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Luo Y, Zhou T, Liu D, Wang F, Zhao Q. AIMER: A SNP-independent software for identifying imprinting-like allelic methylated regions from DNA methylome. Comput Struct Biotechnol J 2024; 23:566-576. [PMID: 38274999 PMCID: PMC10809074 DOI: 10.1016/j.csbj.2023.12.038] [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: 10/06/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Genomic imprinting is essential for mammalian growth and embryogenesis. High-throughput bisulfite sequencing accompanied with parental haplotype-specific information allows analysis of imprinted genes and imprinting control regions (ICRs) on a large scale. Currently, although several allelic methylated regions (AMRs) detection software were developed, methods for detecting imprinted AMRs is still limited. Here, we developed a SNP-independent statistical approach, AIMER, to detect imprinting-like AMRs. By using the mouse frontal cortex methylome as input, we demonstrated that AIMER performs very well in detecting known germline ICRs compared with other methods. Furthermore, we found the putative parental AMRs AIMER detected could be distinguished from sequence-dependent AMRs. Finally, we found a novel germline imprinting-like AMR using WGBS data from 17 distinct mouse tissue samples. The results indicate that AIMER is a good choice for detecting imprinting-like (parent-of-origin-dependent) AMRs. We hope this method will be helpful for future genomic imprinting studies. The Python source code for our project is now publicly available on both GitHub (https://github.com/ZhaoLab-TMU/AIMER) and Gitee (https://gitee.com/zhaolab_tmu/AIMER).
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Affiliation(s)
| | | | - Deng Liu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Fan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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2
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Blanchett R, Lau KH, Pfeifer GP. Homeobox and Polycomb target gene methylation in human solid tumors. Sci Rep 2024; 14:13912. [PMID: 38886487 DOI: 10.1038/s41598-024-64569-5] [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: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
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Affiliation(s)
- Reid Blanchett
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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3
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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024; 13:313-337. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-y] [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] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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4
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Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C. The genome of Przewalski's horse ( Equus ferus przewalskii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581252. [PMID: 38464182 PMCID: PMC10925127 DOI: 10.1101/2024.02.20.581252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Lauren Hughes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Jacob Cassens
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota Minneapolis, MN, USA
| | - Maya Enriquez
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Samrawit Gebeyehu
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | | | - Jason Hatfield
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Anna Kauffman
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Baylor Brown
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Caitlin Klaeui
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Islam F. Mabrouk
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Carrie Walls
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | - Taylor Yeater
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | | | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
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Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet 2024; 15:1346150. [PMID: 38444759 PMCID: PMC10912962 DOI: 10.3389/fgene.2024.1346150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
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Affiliation(s)
- Md Nazmul Hossain
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
- Department of Livestock Production and Management, Faculty of Veterinary, Animal, and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yao Gao
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Michael J. Hatfield
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Jeanene M. de Avila
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | | | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
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6
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Yu ST, Zhao R, Sun XQ, Hou MX, Cao YM, Zhang J, Chen YJ, Wang KK, Zhang Y, Li JT, Wang Q. DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp ( Cyprinus carpio). Int J Mol Sci 2024; 25:1635. [PMID: 38338913 PMCID: PMC10855618 DOI: 10.3390/ijms25031635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
DNA methylation and chromatin accessibility play important roles in gene expression, but their function in subgenome expression dominance remains largely unknown. We conducted comprehensive analyses of the transcriptome, DNA methylation, and chromatin accessibility in liver and muscle tissues of allotetraploid common carp, aiming to reveal the function of epigenetic modifications in subgenome expression dominance. A noteworthy overlap in differential expressed genes (DEGs) as well as their functions was observed across the two subgenomes. In the promoter and gene body, the DNA methylation level of the B subgenome was significantly different than that of the A subgenome. Nevertheless, differences in DNA methylation did not align with changes in homoeologous biased expression across liver and muscle tissues. Moreover, the B subgenome exhibited a higher prevalence of open chromatin regions and greater chromatin accessibility, in comparison to the A subgenome. The expression levels of genes located proximally to open chromatin regions were significantly higher than others. Genes with higher chromatin accessibility in the B subgenome exhibited significantly elevated expression levels compared to the A subgenome. Contrastingly, genes without accessibility exhibited similar expression levels in both subgenomes. This study contributes to understanding the regulation of subgenome expression dominance in allotetraploid common carp.
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Affiliation(s)
- Shuang-Ting Yu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ming-Xi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yi-Ming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ying-Jie Chen
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Kai-Kuo Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
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7
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Arai K, Qi H, Inoue-Murayama M. Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM). PLoS One 2023; 18:e0294994. [PMID: 38079426 PMCID: PMC10712859 DOI: 10.1371/journal.pone.0294994] [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: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour-, time-, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.
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Affiliation(s)
- Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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8
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Wen R, Zhou L, Jiang S, Fan H, Zheng K, Yu Y, Gao X, Hao L, Lou Z, Yu G, Yang F, Zhang W. DSTN Hypomethylation Promotes Radiotherapy Resistance of Rectal Cancer by Activating the Wnt/β-Catenin Signaling Pathway. Int J Radiat Oncol Biol Phys 2023; 117:198-210. [PMID: 37019366 DOI: 10.1016/j.ijrobp.2023.03.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
PURPOSE Although surgical resection combined with neoadjuvant radiation therapy can reduce the local recurrence rate of rectal cancer, not all patients benefit from neoadjuvant radiation therapy. Therefore, screening for patients with rectal cancer who are sensitive or resistant to radiation therapy has great clinical significance. METHODS AND MATERIALS Patients with rectal cancer were selected according to postoperative tumor regression grade, and tumor samples were taken for detection. Differential genes between radiation-resistant and radiation-sensitive tissues were screened and validated by Illumina Infinium MethylationEPIC BeadChip, proteomics, Agena MassARRAY methylation, reverse transcription quantitative real-time polymerase chain reaction, and immunohistochemistry. In vitro and in vivo functional experiments verified the role of DSTN. Protein coimmunoprecipitation, western blot, and immunofluorescence were used to investigate the mechanisms of DSTN-related radiation resistance. RESULTS DSTN was found to be highly expressed (P < .05) and hypomethylated (P < .01) in rectal cancer tissues resistant to neoadjuvant radiation therapy. Follow-up data confirmed that patients with high expression of DSTN in neoadjuvant radiation therapy-resistant rectal cancer tissues had shorter disease-free survival (P < .05). DSTN expression increased after methyltransferase inhibitor inhibition of DNA methylation in colorectal cancer cells (P < .05). In vitro and in vivo experiments showed that knockdown of DSTN promoted the sensitivity of colorectal cancer cells to radiation therapy, and overexpression of DSTN promoted the resistance of colorectal cancer cells to radiation (P < .05). The Wnt/β-catenin signaling pathway was activated in colorectal cancer cells overexpressing DSTN. β-catenin was highly expressed in radiation therapy-resistant tissues, and there was a linear correlation between the expression of DSTN and β-catenin (P < .0001). Further studies showed that DSTN can bind to β-catenin and increase its stability. CONCLUSIONS The degree of DNA methylation and the expression level of DSTN can be used as biomarkers to predict the sensitivity of neoadjuvant radiation therapy for rectal cancer. DSTN and β-catenin are also expected to become a reference for the selection of neoadjuvant radiation therapy.
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Affiliation(s)
- Rongbo Wen
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Leqi Zhou
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Siyuan Jiang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hao Fan
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Kuo Zheng
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yue Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xianhua Gao
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Liqiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zheng Lou
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Guanyu Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Fu Yang
- Department of Medical Genetics, Naval Medical University, Shanghai, China.
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
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9
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Acharya SN, Nichols RV, Rylaarsdam LE, O’Connell BL, Braun TP, Adey AC. sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548718. [PMID: 37502923 PMCID: PMC10369954 DOI: 10.1101/2023.07.12.548718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Sufficient off-target coverage further enables the production of near-complete methylomes for individual cell types. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).
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Affiliation(s)
- Sonia N. Acharya
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Ruth V. Nichols
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Lauren E. Rylaarsdam
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Brendan L. O’Connell
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Theodore P. Braun
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Hematology/Medical Oncology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andrew C. Adey
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
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10
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Walton E, Baltramonaityte V, Calhoun V, Heijmans BT, Thompson PM, Cecil CAM. A systematic review of neuroimaging epigenetic research: calling for an increased focus on development. Mol Psychiatry 2023; 28:2839-2847. [PMID: 37185958 PMCID: PMC10615743 DOI: 10.1038/s41380-023-02067-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
Epigenetic mechanisms, such as DNA methylation (DNAm), have gained increasing attention as potential biomarkers and mechanisms underlying risk for neurodevelopmental, psychiatric and other brain-based disorders. Yet, surprisingly little is known about the extent to which DNAm is linked to individual differences in the brain itself, and how these associations may unfold across development - a time of life when many of these disorders emerge. Here, we systematically review evidence from the nascent field of Neuroimaging Epigenetics, combining structural or functional neuroimaging measures with DNAm, and the extent to which the developmental period (birth to adolescence) is represented in these studies. We identified 111 articles published between 2011-2021, out of which only a minority (21%) included samples under 18 years of age. Most studies were cross-sectional (85%), employed a candidate-gene approach (67%), and examined DNAm-brain associations in the context of health and behavioral outcomes (75%). Nearly half incorporated genetic data, and a fourth investigated environmental influences. Overall, studies support a link between peripheral DNAm and brain imaging measures, but there is little consistency in specific findings and it remains unclear whether DNAm markers present a cause, correlate or consequence of brain alterations. Overall, there is large heterogeneity in sample characteristics, peripheral tissue and brain outcome examined as well as the methods used. Sample sizes were generally low to moderate (median nall = 98, ndevelopmental = 80), and attempts at replication or meta-analysis were rare. Based on the strengths and weaknesses of existing studies, we propose three recommendations on how advance the field of Neuroimaging Epigenetics. We advocate for: (1) a greater focus on developmentally oriented research (i.e. pre-birth to adolescence); (2) the analysis of large, prospective, pediatric cohorts with repeated measures of DNAm and imaging to assess directionality; and (3) collaborative, interdisciplinary science to identify robust signals, triangulate findings and enhance translational potential.
