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Naderi S, Maali-Amiri R, Sadeghi L, Hamidi A. Physio-biochemical and DNA methylation analysis of the defense response network of wheat to drought stress. Plant Physiol Biochem 2024; 209:108516. [PMID: 38537384 DOI: 10.1016/j.plaphy.2024.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
In the present work, physio-biochemical and DNA methylation analysis were conducted in wheat (Triticum aestivum L.) cultivars "Bolani" (drought-tolerant) and "Sistan" (drought-sensitive) during drought treatments: well-watered (at 90% field capacity (FC)), mild stress (at 50% FC, and severe stress (at 25% FC). During severe stress, O2•- and H2O2 content in cultivar Sistan showed significant increase (by 1.3 and 2.5-fold, respectively) relative to cultivar Bolani. In Bolani, the increased levels of radical scavenging activity (by 32%), glycine betaine (GB) (by 11.44%), proline (4-fold), abscisic acid (by 63.76%), and more stability of relative water content (RWC) (2-fold) were observed against drought-induced oxidative stress. Methylation level significantly decreased from 70.26% to 60.64% in Bolani and from 69.06% to 59.85% in Sistan during stress, and higher decreased tendency was related to CG and CHG in Bolani but CG in Sistan under severe stress. Methylation patterns showed that the highest polymorphism in Bolani was mainly as CG. As the intensity of stress increased, the enhanced physio-biochemical responses of Bolani cultivar were accompanied by a more decrease in the number of unchanged bands. According to heat map analysis, the highest difference (84.38%) in methylation patterns was observed between control and severe stress. Multivariate analysis using principal component analysis (PCA) showed a cultivar-specific methylation during stress and that methylation changes between cultivars are much higher than that of within a cultivar. Higher methylation to demethylation in Bolani (30.06 vs. 22.12%) compared to that of cultivar Sistan (23.21 vs. 30.15%) indicated more demethylation did not induce tolerance responses in Sistan. Sequencing differentially methylated fragments along with qRT-PCR analysis showed the efficient role of various DNA fragments, including demethylated fragments such as phosphoenol pyruvate carboxylase (PEPC), beta-glucosidase (BGlu), glycosyltransferase (GT), glutathione S-transferase (GST) and lysine demethylase (LSD) genes and methylated fragments like ubiquitin E2 enzyme genes in the development of drought tolerance. These results suggested the specific roles of DNA methylation in development of drought tolerance in wheat landrace.
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Affiliation(s)
- Salehe Naderi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran.
| | - Leila Sadeghi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
| | - Aidin Hamidi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
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Opsahl JO, Fragoso-Bargas N, Lee Y, Carlsen EØ, Lekanova N, Qvigstad E, Sletner L, Jenum AK, Lee-Ødegård S, Prasad RB, Birkeland KI, Moen GH, Sommer C. Epigenome-wide association study of DNA methylation in maternal blood leukocytes with BMI in pregnancy and gestational weight gain. Int J Obes (Lond) 2024; 48:584-593. [PMID: 38219005 PMCID: PMC10978488 DOI: 10.1038/s41366-024-01458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/17/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
OBJECTIVES We aimed to discover CpG sites with differential DNA methylation in peripheral blood leukocytes associated with body mass index (BMI) in pregnancy and gestational weight gain (GWG) in women of European and South Asian ancestry. Furthermore, we aimed to investigate how the identified sites were associated with methylation quantitative trait loci, gene ontology, and cardiometabolic parameters. METHODS In the Epigenetics in pregnancy (EPIPREG) sample we quantified maternal DNA methylation in peripheral blood leukocytes in gestational week 28 with Illumina's MethylationEPIC BeadChip. In women with European (n = 303) and South Asian (n = 164) ancestry, we performed an epigenome-wide association study of BMI in gestational week 28 and GWG between gestational weeks 15 and 28 using a meta-analysis approach. Replication was performed in the Norwegian Mother, Father, and Child Cohort Study, the Study of Assisted Reproductive Technologies (MoBa-START) (n = 877, mainly European/Norwegian). RESULTS We identified one CpG site significantly associated with GWG (p 5.8 × 10-8) and five CpG sites associated with BMI at gestational week 28 (p from 4.0 × 10-8 to 2.1 × 10-10). Of these, we were able to replicate three in MoBa-START; cg02786370, cg19758958 and cg10472537. Two sites are located in genes previously associated with blood pressure and BMI. DNA methylation at the three replicated CpG sites were associated with levels of blood pressure, lipids and glucose in EPIPREG (p from 1.2 × 10-8 to 0.04). CONCLUSIONS We identified five CpG sites associated with BMI at gestational week 28, and one with GWG. Three of the sites were replicated in an independent cohort. Several genetic variants were associated with DNA methylation at cg02786379 and cg16733643 suggesting a genetic component influencing differential methylation. The identified CpG sites were associated with cardiometabolic traits. CLINICALTRIALS GOV REGISTRATION NO Not applicable.
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Affiliation(s)
- J O Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - N Fragoso-Bargas
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Y Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - E Ø Carlsen
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - N Lekanova
- Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - E Qvigstad
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - L Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - A K Jenum
- General Practice Research Unit, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - S Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - R B Prasad
- Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - K I Birkeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - G-H Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - C Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway.
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53
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Leri J, Liu J, Kelly M, Kertes DA. A preliminary investigation of epigenome-wide DNA methylation and temperament during infancy. Dev Psychobiol 2024; 66:e22475. [PMID: 38470455 DOI: 10.1002/dev.22475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
This study provides preliminary evidence for an epigenetic architecture of infant temperament. At 12 months of age, blood was collected and assayed for DNA methylation and maternally reported infant temperament was assessed using the Infant Behavior Questionnaire in 67 mother-infant dyads. Epigenome-wide analyses showed that the higher order temperament dimensions Surgency and Negative Affect were associated with DNA methylation. The epigenetic signatures of Surgency and Negative Affect were situated at genes involved in synaptic signaling and plasticity. Although replication is required, these results are consistent with a biologically based model of temperament, create new avenues for hypothesis-driven research into epigenetic pathways that underlie individual differences in temperament, and demonstrate that infant temperament has a widespread epigenetic signature in the methylome.
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Affiliation(s)
- John Leri
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Jingwen Liu
- Department of Psychology, University of Florida, Gainesville, Florida, USA
| | - Maria Kelly
- Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Darlene A Kertes
- Department of Psychology, University of Florida, Gainesville, Florida, USA
- UF Genetics Institute, University of Florida, Gainesville, USA
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Miao L, Xu W, Liu Y, Huang X, Chen Z, Wang H, Wang Z, Chen Y, Song Q, Zhang J, Han F, Peng H, Yao Y, Xin M, Hu Z, Ni Z, Sun Q, Xing J, Guo W. Reshaped DNA methylation cooperating with homoeolog-divergent expression promotes improved root traits in synthesized tetraploid wheat. New Phytol 2024; 242:507-523. [PMID: 38362849 DOI: 10.1111/nph.19593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive. Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (SlSl and AA) and their synthetic allotetraploid wheat line (SlSlAA), which displayed elongated root hair and improved root capability for nitrate uptake and assimilation after tetraploidization. Globally decreased DNA methylation levels with a reduced difference between subgenomes were observed in the roots of SlSlAA. DNA methylation changes in first exon showed strong connections with altered transcription during tetraploidization. Homoeolog-specific transcription was associated with biased DNA methylation as shaped by homoeologous sequence variation. The hypomethylated promoters showed significantly enriched binding sites for MYB, which may affect gene transcription in response to root hair growth. Two master regulators in root hair elongation pathway, AlCPC and TuRSL4, exhibited upregulated transcription levels accompanied by hypomethylation in promoter, which may contribute to the elongated root hair. The upregulated nitrate transporter genes, including NPFs and NRTs, also are significantly associated with hypomethylation, indicating an epigenetic-incorporated regulation manner in improving nitrogen use efficiency. Collectively, these results provided new insights into epigenetic changes in response to crop polyploidization and underscored the importance of epigenetic regulation in improving crop traits.
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Affiliation(s)
- Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weiya Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiangyi Huang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhe Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huifang Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, 266000, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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Yang Q, Cao Q, Yu Y, Lai X, Feng J, Li X, Jiang Y, Sun Y, Zhou ZW, Li X. Epigenetic and transcriptional landscapes during cerebral cortex development in a microcephaly mouse model. J Genet Genomics 2024; 51:419-432. [PMID: 37923173 DOI: 10.1016/j.jgg.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
The cerebral cortex is a pivotal structure integral to advanced brain functions within the mammalian central nervous system. DNA methylation and hydroxymethylation play important roles in regulating cerebral cortex development. However, it remains unclear whether abnormal cerebral cortex development, such as microcephaly, could rescale the epigenetic landscape, potentially contributing to dysregulated gene expression during brain development. In this study, we characterize and compare the DNA methylome/hydroxymethylome and transcriptome profiles of the cerebral cortex across several developmental stages in wild-type (WT) mice and Mcph1 knockout (Mcph1-del) mice with severe microcephaly. Intriguingly, we discover a global reduction of 5'-hydroxymethylcytosine (5hmC) level, primarily in TET1-binding regions, in Mcph1-del mice compared to WT mice during juvenile and adult stages. Notably, genes exhibiting diminished 5hmC levels and concurrently decreased expression are essential for neurodevelopment and brain functions. Additionally, genes displaying a delayed accumulation of 5hmC in Mcph1-del mice are significantly associated with the establishment and maintenance of the nervous system during the adult stage. These findings reveal that aberrant cerebral cortex development in the early stages profoundly alters the epigenetic regulation program, which provides unique insights into the molecular mechanisms underpinning diseases related to cerebral cortex development.
