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Konstantinidis I, Sætrom P, Brieuc S, Jakobsen KS, Liedtke H, Pohlmann C, Tsoulia T, Fernandes JMO. DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics 2023; 18:2282323. [PMID: 38010265 PMCID: PMC10732659 DOI: 10.1080/15592294.2023.2282323] [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: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S.O. Brieuc
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannes Liedtke
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Caroline Pohlmann
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thomais Tsoulia
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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2
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Yu J, Zhang Y, Xun Y, Tang H, Fu X, Zhang R, Zhu F, Zhang J. Methylation and expression quantitative trait loci rs1799971 in the OPRM1 gene and rs4654327 in the OPRD1 gene are associated with opioid use disorder. Neurosci Lett 2023; 814:137468. [PMID: 37660978 DOI: 10.1016/j.neulet.2023.137468] [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: 02/27/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Opioid use disorder (OUD) is a chronic and relapsing brain disease that results in significant mortality worldwide. Genetic factors are estimated to contribute to 40%-60% of the liability, with polymorphisms of opioid receptor genes implicated in this disorder. However, the mechanisms underlying these associations are not yet fully understood. In the present study, we first examined the methylation levels in the promoter region of the OPRM1, OPRD1, and OPRK1 genes in 111 healthy controls (HCs) and 120 patients with OUD, and genotyped three tag SNPs in these genes. Correlations between these SNPs and the methylation levels of the CpG sites and expression levels of the genes were analyzed. After identifying the mQTLs and eQTLs, we determined the associations between the mQTLs/eQTLs and susceptibility to and characteristics of OUD in 930 HCs and 801 patients with OUD. Our results demonstrated that SNPs rs1799971 in the OPRM1 gene and rs4654327 in the OPRD1 gene were both mQTLs and eQTLs. We observed unique correlations between mQTLs and methylation levels of several CpG sites in the OUD group compared to the HC group. Interestingly, both the two mQTLs and eQTLs were associated with the susceptibility to OUD. In conclusion, we suppose that mQTLs and eQTLs in genes may underlie the associations between certain risk genetic polymorphisms and OUD. These mQTLs and eQTLs could potentially serve as promising biomarkers for better management of opioid misuse.
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Affiliation(s)
- Jiao Yu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, China
| | - Yudan Zhang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Yufeng Xun
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Hua Tang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Xi'an International Medical Center Hospital, Xi'an, Shaanxi 710061, China
| | - Xiaoyu Fu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Rui Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi 710061, China
| | - Feng Zhu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Jianbo Zhang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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3
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Konstantinidis I, Sætrom P, Fernandes JMO. Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance. Sci Data 2023; 10:114. [PMID: 36859394 PMCID: PMC9977925 DOI: 10.1038/s41597-023-01996-5] [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: 09/02/2021] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,Department of Computer Science, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
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4
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Petrova V, Song R, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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5
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Song R, Tikoo S, Jain R, Pinello N, Au AY, Nagarajah R, Porse B, Rasko JEJ, Wong JJL. Dynamic intron retention modulates gene expression in the monocytic differentiation pathway. Immunology 2021; 165:274-286. [PMID: 34775600 DOI: 10.1111/imm.13435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/01/2022] Open
Abstract
Monocytes play a crucial role in maintaining homeostasis and mediating a successful innate immune response. They also act as central players in diverse pathological conditions, thus making them an attractive therapeutic target. Within the bone marrow, monocytes arise from a committed precursor termed cMoP (Common Monocyte Progenitor). However, molecular mechanisms that regulate the differentiation of cMoP to various monocytic subsets remain unclear. Herein, we purified murine myeloid precursors for deep poly-A enriched RNA sequencing to understand the role of alternative splicing in the development and differentiation of monocytes under homeostasis. Our analyses revealed intron retention to be the major alternative splicing mechanism involved in the monocyte differentiation cascade, especially in the differentiation of Ly6Chi monocytes to Ly6Clo monocytes. Furthermore, we found that the key genes regulated by intron retention in the differentiation of murine Ly6Chi to Ly6Clo monocytes were also conserved in humans. Our data highlight the unique role of intron retention in the regulation of the monocytic differentiation pathway.
