (Dnmts), has been widely studied because it is essential for imprinting and regulation of gene expression. In our previous study, we showed that the levels of Dnmt1, Dnmt3a and global DNA methylation was dramatically altered in the testis and ovary of high-fat diet (HFD)-induced obese mice. However, the effect of HFD on Dnmts and global DNA methylation in mouse uterus has not yet been demonstrated. Therefore, in the present study, we aimed to evaluate the effect of HFD on the level of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l and global DNA methylation in uterus. Our results showed that HFD significantly altered the levels of Dnmts and global DNA methylation in the uterus. The total expression of Dnmt1, Dnmt3a and Dnmt3b was significantly upregulated, while level of Dnmt3l and global DNA methylation were dramatically decreased (p < 0.05). Furthermore, we observed that the expression of Dnmt3b and Dnmt3l was significantly increased in endometrium including gland and epithelium (p < 0.05). Although Dnmt3b was the only protein whose expression significantly increased, the level of global DNA methylation and Dnmt3l significantly decreased in stroma and myometrium (p < 0.05). In conclusion, our results show for the first time that obesity dramatically alters global DNA methylation and expression of Dnmts, and decreased DNA methylation and Dnmt expression may cause abnormal gene expression, especially in the endometrium.
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Affiliation(s)
- Nazlican Bozdemir
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey
| | - Tuba Kablan
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey
| | - Mehmet Ozgen Altintas
- Department of Physiology, Ankara Medipol University School of Medicine, Ankara, Turkey
- Department of Physiology, Istanbul Medipol University Institute of Health Sciences, Istanbul, Turkey
| | - Gozde Sukur
- Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Ozgur Cinar
- Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Fatma Uysal
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey.
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Yang Q, Chen L, Zhang H, Li M, Sun L, Wu X, Zhao H, Qu X, An X, Wang T. DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner. Cell Death Differ 2024; 31:999-1012. [PMID: 38719927 PMCID: PMC11303534 DOI: 10.1038/s41418-024-01305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 08/09/2024] Open
Abstract
The dynamic balance of DNA methylation and demethylation is required for erythropoiesis. Our previous transcriptomic analyses revealed that DNA methyltransferase 1 (DNMT1) is abundantly expressed in erythroid cells at all developmental stages. However, the role and molecular mechanisms of DNMT1 in human erythropoiesis remain unknown. Here we found that DNMT1 deficiency led to cell cycle arrest of erythroid progenitors which was partially rescued by treatment with a p21 inhibitor UC2288. Mechanically, this is due to decreased DNA methylation of p21 promoter, leading to upregulation of p21 expression. In contrast, DNMT1 deficiency led to increased apoptosis during terminal stage by inducing endoplasmic reticulum (ER) stress in a p21 independent manner. ER stress was attributed to the upregulation of RPL15 expression due to the decreased DNA methylation at RPL15 promoter. The upregulated RPL15 expression subsequently caused a significant upregulation of core ribosomal proteins (RPs) and thus ultimately activated all branches of unfolded protein response (UPR) leading to the excessive ER stress, suggesting a role of DNMT1 in maintaining protein homeostasis during terminal erythroid differentiation. Furthermore, the increased apoptosis was significantly rescued by the treatment of ER stress inhibitor TUDCA. Our findings demonstrate the stage-specific role of DNMT1 in regulating human erythropoiesis and provide new insights into regulation of human erythropoiesis.
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Affiliation(s)
- Qianqian Yang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Lixiang Chen
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Hengchao Zhang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Mengjia Li
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
- Department of Hematology, First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Zhengzhou, 450052, China
| | - Lei Sun
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Xiuyun Wu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Huizhi Zhao
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China
| | - Xiaoli Qu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China.
| | - Xiuli An
- Laboratory of Membrane Biology, New York Blood Center, 310 East, 67th Street, New York, NY, 10065, USA.
| | - Ting Wang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, 450001, China.
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17
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Yousefi Y, Nejati R, Eslahi A, Alizadeh F, Farrokhi S, Asoodeh A, Mojarrad M. Enhancing Temozolomide (TMZ) chemosensitivity using CRISPR-dCas9-mediated downregulation of O 6-methylguanine DNA methyltransferase (MGMT). J Neurooncol 2024; 169:129-135. [PMID: 38762829 DOI: 10.1007/s11060-024-04708-0] [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: 03/29/2024] [Accepted: 05/02/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE Glioblastoma (GBM) stands out as the most prevalent and aggressive intracranial tumor, notorious for its poor prognosis. The current standard-of-care for GBM patients involves surgical resection followed by radiotherapy, combined with concurrent and adjuvant chemotherapy using Temozolomide (TMZ). The effectiveness of TMZ primarily relies on the activity of O6-methylguanine DNA methyltransferase (MGMT), which removes alkyl adducts from the O6 position of guanine at the DNA level, thereby counteracting the toxic effects of TMZ. METHOD In this study, we employed fusions of catalytically-inactive Cas9 (dCas9) to DNA methyltransferases (dCas9-DNMT3A) to selectively downregulation MGMT transcription by inducing methylation at MGMT promoter and K-M enhancer. RESULT Our findings demonstrate a significant reduction in MGMT expression, leading to intensified TMZ sensitivity in the HEK293T cell line. CONCLUSION This study serves as a proof of concept for the utilization of CRISPR-based gene suppression to overcome TMZ resistance and enhance the lethal effect of TMZ in glioblastoma tumor cells.
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Affiliation(s)
- Yasamin Yousefi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, 19111, Philadelphia, PA, USA
| | - Atiye Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Alizadeh
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Farrokhi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ahmad Asoodeh
- Department of chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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18
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Teragawa S, Wang L, Liu Y. DeepPGD: A Deep Learning Model for DNA Methylation Prediction Using Temporal Convolution, BiLSTM, and Attention Mechanism. Int J Mol Sci 2024; 25:8146. [PMID: 39125714 PMCID: PMC11311892 DOI: 10.3390/ijms25158146] [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: 05/03/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 08/12/2024] Open
Abstract
As part of the field of DNA methylation identification, this study tackles the challenge of enhancing recognition performance by introducing a specialized deep learning framework called DeepPGD. DNA methylation, a crucial biological modification, plays a vital role in gene expression analyses, cellular differentiation, and the study of disease progression. However, accurately and efficiently identifying DNA methylation sites remains a pivotal concern in the field of bioinformatics. The issue addressed in this paper is the presence of methylation in DNA, which is a binary classification problem. To address this, our research aimed to develop a deep learning algorithm capable of more precisely identifying these sites. The DeepPGD framework combined a dual residual structure involving Temporal convolutional networks (TCNs) and bidirectional long short-term memory (BiLSTM) networks to effectively extract intricate DNA structural and sequence features. Additionally, to meet the practical requirements of DNA methylation identification, extensive experiments were conducted across a variety of biological species. The experimental results highlighted DeepPGD's exceptional performance across multiple evaluation metrics, including accuracy, Matthews' correlation coefficient (MCC), and the area under the curve (AUC). In comparison to other algorithms in the same domain, DeepPGD demonstrated superior classification and predictive capabilities across various biological species datasets. This significant advancement in algorithmic prowess not only offers substantial technical support, but also holds potential for research and practical implementation within the DNA methylation identification domain. Moreover, the DeepPGD framework shows potential for application in genomics research, biomedicine, and disease diagnostics, among other fields.
