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da Silva Santos R, Pascoalino Pinheiro D, Gustavo Hirth C, Barbosa Bezerra MJ, Joyce de Lima Silva-Fernandes I, Andréa da Silva Oliveira F, Viana de Holanda Barros M, Silveira Ramos E, A. Moura A, Filho ODMM, Pessoa C, Miranda Furtado CL. Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection. Epigenetics 2024; 19:2305081. [PMID: 38245880 PMCID: PMC10802203 DOI: 10.1080/15592294.2024.2305081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Penile squamous cell carcinoma (SCC) is a rare and aggressive tumour mainly related to lifestyle behaviour and human papillomavirus (HPV) infection. Environmentally induced loss of imprinting (LOI) at the H19 differentially methylated region (H19DMR) is associated with many cancers in the early events of tumorigenesis and may be involved in the pathogenesis of penile SCC. We sought to evaluate the DNA methylation pattern at H19DMR and its association with HPV infection in men with penile SCC by bisulfite sequencing (bis-seq). We observed an average methylation of 32.2% ± 11.6% at the H19DMR of penile SCC and did not observe an association between the p16INK4a+ (p = 0.59) and high-risk HPV+ (p = 0.338) markers with methylation level. The average methylation did not change according to HPV positive for p16INK4a+ or hrHPV+ (35.4% ± 10%) and negative for both markers (32.4% ± 10.1%) groups. As the region analysed has a binding site for the CTCF protein, the hypomethylation at the surrounding CpG sites might alter its insulator function. In addition, there was a positive correlation between intense polymorphonuclear cell infiltration and hypomethylation at H19DMR (p = 0.035). Here, we report that hypomethylation at H19DMR in penile SCC might contribute to tumour progression and aggressiveness regardless of HPV infection.
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Affiliation(s)
- Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | | | | | | | - Maisa Viana de Holanda Barros
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Arlindo A. Moura
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Animal Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Odorico de Moraes Manoel Filho
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil
- Graduate Program in Medical Sciences, Universidade de Fortaleza, Fortaleza, Ceará, Brazil
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2
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Xie G, Si Q, Zhang G, Fan Y, Li Q, Leng P, Qiao F, Liang S, Yu R, Wang Y. The role of imprinting genes' loss of imprints in cancers and their clinical implications. Front Oncol 2024; 14:1365474. [PMID: 38812777 PMCID: PMC11133587 DOI: 10.3389/fonc.2024.1365474] [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: 01/04/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024] Open
Abstract
Genomic imprinting plays an important role in the growth and development of mammals. When the original imprint status of these genes is lost, known as loss of imprinting (LOI), it may affect growth, neurocognitive development, metabolism, and even tumor susceptibility. The LOI of imprint genes has gradually been found not only as an early event in tumorigenesis, but also to be involved in progression. More than 120 imprinted genes had been identified in humans. In this review, we summarized the most studied LOI of two gene clusters and 13 single genes in cancers. We focused on the roles they played, that is, as growth suppressors and anti-apoptosis agents, sustaining proliferative signaling or inducing angiogenesis; the molecular pathways they regulated; and especially their clinical significance. It is notable that 12 combined forms of multi-genes' LOI, 3 of which have already been used as diagnostic models, achieved good sensitivity, specificity, and accuracy. In addition, the methods used for LOI detection in existing research are classified into detection of biallelic expression (BAE), differentially methylated regions (DMRs), methylation, and single-nucleotide polymorphisms (SNPs). These all indicated that the detection of imprinting genes' LOI has potential clinical significance in cancer diagnosis, treatment, and prognosis.