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Affiliation(s)
- Esther Walton
- Department of Psychology, University of Bath, Bath, UK.
| | | | - Vince Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Dept. of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | - Charlotte A M Cecil
- Molecular Epidemiology, Dept. of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
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11
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Shi Q, Qi K. Developmental origins of health and disease: Impact of paternal nutrition and lifestyle. Pediatr Investig 2023; 7:111-131. [PMID: 37324600 PMCID: PMC10262906 DOI: 10.1002/ped4.12367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/29/2023] [Indexed: 09/20/2023] Open
Abstract
Most epidemiological and experimental studies have focused on maternal influences on offspring's health. The impact of maternal undernutrition, overnutrition, hypoxia, and stress is linked to adverse offspring outcomes across a range of systems including cardiometabolic, respiratory, endocrine, and reproduction among others. During the past decade, it has become evident that paternal environmental factors are also linked to the development of diseases in offspring. In this article, we aim to outline the current understanding of the impact of male health and environmental exposure on offspring development, health, and disease and explore the mechanisms underlying the paternal programming of offspring health. The available evidence suggests that poor paternal pre-conceptional nutrition and lifestyle, and advanced age can increase the risk of negative outcomes in offspring, via both direct (genetic/epigenetic) and indirect (maternal uterine environment) effects. Beginning at preconception, and during utero and the early life after birth, cells acquire an epigenetic memory of the early exposure which can be influential across the entire lifespan and program a child's health. Potentially not only mothers but also fathers should be advised that maintaining a healthy diet and lifestyle is important to improve offspring health as well as the parental health status. However, the evidence is mostly based on animal studies, and well-designed human studies are urgently needed to verify findings from animal data.
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Affiliation(s)
- Qiaoyu Shi
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's HospitalCapital Medical University, National Center for Children's HealthBeijingChina
| | - Kemin Qi
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's HospitalCapital Medical University, National Center for Children's HealthBeijingChina
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12
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Vasconcelos S, Caniçais C, Chuva de Sousa Lopes SM, Marques CJ, Dória S. The role of DNA hydroxymethylation and TET enzymes in placental development and pregnancy outcome. Clin Epigenetics 2023; 15:66. [PMID: 37095555 PMCID: PMC10127343 DOI: 10.1186/s13148-023-01483-z] [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: 09/13/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
The placenta is a temporary organ that is essential for supporting mammalian embryo and fetal development. Understanding the molecular mechanisms underlying trophoblast differentiation and placental function may contribute to improving the diagnosis and treatment of obstetric complications. Epigenetics plays a significant role in the regulation of gene expression, particularly at imprinted genes, which are fundamental in the control of placental development. The Ten-Eleven-Translocation enzymes are part of the epigenetic machinery, converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). DNA hydroxymethylation is thought to act as an intermediate in the DNA demethylation mechanism and potentially be a stable and functionally relevant epigenetic mark on its own. The role of DNA hydroxymethylation during differentiation and development of the placenta is not fully understood but increasing knowledge in this field will help to evaluate its potential role in pregnancy complications. This review focuses on DNA hydroxymethylation and its epigenetic regulators in human and mouse placental development and function. Additionally, we address 5hmC in the context of genomic imprinting mechanism and in pregnancy complications, such as intrauterine growth restriction, preeclampsia and pregnancy loss. The cumulative findings show that DNA hydroxymethylation might be important for the control of gene expression in the placenta and suggest a dynamic role in the differentiation of trophoblast cell types during gestation.
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Affiliation(s)
- Sara Vasconcelos
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Carla Caniçais
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | | | - C Joana Marques
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal.
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
| | - Sofia Dória
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal.
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
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13
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Breton-Larrivée M, Elder E, Legault LM, Langford-Avelar A, MacFarlane AJ, McGraw S. Mitigating the detrimental developmental impact of early fetal alcohol exposure using a maternal methyl donor-enriched diet. FASEB J 2023; 37:e22829. [PMID: 36856720 DOI: 10.1096/fj.202201564r] [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: 09/27/2022] [Revised: 01/23/2023] [Accepted: 02/03/2023] [Indexed: 03/02/2023]
Abstract
Fetal alcohol exposure at any stage of pregnancy can lead to fetal alcohol spectrum disorder (FASD), a group of life-long conditions characterized by congenital malformations, as well as cognitive, behavioral, and emotional impairments. The teratogenic effects of alcohol have long been publicized; yet fetal alcohol exposure is one of the most common preventable causes of birth defects. Currently, alcohol abstinence during pregnancy is the best and only way to prevent FASD. However, alcohol consumption remains astoundingly prevalent among pregnant women; therefore, additional measures need to be made available to help protect the developing embryo before irreparable damage is done. Maternal nutritional interventions using methyl donors have been investigated as potential preventative measures to mitigate the adverse effects of fetal alcohol exposure. Here, we show that a single acute preimplantation (E2.5; 8-cell stage) fetal alcohol exposure (2 × 2.5 g/kg ethanol with a 2h interval) in mice leads to long-term FASD-like morphological phenotypes (e.g. growth restriction, brain malformations, skeletal delays) in late-gestation embryos (E18.5) and demonstrate that supplementing the maternal diet with a combination of four methyl donor nutrients, folic acid, choline, betaine, and vitamin B12, prior to conception and throughout gestation effectively reduces the incidence and severity of alcohol-induced morphological defects without altering DNA methylation status of imprinting control regions and regulation of associated imprinted genes. This study clearly supports that preimplantation embryos are vulnerable to the teratogenic effects of alcohol, emphasizes the dangers of maternal alcohol consumption during early gestation, and provides a potential proactive maternal nutritional intervention to minimize FASD progression, reinforcing the importance of adequate preconception and prenatal nutrition.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Elizabeth Elder
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Lisa-Marie Legault
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Alexandra Langford-Avelar
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
| | - Amanda J MacFarlane
- Agriculture, Food, and Nutrition Evidence Center, Texas A&M University, Texas, Fort Worth, USA.,Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Serge McGraw
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada.,Department of Obstetrics and Gynecology, Université de Montréal, Montreal, Canada
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14
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Detection of aberrant DNA methylation patterns in sperm of male recurrent spontaneous abortion patients. ZYGOTE 2023; 31:163-172. [PMID: 36617979 DOI: 10.1017/s0967199422000648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Aberrant DNA methylation patterns in sperm are a cause of embryonic failure and infertility, and could be a critical factor contributing to male recurrent spontaneous abortion (RSA). The purpose of this study was to reveal the potential effects of sperm DNA methylation levels in patients with male RSA. We compared sperm samples collected from fertile men and oligoasthenospermia patients. Differentially methylated sequences were identified by reduced representation bisulfite sequencing (RRBS) methods. The DNA methylation levels of the two groups were compared and qRT-PCR was used to validate the expression of genes showing differential methylation. The results indicated that no difference in base distribution was observed between the normal group and the patient group. However, the chromosome methylation in these two groups was markedly different. One site was located on chromosome 8 and measured 150 bp, while the other sites were on chromosomes 9, 10, and X and measured 135 bp, 68 bp, and 136 bp, respectively. In particular, two genes were found to be hypermethylated in these patients, one gene was DYDC2 (placed in the differential methylation region of chromosome 10), and the other gene was NXF3 (located on chromosome X). Expression levels of DYDC2 and NXF3 in the RSA group were significantly lower than those in the normal group (P < 0.05). Collectively, these results demonstrated that changes in DNA methylation might be related to male RSA. Our findings provide important information regarding the potential role of sperm DNA methylation in human development.
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15
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Hosseini M, Lotfi‐Shahreza M, Nikpour P. Integrative analysis of DNA methylation and gene expression through machine learning identifies stomach cancer diagnostic and prognostic biomarkers. J Cell Mol Med 2023; 27:714-726. [PMID: 36779430 PMCID: PMC9983314 DOI: 10.1111/jcmm.17693] [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: 10/15/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 02/14/2023] Open
Abstract
DNA methylation is an early event in tumorigenesis. Here, by integrative analysis of DNA methylation and gene expression and utilizing machine learning approaches, we introduced potential diagnostic and prognostic methylation signatures for stomach cancer. Differentially-methylated positions (DMPs) and differentially-expressed genes (DEGs) were identified using The Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) data. A total of 256 DMPs consisting of 140 and 116 hyper- and hypomethylated positions were identified between 443 tumour and 27 nontumour STAD samples. Gene expression analysis revealed a total of 2821 DEGs with 1247 upregulated and 1574 downregulated genes. By analysing the impact of cis and trans regulation of methylation on gene expression, a dominant negative correlation between methylation and expression was observed, while for trans regulation, in hypermethylated and hypomethylated genes, there was mainly a negative and positive correlation with gene expression, respectively. To find diagnostic biomarkers, we used 28 hypermethylated probes locating in the promoter of 27 downregulated genes. By implementing a feature selection approach, eight probes were selected and then used to build a support vector machine diagnostic model, which had an area under the curve of 0.99 and 0.97 in the training and validation (GSE30601 with 203 tumour and 94 nontumour samples) cohorts, respectively. Using 412 TCGA-STAD samples with both methylation and clinical data, we also identified four prognostic probes by implementing univariate and multivariate Cox regression analysis. In summary, our study introduced potential diagnostic and prognostic biomarkers for STAD, which demands further validation.