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Affiliation(s)
- Shoryu Teragawa
- School of Software, Dalian University of Technology, Dalian 116024, China;
| | - Lei Wang
- School of Software, Dalian University of Technology, Dalian 116024, China;
| | - Yi Liu
- School of Engineering, University of Southern Queensland, 487-535 West Street, Toowoomba, QLD 4350, Australia;
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Xu S, Zhang Y, Yang Y, Dong K, Zhang H, Luo C, Liu SM. A m 6A regulators-related classifier for prognosis and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1374465. [PMID: 39119345 PMCID: PMC11306056 DOI: 10.3389/fimmu.2024.1374465] [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: 01/22/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background Increasing evidence have highlighted the biological significance of mRNA N6-methyladenosine (m6A) modification in regulating tumorigenicity and progression. However, the potential roles of m6A regulators in tumor microenvironment (TME) formation and immune cell infiltration in liver hepatocellular carcinoma (LIHC or HCC) requires further clarification. Method RNA sequencing data were obtained from TCGA-LIHC databases and ICGC-LIRI-JP databases. Consensus clustering algorithm was used to identify m6A regulators cluster subtypes. Weighted gene co-expression network analysis (WGCNA), LASSO regression, Random Forest (RF), and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) were applied to identify candidate biomarkers, and then a m6Arisk score model was constructed. The correlations of m6Arisk score with immunological characteristics (immunomodulators, cancer immunity cycles, tumor-infiltrating immune cells (TIICs), and immune checkpoints) were systematically evaluated. The effective performance of nomogram was evaluated using concordance index (C-index), calibration plots, decision curve analysis (DCA), and receiver operating characteristic curve (ROC). Results Two distinct m6A modification patterns were identified based on 23 m6A regulators, which were correlated with different clinical outcomes and biological functions. Based on the constructed m6Arisk score model, HCC patients can be divided into two distinct risk score subgroups. Further analysis indicated that the m6Arisk score showed excellent prognostic performance. Patients with a high m6Arisk score was significantly associated with poorer clinical outcome, lower drug sensitivity, and higher immune infiltration. Moreover, we developed a nomogram model by incorporating the m6Arisk score and clinicopathological features. The application of the m6Arisk score for the prognostic stratification of HCC has good clinical applicability and clinical net benefit. Conclusion Our findings reveal the crucial role of m6A modification patterns for predicting HCC TME status and prognosis, and highlight the good clinical applicability and net benefit of m6Arisk score in terms of prognosis, immunophenotype, and drug therapy in HCC patients.
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Affiliation(s)
- Shaohua Xu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yi Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kexin Dong
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hanfei Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
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Zhu PK, Lin MX, Zeng MY, Tang Y, Li XR, He TY, Zheng YS, Chen LY. Expression of Iron Metabolism Genes Is Potentially Regulated by DOF Transcription Factors in Dendrocalamus latiflorus Leaves. Int J Mol Sci 2024; 25:8114. [PMID: 39125685 PMCID: PMC11311721 DOI: 10.3390/ijms25158114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Transcription factors (TFs) are crucial pre-transcriptional regulatory mechanisms that can modulate the expression of downstream genes by binding to their promoter regions. DOF (DNA binding with One Finger) proteins are a unique class of TFs with extensive roles in plant growth and development. Our previous research indicated that iron content varies among bamboo leaves of different colors. However, to our knowledge, genes related to iron metabolism pathways in bamboo species have not yet been studied. Therefore, in the current study, we identified iron metabolism related (IMR) genes in bamboo and determined the TFs that significantly influence them. Among these, DOFs were found to have widespread effects and potentially significant impacts on their expression. We identified specific DOF members in Dendrocalamus latiflorus with binding abilities through homology with Arabidopsis DOF proteins, and established connections between some of these members and IMR genes using RNA-seq data. Additionally, molecular docking confirmed the binding interactions between these DlDOFs and the DOF binding sites in the promoter regions of IMR genes. The co-expression relationship between the two gene sets was further validated using q-PCR experiments. This study paves the way for research into iron metabolism pathways in bamboo and lays the foundation for understanding the role of DOF TFs in D. latiflorus.
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Affiliation(s)
- Peng-Kai Zhu
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei-Xia Lin
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei-Yin Zeng
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Tang
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin-Rui Li
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tian-You He
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu-Shan Zheng
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ling-Yan Chen
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Ren Y, Zhang P, Li L, Wang M, Hu H, Shen Y, Xu P, Wu Q, Li F. Hyper-methylation and DNMT3A mediated LTC4S downregulation promoted lung adenocarcinoma tumorigenesis via mTORC1 signaling pathway. Heliyon 2024; 10:e33203. [PMID: 39027522 PMCID: PMC11255598 DOI: 10.1016/j.heliyon.2024.e33203] [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: 08/30/2023] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
Background Lung adenocarcinoma is a malignancy characterized by high mortality rates and unfavorable prognosis. However, the role of Leukotriene C4 Synthase (LTC4S) in lung cancer remains uninvestigated. Methods The expression and prognostic value of LTC4S in LUAD were analyzed using the GEPIA online database. Subsequently, the function of LTC4S in lung cancer cells was examined through gain-of function experiments, using assays to evaluate tumor malignant behavior. Subcutaneous xenograft experiments in vivo was used for investigating the functions of LTC4S. Then, tumor hallmark pathways were analyzed by GSEA. Western blot assay was used to validate the impact of LTC4S on mTORC1 pathway. Finally, the correlation of mRNA and methylation of LTC4S were analyzed by cBioPortal. qRT-PCR, ChIP-qPCR and ChIP-Atlas were used to verify the regulation factors of LTC4S low expression in LUAD cells. Results LTC4S presented significant decreased expression and favorable prognostic significance in LUAD. LTC4S was correlated with clinical stages in LUAD, which showed decreased expression gradually and significantly along with TNM stages. LTC4S-co-expressed genes were closely related to Ras signaling pathway, and MAPK signaling pathway. Overexpression of LTC4S inhibited cancer malignant phenotype and tumor growth in vitro and vivo. GSEA analysis and Western blot assay suggested low expression of LTC4S activated mTORC1 signaling pathway in LUAD. Moreover, the DNA methylation level of LTC4S in LUAD tissue was markedly elevated compared to normal tissue. The hypermethylation of the LTC4S promoter by DNMT3A leads to the decreased expression of LTC4S in LUAD. Conclusions In conclusion, low expression of LTC4S serves as an unfavorable prognostic marker and the critical function of LTC4S in controlling the progression of LUAD. This highlights the promise for exploring the clinical benefits of manipulating LTC4S in LUAD targeted therapies.
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Affiliation(s)
- Yang Ren
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Peng Zhang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Liqun Li
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Mei Wang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Huiliang Hu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yidan Shen
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ping Xu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qingguo Wu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Feng Li
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
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22
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [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: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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23
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Su X, Li Y, Ren Y, Cao M, Yang G, Luo J, Hu Z, Deng H, Deng M, Liu B, Yao Z. A new strategy for overcoming drug resistance in liver cancer: Epigenetic regulation. Biomed Pharmacother 2024; 176:116902. [PMID: 38870626 DOI: 10.1016/j.biopha.2024.116902] [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: 03/09/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Drug resistance in hepatocellular carcinoma has posed significant obstacles to effective treatment. Recent evidence indicates that, in addition to traditional gene mutations, epigenetic recoding plays a crucial role in HCC drug resistance. Unlike irreversible gene mutations, epigenetic changes are reversible, offering a promising avenue for preventing and overcoming drug resistance in liver cancer. This review focuses on various epigenetic modifications relevant to drug resistance in HCC and their underlying mechanisms. Additionally, we introduce current clinical epigenetic drugs and clinical trials of these drugs as regulators of drug resistance in other solid tumors. Although there is no clinical study to prevent the occurrence of drug resistance in liver cancer, the development of liquid biopsy and other technologies has provided a bridge to achieve this goal.