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Affiliation(s)
- Qing Yang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qiang Cao
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yue Yu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianxin Lai
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiahao Feng
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xinjie Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yinan Jiang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yazhou Sun
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhong-Wei Zhou
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Xin Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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56
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Kakoulidou I, Piecyk RS, Meyer RC, Kuhlmann M, Gutjahr C, Altmann T, Johannes F. Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids. Life Sci Alliance 2024; 7:e202402599. [PMID: 38290756 PMCID: PMC10828516 DOI: 10.26508/lsa.202402599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns. Using a combination of multi-omic profiling and epigenetic mapping strategies we show that differentially methylated regions in parental pericentromeres act as major reorganizers of hybrid methylomes and transcriptomes, even in the absence of genetic variation. These parental differentially methylated regions are associated with hybrid methylation remodeling events at thousands of target regions throughout the genome, both locally (in cis) and distally (in trans). Many of these distally-induced methylation changes lead to nonadditive expression of nearby genes and associate with phenotypic heterosis. Our study highlights the pleiotropic potential of parental pericentromeres in the functional remodeling of hybrid genomes and phenotypes.
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Affiliation(s)
- Ioanna Kakoulidou
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Robert S Piecyk
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Rhonda C Meyer
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Kuhlmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Thomas Altmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Johannes
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- https://ror.org/02kkvpp62 Institute of Advanced Studies, Technical University of Munich, Munich, Germany
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Zhang Y, Chen J, Zheng B, Teng J, Lou Z, Feng H, Zhao S, Xue L. Genome-wide identification, evolution of DNA methyltransferases and their expression under salinity stress in Larimichthys crocea. Int J Biol Macromol 2024; 264:130603. [PMID: 38447841 DOI: 10.1016/j.ijbiomac.2024.130603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
DNA methyltransferases (Dnmts) are responsible for DNA methylation which influences patterns of gene expression and plays a crucial role in response to environmental changes. In this study, 7 LcDnmt genes were identified in the genome of large yellow croaker (Larimichthys crocea). The comprehensive analysis was conducted on gene structure, protein and location site of LcDnmts. LcDnmt proteins belonged to three groups (Dnmt1, Dnmt2, and Dnmt3) according to their conserved domains and phylogenetic analysis. Although Dnmt3 can be further divided into three sub groups (Dnmt3a, Dnmt3b, and Dnmt3l), there is no Dnmnt3l member in the large yellow croaker. Phylogenetic analysis revealed that the Dnmt family was highly conserved in teleosts. Expression patterns derived from the RNA-seq, qRT-PCR and Western blot analysis revealed that 2 LcDnmt genes (LcDnmt1 and LcDnmt3a2) significantly regulated under salinity stress in the liver, which was found to be dominantly expressed in the intestine and brain, respectively. These two genes may play an important role in the salinity stress of large yellow croaker and represent candidates for future functional analysis. Our results revealed the conservation of Dnmts during evolution and indicated a potential role of Dnmts in epigenetic regulation of response to salinity stress.
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Affiliation(s)
- Yu Zhang
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Jiaqian Chen
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Baoxiao Zheng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Jian Teng
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Zhengjia Lou
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Huijie Feng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Shiqi Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Liangyi Xue
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.
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58
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Liu Z, Gao L, Kan C, Chen X, Shi K, Wang W. DNMT1 methylation of LncRNA-ANRIL causes myocardial fibrosis pyroptosis by interfering with the NLRP3/Caspase-1 pathway. Cell Mol Biol (Noisy-le-grand) 2024; 70:197-203. [PMID: 38650132 DOI: 10.14715/cmb/2024.70.3.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Indexed: 04/25/2024]
Abstract
Myocardial fibrosis is a common pathological manifestation that occurs in various cardiac diseases. The present investigation aims to reveal how DNMT1/lncRNA-ANRIL/NLRP3 influences fibrosis and cardiac fibroblast pyroptosis. Here, we used ISO to induce myocardial fibrosis in mice, and LPS and ATP to induce myocardial fibroblast pyroptosis. The results showed that DNMT1, Caspase-1, and NLRP3 expression were significantly increased in fibrotic murine myocardium and pyroptotic cardiac fibroblasts, whereas LncRNA-ANRIL expression was decreased. DNMT1 overexpression decreased the level of LncRNA-ANRIL while increasing the levels of NLRP3 and Caspase-1. Contrarily, silencing DNMT1 increased the LncRNA-ANRIL and decreased the levels of NLRP3 and Caspase-1. Silencing LncRNA-ANRIL increased the levels of NLRP3 and Caspase-1. The present findings suggest that DNMT1 can methylate LncRNA-ANRIL during the development of myocardial fibrosis and CFs cell scorching, resulting in low LncRNA-ANRIL expression, thereby influencing myocardial fibrosis and cardiac fibroblast pyroptosis.
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Affiliation(s)
- Zuntao Liu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China.
| | - Lei Gao
- Department of Integrated Chinese and Western Medicine, School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Chenjing Kan
- Wang Jing Hospital of CACMS, Beijing 100102, China.
| | - Xin Chen
- Department of Interventional Radiology, Liyang Hospital of Traditional Chinese Medicine, Liyang, Jiangsu 213399, China.
| | - Kaihu Shi
- Department of Cardiothoracic Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China.
| | - Wei Wang
- Department of Cardiothoracic Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China.
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nat Commun 2024; 15:2790. [PMID: 38555308 PMCID: PMC10981715 DOI: 10.1038/s41467-024-47196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45229, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christopher Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Samuel Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David W Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. Plant Physiol 2024; 194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in 3 additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these 3 species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
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Affiliation(s)
- Kelly J Dew-Budd
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Hiu Tung Chow
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brandon C David
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - James A Rozelle
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Li D, Yang W, Pang J, Yu G. Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis. Mol Biol Rep 2024; 51:475. [PMID: 38553662 DOI: 10.1007/s11033-024-09416-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/05/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Patients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of extracellular matrix (ECM) proteins. While ECM accumulation can prevent liver infection and injury, it can destroy normal liver function and architecture. miRNA's own regulation was involved in DNA methylation change. The purpose of this study is to detect DNA methylation landscape of miRNAs genes in mice liver fibrosis tissues. METHODS Male mice (10-12 weeks) were injected CCl4 from abdominal cavity to induced liver fibrosis. 850 K BeadChips were used to examine DNA methylation change in whole genome. The methylation change of 16 CpG dinucleotides located in promoter regions of 4 miRNA genes were detected by bisulfite sequencing polymerase chain reaction (BSP) to verify chip data accuracy, and these 4 miRNA genes' expressions were detected by RT-qPCR methods. RESULTS There are 769 differential methylation sites (DMS) in total between fibrotic liver tissue and normal mice liver tissue, which were related with 148 different miRNA genes. Chips array data were confirmed by bisulfite sequencing polymerase chain reaction (R = 0.953; P < 0.01). GO analysis of the target genes of 2 miRNA revealed that protein binding, cytoplasm and chromatin binding activity were commonly enriched; KEGG pathway enrichment analysis displayed that TGF-beta signaling pathway was commonly enriched. CONCLUSION The DNA of 148 miRNA genes was found to have methylation change in liver fibrosis tissue. These discoveries in miRNA genes are beneficial to future miRNA function research in liver fibrosis.
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Affiliation(s)
- Deming Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Wentong Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jiaojiao Pang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China.
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Liu J, Zhong X. Population epigenetics: DNA methylation in the plant omics era. Plant Physiol 2024; 194:2039-2048. [PMID: 38366882 PMCID: PMC10980424 DOI: 10.1093/plphys/kiae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
DNA methylation plays an important role in many biological processes. The mechanisms underlying the establishment and maintenance of DNA methylation are well understood thanks to decades of research using DNA methylation mutants, primarily in Arabidopsis (Arabidopsis thaliana) accession Col-0. Recent genome-wide association studies (GWASs) using the methylomes of natural accessions have uncovered a complex and distinct genetic basis of variation in DNA methylation at the population level. Sequencing following bisulfite treatment has served as an excellent method for quantifying DNA methylation. Unlike studies focusing on specific accessions with reference genomes, population-scale methylome research often requires an additional round of sequencing beyond obtaining genome assemblies or genetic variations from whole-genome sequencing data, which can be cost prohibitive. Here, we provide an overview of recently developed bisulfite-free methods for quantifying methylation and cost-effective approaches for the simultaneous detection of genetic and epigenetic information. We also discuss the plasticity of DNA methylation in a specific Arabidopsis accession, the contribution of DNA methylation to plant adaptation, and the genetic determinants of variation in DNA methylation in natural populations. The recently developed technology and knowledge will greatly benefit future studies in population epigenomes.
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Affiliation(s)
- Jie Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xuehua Zhong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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63
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Cao X, Li X, Su Y, Zhang C, Wei C, Chen K, Grierson D, Zhang B. Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening. Plant Physiol 2024; 194:2049-2068. [PMID: 37992120 DOI: 10.1093/plphys/kiad627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.
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Affiliation(s)
- Xiangmei Cao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xinzhao Li
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yike Su
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chunyan Wei
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Desheng Middle Road No. 298, Hangzhou, Zhejiang Province 310021, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. Plant Physiol 2024; 194:2511-2532. [PMID: 38109503 PMCID: PMC10980416 DOI: 10.1093/plphys/kiad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (Mediator of paramutation1), with that of their parents, wild-type siblings, and backcrossed progeny in maize (Zea mays). Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of these DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that both TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in most TCM DMRs in F1 plants required Mop1, initiation of a new epigenetic state of these DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is independent of RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Xu D, Zeng L, Wang L, Yang DL. Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity. Plant Physiol 2024; 194:2149-2164. [PMID: 37992039 DOI: 10.1093/plphys/kiad624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.
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Affiliation(s)
- Dachao Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjun Zeng
- Institute of Crop Sciences, Yichun Academy of Sciences, Yichun, 336000 Jiangxi, China
| | - Lili Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Ren Z, Gou R, Zhuo W, Chen Z, Yin X, Cao Y, Wang Y, Mi Y, Liu Y, Wang Y, Fan LM, Deng XW, Qian W. The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis. Plant Cell 2024; 36:1098-1118. [PMID: 38092516 PMCID: PMC10980342 DOI: 10.1093/plcell/koad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/11/2023] [Indexed: 04/01/2024]
Abstract
DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.
