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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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2
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Rashidiani S, Mamo G, Farkas B, Szabadi A, Farkas B, Uszkai V, Császár A, Brandt B, Kovács K, Pap M, Rauch TA. Integrative Epigenetic and Molecular Analysis Reveals a Novel Promoter for a New Isoform of the Transcription Factor TEAD4. Int J Mol Sci 2024; 25:2223. [PMID: 38396900 PMCID: PMC10888684 DOI: 10.3390/ijms25042223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
TEAD4 is a transcription factor that plays a crucial role in the Hippo pathway by regulating the expression of genes related to proliferation and apoptosis. It is also involved in the maintenance and differentiation of the trophectoderm during pre- and post-implantation embryonic development. An alternative promoter for the TEAD4 gene was identified through epigenetic profile analysis, and a new transcript from the intronic region of TEAD4 was discovered using the 5'RACE method. The transcript of the novel promoter encodes a TEAD4 isoform (TEAD4-ΔN) that lacks the DNA-binding domain but retains the C-terminal protein-protein interaction domain. Gene expression studies, including end-point PCR and Western blotting, showed that full-length TEAD4 was present in all investigated tissues. However, TEAD4-ΔN was only detectable in certain cell types. The TEAD4-ΔN promoter is conserved throughout evolution and demonstrates transcriptional activity in transient-expression experiments. Our study reveals that TEAD4 interacts with the alternative promoter and increases the expression of the truncated isoform. DNA methylation plays a crucial function in the restricted expression of the TEAD4-ΔN isoform in specific tissues, including the umbilical cord and the placenta. The data presented indicate that the DNA-methylation status of the TEAD4-ΔN promoter plays a critical role in regulating organ size, cancer development, and placenta differentiation.
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Affiliation(s)
- Shima Rashidiani
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - Gizaw Mamo
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - Benjámin Farkas
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
| | - András Szabadi
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
- Department of Dentistry, Oral and Maxillofacial Surgery, Medical School, University of Pécs, 7623 Pécs, Hungary
| | - Bálint Farkas
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
- National Laboratory of Human Reproduction, University of Pécs, 7624 Pécs, Hungary
| | - Veronika Uszkai
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
| | - András Császár
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
| | - Barbara Brandt
- Department of Medical Biology and Central Electron Microscope Laboratory, Medical School, University of Pécs, 7624 Pécs, Hungary (M.P.)
| | - Kálmán Kovács
- Department of Obstetrics and Gynecology, Medical School, University of Pécs, 7624 Pécs, Hungary; (B.F.); (V.U.); (A.C.)
- National Laboratory of Human Reproduction, University of Pécs, 7624 Pécs, Hungary
| | - Marianna Pap
- Department of Medical Biology and Central Electron Microscope Laboratory, Medical School, University of Pécs, 7624 Pécs, Hungary (M.P.)
| | - Tibor A. Rauch
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary; (S.R.); (G.M.); (B.F.); (A.S.)
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3
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Promoter-Adjacent DNA Hypermethylation Can Downmodulate Gene Expression: TBX15 in the Muscle Lineage. EPIGENOMES 2022; 6:epigenomes6040043. [PMID: 36547252 PMCID: PMC9778270 DOI: 10.3390/epigenomes6040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border both sides of a constitutively unmethylated promoter. To understand the functionality of this DNA hypermethylation, we cloned the differentially methylated sequences (DMRs) in CpG-free reporter vectors and tested them for promoter or enhancer activity upon transient transfection. These cloned regions exhibited strong promoter activity and, when placed upstream of a weak promoter, strong enhancer activity specifically in myoblast host cells. In vitro CpG methylation targeted to the DMR sequences in the plasmids resulted in 86−100% loss of promoter or enhancer activity, depending on the insert sequence. These results as well as chromatin epigenetic and transcription profiles for this gene in various cell types support the hypothesis that DNA hypermethylation immediately upstream and downstream of the unmethylated promoter region suppresses enhancer/extended promoter activity, thereby downmodulating, but not silencing, expression in myoblasts and certain kinds of skeletal muscle. This promoter-border hypermethylation was not found in cell types with a silent TBX15 gene, and these cells, instead, exhibit repressive chromatin in and around the promoter. TBX18, TBX2, TBX3 and TBX1 display TBX15-like hypermethylated DMRs at their promoter borders and preferential expression in myoblasts. Therefore, promoter-adjacent DNA hypermethylation for downmodulating transcription to prevent overexpression may be used more frequently for transcription regulation than currently appreciated.