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Affiliation(s)
- Maryam Hosseini
- Department of Genetics and Molecular Biology, Faculty of MedicineIsfahan University of Medical SciencesIsfahanIran
| | | | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of MedicineIsfahan University of Medical SciencesIsfahanIran
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16
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Shi Q, Liu X, Fan X, Wang R, Qi K. Paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids programs offspring leptin expression and gene imprinting in mice. Front Nutr 2022; 9:1043876. [PMID: 36618698 PMCID: PMC9816484 DOI: 10.3389/fnut.2022.1043876] [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: 09/15/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Background This study determined the effects of the paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids (PUFAs) on leptin expression in the offspring and associated gene imprinting in a mouse model. Methods Three- to four-week-old male C57BL/6J mice (F0) were fed an n-3 PUFA-deficient (n-3 D) diet, a diet with normal n-3 PUFA content (n-3 N; n-6: n-3 = 4.3:1), or a diet with a high n-3 PUFA content (n-3 H; n-6: n-3 = 1.5:1) for 8 weeks. Two subsequent generations were generated by mating F0 and F1 male mice with 10-week-old virgin female C57 BL/6J mice, to produce F1 and F2 offspring. Results Compared to the paternal n-3 D diet, paternal n-3 N and n-3 H diets reduced adipose mRNA expression of leptin (Lep) and its plasma concentrations in juvenile F1 male and female offspring, and adult F1 male and F2 female offspring, with upregulated Lep receptor mRNA expression in the hypothalamus. Meanwhile, paternal n-3 N and n-3 H diets altered the expression of the imprinted genes H19, Igf2, Igf2r, Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10 in the adipose tissue of juvenile and adult F1 males, with almost no effects on F1 females, while more effects were observed in the adult F2 females than F2 males. Principal component analysis verified that Plagl1, Cdkn1c, and Kcnq1ot1 contributed the most to variation in adipose tissue expression in all offspring. Some of these genes (Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10) were altered by the paternal n-3 N and n-3 H diets in the F1 and F2 generation testes as well. Furthermore, adipose Lep expression was positively correlated with expressions of H19, Igf2r, Plagl1, and Kcnq1ot1 in juvenile F1 males and females, negatively correlated with the Kcnq1ot1 expression in adult F1 males, and positively correlated with the Plagl1 expression in adult F2 females. Conclusion These data imply that paternal Plagl1, Cdkn1c, and Kcnq1ot1 might be part of the pathways involved in offspring leptin programming. Therefore, a lower ratio of n-6: n-3 PUFAs, with higher intake of n-3 PUFAs in paternal pre-conception, may help maintain the offspring's optimal leptin pattern in a sex-specific manner through multiple generations, and thereby, be beneficial for the offspring's long-term health.
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17
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Chen H, Zhang L, Meng L, Liang L, Zhang C. Advantages of vitrification preservation in assisted reproduction and potential influences on imprinted genes. Clin Epigenetics 2022; 14:141. [PMID: 36324168 PMCID: PMC9632035 DOI: 10.1186/s13148-022-01355-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Cryopreservation has important application in assisted reproductive technology (ART). The vitrification technique has been widely used in the cryopreservation of oocytes and embryos, as a large number of clinical results and experimental studies have shown that vitrification can achieve a higher cell survival rate and preimplantation development rate and better pregnancy outcomes. Ovarian tissue vitrification is an alternative method to slow freezing that causes comparatively less damage to the original follicular DNA. At present, sperm preservation mainly adopts slow freezing or rapid freezing (LN2 vapor method), although the vitrification method can achieve higher sperm motility after warming. However, due to the use of high-concentration cryoprotectants and ultra-rapid cooling, vitrification may cause strong stress to gametes, embryos and tissue cells, resulting in potentially adverse effects. Imprinted genes are regulated by epigenetic modifications, including DNA methylation, and show single allele expression. Their accurate regulation and correct expression are very important for the placenta, fetal development and offspring health. Considering that genome imprinting is very sensitive to changes in the external environment, we comprehensively summarized the effect of cryopreservation—especially the vitrification method in ART—on imprinted genes. Animal studies have found that the vitrification of oocytes and embryos can have a significant impact on some imprinted genes and DNA methylation, but the few studies in humans have reported almost no influence, which need to be further explored. This review provides useful information for the safety assessment and further optimization of the current cryopreservation techniques in ART.
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Affiliation(s)
- Huanhuan Chen
- Reproductive Medicine Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou, Henan, China.,Henan Joint International Research Laboratory of Reproductive Bioengineering, Zhengzhou, Henan Province, China
| | - Lei Zhang
- Reproductive Medicine Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou, Henan, China.,Henan Joint International Research Laboratory of Reproductive Bioengineering, Zhengzhou, Henan Province, China
| | - Li Meng
- Reproductive Medicine Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou, Henan, China.,Henan Joint International Research Laboratory of Reproductive Bioengineering, Zhengzhou, Henan Province, China
| | - Linlin Liang
- Reproductive Medicine Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou, Henan, China. .,Henan Joint International Research Laboratory of Reproductive Bioengineering, Zhengzhou, Henan Province, China.
| | - Cuilian Zhang
- Reproductive Medicine Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou, Henan, China. .,Henan Joint International Research Laboratory of Reproductive Bioengineering, Zhengzhou, Henan Province, China.
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18
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Cecil CAM, Nigg JT. Epigenetics and ADHD: Reflections on Current Knowledge, Research Priorities and Translational Potential. Mol Diagn Ther 2022; 26:581-606. [PMID: 35933504 PMCID: PMC7613776 DOI: 10.1007/s40291-022-00609-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common and debilitating neurodevelopmental disorder influenced by both genetic and environmental factors, typically identified in the school-age years but hypothesized to have developmental origins beginning in utero. To improve current strategies for prediction, prevention and treatment, a central challenge is to delineate how, at a molecular level, genetic and environmental influences jointly shape ADHD risk, phenotypic presentation, and developmental course. Epigenetic processes that regulate gene expression, such as DNA methylation, have emerged as a promising molecular system in the search for both biomarkers and mechanisms to address this challenge. In this Current Opinion, we discuss the relevance of epigenetics (specifically DNA methylation) for ADHD research and clinical practice, starting with the current state of knowledge, what challenges we have yet to overcome, and what the future may hold in terms of methylation-based applications for personalized medicine in ADHD. We conclude that the field of epigenetics and ADHD is promising but is still in its infancy, and the potential for transformative translational applications remains a distant goal. Nevertheless, rapid methodological advances, together with the rise of collaborative science and increased availability of high-quality, longitudinal data make this a thriving research area that in future may contribute to the development of new tools for improved prediction, management, and treatment of ADHD.
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Affiliation(s)
- Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC-Sophia, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.
| | - Joel T Nigg
- Division of Psychology, Department of Psychiatry, Oregon Health and Science University, Portland, OR, USA
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Zhang H, Liu Y, Xie Y, Zhu Y, Liu J, Lu F. H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1685-1700. [PMID: 35831553 DOI: 10.1007/s11427-022-2155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation and histone lysine tri-methylation at H3K27 (H3K27me3) are two chromatin modifications for transcriptional gene silencing, which play important roles in diverse biological processes, including cell fate determination and cell lineage commitment. These two marks are largely mutually exclusive and target distinct sets of genes in the mammalian genome. However, how H3K27me3 shapes the DNA methylome remains elusive. Here, we report that the loss of H3K27me3 modification leads to increased DNA methylation at previously marked H3K27me3 sites, indicating that H3K27me3 negatively regulates DNA methylation. Genome-wide analysis of H3 ubiquitination, essential for recruitment and activation of DNA methyltransferase DNMT1, reveals the absence of H3 ubiquitination at H3K27me3 marked nucleosomes. Moreover, loss of H3K27me3 modification induces an increase in H3K18 ubiquitination at the corresponding hyper-methylated loci. Importantly, we show that H3K27me3 directly inhibits UHRF1-mediated H3 ubiquitination toward nucleosomes in a defined biochemical assay. Taken together, our findings reveal a general mechanism for H3K27me3-mediated shaping of the mammalian DNA methylome via modulation of H3 ubiquitination.
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Affiliation(s)
- Honglian Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunji Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwen Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Dvoran M, Nemcova L, Kalous J. An Interplay between Epigenetics and Translation in Oocyte Maturation and Embryo Development: Assisted Reproduction Perspective. Biomedicines 2022; 10:biomedicines10071689. [PMID: 35884994 PMCID: PMC9313063 DOI: 10.3390/biomedicines10071689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
Germ cell quality is a key prerequisite for successful fertilization and early embryo development. The quality is determined by the fine regulation of transcriptomic and proteomic profiles, which are prone to alteration by assisted reproduction technology (ART)-introduced in vitro methods. Gaining evidence shows the ART can influence preset epigenetic modifications within cultured oocytes or early embryos and affect their developmental competency. The aim of this review is to describe ART-determined epigenetic changes related to the oogenesis, early embryogenesis, and further in utero development. We confront the latest epigenetic, related epitranscriptomic, and translational regulation findings with the processes of meiotic maturation, fertilization, and early embryogenesis that impact the developmental competency and embryo quality. Post-ART embryo transfer, in utero implantation, and development (placentation, fetal development) are influenced by environmental and lifestyle factors. The review is emphasizing their epigenetic and ART contribution to fetal development. An epigenetic parallel among mouse, porcine, and bovine animal models and human ART is drawn to illustrate possible future mechanisms of infertility management as well as increase the awareness of the underlying mechanisms governing oocyte and embryo developmental complexity under ART conditions.