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Affiliation(s)
- Zhitong Ren
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Runyu Gou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wanqing Zhuo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaochang Yin
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yuxin Cao
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingjie Mi
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yannan Liu
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- College of Life Sciences, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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Mezzacappa C, Wang Z, Lu L, Risch H, Taddei T, Yu H. Detection of hepatocellular carcinoma methylation markers in salivary DNA. Biosci Rep 2024; 44:BSR20232063. [PMID: 38457142 PMCID: PMC10958141 DOI: 10.1042/bsr20232063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/21/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Alterations to DNA methylation have been identified in both hepatocellular carcinoma (HCC) tumor and circulating DNA from affected individuals. These markers have potential utility in HCC screening. Adherence to HCC screening is poor and acceptable HCC screening tests are needed. METHODS A feasibility study was performed on a subset of case patients and control subjects from a prior study of risk factors for HCC. Case patients (n=12) included adults aged 47-85 years with a first diagnosis of HCC between 2011 and 2016 and without viral hepatitis. Control subjects (n=12) were matched on age, sex, and state of residence. Participants provided saliva samples for DNA genotyping. Log fold change in salivary DNA methylation at 1359 CpG sites representing 25 candidate genes previously associated with HCC was compared across case patients and control subjects. RESULTS The quantity of DNA ranged from 9.65 to 257.79 μg. The purity of DNA isolates was good, with mean OD260/280 ratio of 1.78 (SD: 0.14). Of 25 candidate genes, 16 had at ≥1 CpG site with detectable differences in methylation across HCC case patients and control subjects. Sites differentially methylated in HCC case patients included genes encoding tumor suppressors (PRDM2, RUNX3, p15/16, and RASSF1/5), regulators of cell cycle progression (DAPK1 and TP73), and DNA repair (MGMT and GSTP1). No associations met the significance threshold 3.7 × 10-5 required for multiple comparisons. CONCLUSIONS Salivary DNA may be a feasible alternative to blood samples in the era of novel DNA-based screening tests for HCC. The ease of saliva-based testing supports further investigation of its potential.
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Affiliation(s)
- Catherine Mezzacappa
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Zhanwei Wang
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Harvey Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Tamar Taddei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Herbert Yu
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
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68
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Luo JH, Guo T, Wang M, Liu JH, Zheng LM, He Y. RNA m6A modification facilitates DNA methylation during maize kernel development. Plant Physiol 2024; 194:2165-2182. [PMID: 37995374 DOI: 10.1093/plphys/kiad625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.
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Affiliation(s)
- Jin-Hong Luo
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Guo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Min Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jing-Han Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lei-Ming Zheng
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Cao D. RNA-directed DNA methylation as a weapon in parental conflict. Plant Physiol 2024; 194:1931-1933. [PMID: 38095352 PMCID: PMC10980382 DOI: 10.1093/plphys/kiad664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 04/01/2024]
Affiliation(s)
- Dechang Cao
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Huo H, Zhang C, Wang K, Wang S, Chen W, Zhang Y, Yu W, Li S, Li S. A novel imprinted locus on bovine chromosome 18 homologous with human chromosome 16q24.1. Mol Genet Genomics 2024; 299:40. [PMID: 38546894 DOI: 10.1007/s00438-024-02123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/02/2024] [Indexed: 04/02/2024]
Abstract
Genomic imprinting is an epigenetic regulation mechanism in mammals resulting in the parentally dependent monoallelic expression of genes. Imprinting disorders in humans are associated with several congenital syndromes and cancers and remain the focus of many medical studies. Cattle is a better model organism for investigating human embryo development than mice. Imprinted genes usually cluster on chromosomes and are regulated by different methylation regions (DMRs) located in imprinting control regions that control gene expression in cis. There is an imprinted locus on human chromosome 16q24.1 associated with congenital lethal developmental lung disease in newborns. However, genomic imprinting on bovine chromosome 18, which is homologous with human chromosome 16 has not been systematically studied. The aim of this study was to analyze the allelic expressions of eight genes (CDH13, ATP2C2, TLDC1, COTL1, CRISPLD2, ZDHHC7, KIAA0513, and GSE1) on bovine chromosome 18 and to search the DMRs associated gene allelic expression. Three transcript variants of the ZDHHC7 gene (X1, X2, and X5) showed maternal imprinting in bovine placentas. In addition, the monoallelic expression of X2 and X5 was tissue-specific. Five transcripts of the KIAA0513 gene showed tissue- and isoform-specific monoallelic expression. The CDH13, ATP2C2, and TLDC1 genes exhibited tissue-specific imprinting, however, COTL1, CRISLPLD2, and GSE1 escaped imprinting. Four DMRs, established after fertilization, were found in this region. Two DMRs were located between the ZDHHC7 and KIAA0513 genes, and two were in exon 1 of the CDH13 and ATP2C2 genes, respectively. The results from this study support future studies on the molecular mechanism to regulate the imprinting of candidate genes on bovine chromosome 18.
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Affiliation(s)
- Haonan Huo
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Cui Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Kun Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Crop Cultivation Physiology and Green Production in Hebei Province, Shijiazhuang, China
| | - Siwei Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Crop Cultivation Physiology and Green Production in Hebei Province, Shijiazhuang, China
| | - Weina Chen
- College of Medical Science, Hebei University, Baoding, Hebei, China
| | - Yinjiao Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Wenli Yu
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang, Hebei, China
| | - Shujing Li
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang, Hebei, China.
| | - Shijie Li
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China.
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Caldwell BA, Wu Y, Wang J, Li L. Altered DNA methylation underlies monocyte dysregulation and immune exhaustion memory in sepsis. Cell Rep 2024; 43:113894. [PMID: 38442017 DOI: 10.1016/j.celrep.2024.113894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Monocytes can develop an exhausted memory state characterized by reduced differentiation, pathogenic inflammation, and immune suppression that drives immune dysregulation during sepsis. Chromatin alterations, notably via histone modifications, underlie innate immune memory, but the contribution of DNA methylation remains poorly understood. Using an ex vivo sepsis model, we show altered DNA methylation throughout the genome of exhausted monocytes, including genes implicated in immune dysregulation during sepsis and COVID-19 infection (e.g., Plac8). These changes are recapitulated in septic mice induced by cecal slurry injection. Methylation profiles developed in septic mice are maintained during ex vivo culture, supporting the involvement of DNA methylation in stable monocyte exhaustion memory. Methylome reprogramming is driven in part by Wnt signaling inhibition in exhausted monocytes and can be reversed with DNA methyltransferase inhibitors, Wnt agonists, or immune training molecules. Our study demonstrates the significance of altered DNA methylation in the maintenance of stable monocyte exhaustion memory.
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Affiliation(s)
- Blake A Caldwell
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Yajun Wu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Jing Wang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA.
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Li D, Yuan Y, Meng C, Lin Z, Zhao M, Shi L, Li M, Ye D, Cai Y, He X, Ye H, Zhou S, Zhou H, Gao S. Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax. Clin Epigenetics 2024; 16:48. [PMID: 38528641 PMCID: PMC10964616 DOI: 10.1186/s13148-024-01658-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND miR-182 promoter hypermethylation frequently occurs in various tumors, including acute myeloid leukemia, and leads to low expression of miR-182. However, whether adult acute lymphocyte leukemia (ALL) cells have high miR-182 promoter methylation has not been determined. METHODS To assess the methylation status of the miR-182 promoter, methylation and unmethylation-specific PCR analysis, bisulfite-sequencing analysis, and MethylTarget™ assays were performed to measure the frequency of methylation at the miR-182 promoter. Bone marrow cells were isolated from miR-182 knockout (182KO) and 182 wild type (182WT) mice to construct BCR-ABL (P190) and Notch-induced murine B-ALL and T-ALL models, respectively. Primary ALL samples were performed to investigate synergistic effects of the hypomethylation agents (HMAs) and the BCL2 inhibitor venetoclax (Ven) in vitro. RESULTS miR-182 (miR-182-5P) expression was substantially lower in ALL blasts than in normal controls (NCs) because of DNA hypermethylation at the miR-182 promoter in ALL blasts but not in normal controls (NCs). Knockout of miR-182 (182KO) markedly accelerated ALL development, facilitated the infiltration, and shortened the OS in a BCR-ABL (P190)-induced murine B-ALL model. Furthermore, the 182KO ALL cell population was enriched with more leukemia-initiating cells (CD43+B220+ cells, LICs) and presented higher leukemogenic activity than the 182WT ALL population. Furthermore, depletion of miR-182 reduced the OS in a Notch-induced murine T-ALL model, suggesting that miR-182 knockout accelerates ALL development. Mechanistically, overexpression of miR-182 inhibited proliferation and induced apoptosis by directly targeting PBX3 and BCL2, two well-known oncogenes, that are key targets of miR-182. Most importantly, DAC in combination with Ven had synergistic effects on ALL cells with miR-182 promoter hypermethylation, but not on ALL cells with miR-182 promoter hypomethylation. CONCLUSIONS Collectively, we identified miR-182 as a tumor suppressor gene in ALL cells and low expression of miR-182 because of hypermethylation facilitates the malignant phenotype of ALL cells. DAC + Ven cotreatment might has been applied in the clinical try for ALL patients with miR-182 promoter hypermethylation. Furthermore, the methylation frequency at the miR-182 promoter should be a potential biomarker for DAC + Ven treatment in ALL patients.
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Affiliation(s)
- Danyang Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Yigang Yuan
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Chen Meng
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Zihan Lin
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Min Zhao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Liuzhi Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Min Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Daijiao Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Yue Cai
- Department of Clinical Medicine, Wenzhou Medical University, Chashan District, Wenzhou, Zhejiang Province, China
| | - Xiaofei He
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
- The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xuanyuanxi Road, Wenzhou, Zhejiang Province, China
| | - Haige Ye
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Shujuan Zhou
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Haixia Zhou
- The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xuanyuanxi Road, Wenzhou, Zhejiang Province, China.
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xuanyuanxi Road, Wenzhou, Zhejiang Province, China.
| | - Shenmeng Gao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China.
- The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xuanyuanxi Road, Wenzhou, Zhejiang Province, China.