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Affiliation(s)
- Guojing Xie
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qin Si
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guangjie Zhang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Clinical Laboratory, Chengdu Fifth People’s Hospital, Chengdu, China
| | - Yu Fan
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Qinghua Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ping Leng
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Fengling Qiao
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Simin Liang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Yu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
| | - Yingshuang Wang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Sichuan Key Laboratory of Medical Molecular Testing, Chengdu, China
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3
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Weinberg-Shukron A, Youngson NA, Ferguson-Smith AC, Edwards CA. Epigenetic control and genomic imprinting dynamics of the Dlk1-Dio3 domain. Front Cell Dev Biol 2023; 11:1328806. [PMID: 38155837 PMCID: PMC10754522 DOI: 10.3389/fcell.2023.1328806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
Genomic imprinting is an epigenetic process whereby genes are monoallelically expressed in a parent-of-origin-specific manner. Imprinted genes are frequently found clustered in the genome, likely illustrating their need for both shared regulatory control and functional inter-dependence. The Dlk1-Dio3 domain is one of the largest imprinted clusters. Genes in this region are involved in development, behavior, and postnatal metabolism: failure to correctly regulate the domain leads to Kagami-Ogata or Temple syndromes in humans. The region contains many of the hallmarks of other imprinted domains, such as long non-coding RNAs and parental origin-specific CTCF binding. Recent studies have shown that the Dlk1-Dio3 domain is exquisitely regulated via a bipartite imprinting control region (ICR) which functions differently on the two parental chromosomes to establish monoallelic expression. Furthermore, the Dlk1 gene displays a selective absence of imprinting in the neurogenic niche, illustrating the need for precise dosage modulation of this domain in different tissues. Here, we discuss the following: how differential epigenetic marks laid down in the gametes cause a cascade of events that leads to imprinting in the region, how this mechanism is selectively switched off in the neurogenic niche, and why studying this imprinted region has added a layer of sophistication to how we think about the hierarchical epigenetic control of genome function.
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Affiliation(s)
| | - Neil A. Youngson
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Carol A. Edwards
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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Fanis P, Morrou M, Tomazou M, Michailidou K, Spyrou GM, Toumba M, Skordis N, Neocleous V, Phylactou LA. Methylation status of hypothalamic Mkrn3 promoter across puberty. Front Endocrinol (Lausanne) 2022; 13:1075341. [PMID: 36714607 PMCID: PMC9880154 DOI: 10.3389/fendo.2022.1075341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Makorin RING finger protein 3 (MKRN3) is an important factor located on chromosome 15 in the imprinting region associated with Prader-Willi syndrome. Imprinted MKRN3 is expressed in hypothalamic regions essential for the onset of puberty and mutations in the gene have been found in patients with central precocious puberty. The pubertal process is largely controlled by epigenetic mechanisms that include, among other things, DNA methylation at CpG dinucleotides of puberty-related genes. In the present study, we investigated the methylation status of the Mkrn3 promoter in the hypothalamus of the female mouse before, during and after puberty. Initially, we mapped the 32 CpG dinucleotides in the promoter, the 5'UTR and the first 50 nucleotides of the coding region of the Mkrn3 gene. Moreover, we identified a short CpG island region (CpG islet) located within the promoter. Methylation analysis using bisulfite sequencing revealed that CpG dinucleotides were methylated regardless of developmental stage, with the lowest levels of methylation being found within the CpG islet region. In addition, the CpG islet region showed significantly lower methylation levels at the pre-pubertal stage when compared with the pubertal or post-pubertal stage. Finally, in silico analysis of transcription factor binding sites on the Mkrn3 CpG islet identified the recruitment of 29 transcriptional regulators of which 14 were transcriptional repressors. Our findings demonstrate the characterization and differential methylation of the CpG dinucleotides located in the Mkrn3 promoter that could influence the transcriptional activity in pre-pubertal compared to pubertal or post-pubertal period. Further studies are needed to clarify the possible mechanisms and effects of differential methylation of the Mkrn3 promoter.