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21
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Gonçalves BM, Graceli JB, da Rocha PB, Tilli HP, Vieira EM, de Sibio MT, Peghinelli VV, Deprá IC, Mathias LS, Olímpio RMC, Belik VC, Nogueira CR. Placental model as an important tool to study maternal-fetal interface. Reprod Toxicol 2022; 112:7-13. [PMID: 35714933 DOI: 10.1016/j.reprotox.2022.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/29/2022] [Accepted: 06/09/2022] [Indexed: 10/18/2022]
Abstract
The placenta is a temporary organ that plays critical roles at the maternal-fetal interface. Normal development and function of the placenta is dependent on hormonal signaling pathways that make the placenta a target of endocrine disrupting chemical (EDC) action. Studies showing association between prenatal exposure, hormone disruption, and reproductive damage indicate that EDCs are developmentally toxic and can impact future generations. In this context, new placental models (trophoblast-derived cell lines, organotypic or 3D cell models, and physiologically based kinetic models) have been developed in order to create new approach methodology (NAM) to assess and even prevent such disastrous toxic harm in future generations. With the widespread discouragement of conducting animal studies, it has become irrefutable to develop in vitro models that can serve as a substitute for in vivo models. The goal of this review is to discuss the newest in vitro models to understand the maternal-fetal interface and predict placental development, physiology, and dysfunction generated by failures in molecular hormone control mechanisms, which, consequently, may change epigenetic programming to increase susceptibility to metabolic and other disorders in the offspring. We summarize the latest placental models for developmental toxicology studies, focusing mainly on three-dimensional (3D) culture models.
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Affiliation(s)
- Bianca M Gonçalves
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Jones B Graceli
- Department of Morphology, Health Sciences Center, Federal University of Espirito Santo (UFES), Vitória, ES, Brazil
| | - Paula B da Rocha
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Helena P Tilli
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Ester M Vieira
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria T de Sibio
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Vinícius V Peghinelli
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Igor C Deprá
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Lucas S Mathias
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Regiane M C Olímpio
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Virgínia C Belik
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Célia R Nogueira
- Department of Clinical Medicine, Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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22
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Zhang Y, Li T, Pan C, Khan IA, Chen Z, Yue Y, Yang M. Intergenerational toxic effects of parental exposure to bisphenol AF on offspring and epigenetic modulations in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153714. [PMID: 35143790 DOI: 10.1016/j.scitotenv.2022.153714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Bisphenol AF (BPAF), an endocrine-disrupting chemical, has been detected in various environmental media because of its wide industrial applications. Meanwhile, substances that are known to be toxic to the reproductive system have been observed to interfere with the development of the offspring following parental exposure. This study was aimed at determining the gender-dependent intergenerational effects of BPAF on offspring development following either paternal or maternal exposure of adult zebrafish to an environmental concentration of BPAF. Four-month-old zebrafish (F0) were exposed to 10 μg/L of BPAF for 28 days, the developmental endpoints of F1 embryos were then tested without further treatment with BPAF. The results show that paternal BPAF exposure decreased the hatching rate, increased mortality, and shortened the body lengths of F1 larval offspring. In addition, it changed DNA and m6A RNA methylation gene expression levels in F0 testes and F1 larvae. Although maternal exposure increased mortality and enhanced antioxidant enzyme activities in F1 larvae, only DNA methylation gene expression was altered in F0 ovaries and F1 larvae. In addition, a short term BPAF exposure of zebrafish embryos from 4 h post-fertilization (hpf) until 120 hpf similarly impaired the early development of the larvae but only at a level relatively higher than 10 μg/L; and DNA and RNA methylation gene expression was regulated to some extent in BPAF exposure groups. Overall, our results indicate the gender-specific effects of BPAF on offspring development and epigenetic modulations, suggesting a relatively high susceptibility within the exposure window during gametogenesis and early embryonic developmental stages to environmental chemicals.
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Affiliation(s)
- Yuanyuan Zhang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Tianjie Li
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Chenyuan Pan
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Imran Ahamed Khan
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Zhong Chen
- Department of Cardiology, the Affiliated Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201306, China.
| | - Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China.
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Siddeek B, Simeoni U. Epigenetics provides a bridge between early nutrition and long-term health and a target for disease prevention. Acta Paediatr 2022; 111:927-934. [PMID: 35038770 PMCID: PMC9305224 DOI: 10.1111/apa.16258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/19/2022]
Abstract
Exposure to nutritional imbalance during early life can influence disease risk lifelong and across generations. In this long‐term conditioning, epigenetics constitutes a key mechanism. They bridge environmental cues and the expression of genes involved in the setting of long‐standing biological regulations in numerous organs and species. Epigenetic marks are proposed as innovative diagnostic biomarkers and potential targets in the prevention of diseases. However, a number of uncertainties make them difficult to use in clinical approaches in the context of early exposure to nutritional challenge. In conclusion, active investigations in this field are still needed before clinical applications are considered.
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Affiliation(s)
- Benazir Siddeek
- DOHaD Laboratory Division of Pediatrics Woman‐Mother‐Child‐Department Centre Hospitalier Universitaire Vaudois and University of Lausanne Lausanne Switzerland
| | - Umberto Simeoni
- DOHaD Laboratory Division of Pediatrics Woman‐Mother‐Child‐Department Centre Hospitalier Universitaire Vaudois and University of Lausanne Lausanne Switzerland
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24
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Epigenetic Effect of Maternal Methyl-Group Donor Intake on Offspring’s Health and Disease. Life (Basel) 2022; 12:life12050609. [PMID: 35629277 PMCID: PMC9145757 DOI: 10.3390/life12050609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/02/2022] [Accepted: 04/15/2022] [Indexed: 01/16/2023] Open
Abstract
Maternal exposure to some dietary and environmental factors during embryonic development can affect offspring’s phenotype and, furthermore, the risk of developing diseases later in life. One potential mechanism responsible for this early programming may be the modification of the epigenome, such as DNA methylation. Methyl-group donors are essential for DNA methylation and are shown to have an important role in fetal development and later health. The main goal of the present review is to summarize the available literature data on the epigenetic effect (DNA methylation) of maternal methyl-group donor availability on reproductivity, perinatal outcome, and later health of the offspring. In our literature search, we found evidence for the association between alterations in DNA methylation patterns caused by different maternal methyl-group donor (folate, choline, methionine, betaine) intake and reproductivity, birth weight, neural tube defect, congenital heart defect, cleft lip and palate, brain development, and the development of obesity and associated non-communicable diseases in later life. We can conclude that maternal methyl-group donor availability could affect offspring’s health via alterations in DNA methylation and may be a major link between early environmental exposure and the development of diseases in the offspring. However, still, further studies are necessary to confirm the associations and causal relationships.
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25
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Mlodawska OW, Saini P, Parker JB, Wei JJ, Bulun SE, Simon MA, Chakravarti D. Epigenomic and enhancer dysregulation in uterine leiomyomas. Hum Reprod Update 2022; 28:518-547. [PMID: 35199155 PMCID: PMC9247409 DOI: 10.1093/humupd/dmac008] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Uterine leiomyomas, also known as uterine fibroids or myomas, are the most common benign gynecological tumors and are found in women of reproductive and postmenopausal age. There is an exceptionally high prevalence of this tumor in women by the age of 50 years. Black women are particularly affected, with an increased incidence, earlier age of onset, larger and faster growing fibroids and greater severity of symptoms as compared to White women. Although advances in identifying genetic and environmental factors to delineate these fibroids have already been made, only recently has the role of epigenomics in the pathogenesis of this disease been considered. OBJECTIVE AND RATIONALE Over recent years, studies have identified multiple epigenomic aberrations that may contribute to leiomyoma development and growth. This review will focus on the most recent discoveries in three categories of epigenomic changes found in uterine fibroids, namely aberrant DNA methylation, histone tail modifications and histone variant exchange, and their translation into altered target gene architecture and transcriptional outcome. The findings demonstrating how the altered 3D shape of the enhancer can regulate gene expression from millions of base pairs away will be discussed. Additionally, translational implications of these discoveries and potential roadblocks in leiomyoma treatment will be addressed. SEARCH METHODS A comprehensive PubMed search was performed to identify published articles containing keywords relevant to the focus of the review, such as: uterine leiomyoma, uterine fibroids, epigenetic alterations, epigenomics, stem cells, chromatin modifications, extracellular matrix [ECM] organization, DNA methylation, enhancer, histone post-translational modifications and dysregulated gene expression. Articles until September 2021 were explored and evaluated to identify relevant updates in the field. Most of the articles focused on in the discussion were published between 2015 and 2021, although some key discoveries made before 2015 were included for background information and foundational purposes. We apologize to the authors whose work was not included because of space restrictions or inadvertent omission. OUTCOMES Chemical alterations to the DNA structure and of nucleosomal histones, without changing the underlying DNA sequence, have now been implicated in the phenotypic manifestation of uterine leiomyomas. Genome-wide DNA methylation analysis has revealed subsets of either suppressed or overexpressed genes accompanied by aberrant promoter methylation. Furthermore, differential promoter access resulting from altered 3D chromatin structure and histone modifications plays a role in regulating transcription of key genes thought to be involved in leiomyoma etiology. The dysregulated genes function in tumor suppression, apoptosis, angiogenesis, ECM formation, a variety of cancer-related signaling pathways and stem cell differentiation. Aberrant DNA methylation or histone modification is also observed in altering enhancer architecture, which leads to changes in enhancer-promoter contact strength, producing novel explanations for the overexpression of high mobility group AT-hook 2 and gene dysregulation found in mediator complex subunit 12 mutant fibroids. While many molecular mechanisms and epigenomic features have been investigated, the basis for the racial disparity observed among those in the Black population remains unclear. WIDER IMPLICATIONS A comprehensive understanding of the exact pathogenesis of uterine leiomyoma is lacking and requires attention as it can provide clues for prevention and viable non-surgical treatment. These findings will widen our knowledge of the role epigenomics plays in the mechanisms related to uterine leiomyoma development and highlight novel approaches for the prevention and identification of epigenome targets for long-term non-invasive treatment options of this significantly common disease.