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Wang L, Yang X, Zhao K, Huang S, Qin Y, Chen Z, Hu X, Jin G, Zhou Z. MOF-mediated acetylation of UHRF1 enhances UHRF1 E3 ligase activity to facilitate DNA methylation maintenance. Cell Rep 2024; 43:113908. [PMID: 38446667 DOI: 10.1016/j.celrep.2024.113908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 01/11/2024] [Accepted: 02/18/2024] [Indexed: 03/08/2024] Open
Abstract
The multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 for DNA methylation maintenance during DNA replication. Here, we show that MOF (males absent on the first) acetylates UHRF1 at K670 in the pre-RING linker region, whereas HDAC1 deacetylates UHRF1 at the same site. We also identify that K667 and K668 can also be acetylated by MOF when K670 is mutated. The MOF/HDAC1-mediated acetylation in UHRF1 is cell-cycle regulated and peaks at G1/S phase, in line with the function of UHRF1 in recruiting DNMT1 to maintain DNA methylation. In addition, UHRF1 acetylation significantly enhances its E3 ligase activity. Abolishing UHRF1 acetylation at these sites attenuates UHRF1-mediated H3 ubiquitination, which in turn impairs DNMT1 recruitment and DNA methylation. Taken together, these findings identify MOF as an acetyltransferase for UHRF1 and define a mechanism underlying the regulation of DNA methylation maintenance through MOF-mediated UHRF1 acetylation.
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Affiliation(s)
- Linsheng Wang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China; School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Xi Yang
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kaiqiang Zhao
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong; Dongguang Children's Hospital, Dongguan Pediatric Research Institute, Dongguan, P.R. China
| | - Shengshuo Huang
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yiming Qin
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China
| | - Zixin Chen
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China
| | - Xiaobin Hu
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Guoxiang Jin
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China.
| | - Zhongjun Zhou
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China; School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong; Orthopedic Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, P.R. China.
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Fitzgerald S, Bhat B, Print C, Jones GT. A validated restriction enzyme ddPCR cg05575921 (AHRR) assay to accurately assess smoking exposure. Clin Epigenetics 2024; 16:45. [PMID: 38528596 PMCID: PMC10962207 DOI: 10.1186/s13148-024-01659-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND & METHODS In this study, a novel restriction enzyme (RE) digestion-based droplet digital polymerase chain reaction (ddPCR) assay was designed for cg005575921 within the AHRR gene body and compared with matching results obtained by bisulfite conversion (BIS) ddPCR and Illumina DNA methylation array. RESULTS The RE ddPCR cg05575921 assay appeared concordant with BIS ddPCR (r2 = 0.94, P < 0.0001) and, when compared with the Illumina array, had significantly better smoking status classification performance for current versus never smoked (AUC 0.96 versus 0.93, P < 0.04) and current versus ex-smoker (AUC 0.88 versus 0.83, P < 0.04) comparisons. CONCLUSIONS The RE ddPCR cg05575921 assay accurately predicts smoking status and could be a useful component of 'precision-medicine' chronic disease risk screening tools.
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Affiliation(s)
- Sandra Fitzgerald
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | - Basharat Bhat
- Vascular Research Group, Department of Surgical Sciences, Dunedin Medical School, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Cristin Print
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | - Gregory T Jones
- Vascular Research Group, Department of Surgical Sciences, Dunedin Medical School, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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Gibson D, Vo AH, Lambing H, Bhattacharya P, Tahir P, Chehab FF, Butowski N. A systematic review of high impact CpG sites and regions for MGMT methylation in glioblastoma [A systematic review of MGMT methylation in GBM]. BMC Neurol 2024; 24:103. [PMID: 38521933 PMCID: PMC10960428 DOI: 10.1186/s12883-024-03605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/17/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND MGMT (O 6 -methylguanine-DNA methyltransferase) promoter methylation is a commonly assessed prognostic marker in glioblastoma (GBM). Epigenetic silencing of the MGMT gene by promoter methylation is associated with greater overall and progression free survival with alkylating agent regimens. To date, there is marked heterogeneity in how MGMT promoter methylation is tested and which CpG sites are interrogated. METHODS To further elucidate which MGMT promoter CpG sites are of greatest interest, we performed comprehensive searches in PubMed, Web of Science, and Embase and reviewed 2,925 article abstracts. We followed the GRADE scoring system to assess risk of bias and the quality of the studies we included. RESULTS We included articles on adult glioblastoma that examined significant sites or regions within MGMT promoter for the outcomes: overall survival, progression free survival, and/or MGMT expression. We excluded systemic reviews and articles on lower grade glioma. fifteen articles met inclusion criteria with variable overlap in laboratory and statistical methods employed, as well as CpG sites interrogated. Pyrosequencing or BeadChip arrays were the most popular methods utilized, and CpG sites between CpG's 70-90 were most frequently investigated. Overall, there was moderate concordance between the CpG sites that the studies reported to be highly predictive of prognosis. Combinations or means of sites between CpG's 73-89 were associated with improved OS and PFS. Six studies identified CpG sites associated with prognosis that were closer to the transcription start site: CpG's 8, 19, 22, 25, 27, 32,38, and CpG sites 21-37, as well as low methylation level of the enhancer regions. CONCLUSION The following systematic review details a comprehensive investigation of the current literature and highlights several potential key CpG sites that demonstrate significant association with OS, PFS, and MGMT expression. However, the relationship between extent of MGMT promoter methylation and survival may be non-linear and could be influenced by potential CpG hotspots, the extent of methylation at each CpG site, and MGMT enhancer methylation status. There were several limitations within the studies such as smaller sample sizes, variance between methylation testing methods, and differences in the various statistical methods to test for association to outcome. Further studies of high impact CpG sites in MGMT methylation is warranted.
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Affiliation(s)
- David Gibson
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
- Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anh Huan Vo
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA.
| | - Hannah Lambing
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prithanjan Bhattacharya
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
| | - Peggy Tahir
- University of California, San Francisco Library, San Francisco, CA, USA
| | - Farid F Chehab
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas Butowski
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
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Muhammad N, Fasih S, Malik B, Hameed S, Loya A, Rashid MU. Predominance of MGMT promoter methylation among Pakistani glioblastoma patients. Mol Biol Rep 2024; 51:433. [PMID: 38520591 DOI: 10.1007/s11033-024-09363-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Glioblastoma multiforme (GBM), the most prevalent subgroup of neuroepithelial tumors, is characterized by dismal overall survival (OS). Several studies have linked O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation to OS in GBM patients. However, MGMT methylation frequencies vary geographically and across ethnicities, with limited data for South Asian populations, including Pakistan. This study aimed to analyze MGMT promoter methylation in Pakistani GBM patients. METHODS Consecutive primary GBM patients diagnosed ≥ 18 years-of-age, with no prior chemotherapy or radiotherapy history, were retrospectively selected. DNA was isolated from formalin-fixed-paraffin-embedded tissues. MGMT promoter methylation was analyzed using methylation-specific PCR. Clinical, pathological, and treatment data were assessed using Fisher's exact/Chi-squared tests. OS was calculated using Kaplan-Meier analysis in SPSS 27.0.1. RESULTS The study included 48 GBM patients, comprising 38 (79.2%) males and 10 (20.8%) females. The median diagnosis age was 49.5 years (range 18-70). MGMT methylation was observed in 87.5% (42/48) of all cases. Patients with MGMT methylation undergoing radiotherapy or radiotherapy plus chemotherapy exhibited significantly improved median OS of 7.2 months (95% CI, 3.7-10.7; P < 0.001) and 16.9 months (95% CI, 15.9-17.9; P < 0.001), respectively, compared to those undergoing surgical resection only (OS: 2.2 months, 95% CI, 0.8-3.6). CONCLUSION This is the first comprehensive study highlighting a predominance of MGMT methylation in Pakistani GBM patients. Furthermore, our findings underscore the association of MGMT methylation with improved OS across diverse treatment modalities. Larger studies are imperative to validate our findings for better management of Pakistani GBM patients.
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Affiliation(s)
- Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Samir Fasih
- Department of Medical Oncology, SKMCH&RC, Lahore, Pakistan
| | - Bilal Malik
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Shahid Hameed
- Department of Radiation Oncology, SKMCH&RC, Lahore, Pakistan
| | - Asif Loya
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
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78
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Giaccari C, Cecere F, Argenziano L, Pagano A, Galvao A, Acampora D, Rossi G, Hay Mele B, Acurzio B, Coonrod S, Cubellis MV, Cerrato F, Andrews S, Cecconi S, Kelsey G, Riccio A. A maternal-effect Padi6 variant causes nuclear and cytoplasmic abnormalities in oocytes, as well as failure of epigenetic reprogramming and zygotic genome activation in embryos. Genes Dev 2024; 38:131-150. [PMID: 38453481 PMCID: PMC10982689 DOI: 10.1101/gad.351238.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Maternal inactivation of genes encoding components of the subcortical maternal complex (SCMC) and its associated member, PADI6, generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multilocus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. We generated a mouse line carrying a Padi6 missense variant that was identified in a family with Beckwith-Wiedemann syndrome and MLID. If homozygous in female mice, this variant resulted in interruption of embryo development at the two-cell stage. Single-cell multiomic analyses demonstrated defective maturation of Padi6 mutant oocytes and incomplete DNA demethylation, down-regulation of zygotic genome activation (ZGA) genes, up-regulation of maternal decay genes, and developmental delay in two-cell embryos developing from Padi6 mutant oocytes but little effect on genomic imprinting. Western blotting and immunofluorescence analyses showed reduced levels of UHRF1 in oocytes and abnormal localization of DNMT1 and UHRF1 in both oocytes and zygotes. Treatment with 5-azacytidine reverted DNA hypermethylation but did not rescue the developmental arrest of mutant embryos. Taken together, this study demonstrates that PADI6 controls both nuclear and cytoplasmic oocyte processes that are necessary for preimplantation epigenetic reprogramming and ZGA.
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Affiliation(s)
- Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Lucia Argenziano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Angela Pagano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Antonio Galvao
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn 10-748, Poland
| | - Dario Acampora
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
| | - Gianna Rossi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Naples "Federico II," Napoli 80126, Italy
| | - Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Scott Coonrod
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | | | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Simon Andrews
- Bioinformatics Unit, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sandra Cecconi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy;
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
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79
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Xiong X, Chen H, Zhang Q, Liu Y, Xu C. Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing. Nucleic Acids Res 2024; 52:e24. [PMID: 38261991 PMCID: PMC10954476 DOI: 10.1093/nar/gkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.