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Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Morrou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- Medical School, University of Nicosia, Nicosia, Cyprus
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou,
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5
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Zhou J, Cheng T, Li X, Hu J, Li E, Ding M, Shen R, Pineda JP, Li C, Lu S, Yu H, Sun J, Huang W, Wang X, Si H, Shi P, Liu J, Chang M, Dou M, Shi M, Chen X, Yung RC, Wang Q, Zhou N, Bai C. Epigenetic imprinting alterations as effective diagnostic biomarkers for early-stage lung cancer and small pulmonary nodules. Clin Epigenetics 2021; 13:220. [PMID: 34906185 PMCID: PMC8672623 DOI: 10.1186/s13148-021-01203-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/28/2021] [Indexed: 01/18/2023] Open
Abstract
Background Early lung cancer detection remains a clinical challenge for standard diagnostic biopsies due to insufficient tumor morphological evidence. As epigenetic alterations precede morphological changes, expression alterations of certain imprinted genes could serve as actionable diagnostic biomarkers for malignant lung lesions. Results Using the previously established quantitative chromogenic imprinted gene in situ hybridization (QCIGISH) method, elevated aberrant allelic expression of imprinted genes GNAS, GRB10, SNRPN and HM13 was observed in lung cancers over benign lesions and normal controls, which were pathologically confirmed among histologically stained normal, paracancerous and malignant tissue sections. Based on the differential imprinting signatures, a diagnostic grading model was built on 246 formalin-fixed and paraffin-embedded (FFPE) surgically resected lung tissue specimens, tested against 30 lung cytology and small biopsy specimens, and blindly validated in an independent cohort of 155 patients. The QCIGISH diagnostic model demonstrated 99.1% sensitivity (95% CI 97.5–100.0%) and 92.1% specificity (95% CI 83.5–100.0%) in the blinded validation set. Of particular importance, QCIGISH achieved 97.1% sensitivity (95% CI 91.6–100.0%) for carcinoma in situ to stage IB cancers with 100% sensitivity and 91.7% specificity (95% CI 76.0–100.0%) noted for pulmonary nodules with diameters ≤ 2 cm. Conclusions Our findings demonstrated the diagnostic value of epigenetic imprinting alterations as highly accurate translational biomarkers for a more definitive diagnosis of suspicious lung lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01203-5.
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Affiliation(s)
- Jian Zhou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, 200032, China
| | - Tong Cheng
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Xing Li
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Jie Hu
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Encheng Li
- Department of Respiratory Medicine, The Second Hospital Affiliated to Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Ming Ding
- Department of Respiratory Medicine, The Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Rulong Shen
- Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - John P Pineda
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Chun Li
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shaohua Lu
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hongyu Yu
- Department of Pathology, Changzheng Hospital, Navy Medical University, Shanghai, 200003, China
| | - Jiayuan Sun
- Department of Respiratory Endoscopy and Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenbin Huang
- Department of Pathology, Nanjing First Hospital, Nanjing, 210006, Jiangsu, China
| | - Xiaonan Wang
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Han Si
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Panying Shi
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Jing Liu
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, 264000, Shandong, China
| | - Meijia Chang
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Maosen Dou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Meng Shi
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xiaofeng Chen
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Rex C Yung
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21207, USA
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital Affiliated to Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Ning Zhou
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China.
| | - Chunxue Bai
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, 200032, China.
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6
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Li J, Chen W, Li D, Gu S, Liu X, Dong Y, Jin L, Zhang C, Li S. Conservation of Imprinting and Methylation of MKRN3, MAGEL2 and NDN Genes in Cattle. Animals (Basel) 2021; 11:1985. [PMID: 34359112 PMCID: PMC8300276 DOI: 10.3390/ani11071985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Genomic imprinting is the epigenetic mechanism of transcriptional regulation that involves differential DNA methylation modification. Comparative analysis of imprinted genes between species can help us to investigate the biological significance and regulatory mechanisms of genomic imprinting. MKRN3, MAGEL2 and NDN are three maternally imprinted genes identified in the human PWS/AS imprinted locus. This study aimed to assess the allelic expression of MKRN3, MAGEL2 and NDN and to examine the differentially methylated regions (DMRs) of bovine PWS/AS imprinted domains. An expressed single-nucleotide polymorphism (SNP)-based approach was used to investigate the allelic expression of MKRN3, MAGEL2 and NDN genes in bovine adult tissues and placenta. Consistent with the expression in humans and mice, we found that the MKRN3, MAGEL2 and NDN genes exhibit monoallelic expression in bovine somatic tissues and the paternal allele expressed in the bovine placenta. Three DMRs, PWS-IC, MKRN3 and NDN DMR, were identified in the bovine PWS/AS imprinted region by analysis of the DNA methylation status in bovine tissues using the bisulfite sequencing method and were located in the promoter and exon 1 of the SNRPN gene, NDN promoter and 5' untranslated region (5'UTR) of MKRN3 gene, respectively. The PWS-IC DMR is a primary DMR inherited from the male or female gamete, but NDN and MKRN3 DMR are secondary DMRs that occurred after fertilization by examining the methylation status in gametes.