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Affiliation(s)
| | | | - J Brandon Parker
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jian-Jun Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Melissa A Simon
- Department of Obstetrics and Gynecology, Center for Health Equity Transformation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Debabrata Chakravarti
- Correspondence address. Department of Obstetrics and Gynecology, Northwestern University, Feinberg School of Medicine, 303 E Superior Street, Lurie 4-119, Chicago, IL 60611, USA. E-mail:
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26
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Gantenbein KV, Kanaka-Gantenbein C. Highlighting the trajectory from intrauterine growth restriction to future obesity. Front Endocrinol (Lausanne) 2022; 13:1041718. [PMID: 36440208 PMCID: PMC9691665 DOI: 10.3389/fendo.2022.1041718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
During the last decades several lines of evidence reported the association of an adverse intrauterine environment, leading to intrauterine restriction, with future disease, such as obesity and metabolic syndrome, both leading to increased cardiovascular and cancer risk. The underlying explanation for this association has firstly been expressed by the Barker's hypothesis, the "thrifty phenotype hypothesis". According to this hypothesis, a fetus facing an adverse intrauterine environment adapts to this environment through a reprogramming of its endocrine-metabolic status, during the crucial window of developmental plasticity to save energy for survival, providing less energy and nutrients to the organs that are not essential for survival. This theory evolved to the concept of the developmental origin of health and disease (DOHaD). Thus, in the setting of an adverse, f. ex. protein restricted intrauterine environment, while the energy is mainly directed to the brain, the peripheral organs, f.ex. the muscles and the liver undergo an adaptation that is expressed through insulin resistance. The adaptation at the hepatic level predisposes to future dyslipidemia, the modifications at the vascular level to endothelial damage and future hypertension and, overall, through the insulin resistance to the development of metabolic syndrome. All these adaptations are suggested to take place through epigenetic modifications of the expression of genes without change of their amino-acid sequence. The epigenetic modifications leading to future obesity and cardiovascular risk are thought to induce appetite dysregulation, promoting food intake and adipogenesis, facilitating obesity development. The epigenetic modifications may even persist into the next generation even though the subsequent generation has not been exposed to an adverse intrauterine environment, a notion defined as the "transgenerational transfer of environmental information". As a consequence, if the increased public health burden and costs of non-communicable chronic diseases such as obesity, hypertension, metabolic syndrome and type 2 diabetes have to be minimized, special attention should be laid to the healthy lifestyle habits of women of reproductive age, including healthy diet and physical activity to be established long before any pregnancy takes place in order to provide the best conditions for both somatic and mental health of future generations.
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Affiliation(s)
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics Medical School, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens, Greece
- *Correspondence: Christina Kanaka-Gantenbein, ,
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27
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Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ 2022; 70:339-373. [PMID: 36348114 PMCID: PMC9753575 DOI: 10.1007/978-3-031-06573-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epigenetic gene regulatory mechanisms play a central role in the biological control of cell and tissue structure, function, and phenotype. Identification of epigenetic dysregulation in cancer provides mechanistic into tumor initiation and progression and may prove valuable for a variety of clinical applications. We present an overview of epigenetically driven mechanisms that are obligatory for physiological regulation and parameters of epigenetic control that are modified in tumor cells. The interrelationship between nuclear structure and function is not mutually exclusive but synergistic. We explore concepts influencing the maintenance of chromatin structures, including phase separation, recognition signals, factors that mediate enhancer-promoter looping, and insulation and how these are altered during the cell cycle and in cancer. Understanding how these processes are altered in cancer provides a potential for advancing capabilities for the diagnosis and identification of novel therapeutic targets.
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Affiliation(s)
- Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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Fanis P, Morrou M, Tomazou M, Michailidou K, Spyrou GM, Toumba M, Skordis N, Neocleous V, Phylactou LA. Methylation status of hypothalamic Mkrn3 promoter across puberty. Front Endocrinol (Lausanne) 2022; 13:1075341. [PMID: 36714607 PMCID: PMC9880154 DOI: 10.3389/fendo.2022.1075341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Makorin RING finger protein 3 (MKRN3) is an important factor located on chromosome 15 in the imprinting region associated with Prader-Willi syndrome. Imprinted MKRN3 is expressed in hypothalamic regions essential for the onset of puberty and mutations in the gene have been found in patients with central precocious puberty. The pubertal process is largely controlled by epigenetic mechanisms that include, among other things, DNA methylation at CpG dinucleotides of puberty-related genes. In the present study, we investigated the methylation status of the Mkrn3 promoter in the hypothalamus of the female mouse before, during and after puberty. Initially, we mapped the 32 CpG dinucleotides in the promoter, the 5'UTR and the first 50 nucleotides of the coding region of the Mkrn3 gene. Moreover, we identified a short CpG island region (CpG islet) located within the promoter. Methylation analysis using bisulfite sequencing revealed that CpG dinucleotides were methylated regardless of developmental stage, with the lowest levels of methylation being found within the CpG islet region. In addition, the CpG islet region showed significantly lower methylation levels at the pre-pubertal stage when compared with the pubertal or post-pubertal stage. Finally, in silico analysis of transcription factor binding sites on the Mkrn3 CpG islet identified the recruitment of 29 transcriptional regulators of which 14 were transcriptional repressors. Our findings demonstrate the characterization and differential methylation of the CpG dinucleotides located in the Mkrn3 promoter that could influence the transcriptional activity in pre-pubertal compared to pubertal or post-pubertal period. Further studies are needed to clarify the possible mechanisms and effects of differential methylation of the Mkrn3 promoter.
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Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Morrou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- Medical School, University of Nicosia, Nicosia, Cyprus
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou,
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Faienza MF, Urbano F, Moscogiuri LA, Chiarito M, De Santis S, Giordano P. Genetic, epigenetic and enviromental influencing factors on the regulation of precocious and delayed puberty. Front Endocrinol (Lausanne) 2022; 13:1019468. [PMID: 36619551 PMCID: PMC9813382 DOI: 10.3389/fendo.2022.1019468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
The pubertal development onset is controlled by a network of genes that regulate the gonadotropin releasing hormone (GnRH) pulsatile release and the subsequent increase of the circulating levels of pituitary gonadotropins that activate the gonadal function. Although the transition from pre-pubertal condition to puberty occurs physiologically in a delimited age-range, the inception of pubertal development can be anticipated or delayed due to genetic and epigenetic changes or environmental conditions. Most of the genetic and epigenetic alterations concern genes which encode for kisspeptin, GnRH, LH, FSH and their receptor, which represent crucial factors of the hypothalamic-pituitary-gonadal (HPG) axis. Recent data indicate a central role of the epigenome in the regulation of genes in the hypothalamus and pituitary that could mediate the flexibility of pubertal timing. Identification of epigenetically regulated genes, such as Makorin ring finger 3 (MKRN3) and Delta-like 1 homologue (DLK1), respectively responsible for the repression and the activation of pubertal development, provides additional evidence of how epigenetic variations affect pubertal timing. This review aims to investigate genetic, epigenetic, and environmental factors responsible for the regulation of precocious and delayed puberty.
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Affiliation(s)
- Maria Felicia Faienza
- Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, Bari, Italy
- Giovanni XXIII Pediatric Hospital, Bari, Italy
- *Correspondence: Maria Felicia Faienza,
| | | | | | | | - Stefania De Santis
- Department of Pharmacy-Pharmaceutical Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Paola Giordano
- Giovanni XXIII Pediatric Hospital, Bari, Italy
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, Bari, Italy
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30
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Zhang Q, Su R, Qin S, Wei Y. High glucose increases IGF-2/H19 expression by changing DNA methylation in HTR8/SVneo trophoblast cells. Placenta 2021; 118:32-37. [PMID: 35007927 DOI: 10.1016/j.placenta.2021.12.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Gestational diabetes mellitus (GDM) is associated with many adverse outcomes of pregnancy, especially macrosomia. The aim of our study was to verify whether high glucose concentrations change the methylation levels of the insulin-like growth factor-2 (IGF-2)/H19 gene promoters to increase the expression of IGF-2, a key gene in fetal growth regulation. METHODS HTR8/SVneo cells were used to establish a cell model of intrauterine hyperglycemia in pregnant women with GDM. The RNA expression levels of the IGF-2/H19 genes and the methylation levels of the IGF-2/H19 gene promoter regions were measured. Methylated and unmethylated IGF-2/H19 gene promoter plasmids were transfected into HTR8/SVneo cells. RESULTS Among the five groups of cells, the RNA levels of IGF-2 and H19 were lowest in the 5-mM (physiological blood glucose level) group, which was statistically significant (all P < 0.05). Compared with those in the 5-mM group, two cytosine-phosphate-guanine (CpG) sites in the promoter region of the IGF-2 gene and twelve CpG sites in the promoter region of the H19 gene had statistically significant changes in methylation levels (all P < 0.05). Additionally, luciferase activity was significantly higher in cells transfected with the methylated H19 gene promoter plasmid than in control cells transfected with the unmethylated plasmid (P < 0.01), while the methylated IGF-2 gene promoter plasmid produced lower luciferase activity than the unmethylated plasmid (P < 0.01). DISCUSSION High glucose concentrations may increase IGF-2/H19 expression by changing the methylation levels of the IGF-2 and H19 gene promoters.
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Affiliation(s)
- Qidi Zhang
- Peking University First Hospital Obstetrics and Gynecology, Beijing Key Laboratory of Maternal-Fetal Medicine of Gestational Diabetes Mellitus, China
| | - Rina Su
- Peking University First Hospital Obstetrics and Gynecology, Beijing Key Laboratory of Maternal-Fetal Medicine of Gestational Diabetes Mellitus, China
| | - Shengtang Qin
- Peking University First Hospital Obstetrics and Gynecology, Beijing Key Laboratory of Maternal-Fetal Medicine of Gestational Diabetes Mellitus, China
| | - Yumei Wei
- Peking University First Hospital Obstetrics and Gynecology, Beijing Key Laboratory of Maternal-Fetal Medicine of Gestational Diabetes Mellitus, China.