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Affiliation(s)
- Xiong Xiong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Hengye Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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80
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Zhou D, Guo S, Wang Y, Zhao J, Liu H, Zhou F, Huang Y, Gu Y, Jin G, Zhang Y. Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer. Brief Funct Genomics 2024; 23:150-162. [PMID: 37279592 DOI: 10.1093/bfgp/elad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/18/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
Abnormalities of DNA modifications are closely related to the pathogenesis and prognosis of pancreatic cancer. The development of third-generation sequencing technology has brought opportunities for the study of new epigenetic modification in cancer. Here, we screened the N6-methyladenine (6mA) and 5-methylcytosine (5mC) modification in pancreatic cancer based on Oxford Nanopore Technologies sequencing. The 6mA levels were lower compared with 5mC and upregulated in pancreatic cancer. We developed a novel method to define differentially methylated deficient region (DMDR), which overlapped 1319 protein-coding genes in pancreatic cancer. Genes screened by DMDRs were more significantly enriched in the cancer genes compared with the traditional differential methylation method (P < 0.001 versus P = 0.21, hypergeometric test). We then identified a survival-related signature based on DMDRs (DMDRSig) that stratified patients into high- and low-risk groups. Functional enrichment analysis indicated that 891 genes were closely related to alternative splicing. Multi-omics data from the cancer genome atlas showed that these genes were frequently altered in cancer samples. Survival analysis indicated that seven genes with high expression (ADAM9, ADAM10, EPS8, FAM83A, FAM111B, LAMA3 and TES) were significantly associated with poor prognosis. In addition, the distinction for pancreatic cancer subtypes was determined using 46 subtype-specific genes and unsupervised clustering. Overall, our study is the first to explore the molecular characteristics of 6mA modifications in pancreatic cancer, indicating that 6mA has the potential to be a target for future clinical treatment.
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Affiliation(s)
- Dianshuang Zhou
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Yangyang Wang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Jiyun Zhao
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Honghao Liu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Feiyang Zhou
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Yan Huang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Yue Gu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Yan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150006, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- College of Pathology, Qiqihar Medical University, Qiqihar 161042, China
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81
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Li Z, Wang W, Li W, Duan H, Xu C, Tian X, Ning F, Zhang D. Co-methylation analyses identify CpGs associated with lipid traits in Chinese discordant monozygotic twins. Hum Mol Genet 2024; 33:583-593. [PMID: 38142287 DOI: 10.1093/hmg/ddad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/25/2023] Open
Abstract
To control genetic background and early life milieu in genome-wide DNA methylation analysis for blood lipids, we recruited Chinese discordant monozygotic twins to explore the relationships between DNA methylations and total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). 132 monozygotic (MZ) twins were included with discordant lipid levels and completed data. A linear mixed model was conducted in Epigenome-wide association study (EWAS). Generalized estimating equation model was for gene expression analysis. We conducted Weighted correlation network analysis (WGCNA) to build co-methylated interconnected network. Additional Qingdao citizens were recruited for validation. Inference about Causation through Examination of Familial Confounding (ICE FALCON) was used to infer the possible direction of these relationships. A total of 476 top CpGs reached suggestively significant level (P < 10-4), of which, 192 CpGs were significantly associated with TG (FDR < 0.05). They were used to build interconnected network and highlight crucial genes from WGCNA. Finally, four CpGs in GATA4 were validated as risk factors for TC; six CpGs at ITFG2-AS1 were negatively associated with TG; two CpGs in PLXND1 played protective roles in HDL-C. ICE FALCON indicated abnormal TC was regarded as the consequence of DNA methylation in CpGs at GATA4, rather than vice versa. Four CpGs in ITFG2-AS1 were both causes and consequences of modified TG levels. Our results indicated that DNA methylation levels of 12 CpGs in GATA4, ITFG2-AS1, and PLXND1 were relevant to TC, TG, and HDL-C, respectively, which might provide new epigenetic insights into potential clinical treatment of dyslipidemia.
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Affiliation(s)
- Zhaoying Li
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9 B, st. tv. Odense C DK-5000, Denmark
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Feng Ning
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
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82
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Deycmar S, Johnson BJ, Ray K, Schaaf GW, Ryan DP, Cullin C, Dozier BL, Ferguson B, Bimber BN, Olson JD, Caudell DL, Whitlow CT, Solingapuram Sai KK, Romero EC, Villinger FJ, Burgos AG, Ainsworth HC, Miller LD, Hawkins GA, Chou JW, Gomes B, Hettich M, Ceppi M, Charo J, Cline JM. Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques. J Transl Med 2024; 22:292. [PMID: 38504345 PMCID: PMC10953092 DOI: 10.1186/s12967-024-04869-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. METHODS We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation. RESULTS Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs. CONCLUSIONS These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.
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Affiliation(s)
- Simon Deycmar
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Roche Postdoctoral Fellowship (RPF) Program, Basel, Switzerland
| | - Brendan J Johnson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Karina Ray
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - George W Schaaf
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Declan Patrick Ryan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cassandra Cullin
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Brandy L Dozier
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - John D Olson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - David L Caudell
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Christopher T Whitlow
- Department of Radiology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Emily C Romero
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Francois J Villinger
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Armando G Burgos
- Caribbean Primate Research Center, University of Puerto Rico, Toa Baja, PR, USA
| | - Hannah C Ainsworth
- Department of Biostatistics and Data Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeff W Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Bruno Gomes
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Hettich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Maurizio Ceppi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- iTeos Therapeutics, Translational Medicine, Gosselies, Belgium
| | - Jehad Charo
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Zurich, Switzerland
| | - J Mark Cline
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
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83
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Han F, Chen S, Zhang K, Zhang K, Wang M, Wang P. Single-cell transcriptomic sequencing data reveal aberrant DNA methylation in SMAD3 promoter region in tumor-associated fibroblasts affecting molecular mechanism of radiosensitivity in non-small cell lung cancer. J Transl Med 2024; 22:288. [PMID: 38493128 PMCID: PMC10944599 DOI: 10.1186/s12967-024-05057-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
OBJECTIVE Non-small cell lung cancer (NSCLC) often exhibits resistance to radiotherapy, posing significant treatment challenges. This study investigates the role of SMAD3 in NSCLC, focusing on its potential in influencing radiosensitivity via the ITGA6/PI3K/Akt pathway. METHODS The study utilized gene expression data from the GEO database to identify differentially expressed genes related to radiotherapy resistance in NSCLC. Using the GSE37745 dataset, prognostic genes were identified through Cox regression and survival analysis. Functional roles of target genes were explored using Gene Set Enrichment Analysis (GSEA) and co-expression analyses. Gene promoter methylation levels were assessed using databases like UALCAN, DNMIVD, and UCSC Xena, while the TISCH database provided insights into the correlation between target genes and CAFs. Experiments included RT-qPCR, Western blot, and immunohistochemistry on NSCLC patient samples, in vitro studies on isolated CAFs cells, and in vivo nude mouse tumor models. RESULTS Fifteen key genes associated with radiotherapy resistance in NSCLC cells were identified. SMAD3 was recognized as an independent prognostic factor for NSCLC, linked to poor patient outcomes. High expression of SMAD3 was correlated with low DNA methylation in its promoter region and was enriched in CAFs. In vitro and in vivo experiments confirmed that SMAD3 promotes radiotherapy resistance by activating the ITGA6/PI3K/Akt signaling pathway. CONCLUSION High expression of SMAD3 in NSCLC tissues, cells, and CAFs is closely associated with poor prognosis and increased radiotherapy resistance. SMAD3 is likely to enhance radiotherapy resistance in NSCLC cells by activating the ITGA6/PI3K/Akt signaling pathway.
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Affiliation(s)
- Fushi Han
- Department of Medical Imaging, Tongji Hospital, School of Medicine, Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
- Institute of Medical Imaging Artificial Intelligence, Tongji University School of Medicine, Shanghai, 200065, China
| | - Shuzhen Chen
- Department of Nuclear Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Kangwei Zhang
- Department of Medical Imaging, Tongji Hospital, School of Medicine, Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
- Institute of Medical Imaging Artificial Intelligence, Tongji University School of Medicine, Shanghai, 200065, China
| | - Kunming Zhang
- Department of Internal Medicine, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Meng Wang
- Department of Radiotherapy, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Peijun Wang
- Department of Medical Imaging, Tongji Hospital, School of Medicine, Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China.
- Institute of Medical Imaging Artificial Intelligence, Tongji University School of Medicine, Shanghai, 200065, China.
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84
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Cao Q, Wang X, Liu J, Dong Y, Wu X, Mi Y, Liu K, Zhang M, Shi Y, Fan R. ICBP90, an epigenetic regulator, induces DKK3 promoter methylation, promotes glioma progression, and reduces sensitivity to cis-platinum. Exp Cell Res 2024; 436:113976. [PMID: 38401687 DOI: 10.1016/j.yexcr.2024.113976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Glioma is the most common brain malignancy, characterized by high morbidity, high mortality, and treatment-resistance. Inverted CCAAT box Binding Protein of 90 kDa (ICBP90) has been reported to be involved in tumor progression and the maintenance of DNA methylation. Herein, we constructed ICBP90 over-expression and knockdown glioma cell lines, and found that ICBP90 knockdown inhibited glioma cell proliferation, migration, and invasion. ICBP90 silencing potentially enhanced cellular sensitivity to cis-platinum (DDP) and exacerbated DDP-induced pyroptosis, manifested by the elevated levels of gasdermin D-N-terminal and cleaved caspase 1; whereas, ICBP90 over-expression exhibited the opposite effects. Consistently, ICBP90 knockdown inhibited tumor growth in an in vivo mouse xenograft study using U251 cells stably expressing sh-ICBP90 and oe-ICBP90. Further experiments found that ICBP90 reduced the expression of Dickkopf 3 homolog (DKK3), a negative regulator of β-catenin, by binding its promoter and inducing DNA methylation. ICBP90 knockdown prevented the nuclear translocation of β-catenin and suppressed the expression of c-Myc and cyclin D1. Besides, DKK3 over-expression restored the effects of ICBP90 over-expression on cell proliferation, migration, invasion, and DDP sensitivity. Our findings suggest that ICBP90 inhibits the expression of DKK3 in glioma by maintaining DKK3 promoter methylation, thereby conducing to ICBP90-mediated carcinogenesis and drug insensitivity.