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Affiliation(s)
- Xiaorui Su
- Department of Hepatobiliary-Pancreatic-Splenic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Yuxuan Li
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Yupeng Ren
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Mingbo Cao
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Gaoyuan Yang
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Jing Luo
- Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Ziyi Hu
- Department of Hepatobiliary-Pancreatic-Splenic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Haixia Deng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Meihai Deng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Bo Liu
- Department of Hepatobiliary-Pancreatic-Splenic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Zhicheng Yao
- Department of Hepatobiliary-Pancreatic-Splenic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
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24
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Park S, Min E, Kim S, Kim S, Na K, Park CH, Jung Y, Oh B, Hong I. Exploring Memory Function Beyond Immune Cells: ANGPTL4-Mediated Memory Functions in Tissue Resident Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307545. [PMID: 38666393 PMCID: PMC11267307 DOI: 10.1002/advs.202307545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/15/2024] [Indexed: 07/25/2024]
Abstract
Adapted immune cells are known to develop memory functions that increase resistance to subsequent infections after initial pathogen exposure, however, it is unclear whether non-immune cells, like tissue-resident stem cells, have similar memory functions. Here, it is found that tissue-resident stem cells crucial for tissue regeneration show diminished adverse effects on diverse stem cell functions against successive exposure to foreign antigen (β-glucan) to maintain tissue homeostasis and stability both in vitro and in vivo. These data suggest that endometrial stem cells may possess a robust memory function, in contrast, fully differentiated cells like fibroblasts and vesicular cells do not show these memory mechanisms upon consecutive antigen exposure. Moreover, the pivotal role of Angiopoietin-like 4 (ANGPTL4) in regulating the memory functions of endometrial stem cells is identified through specific shRNA knockdown in vitro and knockout mice in vivo experiments. ANGPTL4 is associated with the alteration of diverse stem cell functions and epigenetic modifications, notably through histone H3 methylation changes and two pathways (i.e., PI3K/Akt and FAK/ERK1/2 signaling) upon consecutive antigen exposure. These findings imply the existence of inherent self-defense mechanisms through which local stem cells can adapt and protect themselves from recurrent antigenic challenges, ultimately mitigating adverse consequences.
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Affiliation(s)
- Se‐Ra Park
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Eun‐kyung Min
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Soo‐Rim Kim
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Suk‐Kyung Kim
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Kun‐Hee Na
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Microbiology, College of MedicineGachon UniversityIncheon21999Republic of Korea
| | - Chan Hum Park
- Department of Otolaryngology‐Head and Neck Surgery, Chuncheon Sacred Heart HospitalHallym University College of MedicineChuncheon24201Republic of Korea
| | - YunJae Jung
- Department of Microbiology, College of MedicineGachon UniversityIncheon21999Republic of Korea
| | - Byung‐Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes InstituteGachon University College of MedicineIncheon21999Republic of Korea
| | - In‐Sun Hong
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
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25
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Bhargavan B, Chhunchha B, Kubo E, Singh DP. DNA methylation as an epigenetic mechanism in the regulation of LEDGF expression and biological response in aging and oxidative stress. Cell Death Discov 2024; 10:296. [PMID: 38909054 PMCID: PMC11193803 DOI: 10.1038/s41420-024-02076-2] [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: 03/22/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
The physiological quantum of stress-inducible transcriptional protein, Lens Epithelium-Derived Growth Factor (LEDGF), is vital for the maintenance of cellular physiology. Erratic epigenetic reprogramming in response to oxidative stress or with advancing age is found to be a major cause in the gene silencing, leading to pathobiologies. Using aging human (h) eye lens/lens epithelial cells (LECs) coupled with redox-active Peroxiredoxin 6 (Prdx6)-deficient (Prdx6-/-) mLECs as model systems, herein, we showed that in aging/oxidative stress, the human LEDGF gene was regulated by unique methylation patterns of CGs nucleotides within and around the Sp1 binding site(s) of CpG island of the LEDGF promoter (-170 to -27nts). The process caused the repression of LEDGF and its target, Hsp27, resulting in reactive oxygen species (ROS) amplification and cellular insults. This phenomenon was opposed to the unmethylated promoter in LECs. Clinically, we observed that the loss of LEDGF in the Prdx6-/- mLECs or aging lenses/LECs, correlating with increased expression of DNMT1, DNMT3a, and DNMT3b along with the methyl CpG binding protein 2 (MeCP2). Upon oxidative stress, the expression of these molecules was increased with the dramatic reduction in LEDGF expression. While demethylating agent, 5-Aza deoxycytidine (5-AzaC) transposed the aberrant methylation status, and revived LEDGF and Hsp27 expression. Mechanistically, the chloramphenicol acetyltransferase (CAT) reporter gene driven by the LEDGF promoter (-170/ + 35) and ChIP assays uncovered that 5-AzaC acted on GC/Sp1 sites to release LEDGF transcription. The data argued, for the first time, that de novo methylation of CGs around and within Sp1 sites of the CpG island directly disrupted Sp1 activity, which ensued in LEDGF repression and its biological functions. The findings should improve our understanding of cellular insults-associated with aberrant DNMTs-mediated LEDGF's activity, and can offer strategies for therapeutic intervention to halt aging/oxidative stress-induced abnormalities.
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Affiliation(s)
- Biju Bhargavan
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bhavana Chhunchha
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Ishikawa, 9200293, Japan
| | - Dhirendra P Singh
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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26
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Funk HM, Brooks JH, Detmer AE, Creech NN, Guy MP. Identification of Amino Acids in Trm734 Required for 2'- O-Methylation of the tRNA Phe Wobble Residue. ACS OMEGA 2024; 9:25063-25072. [PMID: 38882062 PMCID: PMC11170731 DOI: 10.1021/acsomega.4c02313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024]
Abstract
All organisms methylate their nucleic acids, and this methylation is critical for proper gene expression at both the transcriptional and translational levels. For proper translation in eukaryotes, 2'-O-methylation of C32 (Cm32) and G34 (Gm34) in the anticodon loop of tRNAPhe is critical, with defects in these modifications associated with human disease. In yeast, Cm32 is formed by an enzyme that consists of the methyltransferase Trm7 in complex with the auxiliary protein Trm732, and Gm34 is formed by an enzyme that consists of Trm7 in complex with Trm734. The role of Trm732 and Trm734 in tRNA modification is not fully understood, although previous studies have suggested that Trm734 is important for tRNA binding. In this report, we generated Trm734 variants and tested their ability to work with Trm7 to modify tRNAPhe. Using this approach, we identified several regions of amino acids that are important for Trm734 activity and/or stability. Based on the previously determined Trm7-Trm734 crystal structure, these crucial amino acids are near the active site of Trm7 and are not directly involved in Trm7-Trm734 protein-protein interactions. Immunoprecipitation experiments with these Trm734 variants and Trm7 confirm that these residues are not involved in Trm7-Trm734 binding. Further experiments should help determine if these residues are important for tRNA binding or have another role in the modification of the tRNA. Furthermore, our discovery of a nonfunctional, stable Trm734 variant will be useful in determining if the reported roles of Trm734 in other biological processes such as retromer processing and resistance to Ty1 transposition are due to tRNA modification defects or to other bona fide cellular roles of Trm734.