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Guo W, Ma H, Wang CZ, Wan JY, Yao H, Yuan CS. Epigenetic Studies of Chinese Herbal Medicine: Pleiotropic Role of DNA Methylation. Front Pharmacol 2021; 12:790321. [PMID: 34950039 PMCID: PMC8688941 DOI: 10.3389/fphar.2021.790321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/22/2021] [Indexed: 12/03/2022] Open
Abstract
Accumulating knowledge has been achieved on DNA methylation participating in numerous cellular processes and multiple human diseases; however, few studies have addressed the pleiotropic role of DNA methylation in Chinese herbal medicine (CHM). CHM has been used worldwide for the prevention and treatment of multiple diseases. Newly developed epigenetic techniques have brought great opportunities for the development of CHM. In this review, we summarize the DNA methylation studies and portray the pleiotropic role of DNA methylation in CHM. DNA methylation serves as a mediator participating in plant responses to environmental factors, and thus affecting CHM medicinal plants growth and bioactive compound biosynthesis which are vital for therapeutic effects. Furthermore, DNA methylation helps to uncover the pharmaceutical mechanisms of CHM formulae, herbs, and herbal-derived compounds. It also provides scientific validation for constitution theory and other essential issues of CHM. This newly developed field of DNA methylation is up-and-coming to address many complicated scientific questions of CHM; it thus not only promotes disease treatment but also facilitates health maintenance.
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Affiliation(s)
- Wenqian Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.,National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Han Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.,National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Chong-Zhi Wang
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL, United States.,Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL, United States
| | - Jin-Yi Wan
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.,National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Haiqiang Yao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.,National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL, United States.,Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL, United States
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Abstract
The interaction between the gut and its eventual trillions of microbe inhabitants during microbial colonization, represents a critical time period for establishing the overall health and wellbeing of an individual. The gut microbiome represents a diverse community of microbes that are critical for many physiological roles of the host including host metabolism. These processes are controlled by a fine-tuned chemical cross talk between the host and microbiota. Although the exact mechanisms behind this cross talk remains elusive, microbiota induced epigenetic mechanisms like DNA methylation and histone modifications may be key. This review presents our perspective on the epigenome as a mediator for host-microbiota cross talk, as well as methodology to study epigenetics, the role of dysbiosis in disease, and how the gut microbiome-host axis may be used in personal medicine.
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Wu J, Liu LL, Cao M, Hu A, Hu D, Luo Y, Wang H, Zhong JN. DNA methylation plays important roles in retinal development and diseases. Exp Eye Res 2021; 211:108733. [PMID: 34418429 DOI: 10.1016/j.exer.2021.108733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang Province, China
| | - Lin-Lin Liu
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Miao Cao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Ang Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Die Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Yan Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Hui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
| | - Jia-Ning Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
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Wu HY, Cheng Y, Jin LY, Zhou Y, Pang HY, Zhu H, Yan CC, Yan YS, Yu JE, Sheng JZ, Huang HF. Paternal obesity impairs hepatic gluconeogenesis of offspring by altering Igf2/H19 DNA methylation. Mol Cell Endocrinol 2021; 529:111264. [PMID: 33811969 DOI: 10.1016/j.mce.2021.111264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022]
Abstract
Over the past four decades, the global prevalence of obesity has increased rapidly in all age ranges. Emerging evidence suggests that paternal lifestyle and environmental exposure have a crucial role in the health of offspring. Therefore, the current study investigated the impact of paternal obesity on the metabolic profile of offspring in a male mouse model of obesity. Female offspring of obese fathers fed a high-fat diet (HFD) (60% kcal fat) showed hyperglycemia because of enhanced gluconeogenesis and elevated expression of phosphoenolpyruvate carboxykinase (PEPCK), which is a key enzyme involved in the regulation of gluconeogenesis. Methylation of the Igf2/H19 imprinting control region (ICR) was dysregulated in the liver of offspring, and the sperm, of HFD fathers, suggesting that epigenetic changes in germ cells contribute to this father-offspring transmission. In addition, we explored whether H19 might regulate hepatic gluconeogenesis. Our results showed that overexpression of H19 in Hepa1-6 cells enhanced the expression of PEPCK and gluconeogenesis by promoting nuclear retention of forkhead box O1 (FOXO1), which is involved in the transcriptional regulation of Pepck. Thus, the current study suggests that paternal exposure to HFD impairs the gluconeogenesis of offspring via altered Igf2/H19 DNA methylation.
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Affiliation(s)
- Hai-Yan Wu
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi Cheng
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lu-Yang Jin
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yin Zhou
- Department of Reproductive Medicine, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hai-Yan Pang
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hong Zhu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Cao-Chong Yan
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi-Shang Yan
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia-En Yu
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian-Zhong Sheng
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - He-Feng Huang
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Yan S, Lu J, Jiao K. Epigenetic Regulation of Cardiac Neural Crest Cells. Front Cell Dev Biol 2021; 9:678954. [PMID: 33968946 PMCID: PMC8097001 DOI: 10.3389/fcell.2021.678954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 01/02/2023] Open
Abstract
The cardiac neural crest cells (cNCCs) is a transient, migratory cell population that contribute to the formation of major arteries and the septa and valves of the heart. Abnormal development of cNCCs leads to a spectrum of congenital heart defects that mainly affect the outflow region of the hearts. Signaling molecules and transcription factors are the best studied regulatory events controlling cNCC development. In recent years, however, accumulated evidence supports that epigenetic regulation also plays an important role in cNCC development. Here, we summarize the functions of epigenetic regulators during cNCC development as well as cNCC related cardiovascular defects. These factors include ATP-dependent chromatin remodeling factors, histone modifiers and DNA methylation modulators. In many cases, mutations in the genes encoding these factors are known to cause inborn heart diseases. A better understanding of epigenetic regulators, their activities and their roles during heart development will ultimately contribute to the development of new clinical applications for patients with congenital heart disease.
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Affiliation(s)
| | | | - Kai Jiao
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
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Soeda S, Saito R, Fujii A, Tojo S, Tokumura Y, Taniura H. Abnormal DNA methylation in pluripotent stem cells from a patient with Prader-Willi syndrome results in neuronal differentiation defects. Stem Cell Res 2021; 53:102351. [PMID: 33895503 DOI: 10.1016/j.scr.2021.102351] [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] [Received: 04/13/2020] [Revised: 03/09/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022] Open
Abstract
DNA methylation is a common method of gene expression regulation, and this form of regulation occurs in the neurodevelopmental disorder Prader-Willi syndrome (PWS). Gene expression regulation via methylation is important for humans, although there is little understanding of the role of methylation in neuronal differentiation. We characterized the cellular differentiation potential of iPS cells derived from a patient with PWS with abnormal methylation (M-iPWS cells). A comparative genomic hybridization (CGH) array revealed that, unlike iPWS cells (deletion genes type), the abnormally methylated M-iPWS cells had no deletion in the15q11.2-q13 chromosome region. In addition, methylation-specific PCR showed that M-iPWS cells had strong methylation in CpG island of the small nuclear ribonucleoprotein polypeptide N (SNRPN) on both alleles. To assess the effect of abnormal methylation on cell differentiation, the M-iPWS and iPWS cells were induced to differentiate into embryoid bodies (EBs). The results suggest that iPWS and M-iPWS cells are defective at differentiation into ectoderm. Neural stem cells (NSCs) and neurons derived from M-iPWS cells had fewer NSCs and mature neurons with low expression of NSCs and neuronal markers. We conclude that expression of the downstream of genes in the PWS region regulated by methylation is involved in neuronal differentiation.
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Affiliation(s)
- Shuhei Soeda
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan.
| | - Ryo Saito
- Advanced Clinical Research Center, Southern Tohoku Research Institute for Neuroscience, Kanagawa 215-0026, Japan; Core Research Facilities for Basic Science, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Ai Fujii
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Shusei Tojo
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yuka Tokumura
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Hideo Taniura
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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Genomic Imprinting at the Porcine PLAGL1 Locus and the Orthologous Locus in the Human. Genes (Basel) 2021; 12:genes12040541. [PMID: 33918057 PMCID: PMC8069715 DOI: 10.3390/genes12040541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Implementation of genomic imprinting in mammals often results in cis-acting silencing of a gene cluster and monoallelic expression, which are important for mammalian growth and function. Compared with widely documented imprinting status in humans and mice, current understanding of genomic imprinting in pigs is relatively limited. The objectives of this study were to identify DNA methylation status and allelic expression of alternative spliced isoforms at the porcine PLAGL1 locus and assess the conservation of the locus compared to the orthologous human locus. DNA methylome and transcriptome were constructed using porcine parthenogenetic or biparental control embryos. Using methylome, differentially methylated regions between those embryos were identified. Alternative splicing was identified by differential splicing analysis, and monoallelic expression was examined using single nucleotide polymorphism sites. Moreover, topological boundary regions were identified by analyzing CTCF binding sites and compared with the boundary of human orthologous locus. As a result, it was revealed that the monoallelic expression of the PLAGL1 gene in porcine embryos via genomic imprinting was maintained in the adult stage. The porcine PLAGL1 locus was largely conserved in regard to maternal hypermethylation, tissue distribution of mRNA expression, monoallelic expression, and biallelic CTCF-binding, with exceptions on transcript isoforms produced by alternative splicing instead of alternative promoter usage. These findings laid the groundwork for comparative studies on the imprinted PLAGL1 gene and related regulatory mechanisms across species.
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38
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Macken WL, Vandrovcova J, Hanna MG, Pitceathly RDS. Applying genomic and transcriptomic advances to mitochondrial medicine. Nat Rev Neurol 2021; 17:215-230. [PMID: 33623159 DOI: 10.1038/s41582-021-00455-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which restricts their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering efforts to understand the underlying disease mechanisms. Although they represent a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances in genomics and transcriptomics offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression and the interpretation of rare and novel mitochondrial transfer RNA variants.
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Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK.