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Affiliation(s)
- Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Shweta Tikoo
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rohit Jain
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Amy Ym Au
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Rajini Nagarajah
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
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7
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Tian P, Lin Z, Lin D, Dong S, Huang J, Huang T. The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:841-858. [PMID: 34492142 DOI: 10.1111/tpj.15486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/02/2021] [Indexed: 05/20/2023]
Abstract
DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi-), a common stress that impacts plant growth and productivity. However, in the horticultural model species Solanum lycopersicum (tomato), the dynamics of DNA methylation and its relationship with changes in gene transcription and alternative splicing (AS) under Pi- are unknown. Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi-deficient and -sufficient conditions. We found Pi- caused a slight increase in the overall methylation level, with millions of differentially methylated cytosines (DmCs) and a few hundred differentially methylated regions (DMRs). We also identified thousands of differentially expressed (DE) and differential AS (DAS) genes induced by Pi-, and found that DmCs were more abundant in non-expressed genes than in DE or DAS genes. Moreover, DNA methylation alterations weakly correlated with transcription changes but not with DAS events, and hyper-CHH-DMRs overlapping with transposable elements (TEs) were enriched in a subset of Pi starvation response (PSR) genes. We propose that changes in DNA methylation may be associated with the differential expression of some PSR genes, but that most of these changes probably control the expression of nearby TEs, rather than directly affecting the transcription or AS of PSR genes. Besides, the pattern of methylation changes upon Pi- may largely be shaped by TE distributions. Together, our study provides comprehensive insights into the association of DNA methylation with gene transcription and AS under Pi- in tomato and may contribute to unveiling novel roles of epigenetic mechanisms in plant stress response.
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Affiliation(s)
- Peng Tian
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Zeteng Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Shuangyu Dong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, China
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8
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Li Y, Wang J, Elzo MA, Fan H, Du K, Xia S, Shao J, Lai T, Hu S, Jia X, Lai S. Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits. Curr Issues Mol Biol 2021; 43:1558-1575. [PMID: 34698087 PMCID: PMC8929151 DOI: 10.3390/cimb43030110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022] Open
Abstract
DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.
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Affiliation(s)
- Yanhong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Huimei Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Kun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Siqi Xia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Jiahao Shao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Tianfu Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Shenqiang Hu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Xianbo Jia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
| | - Songjia Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (J.W.); (H.F.); (K.D.); (S.X.); (J.S.); (T.L.); (S.H.); (X.J.)
- Correspondence:
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9
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Candido S, Tomasello BMR, Lavoro A, Falzone L, Gattuso G, Libra M. Novel Insights into Epigenetic Regulation of IL6 Pathway: In Silico Perspective on Inflammation and Cancer Relationship. Int J Mol Sci 2021; 22:ijms221810172. [PMID: 34576335 PMCID: PMC8470126 DOI: 10.3390/ijms221810172] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/05/2023] Open
Abstract
IL-6 pathway is abnormally hyperactivated in several cancers triggering tumor cell growth and immune system inhibition. Along with genomic mutation, the IL6 pathway gene expression can be affected by DNA methylation, microRNAs, and post-translational modifications. Computational analysis was performed on the Cancer Genome Atlas (TCGA) datasets to explore the role of IL6, IL6R, IL6ST, and IL6R transmembrane isoform expression and their epigenetic regulation in different cancer types. IL6 was significantly modulated in 70% of tumor types, revealing either up- or down-regulation in an approximately equal number of tumors. Furthermore, IL6R and IL6ST were downregulated in more than 10 tumors. Interestingly, the correlation analysis demonstrated that only the IL6R expression was negatively affected by the DNA methylation within the promoter region in most tumors. Meanwhile, only the IL6ST expression was extensively modulated by miRNAs including miR-182-5p, which also directly targeted all three genes. In addition, IL6 upregulated miR-181a-3p, mirR-214-3p, miR-18a-5p, and miR-938, which in turn inhibited the expression of IL6 receptors. Finally, the patients’ survival rate was significantly affected by analyzed targets in some tumors. Our results suggest the relevance of epigenetic regulation of IL6 signaling and pave the way for further studies to validate these findings and to assess the prognostic and therapeutic predictive value of these epigenetic markers on the clinical outcome and survival of cancer patients.