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Affiliation(s)
- Holly M Funk
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Jennifer H Brooks
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Alisha E Detmer
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Natalie N Creech
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Michael P Guy
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
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27
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Zhao J, Lu Y, Ren X, Bian T, Feng J, Sun H, Liu L, She B, Liu Y, Ke H. Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma. BMC Cancer 2024; 24:687. [PMID: 38840077 PMCID: PMC11154976 DOI: 10.1186/s12885-024-12452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
Background The methylation of SHOX2 and RASSF1A shows promise as a potential biomarker for the early screening of lung cancer, offering a solution to remedy the limitations of morphological diagnosis. The aim of this study is to diagnose lung adenocarcinoma by measuring the methylation levels of SHOX2 and RASSF1A, and provide an accurate pathological diagnosis to predict the invasiveness of lung cancer prior to surgery.Material and methods The methylation levels of SHOX2 and RASSF1A were quantified using a LungMe® test kit through methylation-specific PCR (MS-PCR). The diagnostic efficacy of SHOX2 and RASSF1A and the cutoff values were validated using ROC curve analysis. The hazardous factors influencing the invasiveness of lung adenocarcinoma were calculated using multiple regression.Results: The cutoff values of SHOX2 and RASSF1A were 8.3 and 12.0, respectively. The sensitivities of LungMe® in IA, MIA and AIS patients were 71.3% (122/171), 41.7% (15/36), and 16.1% (5/31) under the specificity of 94.1% (32/34) for benign lesions. Additionally, the methylation level of SHOX2, RASSF1A and LungMe® correlated with the high invasiveness of clinicopathological features, such as age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The tumor size, age, CTR values and LungMe® methylation levels were identified as independent hazardous factors influencing the invasiveness of lung adenocarcinoma.Conclusion: SHOX2 and RASSF1A combined methylation can be used as an early detection indicator of lung adenocarcinoma. SHOX2 and RASSF1A combined (LungMe®) methylation is significantly correlated to age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The SHOX2 and RASSF1A methylation levels, tumor size and CTR values could predict the invasiveness of the tumor prior to surgery, thereby providing guidance for the surgical procedure.
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Affiliation(s)
- Jiaping Zhao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Yu Lu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Xiaosha Ren
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Jia Feng
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Bin She
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Tellgen Corporation Co. Ltd, No. 115, Lane 572, Bibo Road, Pilot Free Trade Zone, Shanghai, 201203, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
| | - Honggang Ke
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
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28
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He B, Yao H, Yi C. Advances in the joint profiling technologies of 5mC and 5hmC. RSC Chem Biol 2024; 5:500-507. [PMID: 38846078 PMCID: PMC11151843 DOI: 10.1039/d4cb00034j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/21/2024] [Indexed: 06/09/2024] Open
Abstract
DNA cytosine methylation, a crucial epigenetic modification, involves the dynamic interplay of 5-methylcytosine (5mC) and its oxidized form, 5-hydroxymethylcytosine (5hmC), generated by ten-eleven translocation (TET) DNA dioxygenases. This process is central to regulating gene expression, influencing critical biological processes such as development, disease progression, and aging. Recognizing the distinct functions of 5mC and 5hmC, researchers often employ restriction enzyme-based or chemical treatment methods for their simultaneous measurement from the same genomic sample. This enables a detailed understanding of the relationship between these modifications and their collective impact on cellular function. This review focuses on summarizing the technologies for detecting 5mC and 5hmC together but also discusses the limitations and potential future directions in this evolving field.
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Affiliation(s)
- Bo He
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing China
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies Chengdu China
| | - Haojun Yao
- College of Chemistry and Chemical Engineering, Hunan University Changsha China
| | - Chengqi Yi
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University Beijing China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University Beijing China
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29
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Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024; 42:960-974. [PMID: 37640946 DOI: 10.1038/s41587-023-01909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
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Affiliation(s)
- Emily B Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Connolly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Tong Wang
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Flournoy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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30
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Bhole RP, Chikhale RV, Rathi KM. Current biomarkers and treatment strategies in Alzheimer disease: An overview and future perspectives. IBRO Neurosci Rep 2024; 16:8-42. [PMID: 38169888 PMCID: PMC10758887 DOI: 10.1016/j.ibneur.2023.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Alzheimer's disease (AD), a progressive degenerative disorder first identified by Alois Alzheimer in 1907, poses a significant public health challenge. Despite its prevalence and impact, there is currently no definitive ante mortem diagnosis for AD pathogenesis. By 2050, the United States may face a staggering 13.8 million AD patients. This review provides a concise summary of current AD biomarkers, available treatments, and potential future therapeutic approaches. The review begins by outlining existing drug targets and mechanisms in AD, along with a discussion of current treatment options. We explore various approaches targeting Amyloid β (Aβ), Tau Protein aggregation, Tau Kinases, Glycogen Synthase kinase-3β, CDK-5 inhibitors, Heat Shock Proteins (HSP), oxidative stress, inflammation, metals, Apolipoprotein E (ApoE) modulators, and Notch signaling. Additionally, we examine the historical use of Estradiol (E2) as an AD therapy, as well as the outcomes of Randomized Controlled Trials (RCTs) that evaluated antioxidants (e.g., vitamin E) and omega-3 polyunsaturated fatty acids as alternative treatment options. Notably, positive effects of docosahexaenoic acid nutriment in older adults with cognitive impairment or AD are highlighted. Furthermore, this review offers insights into ongoing clinical trials and potential therapies, shedding light on the dynamic research landscape in AD treatment.
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Affiliation(s)
- Ritesh P. Bhole
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil institute of Pharmaceutical Sciences & Research, Pimpri, Pune, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, India
| | | | - Karishma M. Rathi
- Department of Pharmacy Practice, Dr. D. Y. Patil institute of Pharmaceutical Sciences & Research, Pimpri, Pune, India
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31
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Maiques-Diaz A, Martin-Subero JI. Biological, prognostic, and therapeutic impact of the epigenome in CLL. Semin Hematol 2024; 61:172-180. [PMID: 38151379 DOI: 10.1053/j.seminhematol.2023.11.005] [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: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by widespread alterations in the genetic and epigenetic landscapes which seem to underlie the variable clinical manifestations observed in patients. Over the last decade, epigenomic studies have described the whole-genome maps of DNA methylation and chromatin features of CLL and normal B cells, identifying distinct epigenetic mechanisms operating in tumoral cells. DNA methylation analyses have identified that the CLL methylome contains imprints of the cell of origin, as well as of the proliferative history of the tumor cells, with both being strong independent prognostic predictors. Moreover, single-cell analysis revealed a higher degree of DNA methylation noise in CLL cells, which associates with transcriptional plasticity and disease aggressiveness. Integrative analysis of chromatin has uncovered chromatin signatures, as well as regulatory regions specifically active in each CLL subtype or in Richter transformed samples. Unique transcription factor (TF) binding motifs are overrepresented on those regions, suggesting that altered TF networks operate from disease initiation to progression as nongenetic factors mediating the oncogenic transcriptional profiles. Multiomics analysis has identified that response to treatment is modulated by an epigenetic imprint, and that treatments affect chromatin through the activity of particular set of TFs. Additionally, the epigenome is an axis of therapeutic vulnerability in CLL, as it can be targeted by inhibitors of histone modifying enzymes, that have shown promising preclinical results. Altogether, this review aims at summarizing the major findings derived from published literature to distill how altered epigenomic mechanisms contribute to CLL origin, evolution, clinical behavior, and response to treatment.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Prognosis
- Epigenesis, Genetic
- Epigenome
- DNA Methylation/genetics
- Epigenomics
- Chromatin/genetics
- Chromatin/metabolism
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Affiliation(s)
- Alba Maiques-Diaz
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.