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Affiliation(s)
- Junliang Li
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Weina Chen
- Department of Traditional Chinese Medicine, Hebei University, Baoding 071000, China;
| | - Dongjie Li
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050081, China;
| | - Shukai Gu
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Xiaoqian Liu
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Yanqiu Dong
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Lanjie Jin
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Cui Zhang
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
| | - Shijie Li
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China; (J.L.); (S.G.); (X.L.); (Y.D.); (L.J.)
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7
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Lozano-Ureña A, Jiménez-Villalba E, Pinedo-Serrano A, Jordán-Pla A, Kirstein M, Ferrón SR. Aberrations of Genomic Imprinting in Glioblastoma Formation. Front Oncol 2021; 11:630482. [PMID: 33777782 PMCID: PMC7994891 DOI: 10.3389/fonc.2021.630482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
In human glioblastoma (GBM), the presence of a small population of cells with stem cell characteristics, the glioma stem cells (GSCs), has been described. These cells have GBM potential and are responsible for the origin of the tumors. However, whether GSCs originate from normal neural stem cells (NSCs) as a consequence of genetic and epigenetic changes and/or dedifferentiation from somatic cells remains to be investigated. Genomic imprinting is an epigenetic marking process that causes genes to be expressed depending on their parental origin. The dysregulation of the imprinting pattern or the loss of genomic imprinting (LOI) have been described in different tumors including GBM, being one of the earliest and most common events that occurs in human cancers. Here we have gathered the current knowledge of the role of imprinted genes in normal NSCs function and how the imprinting process is altered in human GBM. We also review the changes at particular imprinted loci that might be involved in the development of the tumor. Understanding the mechanistic similarities in the regulation of genomic imprinting between normal NSCs and GBM cells will be helpful to identify molecular players that might be involved in the development of human GBM.
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Affiliation(s)
- Anna Lozano-Ureña
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain.,Departamento de Biología Celular, Universidad de Valencia, Valencia, Spain
| | | | | | | | - Martina Kirstein
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain.,Departamento de Biología Celular, Universidad de Valencia, Valencia, Spain
| | - Sacri R Ferrón
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain.,Departamento de Biología Celular, Universidad de Valencia, Valencia, Spain
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8
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Salgado C, Gruis N, Heijmans BT, Oosting J, van Doorn R. Genome-wide analysis of constitutional DNA methylation in familial melanoma. Clin Epigenetics 2020; 12:43. [PMID: 32143689 PMCID: PMC7060565 DOI: 10.1186/s13148-020-00831-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/20/2020] [Indexed: 12/26/2022] Open
Abstract
Background Heritable epigenetic alterations have been proposed as an explanation for familial clustering of melanoma. Here we performed genome-wide DNA methylation analysis on affected family members not carrying pathogenic variants in established melanoma susceptibility genes, compared with healthy volunteers. Results All melanoma susceptibility genes showed the absence of epimutations in familial melanoma patients, and no loss of imprinting was detected. Unbiased genome-wide DNA methylation analysis revealed significantly different levels of methylation in single CpG sites. The methylation level differences were small and did not affect reported tumour predisposition genes. Conclusion Our results provide no support for heritable epimutations as a cause of familial melanoma.
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Affiliation(s)
- Catarina Salgado
- Department of Dermatology, Leiden University Medical Center, Leiden, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, PO Box 9600, 2300 RC, Leiden, The Netherlands.