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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Folic Acid Treatment Directly Influences the Genetic and Epigenetic Regulation along with the Associated Cellular Maintenance Processes of HT-29 and SW480 Colorectal Cancer Cell Lines. Cancers (Basel) 2022; 14:cancers14071820. [PMID: 35406592 PMCID: PMC8997840 DOI: 10.3390/cancers14071820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Folic acid (FA) participates in DNA synthesis and in DNA methylation; hence, it has a dual role in established neoplasms. We aimed to observe this phenomenon on FA-treated colorectal cancer cell lines (HT-29, SW480). Our results demonstrated that the maintenance processes, namely cell proliferation, cell viability, and DNA repair, were altered in HT-29 cells for short-term FA supplementation, while genetic and epigenetic regulations of SW480 cells were also affected. Despite the fact that FA is a precursor molecule in methyl donor formation, DNA methylation alterations were observed in both directions, primarily influencing the pathways of carcinogenesis. Moreover, behind the great number of differentially expressed genes, other FA-related effects than promoter methylation were suspected. All of our results point beyond the attributes related to FA so far. The different response of the two cell lines is worth considering in clinical practice to facilitate the effectiveness of therapy in the case of tumor heterogeneity. Abstract Folic acid (FA) is a synthetic form of vitamin B9, generally used as a nutritional supplement and an adjunctive medication in cancer therapy. FA is involved in genetic and epigenetic regulation; therefore, it has a dual modulatory role in established neoplasms. We aimed to investigate the effect of short-term (72 h) FA supplementation on colorectal cancer; hence, HT-29 and SW480 cells were exposed to different FA concentrations (0, 100, 10,000 ng/mL). HT-29 cell proliferation and viability levels elevated after 100 ng/mL but decreased for 10,000 ng/mL FA. Additionally, a significant (p ≤ 0.05) improvement of genomic stability was detected in HT-29 cells with micronucleus scoring and comet assay. Conversely, the FA treatment did not alter these parameters in SW480 samples. RRBS results highlighted that DNA methylation changes were bidirectional in both cells, mainly affecting carcinogenesis-related pathways. Based on the microarray analysis, promoter methylation status was in accordance with FA-induced expression alterations of 27 genes. Our study demonstrates that the FA effect was highly dependent on the cell type, which can be attributed to the distinct molecular background and the different expression of proliferation- and DNA-repair-associated genes (YWHAZ, HES1, STAT3, CCL2). Moreover, new aspects of FA-regulated DNA methylation and consecutive gene expression were revealed.
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6
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Abstract
Increasing numbers of studies implicate abnormal DNA methylation in cancer and many non-malignant diseases. This is consistent with numerous findings about differentiation-associated changes in DNA methylation at promoters, enhancers, gene bodies, and sites that control higher-order chromatin structure. Abnormal increases or decreases in DNA methylation contribute to or are markers for cancer formation and tumour progression. Aberrant DNA methylation is also associated with neurological diseases, immunological diseases, atherosclerosis, and osteoporosis. In this review, I discuss DNA hypermethylation in disease and its interrelationships with normal development as well as proposed mechanisms for the origin of and pathogenic consequences of disease-associated hypermethylation. Disease-linked DNA hypermethylation can help drive oncogenesis partly by its effects on cancer stem cells and by the CpG island methylator phenotype (CIMP); atherosclerosis by disease-related cell transdifferentiation; autoimmune and neurological diseases through abnormal perturbations of cell memory; and diverse age-associated diseases by age-related accumulation of epigenetic alterations.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center and Tulane Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA
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7
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Qiu C, Shen H, Fu X, Xu C, Deng H. Meta-Analysis of Genome-Wide Association Studies Identifies Novel Functional CpG-SNPs Associated with Bone Mineral Density at Lumbar Spine. Int J Genomics 2018; 2018:6407257. [PMID: 30159320 PMCID: PMC6109501 DOI: 10.1155/2018/6407257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/19/2018] [Indexed: 12/16/2022] Open
Abstract
Osteoporosis is a serious public health issue, which is mostly characterized by low bone mineral density (BMD). To search for additional genetic susceptibility loci underlying BMD variation, an effective strategy is to focus on testing of specific variants with high potential of functional effects. Single nucleotide polymorphisms (SNPs) that introduce or disrupt CpG dinucleotides (CpG-SNPs) may alter DNA methylation levels and thus represent strong candidate functional variants. Here, we performed a targeted GWAS for 63,627 potential functional CpG-SNPs that may affect DNA methylation in bone-related cells, in five independent cohorts (n = 5905). By meta-analysis, 9 CpG-SNPs achieved a genome-wide significance level (p < 7.86 × 10-7) for association with lumbar spine BMD and additional 15 CpG-SNPs showed suggestive significant (p < 5.00 × 10-5) association, of which 2 novel SNPs rs7231498 (NFATC1) and rs7455028 (ESR1) also reached a genome-wide significance level in the joint analysis. Several identified CpG-SNPs were mapped to genes that have not been reported for association with BMD in previous GWAS, such as NEK3 and NFATC1 genes, highlighting the enhanced power of targeted association analysis for identification of novel associations that were missed by traditional GWAS. Interestingly, several genomic regions, such as NEK3 and LRP5 regions, contained multiple significant/suggestive CpG-SNPs for lumbar spine BMD, suggesting that multiple neighboring CpG-SNPs may synergistically mediate the DNA methylation level and gene expression pattern of target genes. Furthermore, functional annotation analyses suggested a strong regulatory potential of the identified BMD-associated CpG-SNPs and a significant enrichment in biological processes associated with protein localization and protein signal transduction. Our results provided novel insights into the genetic basis of BMD variation and highlighted the close connections between genetic and epigenetic mechanisms of complex disease.