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32
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Khan H, Rafi Z, Khan MY, Maarfi F, Rehman S, Kaur K, Ahmad MK, Shahab U, Ahmad N, Ahmad S. Epigenetic contributions to cancer: Exploring the role of glycation reactions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:143-193. [PMID: 39179346 DOI: 10.1016/bs.ircmb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Advanced Glycation End-products (AGEs), with their prolonged half-life in the human body, are emerging as potent diagnostic indicators. Early intervention studies, focusing on AGE cross-link breakers, have shown encouraging results in heart failure patients, paving the way for disease progression monitoring and therapy effectiveness evaluation. AGEs are the byproducts of a non-enzymatic reaction where sugars interact with proteins, lipids, and nucleic acids. These compounds possess the power to alter numerous biological processes, ranging from disrupting molecular conformation and promoting cross-linking to modifying enzyme activity, reducing clearance, and impairing receptor recognition. The damage inflicted by AGEs through the stimulation of intracellular signaling pathways is associated with the onset of chronic diseases across various organ systems. This review consolidates the characteristics of AGEs and the challenges posed by their expression in diverse physiological and pathological states. Furthermore, it highlights the clinical relevance of AGEs and the latest research breakthroughs aimed at reducing AGE accumulation.
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Affiliation(s)
- Hamda Khan
- Department of Biochemistry, Faculty of Medicine, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Zeeshan Rafi
- Department of Bioengineering, Integral University, Lucknow, India
| | - Mohd Yasir Khan
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | - Farah Maarfi
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | | | - Kirtanjot Kaur
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | | | - Uzma Shahab
- Department of Biochemistry, King George Medical University, Lucknow, India
| | - Naved Ahmad
- Department of Computer Science and Information System, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Saudi Arabia.
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Boman J, Qvarnström A, Mugal CF. Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F 1 hybrids. BMC Biol 2024; 22:124. [PMID: 38807214 PMCID: PMC11134931 DOI: 10.1186/s12915-024-01920-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Regulation of transcription by DNA methylation in 5'-CpG-3' context is a widespread mechanism allowing differential expression of genetically identical cells to persist throughout development. Consequently, differences in DNA methylation can reinforce variation in gene expression among cells, tissues, populations, and species. Despite a surge in studies on DNA methylation, we know little about the importance of DNA methylation in population differentiation and speciation. Here we investigate the regulatory and evolutionary impact of DNA methylation in five tissues of two Ficedula flycatcher species and their naturally occurring F1 hybrids. RESULTS We show that the density of CpG in the promoters of genes determines the strength of the association between DNA methylation and gene expression. The impact of DNA methylation on gene expression varies among tissues with the brain showing unique patterns. Differentially expressed genes between parental species are predicted by genetic and methylation differentiation in CpG-rich promoters. However, both these factors fail to predict hybrid misexpression suggesting that promoter mismethylation is not a main determinant of hybrid misexpression in Ficedula flycatchers. Using allele-specific methylation estimates in hybrids, we also determine the genome-wide contribution of cis- and trans effects in DNA methylation differentiation. These distinct mechanisms are roughly balanced in all tissues except the brain, where trans differences predominate. CONCLUSIONS Overall, this study provides insight on the regulatory and evolutionary impact of DNA methylation in songbirds.
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Affiliation(s)
- Jesper Boman
- Department of Ecology and Genetics (IEG), Division of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden.
| | - Anna Qvarnström
- Department of Ecology and Genetics (IEG), Division of Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden
| | - Carina F Mugal
- Department of Ecology and Genetics (IEG), Division of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden.
- CNRS, Laboratory of Biometry and Evolutionary Biology (LBBE), UMR 5558, University of Lyon 1, Villeurbanne, France.
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Li Piani L, Somigliana E, Micci LG, Spinelli G, Barbara G. Going Beyond Childhood and Gender-Based Violence: Epigenetic Modifications and Inheritance. WOMEN'S HEALTH REPORTS (NEW ROCHELLE, N.Y.) 2024; 5:473-484. [PMID: 39035135 PMCID: PMC11257107 DOI: 10.1089/whr.2024.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/28/2024] [Indexed: 07/23/2024]
Abstract
Being exposed to childhood or gender-based violence is associated with subsequent adverse events in individual lives. Not only can it cause psychological distress but violence survivors suffer from a range of long-term adverse health outcomes, including higher morbidity, higher mortality, and higher risk of chronic diseases. Epigenetics may be involved in the determinisms of these long-term detrimental effects. A large body of evidence supports this biological mechanism to explain violence-related health impairment in the long term. However, studies specifically focusing on violence are scant and nonunivocal. Epigenetic modifications of genes involved in stress response and in the hypothalamus-pituitary-adrenal axis regulation are the most commonly and consistently reported. Promising evidence also emerged for the use of epigenetic clocks. Finally, although very limited, there is evidence supporting the notion that long-term health impairment may be transmitted from one generation to the other. Overall, despite promising, available evidence is yet incomplete. The overlap with pure psychological mechanisms of health impairment exposes the findings to confounders and hampers strong conclusions. Based on a literature search on PubMed/Embase, our narrative review aims to illustrate the evidence concerning the potential bond between epigenetics and violence, including also possible impacts on later generations. The goal is to encourage further research to help the development of a more holistic approach for such a vulnerable and often neglected population. Further research is warranted to precisely disentangle the role of epigenetics in mediating the long-term health impairment associated with childhood or gender-based violence. Advances in this area may open new avenues of treatment. Epigenetic modifications may indeed be reversible and could be an attractive therapeutic target to minimize the long-term consequences of childhood or gender-based violence.
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Affiliation(s)
- Letizia Li Piani
- Dept of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edgardo Somigliana
- Dept of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- SVSeD - Service for Sexual and Domestic Violence, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laila Giorgia Micci
- SVSeD - Service for Sexual and Domestic Violence, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gaia Spinelli
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- SVSeD - Service for Sexual and Domestic Violence, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giussy Barbara
- Dept of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- SVSeD - Service for Sexual and Domestic Violence, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Huang L, Chen X, Yang X, Zhang Y, Liang Y, Qiu X. Elucidating epigenetic mechanisms governing odontogenic differentiation in dental pulp stem cells: an in-depth exploration. Front Cell Dev Biol 2024; 12:1394582. [PMID: 38863943 PMCID: PMC11165363 DOI: 10.3389/fcell.2024.1394582] [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: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Epigenetics refers to the mechanisms such as DNA methylation and histone modification that influence gene expression without altering the DNA sequence. These epigenetic modifications can regulate gene transcription, splicing, and stability, thereby impacting cell differentiation, development, and disease occurrence. The formation of dentin is intrinsically linked to the odontogenic differentiation of dental pulp stem cells (DPSCs), which are recognized as the optimal cell source for dentin-pulp regeneration due to their varied odontogenic potential, strong proliferative and angiogenic characteristics, and ready accessibility Numerous studies have demonstrated the critical role of epigenetic regulation in DPSCs differentiation into specific cell types. This review thus provides a comprehensive review of the mechanisms by which epigenetic regulation controls the odontogenesis fate of DPSCs.