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Affiliation(s)
- Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
| | | | - Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
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10
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Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics 2021; 113:2953-2964. [PMID: 34214627 PMCID: PMC7611323 DOI: 10.1016/j.ygeno.2021.06.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/25/2021] [Indexed: 12/29/2022]
Abstract
In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis.
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11
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Li D, Ji Y, Guo J, Guo Q. Upregulated expression of MTFR2 as a novel biomarker predicts poor prognosis in hepatocellular carcinoma by bioinformatics analysis. Future Oncol 2021; 17:3187-3201. [PMID: 34156259 DOI: 10.2217/fon-2020-1160] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: The authors investigated the clinical role of MTFR2 in hepatocellular carcinoma (HCC) progression. Results: MTFR2 expression and methylation were abnormal in HCC tissues, and HCC patients with increased MTFR2 expression or methylation had poor or better overall survival, respectively. In addition, increased MTFR2 expression was correlated with age, grade, cancer stage and T stage. MTFR2 was an independent predictor of dismal prognosis in HCC patients. MTFR2 was involved in HCC progression by modulating the cell cycle, homologous recombination, DNA replication, p53 signaling pathway, etc. The ten hub genes were overexpressed in HCC tissues and were linked to cancer stage and dismal prognosis in HCC patients. Conclusion: MTFR2 could be a prospective biomarker of poor prognosis in individuals with HCC.
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Affiliation(s)
- Dan Li
- Department of Thoracic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.,Department of Oncology, Huanggang Central Hospital, Huanggang, Hubei, 435300, China
| | - YanMei Ji
- Department of Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - JiaLong Guo
- Department of Thoracic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Qiang Guo
- Department of Thoracic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.,Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei, 430030, China
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12
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Schmitz U, Shah JS, Dhungel BP, Monteuuis G, Luu PL, Petrova V, Metierre C, Nair SS, Bailey CG, Saunders VA, Turhan AG, White DL, Branford S, Clark SJ, Hughes TP, Wong JJL, Rasko JE. Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients. Cancers (Basel) 2020; 12:cancers12123738. [PMID: 33322625 PMCID: PMC7764299 DOI: 10.3390/cancers12123738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary This study provides new insights into the changing transcriptomic and epigenomic landscapes in chronic myeloid leukaemia (CML) patients who are receiving tyrosine kinase inhibitor (TKI) therapy (often life-long). Alternative splicing, vital for cellular homeostasis, is dysregulated in human cancers. Remarkably, we found abnormal splicing patterns despite molecular remission in peripheral blood cells of chronic-phase CML patients. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Abstract Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
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Affiliation(s)
- Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Jaynish S. Shah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Geoffray Monteuuis
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
| | - Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
| | - Cynthia Metierre
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Shalima S. Nair
- Kinghorn Centre for Clinical Genomics Core Facility, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Verity A. Saunders
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
| | - Ali G. Turhan
- APHP, Division of Hematology, Paris Sud University Hospitals and Inserm U935 INGESTEM Pluripotent Stem Cell Infrastructure 78 Rue du Général Leclerc, 94275 Le Kremlin Bicetre, France;
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Susan Branford
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Susan J. Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Timothy P. Hughes
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Department of Haematology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5001, Australia
| | - Justin J.-L. Wong
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Correspondence: ; Tel.: +61-2-9565-6160
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13
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Zhang E, Zhang M, Shi C, Sun L, Shan L, Zhang H, Song Y. An overview of advances in multi-omics analysis in prostate cancer. Life Sci 2020; 260:118376. [PMID: 32898525 DOI: 10.1016/j.lfs.2020.118376] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 02/09/2023]
Abstract
Prostate cancer (PCa) is a deadly disease for men, and studies of all types of omics data are necessary to promote precision medicine. The maturity of sequencing technology, the improvements of computer processing power, and the progress achieved in omics analysis methods have improved research efficiency and saved research costs. The occurrence and development of PCa is due to multisystem and multilevel pathological changes. Although omics research at a single level is important, this approach often has limitations. In contrast, the combined analysis of multiple types of omics data can better analyze PCa changes as a whole, thus ensuring the validity of research results to the greatest extent. This paper introduces the applications of single omics in PCa and then summarizes research progress in the combined analysis of two or more types of omics data, so as to systematically and comprehensively analyze the necessity of combined analysis of multiple omics data in PCa.