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Patel J, Bircan E, Tang X, Orloff M, Hobbs CA, Browne ML, Botto LD, Finnell RH, Jenkins MM, Olshan A, Romitti PA, Shaw GM, Werler MM, Li J, Nembhard WN. Paternal genetic variants and risk of obstructive heart defects: A parent-of-origin approach. PLoS Genet 2021; 17:e1009413. [PMID: 33684136 PMCID: PMC7971842 DOI: 10.1371/journal.pgen.1009413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/18/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Previous research on risk factors for obstructive heart defects (OHDs) focused on maternal and infant genetic variants, prenatal environmental exposures, and their potential interaction effects. Less is known about the role of paternal genetic variants or environmental exposures and risk of OHDs. We examined parent-of-origin effects in transmission of alleles in the folate, homocysteine, or transsulfuration pathway genes on OHD occurrence in offspring. We used data on 569 families of liveborn infants with OHDs born between October 1997 and August 2008 from the National Birth Defects Prevention Study to conduct a family-based case-only study. Maternal, paternal, and infant DNA were genotyped using an Illumina Golden Gate custom single nucleotide polymorphism (SNP) panel. Relative risks (RR), 95% confidence interval (CI), and likelihood ratio tests from log-linear models were used to estimate the parent-of-origin effect of 877 SNPs in 60 candidate genes in the folate, homocysteine, and transsulfuration pathways on the risk of OHDs. Bonferroni correction was applied for multiple testing. We identified 3 SNPs in the transsulfuration pathway and 1 SNP in the folate pathway that were statistically significant after Bonferroni correction. Among infants who inherited paternally-derived copies of the G allele for rs6812588 in the RFC1 gene, the G allele for rs1762430 in the MGMT gene, and the A allele for rs9296695 and rs4712023 in the GSTA3 gene, RRs for OHD were 0.11 (95% CI: 0.04, 0.29, P = 9.16x10-7), 0.30 (95% CI: 0.17, 0.53, P = 9.80x10-6), 0.34 (95% CI: 0.20, 0.57, P = 2.28x10-5), and 0.34 (95% CI: 0.20, 0.58, P = 3.77x10-5), respectively, compared to infants who inherited maternally-derived copies of the same alleles. We observed statistically significant decreased risk of OHDs among infants who inherited paternal gene variants involved in folate and transsulfuration pathways. Obstructive heart defects are birth defects that cause obstruction to the blood flow of the developing heart. Common OHDs include coarctation of the aorta, aortic stenosis and pulmonary stenosis. While there is a fair amount of literature indicating an association between maternal genetic variants and OHDs, less is known about the role of paternal genetic variants in the etiology of OHDs. We used a genotype clustering algorithm, SNPMClust, that was developed in-house at the Arkansas Center for Birth Defects Research and Prevention to study the role of paternal genetic variants in the folate, homocysteine and transsulfuration pathways. Maternal, paternal, and infant DNA specimens were collected from participants of the National Birth Defects Prevention Study, a large population-based case-control study in the United States, and were genotyped using an Illumina Golden Gate custom single nucleotide polymorphism (SNP) panel. We identified 4 SNPs in the folate and transsulfuration pathways, rs6812588, rs1762430, rs9296695, and rs4712023, that were associated with a statistically significant decreased risk of OHDs for infants who inherited a paternally-derived copy of the variant allele compared to infants who inherited a maternal copy of the variant allele. In conclusion, we observed a significantly decreased risk and less epigenetic influence of paternal genetic variants on OHDs compared to maternally-derived variants.
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Affiliation(s)
- Jenil Patel
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston (UTHealth) School of Public Health, Dallas, TX, United States of America
| | - Emine Bircan
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Xinyu Tang
- Biostatistics Program, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR, United States of America
| | - Mohammed Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Marilyn L. Browne
- Birth Defects Research Section, New York State Department of Health, Albany, NY, United States of America
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, United States of America
| | - Lorenzo D. Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, United States of America
| | - Richard H. Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States of America
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Andrew Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, United States of America
| | - Gary M. Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Martha M. Werler
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, United States of America
| | - Jingyun Li
- Biostatistics Program, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR, United States of America
| | - Wendy N. Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- * E-mail:
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40
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Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D, Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T, Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G. Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet 2021; 53:215-229. [PMID: 33526924 PMCID: PMC7116828 DOI: 10.1038/s41588-020-00770-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.
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Affiliation(s)
- Riccardo M Betto
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Neuroscience Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Giovanni Rigoni
- Department of Biology, University of Padua, Padua, Italy
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vincent Guerineau
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | - Tim Lohoff
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy.
- Department of Biology, University of Padua, Padua, Italy.
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Gurugubelli KR, Ballambattu VB, Bobby Z. Global DNA Methylation in Cord Blood and Neurodevelopmental Outcome at 18 Months of Age among Intrauterine Growth Restricted and Appropriate for Gestational Age Infants. J Trop Pediatr 2021; 67:6024571. [PMID: 33277909 DOI: 10.1093/tropej/fmaa108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) is associated with faltered growth and development later in life. Alteration in DNA methylation may occur among IUGR babies and it can have bearing on the outcome. OBJECTIVES To compare the DNA methylation in the cord blood among IUGR and appropriate for gestational age (AGA) babies and find it is association with their neurodevelopmental outcome at 18 months of age. METHODOLOGY Genomic DNA methylation among 40 IUGR and equal number of AGA neonates was estimated by using 5-mC ELISA kit in the cord blood. Infants were assessed at birth and their anthropometric measurements were taken. They were regularly followed up and assessed for neurodevelopment outcome till 18 months of age using DASII (Developmental Assessment Scale for Indian Infants). DNA methylation was correlated with neurodevelopmental outcome. Numbers and percentages were used for categorical data. Mean and SD were used for continuous variables. The significant mean difference between IUGR and AGA was determined by independent Student t-test. To study the association between the DNA methylation and outcome, Spearman correlation was used. A p < 0.05 was considered as statistically significant. RESULTS Significant difference in DNA methylation was observed between IUGR and AGA infants (IUGR: 3.12 ± 1.24; AGA: 4.40 ± 2.03; p < 0.001). Anthropometry (weight, length and head circumference) at birth was significantly decreased among IUGR infants. Hospital stay was significantly longer for IUGR infants. Motor (IUGR: 89.98 ± 18.77; AGA: 101.75 ± 9.62; p < 0.001), and mental (IUGR: 90.81 ± 11.13; AGA: 105.71 ± 7.20; p < 0.001) scores were significantly decreased among IUGR compared with AGA neonates at 18 months of follow-up. Global DNA methylation had a significant positive correlation with mental score but not with motor developmental score. CONCLUSION IUGR babies had lower motor and mental score compared with AGA babies. Cord blood global DNA methylation significantly correlated with mental development score but not with motor development at 18 months of age.
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Affiliation(s)
- Krishna Rao Gurugubelli
- Department of Biochemistry, AIIMS, Mangalagiri, Andhra Pradesh 522503, India.,Neonatology, JIPMER, Puducherry 605006, India
| | - Vishnu Bhat Ballambattu
- Neonatology, JIPMER, Puducherry 605006, India.,Pediatrics and Neonatology, AVMC & H, Puducherry 607403, India
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Chang S, Wang Y, Xin Y, Wang S, Luo Y, Wang L, Zhang H, Li J. DNA methylation abnormalities of imprinted genes in congenital heart disease: a pilot study. BMC Med Genomics 2021; 14:4. [PMID: 33407475 PMCID: PMC7789576 DOI: 10.1186/s12920-020-00848-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
Background Congenital heart disease (CHD) is resulted from the interaction of genetic aberration and environmental factors. Imprinted genes, which are regulated by epigenetic modifications, are essential for the normal embryonic development. However, the role of imprinted genes in the etiology of CHD remains unclear. Methods After the samples were treated with bisulfate salt, imprinted genes methylation were measured by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. T test and One-way ANOVA were performed to evaluate the differences among groups. Odds ratios (ORs) were performed to evaluate the incidence risk of CHD in relation to methylation levels. Results We investigated the alterations of imprinted gene germline differential methylation regions (gDMRs) methylation in patients with CHD. Eighteen imprinted genes that are known to affect early embryonic development were selected and the methylation modification genes were detected by massarray in 27 CHD children and 28 healthy children. Altered gDMR methylation level of 8 imprinted genes was found, including 2 imprinted genes with hypermethylation of GRB10 and MEST and 6 genes with hypomethylation of PEG10, NAP1L5, INPP5F, PLAGL1, NESP and MEG3. Stratified analysis showed that the methylation degree of imprinted genes was different in different types of CHD. Risk analysis showed that 6 imprinted genes, except MEST and NAP1L5, within a specific methylation level range were the risk factors for CHD Conclusion Altered methylation of imprinted genes is associated with CHD and varies in different types of CHD. Further experiments are warranted to identify the methylation characteristics of imprinted genes in different types of CHD and clarify the etiologies of imprinted genes in CHD.
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Affiliation(s)
- Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yubo Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yu Xin
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shuangxing Wang
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China
| | - Yi Luo
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Hui Zhang
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China.
| | - Jia Li
- Clinical Physiology Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Tianhe District, Guangzhou City, 510000, Guangdong Province, China. .,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, Guangdong Province, China.
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Gross N, Taylor T, Crenshaw T, Khatib H. The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep. Front Genet 2020; 11:597943. [PMID: 33250925 PMCID: PMC7674940 DOI: 10.3389/fgene.2020.597943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022] Open
Abstract
Knowledge of non-genomic inheritance of traits is currently limited. Although it is well established that maternal diet influences offspring inheritance of traits through DNA methylation, studies on the impact of prepubertal paternal diet on DNA methylation are rare. This study aimed to evaluate the impact of prepubertal diet in Polypay rams on complex traits, DNA methylation, and transmission of traits to offspring. A total of 10 littermate pairs of F0 rams were divided so that one ram was fed a control diet, and the other was fed the control diet with supplemental methionine. Diet was associated with earlier age at puberty in treatment vs. control F0 rams. F0 treatment rams tended to show decreased pubertal weight compared to control rams; however, no differences were detected in overall growth. A total of ten F0 rams were bred, and the entire F1 generation was fed a control diet. Diet of F0 rams had a significant association with scrotal circumference (SC) and weight at puberty of F1 offspring. The paternal diet was not significantly associated with F1 ram growth or age at puberty. The DNA methylation of F0 ram sperm was assessed, and genes related to both sexual development (e.g., DAZAP1, CHD7, TAB1, MTMR2, CELSR1, MGAT1) and body weight (e.g., DUOX2, DUOXA2) were prevalent in the data. These results provide novel information about the mechanisms through which the prepubertal paternal diet may alter body weight at puberty and sexual development.