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Affiliation(s)
| | | | | | | | | | - Xiaoling Qiu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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Sala-Cholewa K, Tomasiak A, Nowak K, Piński A, Betekhtin A. DNA methylation analysis of floral parts revealed dynamic changes during the development of homostylous Fagopyrum tataricum and heterostylous F. esculentum flowers. BMC PLANT BIOLOGY 2024; 24:448. [PMID: 38783206 PMCID: PMC11112930 DOI: 10.1186/s12870-024-05162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Proper flower development is essential for plant reproduction, a crucial aspect of the plant life cycle. This process involves precisely coordinating transcription factors, enzymes, and epigenetic modifications. DNA methylation, a ubiquitous and heritable epigenetic mechanism, is pivotal in regulating gene expression and shaping chromatin structure. Fagopyrum esculentum demonstrates anti-hypertensive, anti-diabetic, anti-inflammatory, cardio-protective, hepato-protective, and neuroprotective properties. However, the heteromorphic heterostyly observed in F. esculentum poses a significant challenge in breeding efforts. F. tataricum has better resistance to high altitudes and harsh weather conditions such as drought, frost, UV-B radiation damage, and pests. Moreover, F. tataricum contains significantly higher levels of rutin and other phenolics, more flavonoids, and a balanced amino acid profile compared to common buckwheat, being recognised as functional food, rendering it an excellent candidate for functional food applications. RESULTS This study aimed to compare the DNA methylation profiles between the Pin and Thrum flower components of F. esculentum, with those of self-fertile species of F. tataricum, to understand the potential role of this epigenetic mechanism in Fagopyrum floral development. Notably, F. tataricum flowers are smaller than those of F. esculentum (Pin and Thrum morphs). The decline in DNA methylation levels in the developed open flower components, such as petals, stigmas and ovules, was consistent across both species, except for the ovule in the Thrum morph. Conversely, Pin and Tartary ovules exhibited a minor decrease in DNA methylation levels. The highest DNA methylation level was observed in Pin stigma from closed flowers, and the most significant decrease was in Pin stigma from open flowers. In opposition, the nectaries of open flowers exhibited higher levels of DNA methylation than those of closed flowers. The decrease in DNA methylation might correspond with the downregulation of genes encoding methyltransferases. CONCLUSIONS Reduced overall DNA methylation and the expression of genes associated with these epigenetic markers in fully opened flowers of both species may indicate that demethylation is necessary to activate the expression of genes involved in floral development.
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Affiliation(s)
- Katarzyna Sala-Cholewa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland.
| | - Alicja Tomasiak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Katarzyna Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland.
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Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.
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Affiliation(s)
- David C Goldberg
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Cameron Cloud
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | - Elliot Kim
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | | | | | | | | | | | | | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Shin Y, Kim S, An W. Promoter hypermethylation as a novel regulator of ANO1 expression and function in prostate cancer bone metastasis. Sci Rep 2024; 14:11595. [PMID: 38773164 PMCID: PMC11109272 DOI: 10.1038/s41598-024-62478-1] [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: 11/30/2023] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Despite growing evidence implicating the calcium-activated chloride channel anoctamin1 (ANO1) in cancer metastasis, its direct impact on the metastatic potential of prostate cancer and the possible significance of epigenetic alteration in this process are not fully understood. Here, we show that ANO1 is minimally expressed in LNCap and DU145 prostate cancer cell lines with low metastatic potential but overexpressed in high metastatic PC3 prostate cancer cell line. The treatment of LNCap and DU145 cells with DNMT inhibitor 5-aza-2'-deoxycytidine (5-Aza-CdR) potentiates ANO1 expression, suggesting that DNA methylation is one of the mechanisms controlling ANO1 expression. Consistent with this notion, hypermethylation was detected at the CpG island of ANO1 promoter region in LNCap and DU145 cells, and 5-Aza-CdR treatment resulted in a drastic demethylation at promoter CpG methylation sites. Upon 5-Aza-CdR treatment, metastatic indexes, such as cell motility, invasion, and metastasis-related gene expression, were significantly altered in LNCap and DU145 cells. These 5-Aza-CdR-induced metastatic hallmarks were, however, almost completely ablated by stable knockdown of ANO1. These in vitro discoveries were further supported by our in vivo observation that ANO1 expression in xenograft mouse models enhances the metastatic dissemination of prostate cancer cells into tibial bone and the development of osteolytic lesions. Collectively, our results help elucidate the critical role of ANO1 expression in prostate cancer bone metastases, which is epigenetically modulated by promoter CpG methylation.
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Affiliation(s)
- Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Sungmin Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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Santourlidis S, Araúzo-Bravo MJ, Erichsen L, Bendhack ML. Epigenetics Meets CAR-T-Cell Therapy to Fight Cancer. Cancers (Basel) 2024; 16:1941. [PMID: 38792020 PMCID: PMC11119853 DOI: 10.3390/cancers16101941] [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: 04/04/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Based on the impressive success of Car-T-cell therapy in the treatment of hematological malignancies, a broad application for solid tumors also appears promising. However, some important hurdles need to be overcome. One of these is certainly the identification of specific target antigens on cancer cells. Hypomethylation is a characteristic epigenetic aberration in many tumor entities. Genome-wide screenings for consistent DNA hypomethylations in tumors enable the identification of aberrantly upregulated transcripts, which might result in cell surface proteins. Thus, this approach provides a new perspective for the discovery of potential new Car-T-cell target antigens for almost every tumor entity. First, we focus on this approach as a possible treatment for prostate cancer.
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Affiliation(s)
- Simeon Santourlidis
- Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany;
| | - Marcos J. Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Lars Erichsen
- Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany;
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Marcelo L. Bendhack
- Department of Urology, Red Cross University Hospital, Positivo University, Rua Mauá 1111, Curitiba 80030-200, Brazil;
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Patil D, Raut S, Joshi M, Bhatt P, Bhatt LK. PAQR4 oncogene: a novel target for cancer therapy. Med Oncol 2024; 41:161. [PMID: 38767705 DOI: 10.1007/s12032-024-02382-w] [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: 01/18/2024] [Accepted: 04/06/2024] [Indexed: 05/22/2024]
Abstract
Despite decades of basic and clinical research and trials of promising new therapies, cancer remains a major cause of morbidity and mortality due to the emergence of drug resistance to anticancer drugs. These resistance events have a very well-understood underlying mechanism, and their therapeutic relevance has long been recognized. Thus, drug resistance continues to be a major obstacle to providing cancer patients with the intended "cure". PAQR4 (Progestin and AdipoQ Receptor Family Member 4) gene is a recently identified novel protein-coding gene associated with various human cancers and acts through different signaling pathways. PAQR4 has a significant influence on multiple proteins that may regulate various gene expressions and may develop chemoresistance. This review discusses the roles of PAQR4 in tumor immunity, carcinogenesis, and chemoresistance. This paper is the first review, discussing PAQR4 in the pathogenesis of cancer. The review further explores the PAQR4 as a potential target in various malignancies.
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Affiliation(s)
- Dipti Patil
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Swapnil Raut
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Mitesh Joshi
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Vile Parle (West), Mumbai, India
| | - Purvi Bhatt
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Vile Parle (West), Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India.