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Affiliation(s)
- Chuan Qiu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Hui Shen
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Xiaoying Fu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Chao Xu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Hongwen Deng
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
- School of Basic Medical Science, Central South University, Changsha 410013, China
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8
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Li Y, Zhao H, Xu Q, Lv N, Jing Y, Wang L, Wang X, Guo J, Zhou L, Liu J, Chen G, Chen C, Li Y, Yu L. Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia. Oncotarget 2017; 8:110444-110459. [PMID: 29299160 PMCID: PMC5746395 DOI: 10.18632/oncotarget.22789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Clinical and genetic features incompletely predict outcome in acute myeloid leukemia (AML). The value of clinical methylation assays for prognostic markers has not been extensively explored. We assess the prognostic implications of methylC-capture sequencing (MCC-Seq) in patients with de novo AML by integrating DNA methylation and genetic risk stratification. MCC-Seq assessed DNA methylation level in 44 samples. The differentially methylated regions associated with prognostic genetic information were identified. The selected prognostic DNA methylation markers were independently validated in two sets. MCC-Seq exhibited good performance in AML patients. A panel of 12 differentially methylated genes was identified with promoter hyper-differentially methylated regions associated with the outcome. Compared with a low M-value, a high M-value was associated with failure to achieve complete remission (p = 0.024), increased hazard for disease-free survival in the study set (p = 0.039) and poor overall survival in The Cancer Genome Atlas set (p = 0.038). Hematopoietic stem cell transplantation and survival outcomes were not adversely affected by a high M-value (p = 0.271). Our study establishes that MCC-Seq is a stable, reproducible, and cost-effective methylation assay in AML. A 12-gene M-value encompassing epigenetic and genetic prognostic information represented a valid prognostic marker for patients with AML.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Qingyu Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
| | - Yu Jing
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lili Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaowen Wang
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Lei Zhou
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guofeng Chen
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Yonghui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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9
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Yu F, Shen H, Deng HW. Systemic analysis of osteoblast-specific DNA methylation marks reveals novel epigenetic basis of osteoblast differentiation. Bone Rep 2017; 6:109-119. [PMID: 28409176 PMCID: PMC5384298 DOI: 10.1016/j.bonr.2017.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 03/20/2017] [Accepted: 04/01/2017] [Indexed: 01/21/2023] Open
Abstract
DNA methylation is an important epigenetic modification that contributes to the lineage commitment and specific functions of different cell types. In this study, we compared ENCODE-generated genome-wide DNA methylation profiles of human osteoblast with 21 other types of human cells in order to identify osteoblast-specific methylation events. For most of the cell strains, data from two isogenic replicates were included, resulting in a total of 51 DNA methylation datasets. We identified 852 significant osteoblast-specific differentially methylated CpGs (DMCs) and 295 significant differentially methylated regions (DMRs). Significant DMCs/DMRs were not enriched in CpG islands (CGIs) and promoters, but more strongly enriched in CGI shores/shelves and in gene body and intergenic regions. The genes associated with significant DMRs were highly enriched in biological processes related to transcriptional regulation and critical for regulating bone metabolism and skeletal development under physiologic and pathologic conditions. By integrating the DMR data with the extensive gene expression and chromatin epigenomics data, we observed complex, context-dependent relationships between DNA methylation, chromatin states, and gene expression, suggesting diverse DNA methylation-mediated regulatory mechanisms. Our results also highlighted a number of novel osteoblast-relevant genes. For example, the integrated evidences from DMR analysis, histone modification and RNA-seq data strongly support that there is a novel isoform of neurexin-2 (NRXN2) gene specifically expressed in osteoblast. NRXN2 was known to function as a cell adhesion molecule in the vertebrate nervous system, but its functional role in bone is completely unknown and thus worth further investigation. In summary, we reported a comprehensive analysis of osteoblast-specific DNA methylation profiles and revealed novel insights into the epigenetic basis of osteoblast differentiation and activity.