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Affiliation(s)
- Nicole Gross
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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Kubiura-Ichimaru M, Ito T, Lefebvre L, Tada M. Cyclic DNA remethylation following active demethylation at euchromatic regions in mouse embryonic stem cells. Chromosome Res 2020; 29:145-157. [PMID: 33205231 DOI: 10.1007/s10577-020-09645-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 11/27/2022]
Abstract
DNA methylation is an essential epigenetic mark that regulates normal mammalian embryonic development. DNA methylation profiles are not always static, especially during germline development. In zygotes, DNA is typically highly methylated but, during preimplantation, DNA methylation is erased globally. Then, at the start of post-implantation development in mouse embryos, DNA again becomes dramatically hypermethylated. Chromatin structure regulates the accessibility of DNA-modifying enzymes to target DNA. Beyond that, however, our understanding of the pathway by which chromatin regulation initiates changes in global DNA methylation during mouse embryonic development remains incomplete. To analyse the relationship between global regulation of DNA methylation and chromatin status, we examined 5-methylcytosine (5mC), modified by the DNA methyltransferase DNMT, and the oxidative derivative 5-hydroxymethylation (5hmC), converted from 5mC by TET-family enzymes, by means of immunofluorescence staining of mitotic chromosomes in mouse embryonic stem cells (ESCs). Our comparison of immunostaining patterns for those epigenetic modifications in wild-type, DNMT-deficient, and TET-deficient ESCs allowed us to visualise cell cycle-mediated DNA methylation changes, especially in euchromatic regions. Our findings suggest that DNA methylation patterns in undifferentiated mouse ESCs are stochastically balanced by the opposing effects of two activities: demethylation by TET and subsequent remethylation by DNMT.
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Affiliation(s)
- Musashi Kubiura-Ichimaru
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba, 274-8510, Japan
| | - Takamasa Ito
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba, 274-8510, Japan
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Masako Tada
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba, 274-8510, Japan.
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Huo P, Deng K, Wang L, Li M, Yao J, Le J, Lei X, Zhang S. The effect of laser-assisted hatching on the methylation and expression pattern of imprinted gene IGF2/H19 in mouse blastocysts and offspring. J Assist Reprod Genet 2020; 37:3057-3067. [PMID: 33089439 DOI: 10.1007/s10815-020-01975-4] [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: 06/19/2020] [Accepted: 10/07/2020] [Indexed: 11/28/2022] Open
Abstract
PURPOSE This study aimed to determine the effects of drilling and thinning treatment of laser-assisted hatching on the expression and methylation of imprinted gene IGF2/H19 in embryos and offspring. METHODS The prehatching blastocysts with treatment of drilling or thinning, or control prehatching blastocysts, were transplanted in surrogate uteri. The DNA methylation of IGF2/H19 imprinting control region (ICR) and the expression of IGF2 and H19 were respectively evaluated using bisulfite conversion-mediated sequencing and real-time PCR. RESULTS The drilling group showed a significant increase in the development rate of hatched blastocysts in comparison with the control and thinning group. DNA methylation level of IGF2/H19 ICR of hatched blastocysts in the thinning group was 27.33% in comparison with the 38.67% and 36% observed in the control and drilling group. The thinning treatment increased the DNA methylation level of IGF2/H19 ICR in the placenta in comparison with the control and drilling group. The drilling and thinning treatment decreased the expression level of H19 mRNA in prehatching and hatched blastocysts as well as placenta, while a significant increase in the expression level of H19 mRNA of offspring was observed in the thinning group. The thinning treatment increased the expression level of IGF2 mRNA of prehatching blastocysts and offspring and a significant decrease in placenta, while the drilling treatment resulted in a significant increase in the expression level of IGF2 mRNA of hatched blastocysts and placenta. CONCLUSION These observations suggested that drilling used for hatching of in vitro cultured mouse blastocysts may improve the production of offspring.
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Affiliation(s)
- Peng Huo
- School of Public and Health, Guilin Medical University, Guilin, 541004, China
| | - Kai Deng
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Lulu Wang
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Man Li
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Jun Yao
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Jianghua Le
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Xiaocan Lei
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, University of South China, Hengyang, 421001, China.
| | - Shun Zhang
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, China.
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Roberts SA, Kaiser UB. GENETICS IN ENDOCRINOLOGY: Genetic etiologies of central precocious puberty and the role of imprinted genes. Eur J Endocrinol 2020; 183:R107-R117. [PMID: 32698138 PMCID: PMC7682746 DOI: 10.1530/eje-20-0103] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Pubertal timing is regulated by the complex interplay of genetic, environmental, nutritional and epigenetic factors. Criteria for determining normal pubertal timing, and thus the definition of precocious puberty, have evolved based on published population studies. The significance of the genetic influence on pubertal timing is supported by familial pubertal timing and twin studies. In contrast to the many monogenic causes associated with hypogonadotropic hypogonadism, only four monogenic causes of central precocious puberty (CPP) have been described. Loss-of-function mutations in Makorin Ring Finger Protein 3(MKRN3), a maternally imprinted gene on chromosome 15 within the Prader-Willi syndrome locus, are the most common identified genetic cause of CPP. More recently, several mutations in a second maternally imprinted gene, Delta-like noncanonical Notch ligand 1 (DLK1), have also been associated with CPP. Polymorphisms in both genes have also been associated with the age of menarche in genome-wide association studies. Mutations in the genes encoding kisspeptin (KISS1) and its receptor (KISS1R), potent activators of GnRH secretion, have also been described in association with CPP, but remain rare monogenic causes. CPP has both short- and long-term health implications for children, highlighting the importance of understanding the mechanisms contributing to early puberty. Additionally, given the role of mutations in the imprinted genes MKRN3 and DLK1 in pubertal timing, other imprinted candidate genes should be considered for a role in puberty initiation.
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Affiliation(s)
- Stephanie A. Roberts
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Ursula B. Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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Yin Q, Yang X, Li L, Xu T, Zhou W, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of S100P and HYAL2 in the Chinese Population. Front Genet 2020; 11:977. [PMID: 33005177 PMCID: PMC7485126 DOI: 10.3389/fgene.2020.00977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 02/05/2023] Open
Abstract
Previous work has shown that DNA methylation in peripheral blood may be associated with malignancy; however, these studies have mainly been conducted within Caucasian populations. Here, we investigated the association between blood-based methylation of S100 calcium-binding protein P gene (S100P) and hyaluronoglucosaminidase 2 gene (HYAL2) and breast cancer (BC) via mass spectrometry in two independent case-control studies of the Chinese population with a total of 351 BC cases and 427 cancer-free female controls. In Study I, in which subjects had an average of 45 years, hypomethylation of S100P showed a protective effect for women ≤45 years (six out of nine CpG sites, p < 0.05) but not for women >45 years. In contrast, hypomethylation of HAYL2 was not correlated with BC in women ≤45 years but was a risk factor for women >45 years (three out of four CpG sites, p < 0.05). We proposed an age-dependent correlation between BC and methylation of S100P and HYAL2 and performed further validation in Study II with older subjects (average age = 52.5 years), where hypomethylation of both S100P and HYAL2 was a risk factor for BC (p < 0.05 for 10 CpG sites) as reported in Caucasians who develop BC around 55 years old. Together with the observation that Chinese cancer-free females having variant basal methylation levels comparing to Caucasians, we assumed that blood-based methylation might be modified by ethnic background, hormone status, and lifestyle. Here, we highlighted that the epigenetic biomarkers warrant validations when its application in variant ethnic groups is considered.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wenjie Zhou
- Chengdu Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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Chi F, Zhao M, Li K, Lin AQ, Li Y, Teng X. DNA methylation status of imprinted H19 and KvDMR1 genes in human placentas after conception using assisted reproductive technology. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:854. [PMID: 32793698 PMCID: PMC7396748 DOI: 10.21037/atm-20-3364] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/28/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Assisted reproductive technologies (ARTs), such as in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI), are thought to destabilize genomic imprints. Previous studies examining the association between ART and aberrant DNA methylation have been inconclusive. METHOD The DNA methylation status of H19 and KvDMR1was compared between newborns conceived through ART and those conceived naturally to evaluate the safety of ART. Placental tissues from 6 full-term, naturally conceived pregnancies (no gestational comorbidities) and six full-term ART pregnancies (no gestational complication) were collected. Genomic DNA (gDNA) and RNA were extracted from both groups. Real-time PCR was used to analyze the mRNA expression levels of H19 and KvDMR1 in the placenta for both groups. A whole-genome DNA methylation microarray was used to examine three placentas from full-term, naturally conceived pregnancies and three placentas from full-term IVF pregnancies. RESULT The expression level of H19 in the IVF group was significantly higher than that in the natural pregnancy group, whereas the expression level of KvDMR1 was significantly lower in the ART group than in the natural pregnancy group. Also, human ART manipulation resulted in placental gDNA methylation modifications. Conclusion: Abnormal methylation patterns were detected in phenotypically normal phenotype conceived by ART, which may occur due to imprinting errors in sperm/oocyte cells or side effects of in vitro embryo culture procedures. Further investigation is necessary to determine whether imprinted gene expression and DNA methylation can be regulated through other mechanisms. KEYWORDS Assisted reproductive technology (ART); placenta; methylation; H19; KvDMR1.
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Affiliation(s)
- Fengli Chi
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Mei Zhao
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kunming Li
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - An-Qi Lin
- Geno Biotech Co. Ltd., Shanghai, China
| | - Yingya Li
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Teng
- Department of Assisted Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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