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Affiliation(s)
- Qinchen Cao
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinxin Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Liu
- Department of Magnetic Resonance Imaging, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Dong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaolong Wu
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yin Mi
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ke Liu
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhi Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yonggang Shi
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruitai Fan
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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85
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Miloro F, Kis A, Havelda Z, Dalmadi Á. Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation. Plant Cell Rep 2024; 43:96. [PMID: 38480545 PMCID: PMC10937801 DOI: 10.1007/s00299-024-03177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
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Affiliation(s)
- Fabio Miloro
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary.
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86
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Ekanayake Weeramange C, Tang KD, Irwin D, Hartel G, Langton-Lockton J, Ladwa R, Kenny L, Taheri T, Whitfield B, Vasani S, Punyadeera C. Human papillomavirus (HPV) DNA methylation changes in HPV-associated head and neck cancer. Carcinogenesis 2024; 45:140-148. [PMID: 38270218 PMCID: PMC10925951 DOI: 10.1093/carcin/bgae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/23/2023] [Accepted: 01/23/2024] [Indexed: 01/26/2024] Open
Abstract
Despite the rising incidence, currently, there are no early detection methods for HPV-driven HNC (HPV-HNC). Cervical cancer studies suggest that HPV DNA methylation changes can be used as a biomarker to discriminate cancer patients from HPV-infected individuals. As such, this study was designed to establish a protocol to evaluate DNA methylation changes in HPV late genes and long control region (LCR) in saliva samples of HPV-HNC patients and HPV-positive controls. Higher methylation levels were detected in HPV late genes (L1 and L2) in both tumour and saliva samples of HPV-HNC patients compared with HPV-positive controls. Moreover, methylation patterns between tumours and corresponding saliva samples were observed to have a strong correlation (Passing-Bablok regression analysis; τ = 0.7483, P < 0.0001). Considering the differences between HNC and controls in methylation levels in late genes, and considering primer amplification efficiencies, 13 CpG sites located at L1 and L2 genes were selected for further evaluation. A total of 18 HNC saliva samples and 10 control saliva samples were assessed for the methylation levels in the selected sites. From the CpG sites evaluated statistically significant differences were identified for CpG sites at L2-CpG 6 (P = 0.0004), L1-CpG 3 (P = 0.0144), L1-CpG 2 (P = 0.0395) and L2-CpG 19 (P = 0.0455). Our pilot data indicate that higher levels of DNA methylation in HPV late genes are indicative of HPV-HNC risk, and it is a potential supplementary biomarker for salivary HPV detection-based HPV-HNC screening.
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Affiliation(s)
- Chameera Ekanayake Weeramange
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, Queensland 4111, Australia
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold Coast, Queensland 4222, Australia
- Faculty of Health, School of Biomedical Science, Centre for Biomedical Technologies, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Kai Dun Tang
- EDA School of Biological Sciences and Biotechnology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300071, P.R. China
| | - Darryl Irwin
- Agena Bioscience, Bowen Hills, Queensland 4006, Australia
| | - Gunter Hartel
- Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
- School of Nursing, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Rahul Ladwa
- Department of Cancer Care Services, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland 4006, Australia
| | - Lizbeth Kenny
- Faculty of Medicine, The University of Queensland, Herston, Queensland 4006, Australia
- Department of Cancer Care Services, Royal Brisbane and Women’s Hospital, Herston, Queensland 4006, Australia
| | - Touraj Taheri
- Faculty of Medicine, The University of Queensland, Herston, Queensland 4006, Australia
- Department of Anatomical Pathology, Royal Brisbane and Women’s Hospital, Herston, Queensland 4006, Australia
| | - Bernard Whitfield
- Department of Otolaryngology, Head and Neck Surgery, Princess Alexandra and Logan Hospitals, Meadowbrook, Queensland 4131, Australia
- School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Sarju Vasani
- Faculty of Medicine, The University of Queensland, Herston, Queensland 4006, Australia
- Department of Otolaryngology, Royal Brisbane and Women’s Hospital, Herston, Queensland 4006, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, Queensland 4111, Australia
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold Coast, Queensland 4222, Australia
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87
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Li Y, Gong J, Sun Q, Vong EG, Cheng X, Wang B, Yuan Y, Jin L, Gamazon ER, Zhou D, Lai M, Zhang D. Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA. Am J Hum Genet 2024; 111:562-583. [PMID: 38367620 PMCID: PMC10940021 DOI: 10.1016/j.ajhg.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024] Open
Abstract
Genetic variants are involved in the orchestration of alternative polyadenylation (APA) events, while the role of DNA methylation in regulating APA remains unclear. We generated a comprehensive atlas of APA quantitative trait methylation sites (apaQTMs) across 21 different types of cancer (1,612 to 60,219 acting in cis and 4,448 to 142,349 in trans). Potential causal apaQTMs in non-cancer samples were also identified. Mechanistically, we observed a strong enrichment of cis-apaQTMs near polyadenylation sites (PASs) and both cis- and trans-apaQTMs in proximity to transcription factor (TF) binding regions. Through the integration of ChIP-signals and RNA-seq data from cell lines, we have identified several regulators of APA events, acting either directly or indirectly, implicating novel functions of some important genes, such as TCF7L2, which is known for its involvement in type 2 diabetes and cancers. Furthermore, we have identified a vast number of QTMs that share the same putative causal CpG sites with five different cancer types, underscoring the roles of QTMs, including apaQTMs, in the process of tumorigenesis. DNA methylation is extensively involved in the regulation of APA events in human cancers. In an attempt to elucidate the potential underlying molecular mechanisms of APA by DNA methylation, our study paves the way for subsequent experimental validations into the intricate biological functions of DNA methylation in APA regulation and the pathogenesis of human cancers. To present a comprehensive catalog of apaQTM patterns, we introduce the Pancan-apaQTM database, available at https://pancan-apaqtm-zju.shinyapps.io/pancanaQTM/.
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Affiliation(s)
- Yige Li
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingwen Gong
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China
| | - Qingrong Sun
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang Province, China; College of Information Science and Technology, ZheJiang Shuren University, Hangzhou 310015, ZheJiang, China
| | - Eu Gene Vong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Biochemistry and Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Binghong Wang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan Zhou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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88
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Huang BZ, Binder AM, Quon B, Patel YM, Lum-Jones A, Tiirikainen M, Murphy SE, Loo L, Maunakea AK, Haiman CA, Wilkens LR, Koh WP, Cai Q, Aldrich MC, Siegmund KD, Hecht SS, Yuan JM, Blot WJ, Stram DO, Le Marchand L, Park SL. Epigenome-wide association study of total nicotine equivalents in multiethnic current smokers from three prospective cohorts. Am J Hum Genet 2024; 111:456-472. [PMID: 38367619 PMCID: PMC10940014 DOI: 10.1016/j.ajhg.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024] Open
Abstract
The impact of tobacco exposure on health varies by race and ethnicity and is closely tied to internal nicotine dose, a marker of carcinogen uptake. DNA methylation is strongly responsive to smoking status and may mediate health effects, but study of associations with internal dose is limited. We performed a blood leukocyte epigenome-wide association study (EWAS) of urinary total nicotine equivalents (TNEs; a measure of nicotine uptake) and DNA methylation measured using the MethylationEPIC v1.0 BeadChip (EPIC) in six racial and ethnic groups across three cohort studies. In the Multiethnic Cohort Study (discovery, n = 1994), TNEs were associated with differential methylation at 408 CpG sites across >250 genomic regions (p < 9 × 10-8). The top significant sites were annotated to AHRR, F2RL3, RARA, GPR15, PRSS23, and 2q37.1, all of which had decreasing methylation with increasing TNEs. We identified 45 novel CpG sites, of which 42 were unique to the EPIC array and eight annotated to genes not previously linked with smoking-related DNA methylation. The most significant signal in a novel gene was cg03748458 in MIR383;SGCZ. Fifty-one of the 408 discovery sites were validated in the Singapore Chinese Health Study (n = 340) and the Southern Community Cohort Study (n = 394) (Bonferroni corrected p < 1.23 × 10-4). Significant heterogeneity by race and ethnicity was detected for CpG sites in MYO1G and CYTH1. Furthermore, TNEs significantly mediated the association between cigarettes per day and DNA methylation at 15 sites (average 22.5%-44.3% proportion mediated). Our multiethnic study highlights the transethnic and ethnic-specific methylation associations with internal nicotine dose, a strong predictor of smoking-related morbidities.
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Affiliation(s)
- Brian Z Huang
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA.
| | - Alexandra M Binder
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA; Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brandon Quon
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yesha M Patel
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Annette Lum-Jones
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Maarit Tiirikainen
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lenora Loo
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Alika K Maunakea
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lynne R Wilkens
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda C Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly D Siegmund
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel O Stram
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Loïc Le Marchand
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sungshim L Park
- Population Sciences of the Pacific Program-Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA.
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89
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Advani J, Mehta PA, Hamel AR, Mehrotra S, Kiel C, Strunz T, Corso-Díaz X, Kwicklis M, van Asten F, Ratnapriya R, Chew EY, Hernandez DG, Montezuma SR, Ferrington DA, Weber BHF, Segrè AV, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. Nat Commun 2024; 15:1972. [PMID: 38438351 PMCID: PMC10912779 DOI: 10.1038/s41467-024-46063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
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Affiliation(s)
- Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Kiel
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
- Doheny Eye Institute, Pasadena, CA, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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90
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Tak Y, Schneider A, Santos E, Randol JL, Tassone F, Hagerman P, Hagerman RJ. Unmethylated Mosaic Full Mutation Males without Fragile X Syndrome. Genes (Basel) 2024; 15:331. [PMID: 38540390 PMCID: PMC10970065 DOI: 10.3390/genes15030331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024] Open
Abstract
Fragile X syndrome (FXS) is the leading inherited cause of intellectual disability (ID) and single gene cause of autism. Although most patients with FXS and the full mutation (FM) have complete methylation of the fragile X messenger ribonucleoprotein 1 (FMR1) gene, some have mosaicism in methylation and/or CGG repeat size, and few have completely unmethylated FM alleles. Those with a complete lack of methylation are rare, with little literature about the cognitive and behavioral phenotypes of these individuals. A review of past literature was conducted regarding individuals with unmethylated and mosaic FMR1 FM. We report three patients with an unmethylated FM FMR1 alleles without any behavioral or cognitive deficits. This is an unusual presentation for men with FM as most patients with an unmethylated FM and no behavioral phenotypes do not receive fragile X DNA testing or a diagnosis of FXS. Our cases showed that mosaic males with unmethylated FMR1 FM alleles may lack behavioral phenotypes due to the presence of smaller alleles producing the FMR1 protein (FMRP). However, these individuals could be at a higher risk of developing fragile X-associated tremor/ataxia syndrome (FXTAS) due to the increased expression of mRNA, similar to those who only have a premutation.