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Affiliation(s)
- Fangtang Yu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
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10
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Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic Adaptive Introgression in TBX15/WARS2. Mol Biol Evol 2017; 34:509-524. [PMID: 28007980 PMCID: PMC5430617 DOI: 10.1093/molbev/msw283] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Matteo Fumagalli
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Amy Ko
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | | | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
- Department of Statistics, University of California Berkeley, Berkeley, CA
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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11
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Andresini O, Ciotti A, Rossi MN, Battistelli C, Carbone M, Maione R. A cross-talk between DNA methylation and H3 lysine 9 dimethylation at the KvDMR1 region controls the induction of Cdkn1c in muscle cells. Epigenetics 2016; 11:791-803. [PMID: 27611768 DOI: 10.1080/15592294.2016.1230576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The cdk inhibitor p57kip2, encoded by the Cdkn1c gene, plays a critical role in mammalian development and in the differentiation of several tissues. Cdkn1c protein levels are carefully regulated via imprinting and other epigenetic mechanisms affecting both the promoter and distant regulatory elements, which restrict its expression to particular developmental phases or specific cell types. Inappropriate activation of these regulatory mechanisms leads to Cdkn1c silencing, causing growth disorders and cancer. We have previously reported that, in skeletal muscle cells, induction of Cdkn1c expression requires the binding of the bHLH myogenic factor MyoD to a long-distance regulatory element within the imprinting control region KvDMR1. Interestingly, MyoD binding to KvDMR1 is prevented in myogenic cell types refractory to the induction of Cdkn1c. In the present work, we took advantage of this model system to investigate the epigenetic determinants of the differential interaction of MyoD with KvDMR1. We show that treatment with the DNA demethylating agent 5-azacytidine restores the binding of MyoD to KvDMR1 in cells unresponsive to Cdkn1c induction. This, in turn, promotes the release of a repressive chromatin loop between KvDMR1 and Cdkn1c promoter and, thus, the upregulation of the gene. Analysis of the chromatin status of Cdkn1c promoter and KvDMR1 in unresponsive compared to responsive cell types showed that their differential responsiveness to the MyoD-dependent induction of the gene does not involve just their methylation status but, rather, the differential H3 lysine 9 dimethylation at KvDMR1. Finally, we report that the same histone modification also marks the KvDMR1 region of human cancer cells in which Cdkn1c is silenced. On the basis of these results, we suggest that the epigenetic status of KvDMR1 represents a critical determinant of the cell type-restricted expression of Cdkn1c and, possibly, of its aberrant silencing in some pathological conditions.
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Affiliation(s)
- Oriella Andresini
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Agnese Ciotti
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Marianna N Rossi
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Cecilia Battistelli
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Mariarosaria Carbone
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Rossella Maione
- a Pasteur Institute-Fondazione Cenci Bolognetti , Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
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Ehrlich M, Ehrlich KC. DNA cytosine methylation and hydroxymethylation at the borders. Epigenomics 2015; 6:563-6. [PMID: 25531248 DOI: 10.2217/epi.14.48] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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13
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Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
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