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Cheng B, Wu C, Wei W, Niu H, Wen Y, Li C, Chen P, Chang H, Yang Z, Zhang F. Identification of cell-specific epigenetic patterns associated with chondroitin sulfate treatment response in an endemic arthritis, Kashin-Beck disease. Bone Joint Res 2024; 13:237-246. [PMID: 38754865 PMCID: PMC11098597 DOI: 10.1302/2046-3758.135.bjr-2023-0271.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Aims To assess the alterations in cell-specific DNA methylation associated with chondroitin sulphate response using peripheral blood collected from Kashin-Beck disease (KBD) patients before initiation of chondroitin sulphate treatment. Methods Peripheral blood samples were collected from KBD patients at baseline of chondroitin sulphate treatment. Methylation profiles were generated using reduced representation bisulphite sequencing (RRBS) from peripheral blood. Differentially methylated regions (DMRs) were identified using MethylKit, while DMR-related genes were defined as those annotated to the gene body or 2.2-kilobase upstream regions of DMRs. Selected DMR-related genes were further validated by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) to assess expression levels. Tensor composition analysis was performed to identify cell-specific differential DNA methylation from bulk tissue. Results This study revealed 21,060 hypermethylated and 44,472 hypomethylated DMRs, and 13,194 hypermethylated and 22,448 hypomethylated CpG islands for differential global methylation for chondroitin sulphate treatment response. A total of 12,666 DMR-related genes containing DMRs were identified in their promoter regions, such as CHL1 (false discovery rate (FDR) = 2.11 × 10-11), RIC8A (FDR = 7.05 × 10-4), and SOX12 (FDR = 1.43 × 10-3). Additionally, RIC8A and CHL1 were hypermethylated in responders, while SOX12 was hypomethylated in responders, all showing decreased gene expression. The patterns of cell-specific differential global methylation associated with chondroitin sulphate response were observed. Specifically, we found that DMRs located in TESPA1 and ATP11A exhibited differential DNA methylation between responders and non-responders in granulocytes, monocytes, and B cells. Conclusion Our study identified cell-specific changes in DNA methylation associated with chondroitin sulphate response in KBD patients.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Wenming Wei
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Hui Niu
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cheng Li
- Research Laboratory of Kashin-Beck Disease and Keshan Disease, Shaanxi Institute for Endemic Disease Prevention and Control, Xi'an, China
| | - Ping Chen
- Research Laboratory of Kashin-Beck Disease and Keshan Disease, Shaanxi Institute for Endemic Disease Prevention and Control, Xi'an, China
| | - Hong Chang
- Research Laboratory of Kashin-Beck Disease and Keshan Disease, Shaanxi Institute for Endemic Disease Prevention and Control, Xi'an, China
| | - Zhengjun Yang
- Research Laboratory of Kashin-Beck Disease and Keshan Disease, Shaanxi Institute for Endemic Disease Prevention and Control, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
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Jilani M, Degras D, Haspel N. Elucidating Cancer Subtypes by Using the Relationship between DNA Methylation and Gene Expression. Genes (Basel) 2024; 15:631. [PMID: 38790260 PMCID: PMC11121157 DOI: 10.3390/genes15050631] [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: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Advancements in the field of next generation sequencing (NGS) have generated vast amounts of data for the same set of subjects. The challenge that arises is how to combine and reconcile results from different omics studies, such as epigenome and transcriptome, to improve the classification of disease subtypes. In this study, we introduce sCClust (sparse canonical correlation analysis with clustering), a technique to combine high-dimensional omics data using sparse canonical correlation analysis (sCCA), such that the correlation between datasets is maximized. This stage is followed by clustering the integrated data in a lower-dimensional space. We apply sCClust to gene expression and DNA methylation data for three cancer genomics datasets from the Cancer Genome Atlas (TCGA) to distinguish between underlying subtypes. We evaluate the identified subtypes using Kaplan-Meier plots and hazard ratio analysis on the three types of cancer-GBM (glioblastoma multiform), lung cancer and colon cancer. Comparison with subtypes identified by both single- and multi-omics studies implies improved clinical association. We also perform pathway over-representation analysis in order to identify up-regulated and down-regulated genes as tentative drug targets. The main goal of the paper is twofold: the integration of epigenomic and transcriptomic datasets followed by elucidating subtypes in the latent space. The significance of this study lies in the enhanced categorization of cancer data, which is crucial to precision medicine.
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Affiliation(s)
- Muneeba Jilani
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA;
| | - David Degras
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Nurit Haspel
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA;
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43
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Khalid S, Kearney M, McReynolds DE. Can social adversity alter the epigenome, trigger oral disease, and affect future generations? Ir J Med Sci 2024:10.1007/s11845-024-03697-3. [PMID: 38740675 DOI: 10.1007/s11845-024-03697-3] [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: 02/23/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
The nature versus nurture debate has intrigued scientific circles for decades. Although extensive research has established a clear relationship between genetics and disease development, recent evidence has highlighted the insufficiency of attributing adverse health outcomes to genetic factors alone. In fact, it has been suggested that environmental influences, such as socioeconomic position (SEP), may play a much larger role in the development of disease than previously thought, with extensive research suggesting that low SEP is associated with adverse health conditions. In relation to oral health, a higher prevalence of caries (tooth decay) exists among those of low SEP. Although little is known about the biological mechanisms underlying this relationship, epigenetic modifications resulting from environmental influences have been suggested to play an important role. This review explores the intersection of health inequalities and epigenetics, the role of early-life social adversity and its long-term epigenetic impacts, and how those living within the lower hierarchies of the socioeconomic pyramid are indeed at higher risk of developing diseases, particularly in relation to oral health. A deeper understanding of these mechanisms could lead to the development of targeted interventions for individuals of low SEP to improve oral health or identify those who are at higher risk of developing oral disease.
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Affiliation(s)
- Sakr Khalid
- Dublin Dental University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Michaela Kearney
- Dublin Dental University Hospital, Trinity College Dublin, Dublin, Ireland
| | - David E McReynolds
- Dublin Dental University Hospital, Trinity College Dublin, Dublin, Ireland.
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44
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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45
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Kotari I, Kosiol C, Borges R. The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases. Mol Biol Evol 2024; 41:msae080. [PMID: 38667829 PMCID: PMC11108087 DOI: 10.1093/molbev/msae080] [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: 05/05/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Different frequencies amongst codons that encode the same amino acid (i.e. synonymous codons) have been observed in multiple species. Studies focused on uncovering the forces that drive such codon usage showed that a combined effect of mutational biases and translational selection works to produce different frequencies of synonymous codons. However, only few have been able to measure and distinguish between these forces that may leave similar traces on the coding regions. Here, we have developed a codon model that allows the disentangling of mutation, selection on amino acids and synonymous codons, and GC-biased gene conversion (gBGC) which we employed on an extensive dataset of 415 chordates and 191 arthropods. We found that chordates need 15 more synonymous codon categories than arthropods to explain the empirical codon frequencies, which suggests that the extent of codon usage can vary greatly between animal phyla. Moreover, methylation at CpG sites seems to partially explain these patterns of codon usage in chordates but not in arthropods. Despite the differences between the two phyla, our findings demonstrate that in both, GC-rich codons are disfavored when mutations are GC-biased, and the opposite is true when mutations are AT-biased. This indicates that selection on the genomic coding regions might act primarily to stabilize its GC/AT content on a genome-wide level. Our study shows that the degree of synonymous codon usage varies considerably among animals, but is likely governed by a common underlying dynamic.
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Affiliation(s)
- Ioanna Kotari
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Carolin Kosiol
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife KY16 9TH, UK
| | - Rui Borges
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
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Sfakianoudis K, Zikopoulos A, Grigoriadis S, Seretis N, Maziotis E, Anifandis G, Xystra P, Kostoulas C, Giougli U, Pantos K, Simopoulou M, Georgiou I. The Role of One-Carbon Metabolism and Methyl Donors in Medically Assisted Reproduction: A Narrative Review of the Literature. Int J Mol Sci 2024; 25:4977. [PMID: 38732193 PMCID: PMC11084717 DOI: 10.3390/ijms25094977] [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: 04/16/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
One-carbon (1-C) metabolic deficiency impairs homeostasis, driving disease development, including infertility. It is of importance to summarize the current evidence regarding the clinical utility of 1-C metabolism-related biomolecules and methyl donors, namely, folate, betaine, choline, vitamin B12, homocysteine (Hcy), and zinc, as potential biomarkers, dietary supplements, and culture media supplements in the context of medically assisted reproduction (MAR). A narrative review of the literature was conducted in the PubMed/Medline database. Diet, ageing, and the endocrine milieu of individuals affect both 1-C metabolism and fertility status. In vitro fertilization (IVF) techniques, and culture conditions in particular, have a direct impact on 1-C metabolic activity in gametes and embryos. Critical analysis indicated that zinc supplementation in cryopreservation media may be a promising approach to reducing oxidative damage, while female serum homocysteine levels may be employed as a possible biomarker for predicting IVF outcomes. Nonetheless, the level of evidence is low, and future studies are needed to verify these data. One-carbon metabolism-related processes, including redox defense and epigenetic regulation, may be compromised in IVF-derived embryos. The study of 1-C metabolism may lead the way towards improving MAR efficiency and safety and ensuring the lifelong health of MAR infants.