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Affiliation(s)
- YeEun Tak
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA 95616, USA; (Y.T.); (E.S.); (F.T.); (P.H.)
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Andrea Schneider
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Ellery Santos
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA 95616, USA; (Y.T.); (E.S.); (F.T.); (P.H.)
| | - Jamie Leah Randol
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Flora Tassone
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA 95616, USA; (Y.T.); (E.S.); (F.T.); (P.H.)
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Paul Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA 95616, USA; (Y.T.); (E.S.); (F.T.); (P.H.)
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Randi J. Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA 95616, USA; (Y.T.); (E.S.); (F.T.); (P.H.)
- Department of Pediatrics, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
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91
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Fedorin DN, Eprintsev AT, Igamberdiev AU. The role of promoter methylation of the genes encoding the enzymes metabolizing di- and tricarboxylic acids in the regulation of plant respiration by light. J Plant Physiol 2024; 294:154195. [PMID: 38377939 DOI: 10.1016/j.jplph.2024.154195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
We discuss the role of epigenetic changes at the level of promoter methylation of the key enzymes of carbon metabolism in the regulation of respiration by light. While the direct regulation of enzymes via modulation of their activity and post-translational modifications is fast and readily reversible, the role of cytosine methylation is important for providing a prolonged response to environmental changes. In addition, adenine methylation can play a role in the regulation of transcription of genes. The mitochondrial and extramitochondrial forms of several enzymes participating in the tricarboxylic acid cycle and associated reactions are regulated via promoter methylation in opposite ways. The mitochondrial forms of citrate synthase, aconitase, fumarase, NAD-malate dehydrogenase are inhibited while the cytosolic forms of aconitase, fumarase, NAD-malate dehydrogenase, and the peroxisomal form of citrate synthase are activated. It is concluded that promoter methylation represents a universal mechanism of the regulation of activity of respiratory enzymes in plant cells by light. The role of the regulation of the mitochondrial and cytosolic forms of respiratory enzymes in the operation of malate and citrate valves and in controlling the redox state and balancing the energy level of photosynthesizing plant cells is discussed.
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Affiliation(s)
- Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada.
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92
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Barata T, Pereira V, Pires das Neves R, Rocha M. Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer. Comput Biol Med 2024; 170:108052. [PMID: 38308868 DOI: 10.1016/j.compbiomed.2024.108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The imbalance of epigenetic regulatory mechanisms such as DNA methylation, which can promote aberrant gene expression profiles without affecting the DNA sequence, may cause the deregulation of signaling, regulatory, and metabolic processes, contributing to a cancerous phenotype. Since some metabolites are substrates and cofactors of epigenetic regulators, their availability can be affected by characteristic cancer cell metabolic shifts, feeding cancer onset and progression through epigenetic deregulation. Hence, there is a need to study the influence of cancer metabolic reprogramming in DNA methylation to design new effective treatments. In this study, a generic Genome-Scale Metabolic Model (GSMM) of a human cell, integrating DNA methylation or demethylation reactions, was obtained and used for the reconstruction of Genome-Scale Metabolic Models enhanced with Enzymatic Constraints using Kinetic and Omics data (GECKOs) of 31 cancer cell lines. Furthermore, cell-line-specific DNA methylation levels were included in the models, as coefficients of a DNA composition pseudo-reaction, to depict the influence of metabolism over global DNA methylation in each of the cancer cell lines. Flux simulations demonstrated the ability of these models to provide simulated fluxes of exchange reactions similar to the equivalent experimentally measured uptake/secretion rates and to make good functional predictions. In addition, simulations found metabolic pathways, reactions and enzymes directly or inversely associated with the gene promoter methylation. Two potential candidates for targeted cancer epigenetic therapy were identified.
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Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Vítor Pereira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal; Department of Informatics, University of Minho, Portugal.
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93
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Layman CE, Ward S, Davis BA, Nevonen KA, Okhovat M, Rincon M, Valent A, Carbone L, Thornburg KL. High-throughput methylome analysis reveals differential methylation for early and late onset preeclampsia for mothers and their children. Physiol Genomics 2024; 56:276-282. [PMID: 38189116 DOI: 10.1152/physiolgenomics.00058.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/14/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024] Open
Abstract
Preeclampsia is a hypertensive disorder of pregnancy that affects ∼2%-5% of all pregnancies, contributes to 4 of the top 10 causes of pregnancy-related deaths, and remains a long-term risk factor for cardiometabolic diseases. Yet, little is still known about the molecular mechanisms that lead to this disease. There is evidence that some cases have a genetic cause. However, it is well appreciated that harmful factors in the environment, such as poor nutrition, stress, and toxins, may lead to epigenetics changes that can contribute to this disease. DNA methylation is one of the epigenetic modifications known to be fairly stable and impact gene expression. Using DNA from buccal swabs, we analyzed global DNA methylation among three groups of individuals: mothers who experienced 1) early-stage preeclampsia (<32 wk), 2) late-stage preeclampsia (>37 wk), or 3) no complications during their pregnancies, as well as the children from these three groups. We found significant differentially methylated regions (DMRs) between mothers who experienced preeclampsia compared with those with no complications adjacent or within genes that are important for placentation, embryonic development, cell adhesion, and inflammation (e.g., the cadherin pathway). A significant portion of DMR genes showed expression in tissues relevant to preeclampsia (i.e., the brain, heart, kidney, uterus, ovaries, and placenta). As this study was performed on DNA extracted from cheek swabs, this opens the way to future studies in different tissues, aimed at identifying possible biomarkers of risk and early detection, developing targeted interventions, and reducing the progression of this life-threatening disease.NEW & NOTEWORTHY Preeclampsia is a life-threatening hypertensive disorder, affecting 2%-5% of pregnancies, that remains poorly understood. This study analyzed DNA methylation from buccal swabs from mothers who experienced early and late-stage preeclampsia and those with uncomplicated pregnancies, along with their children. Differentially methylated regions were found near and within genes crucial for placental function, embryonic development, and inflammation. Many of these genes are expressed in preeclampsia-related tissues, offering hope for future biomarker development for this condition.
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Affiliation(s)
- Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Brett A Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Monica Rincon
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States
| | - Amy Valent
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, United States
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon, United States
| | - Kent L Thornburg
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon, United States
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, United States
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94
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Saarinen A, Marttila S, Mishra PP, Lyytikäinen LP, Raitoharju E, Mononen N, Sormunen E, Kähönen M, Raitakari O, Hietala J, Keltikangas-Järvinen L, Lehtimäki T. Polygenic risk for schizophrenia, social dispositions, and pace of epigenetic aging: Results from the Young Finns Study. Aging Cell 2024; 23:e14052. [PMID: 38031635 DOI: 10.1111/acel.14052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Schizophrenia is often regarded as a disorder of premature aging. We investigated (a) whether polygenic risk for schizophrenia (PRSsch ) relates to pace of epigenetic aging and (b) whether personal dispositions toward active and emotionally close relationships protect against accelerated epigenetic aging in individuals with high PRSsch . The sample came from the population-based Young Finns Study (n = 1348). Epigenetic aging was measured with DNA methylation aging algorithms such as AgeAccelHannum , EEAAHannum , IEAAHannum , IEAAHorvath , AgeAccelHorvath , AgeAccelPheno , AgeAccelGrim , and DunedinPACE. A PRSsch was calculated using summary statistics from the most comprehensive genome-wide association study of schizophrenia to date. Social dispositions were assessed in terms of extraversion, sociability, reward dependence, cooperativeness, and attachment security. We found that PRSsch did not have a statistically significant effect on any studied indicator of epigenetic aging. Instead, PRSsch had a significant interaction with reward dependence (p = 0.001-0.004), cooperation (p = 0.009-0.020), extraversion (p = 0.019-0.041), sociability (p = 0.003-0.016), and attachment security (p = 0.007-0.014) in predicting AgeAccelHannum , EEAAHannum , or IEAAHannum . Specifically, participants with high PRSsch appeared to display accelerated epigenetic aging at higher (vs. lower) levels of extraversion, sociability, attachment security, reward dependence, and cooperativeness. A rather opposite pattern was evident for those with low PRSsch . No such interactions were evident when predicting the other indicators of epigenetic aging. In conclusion, against our hypothesis, frequent social interactions may relate to accelerated epigenetic aging in individuals at risk for psychosis. We speculate that this may be explained by social-cognitive impairments (perceiving social situations as overwhelming or excessively arousing) or ending up in less supportive or deviant social groups.