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Affiliation(s)
- Enchong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Mo Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Changlong Shi
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Li Sun
- Department of Breast Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Liping Shan
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Hui Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
| | - Yongsheng Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
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14
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Hautin M, Mornet C, Chauveau A, Bernard DG, Corcos L, Lippert E. Splicing Anomalies in Myeloproliferative Neoplasms: Paving the Way for New Therapeutic Venues. Cancers (Basel) 2020; 12:E2216. [PMID: 32784800 PMCID: PMC7464941 DOI: 10.3390/cancers12082216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of spliceosome mutations in myeloid malignancies, abnormal pre-mRNA splicing, which has been well studied in various cancers, has attracted novel interest in hematology. However, despite the common occurrence of spliceosome mutations in myelo-proliferative neoplasms (MPN), not much is known regarding the characterization and mechanisms of splicing anomalies in MPN. In this article, we review the current scientific literature regarding "splicing and myeloproliferative neoplasms". We first analyse the clinical series reporting spliceosome mutations in MPN and their clinical correlates. We then present the current knowledge about molecular mechanisms by which these mutations participate in the pathogenesis of MPN or other myeloid malignancies. Beside spliceosome mutations, splicing anomalies have been described in myeloproliferative neoplasms, as well as in acute myeloid leukemias, a dreadful complication of these chronic diseases. Based on splicing anomalies reported in chronic myelogenous leukemia as well as in acute leukemia, and the mechanisms presiding splicing deregulation, we propose that abnormal splicing plays a major role in the evolution of myeloproliferative neoplasms and may be the target of specific therapeutic strategies.
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Affiliation(s)
- Marie Hautin
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Clélia Mornet
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Aurélie Chauveau
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Delphine G. Bernard
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Laurent Corcos
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Eric Lippert
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
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15
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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16
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Beetch M, Harandi-Zadeh S, Shen K, Lubecka K, Kitts DD, O'Hagan HM, Stefanska B. Dietary antioxidants remodel DNA methylation patterns in chronic disease. Br J Pharmacol 2019; 177:1382-1408. [PMID: 31626338 DOI: 10.1111/bph.14888] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic diseases account for over 60% of all deaths worldwide according to the World Health Organization reports. Majority of cases are triggered by environmental exposures that lead to aberrant changes in the epigenome, specifically, the DNA methylation patterns. These changes result in altered expression of gene networks and activity of signalling pathways. Dietary antioxidants, including catechins, flavonoids, anthocyanins, stilbenes and carotenoids, demonstrate benefits in the prevention and/or support of therapy in chronic diseases. This review provides a comprehensive discussion of potential epigenetic mechanisms of antioxidant compounds in reversing altered patterns of DNA methylation in chronic disease. Antioxidants remodel the DNA methylation patterns through multiple mechanisms, including regulation of epigenetic enzymes and chromatin remodelling complexes. These effects can further contribute to antioxidant properties of the compounds. On the other hand, decrease in oxidative stress itself can impact DNA methylation delivering additional link between antioxidant mechanisms and epigenetic effects of the compounds. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Sadaf Harandi-Zadeh
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Kate Shen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Katarzyna Lubecka
- Department of Biomedical Chemistry, Medical University of Lodz, Lodz, Poland
| | - David D Kitts
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M O'Hagan
- Cell, Molecular and Cancer Biology, Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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