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Affiliation(s)
- Konstantinos Sfakianoudis
- Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
| | - Athanasios Zikopoulos
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
- Obstetrics and Gynecology, Royal Cornwall Hospital, Treliske, Truro TR1 3LJ, UK
| | - Sokratis Grigoriadis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Nikolaos Seretis
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Evangelos Maziotis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - George Anifandis
- Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece;
| | - Paraskevi Xystra
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Urania Giougli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Konstantinos Pantos
- Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
| | - Mara Simopoulou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
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47
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Bouyahya A, Bakrim S, Aboulaghras S, El Kadri K, Aanniz T, Khalid A, Abdalla AN, Abdallah AA, Ardianto C, Ming LC, El Omari N. Bioactive compounds from nature: Antioxidants targeting cellular transformation in response to epigenetic perturbations induced by oxidative stress. Biomed Pharmacother 2024; 174:116432. [PMID: 38520868 DOI: 10.1016/j.biopha.2024.116432] [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: 12/17/2023] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Oxidative stress results from a persistent imbalance in oxidation levels that promotes oxidants, playing a crucial role in the early and sustained phases of DNA damage and genomic and epigenetic instability, both of which are intricately linked to the development of tumors. The molecular pathways contributing to carcinogenesis in this context, particularly those related to double-strand and single-strand breaks in DNA, serve as indicators of DNA damage due to oxidation in cancer cases, as well as factors contributing to epigenetic instability through ectopic expressions. Oxidative stress has been considered a therapeutic target for many years, and an increasing number of studies have highlighted the promising effectiveness of natural products in cancer treatment. In this regard, we present significant research on the therapeutic targeting of oxidative stress using natural molecules and underscore the essential role of oxidative stress in cancer. The consequences of stress, especially epigenetic instability, also offer significant therapeutic prospects. In this context, the use of natural epi-drugs capable of modulating and reorganizing the epigenetic network is beginning to emerge remarkably. In this review, we emphasize the close connections between oxidative stress, epigenetic instability, and tumor transformation, while highlighting the role of natural substances as antioxidants and epi-drugs in the anti-tumoral context.
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Affiliation(s)
- Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco.
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir 80000, Morocco
| | - Sara Aboulaghras
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
| | - Kawtar El Kadri
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
| | - Tarik Aanniz
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan PO Box: 114, Saudi Arabia.
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed A Abdallah
- Department of Anatomy, Faculty of Medicine, Umm Alqura University, Makkah 21955, Saudi Arabia
| | - Chrismawan Ardianto
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia.
| | - Long Chiau Ming
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia; School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia; Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam.
| | - Nasreddine El Omari
- High Institute of Nursing Professions and Health Techniques of Tetouan, Tetouan, Morocco
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48
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Zhang Y, Wang B, Sun W, Wang G, Liu Z, Zhang X, Ding J, Han Y, Zhang H. Paternal exposures to endocrine-disrupting chemicals induce intergenerational epigenetic influences on offspring: A review. ENVIRONMENT INTERNATIONAL 2024; 187:108689. [PMID: 38688236 DOI: 10.1016/j.envint.2024.108689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Endocrine-disrupting chemicals (EDCs) are ubiquitous in ecological environments and have become a great issue of public health concern since the 1990 s. There is a deep scientific understanding of the toxicity of EDCs. However, recent studies have found that the abnormal physiological functions of the parents caused by EDCs could be transmitted to their unexposed offspring, leading to intergenerational toxicity. We questioned whether sustained epigenetic changes occur through the male germline. In this review, we (1) systematically searched the available research on the intergenerational impacts of EDCs in aquatic and mammal organisms, including 42 articles, (2) summarized the intergenerational genetic effects, such as decreased offspring survival, abnormal reproductive dysfunction, metabolic disorders, and behavioral abnormalities, (3) summarized the mechanisms of intergenerational toxicity through paternal interactions, and (4) propose suggestions on future research directions to develop a deeper understanding of the ecological risk of EDCs.
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Affiliation(s)
- Yinan Zhang
- Hangzhou Normal University, Hangzhou 310018, China
| | - Bingyi Wang
- Hangzhou Normal University, Hangzhou 310018, China
| | - Wenhui Sun
- Hangzhou Normal University, Hangzhou 310018, China
| | | | - Zhiquan Liu
- Hangzhou Normal University, Hangzhou 310018, China; Hangzhou International Urbanology Research Center, Hangzhou 311121, China
| | | | - Jiafeng Ding
- Hangzhou Normal University, Hangzhou 310018, China
| | - Yu Han
- Hangzhou Normal University, Hangzhou 310018, China
| | - Hangjun Zhang
- Hangzhou Normal University, Hangzhou 310018, China; Hangzhou International Urbanology Research Center, Hangzhou 311121, China.
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49
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Tain YL, Hsu CN. Interplay between maternal nutrition and epigenetic programming on offspring hypertension. J Nutr Biochem 2024; 127:109604. [PMID: 38373508 DOI: 10.1016/j.jnutbio.2024.109604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/19/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
Recent human and animal studies have delineated hypertension can develop in the earliest stage of life. A lack or excess of particular nutrients in the maternal diet may impact the expression of genes associated with BP, leading to an increased risk of hypertension in adulthood. Modulations in gene expression could be caused by epigenetic mechanisms through aberrant DNA methylation, histone modification, and microRNAs (miRNAs). Several molecular mechanisms for the developmental programming of hypertension, including oxidative stress, dysregulated nutrient-sensing signal, aberrant renin-angiotensin system, and dysbiotic gut microbiota have been associated with epigenetic programming. Conversely, maternal nutritional interventions such as amino acids, melatonin, polyphenols, resveratrol or short chain fatty acids may work as epigenetic modifiers to trigger protective epigenetic modifications and prevent offspring hypertension. We present a current perspective of maternal malnutrition that can cause fetal programming and the potential of epigenetic mechanisms lead to offspring hypertension. We also discuss the opportunities of dietary nutrients or nutraceuticals as epigenetic modifiers to counteract those adverse programming actions for hypertension prevention. The extent to which aberrant epigenetic changes can be reprogrammed or reversed by maternal dietary interventions in order to prevent human hypertension remains to be established. Continued research is necessary to evaluate the interaction between maternal malnutrition and epigenetic programming, as well as a greater focus on nutritional interventions for hypertension prevention towards their use in clinical translation.
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Affiliation(s)
- You-Lin Tain
- Division of Pediatric Nephrology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chien-Ning Hsu
- Department of Pharmacy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
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50
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Abebe BK, Wang H, Li A, Zan L. A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle. J Anim Breed Genet 2024; 141:235-256. [PMID: 38146089 DOI: 10.1111/jbg.12841] [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: 09/30/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Department of Animal Science, Werabe University, Werabe, Ethiopia
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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