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Affiliation(s)
- Aino Saarinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Central Hospital, Adolescent Psychiatry Outpatient Clinic, Helsinki, Finland
| | - Saara Marttila
- Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center, Tampere, Finland
| | - Leo-Pekka Lyytikäinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center, Tampere, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
| | - Emma Raitoharju
- Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center, Tampere, Finland
- Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Elina Sormunen
- Department of Psychiatry, University of Turku, Turku, Finland
- Turku University Hospital, Turku, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Olli Raitakari
- Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
- Turku University Hospital, Turku, Finland
- Department of Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | | | - Terho Lehtimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center, Tampere, Finland
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95
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Siller Wilks SJ, Heidinger BJ, Westneat DF, Solomon J, Rubenstein DR. The impact of parental and developmental stress on DNA methylation in the avian hypothalamic-pituitary-adrenal axis. Mol Ecol 2024; 33:e17291. [PMID: 38343177 DOI: 10.1111/mec.17291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024]
Abstract
The hypothalamic-pituitary-adrenal (HPA) axis coordinates an organism's response to environmental stress. The responsiveness and sensitivity of an offspring's stress response may be shaped not only by stressors encountered in their early post-natal environment but also by stressors in their parent's environment. Yet, few studies have considered how stressors encountered in both of these early life environments may function together to impact the developing HPA axis. Here, we manipulated stressors in the parental and post-natal environments in a population of house sparrows (Passer domesticus) to assess their impact on changes in DNA methylation (and corresponding gene expression) in a suite of genes within the HPA axis. We found that nestlings that experienced early life stress across both life-history periods had higher DNA methylation in a critical HPA axis gene, the glucocorticoid receptor (NR3C1). In addition, we found that the life-history stage when stress was encountered impacted some genes (HSD11B1, NR3C1 and NR3C2) differently. We also found evidence for the mitigation of parental stress by post-natal stress (in HSD11B1 and NR3C2). Finally, by assessing DNA methylation in both the brain and blood, we were able to evaluate cross-tissue patterns. While some differentially methylated regions were tissue-specific, we found cross-tissue changes in NR3C2 and NR3C1, suggesting that blood is a suitable tissue for assessing DNA methylation as a biomarker of early life stress. Our results provide a crucial first step in understanding the mechanisms by which early life stress in different life-history periods contributes to changes in the epigenome of the HPA axis.
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Affiliation(s)
- Stefanie J Siller Wilks
- Department of Ecology Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Britt J Heidinger
- Biological Sciences Department, North Dakota State University, Fargo, North Dakota, USA
| | - David F Westneat
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Joseph Solomon
- Department of Ecology Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Dustin R Rubenstein
- Department of Ecology Evolution and Environmental Biology, Columbia University, New York, New York, USA
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96
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Karimi K, Mol MO, Haghshenas S, Relator R, Levy MA, Kerkhof J, McConkey H, Brooks A, Zonneveld-Huijssoon E, Gerkes EH, Tedder ML, Vissers L, Salzano E, Piccione M, Asaftei SD, Carli D, Mussa A, Shukarova-Angelovska E, Trajkova S, Brusco A, Merla G, Alders MM, Bouman A, Sadikovic B. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene. Genet Med 2024; 26:101041. [PMID: 38054406 DOI: 10.1016/j.gim.2023.101041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE The main objective of this study was to assess clinical features and genome-wide DNA methylation profiles in individuals affected by intellectual developmental disorder, autosomal dominant 21 (IDD21) syndrome, caused by variants in the CCCTC-binding factor (CTCF) gene. METHODS DNA samples were extracted from peripheral blood of 16 individuals with clinical features and genetic findings consistent with IDD21. DNA methylation analysis was performed using the Illumina Infinium Methylation EPIC Bead Chip microarrays. The methylation levels were fitted in a multivariate linear regression model to identify the differentially methylated probes. A binary support vector machine classification model was constructed to differentiate IDD21 samples from controls. RESULTS We identified a highly specific, reproducible, and sensitive episignature associated with CTCF variants. Six variants of uncertain significance were tested, of which 2 mapped to the IDD21 episignature and clustered alongside IDD21 cases in both heatmap and multidimensional scaling plots. Comparison of the genomic DNA methylation profile of IDD21 with that of 56 other neurodevelopmental disorders provided insights into the underlying molecular pathophysiology of this disorder. CONCLUSION The robust and specific CTCF/IDD21 episignature expands the growing list of neurodevelopmental disorders with distinct DNA methylation profiles, which can be applied as supporting evidence in variant classification.
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Affiliation(s)
- Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Merel O Mol
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy; Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Sebastian Dorin Asaftei
- Pediatric Onco-Hematology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, Turin, Italy; Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Elena Shukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, North Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Marielle M Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
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97
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Lee SM. Detecting DNA hydroxymethylation: exploring its role in genome regulation. BMB Rep 2024; 57:135-142. [PMID: 38449301 PMCID: PMC10979348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
DNA methylation is one of the most extensively studied epigenetic regulatory mechanisms, known to play crucial roles in various organisms. It has been implicated in the regulation of gene expression and chromatin changes, ranging from global alterations during cell state transitions to locus-specific modifications. 5-hydroxymethylcytosine (5hmC) is produced by a major oxidation, from 5-methylcytosine (5mC), catalyzed by the ten-eleven translocation (TET) enzymes, and is gradually being recognized for its significant role in genome regulation. With the development of state-of-the-art experimental techniques, it has become possible to detect and distinguish 5mC and 5hmC at base resolution. Various techniques have evolved, encompassing chemical and enzymatic approaches, as well as thirdgeneration sequencing techniques. These advancements have paved the way for a thorough exploration of the role of 5hmC across a diverse array of cell types, from embryonic stem cells (ESCs) to various differentiated cells. This review aims to comprehensively report on recent techniques and discuss the emerging roles of 5hmC. [BMB Reports 2024; 57(3): 135-142].
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Affiliation(s)
- Sun-Min Lee
- Department of Physics, Konkuk Univeristy, Seoul 05029, Korea
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98
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Höglund A, Henriksen R, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken. PLoS Genet 2024; 20:e1010719. [PMID: 38457441 PMCID: PMC10954189 DOI: 10.1371/journal.pgen.1010719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 03/20/2024] [Accepted: 01/31/2024] [Indexed: 03/10/2024] Open
Abstract
DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.
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Affiliation(s)
- Andrey Höglund
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M. Guerrero-Bosagna
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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99
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van Toledo DEFWM, Bleijenberg AGC, Venema A, de Wit MJ, van Eeden S, Meijer GA, Carvalho B, Dekker E, Henneman P, IJspeert JEG, van Noesel CJM. Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite-instable colorectal cancers. J Pathol Clin Res 2024; 10:e348. [PMID: 38380944 PMCID: PMC10880511 DOI: 10.1002/cjp2.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/17/2023] [Accepted: 10/15/2023] [Indexed: 02/22/2024]
Abstract
Up to 30% of colorectal cancers (CRCs) develop from sessile serrated lesions (SSLs). Within the serrated neoplasia pathway, at least two principally distinct oncogenetic routes exist generating microsatellite-stable and microsatellite-instable CRCs, respectively. Aberrant DNA methylation (DNAm) is found early in the serrated pathway and might play a role in both oncogenetic routes. We studied a cohort of 23 SSLs with a small focus (<10 mm) of dysplasia or cancer, 10 of which were MLH1 deficient and 13 MLH1 proficient. By comparing, for each SSL, the methylation status of (1) the region of dysplasia or cancer (SSL-D), (2) the nondysplastic SSL (SSL), and (3) adjacent normal mucosa, differentially methylated probes (DMPs) and regions (DMRs) were assessed both genome-wide as well as in a tumor-suppressor gene-focused approach. By comparing DNAm of MLH1-deficient SSL-Ds with their corresponding SSLs, we identified five DMRs, including those annotating for PRDM2 and, not unexpectedly, MLH1. PRDM2 gene promotor methylation was associated with MLH1 expression status, as it was largely hypermethylated in MLH1-deficient SSL-Ds and hypomethylated in MLH1-proficient SSL-Ds. Significantly increased DNAm levels of PRDM2 and MLH1, in particular at 'critical' MLH1 probe sites, were to some extent already visible in SSLs as compared to normal mucosa (p = 0.02, p = 0.01, p < 0.0001, respectively). No DMRs, nor DMPs, were identified for SSLs destined to evolve into MLH1-proficient SSL-Ds. Our data indicate that, within both arms of the serrated CRC pathway, the majority of the epigenetic alterations are introduced early during SSL formation. Promoter hypermethylation of PRDM2 and MLH1 on the other hand specifically initiates in SSLs destined to transform into MLH1-deficient CRCs suggesting that the fate of SSLs may not necessarily result from a stochastic process but possibly is already imprinted and predisposed.
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Affiliation(s)
- David EFWM van Toledo
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Arne GC Bleijenberg
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Andrea Venema
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Mireille J de Wit
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Susanne van Eeden
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Gerrit A Meijer
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Beatrice Carvalho
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Peter Henneman
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Joep EG IJspeert
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Carel JM van Noesel
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
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Yao Z, Li F, Xie W, Chen J, Wu J, Zhan Y, Wu X, Wang Z, Zhang G. DeepSF-4mC: A deep learning model for predicting DNA cytosine 4mC methylation sites leveraging sequence features. Comput Biol Med 2024; 171:108166. [PMID: 38382385 DOI: 10.1016/j.compbiomed.2024.108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
N4-methylcytosine (4mC) is a DNA modification involving the addition of a methyl group to the fourth nitrogen atom of the cytosine base. This modification may influence gene regulation, providing potential insights into gene control mechanisms. Traditional laboratory methods for detecting 4mC DNA methylation have limitations, but the rise of artificial intelligence has introduced efficient computational strategies for 4mC site prediction. Despite this progress, challenges persist in terms of model performance and interpretability. To tackle these challenges, we propose DeepSF-4mC, a deep learning model specifically designed for predicting DNA cytosine 4mC methylation sites by leveraging sequence features. Our approach incorporates multiple encoding techniques to enhance prediction accuracy, increase model stability, and reduce the computational resources needed. Leveraging transfer learning, we harness existing models to enhance performance through learned representations or fine-tuning. Ensemble learning techniques combine predictions from multiple models, boosting robustness and accuracy. This research contributes to DNA methylation analysis and lays the groundwork for understanding 4mC's multifaceted role in biological processes. The web server for DeepSF-4mC is accessible at: http://deepsf-4mc.top/and the original code can be found at: https://github.com/754131799/DeepSF-4mC.
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Affiliation(s)
- Zhaomin Yao
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Fei Li
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Weiming Xie
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Jiaming Chen
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Jiezhang Wu
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Ying Zhan
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China
| | - Xiaodan Wu
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China
| | - Zhiguo Wang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China.
| | - Guoxu Zhang
- Department of Nuclear Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, 110016, China; College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, 110167, China.
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