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9
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Imaizumi Y, Furutachi S, Watanabe T, Miya H, Kawaguchi D, Gotoh Y. Role of the imprinted allele of the Cdkn1c gene in mouse neocortical development. Sci Rep 2020; 10:1884. [PMID: 32024956 PMCID: PMC7002495 DOI: 10.1038/s41598-020-58629-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
Imprinted genes are expressed from only one allele in a parent of origin-specific manner. The cyclin-dependent kinase inhibitor p57kip2 is encoded by an imprinted gene Cdkn1c, with the paternal allele being silenced. The possible expression and function of the paternal allele of Cdkn1c have remained little studied, however. We now show that the paternal allele of the Cdkn1c gene is expressed at a low level in the developing mouse neocortex. Surprisingly, the central nervous system-specific conditional deletion of the paternal allele (pat cKO) at the Cdkn1c locus resulted in a marked reduction in brain size. Furthermore, pat cKO gradually reduced the number of neural stem-progenitor cells (NPCs) during neocortical development, and thus reduced the number of upper-layer neurons, which were derived from late-stage NPCs. Our results thus show that the paternal allele of the Cdkn1c locus plays a key role in maintenance of NPCs during neocortical development.
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Affiliation(s)
- Yui Imaizumi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shohei Furutachi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, W1T 4JG, UK
| | - Tomoyuki Watanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Miya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Daichi Kawaguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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10
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ZNF597 is a maternally expressed imprinted gene in the Holstein breed. Theriogenology 2020; 143:133-138. [PMID: 31874365 DOI: 10.1016/j.theriogenology.2019.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/24/2019] [Accepted: 12/14/2019] [Indexed: 11/22/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon that leads to the preferential expression of genes from either the paternal or maternal allele. Imprinted genes play important roles in mammalian growth and development and a central role in placental function. ZNF597 and NAA60 are two paternally imprinted genes in the human ZNF597-NAA60 imprinted locus, both of which show biallelic expression in the mouse, but their imprinting status in cattle is still unknown. In this study, we examined the allelic expression of ZNF597 and NAA60 in adult bovine placental and somatic tissues. By comparing the mRNA-based genotypes with the genomic DNA-based genotypes, we identified monoallelic expression of ZNF597 in the placenta and in seven other tissues, including the cerebrum, heart, liver, spleen, lung, kidney, and muscle. Nevertheless, analysis revealed biallelic expression of the NAA60 gene in these tissues. Moreover, we tested the imprinting status of ZNF597 and confirmed that the maternal allele is expressed in the bovine placenta. To determine the role of DNA methylation in regulating monoallelic/imprinted expression of bovine ZNF597, the methylation status of two CpG-enriched regions in the bovine ZNF597-NAA60 locus was analyzed using the bisulfite sequencing method. Differentially methylated regions were detected on ten CpG loci in the bovine ZNF597 promoter region. In summary, the bovine ZNF597 gene is a maternally expressed gene, and its expression is regulated by DNA methylation, whereas the NAA60 gene is not imprinted in cattle.
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11
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Zhou T, Lin W, Zhu Q, Renaud H, Liu X, Li R, Tang C, Ma C, Rao T, Tan Z, Guo Y. The role of PEG3 in the occurrence and prognosis of colon cancer. Onco Targets Ther 2019; 12:6001-6012. [PMID: 31413595 PMCID: PMC6662866 DOI: 10.2147/ott.s208060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose Imprinted genes are often identified as key players in the etiology and prognosis of many tumors; however, the role they play in colon cancer remains unclear. Along with the development of big data analysis came the discovery of a wealth of genetic prognostic factors, like microsatellite instability for colon cancer, which need to be taken into consideration when evaluating new biomarkers for the disease. Methods We systematically mined public databases to find recurrence free survival (RFS)-related imprinted genes for colon cancer patients on the mRNA level by univariate and multivariate survival analyses. We then investigated the association of methylation status and microRNA expression of the targeted imprinted genes with survival rate of colon cancer patients. Lastly, in a clinical study we used qRT-PCR and immunohistochemistry to quantify mRNA and protein expression of the imprinted genes that related to RFS in our bioinformatics screening, respectively, in 20 tumor tissues compared to paired adjacent tissues. Results The results show that paternally expressed gene 3 (PEG3) is the only imprinted gene related to colon cancer patient prognosis on the mRNA level in our datasets, and high mRNA expression of PEG3 is associated with a poor prognosis. Furthermore, the methylation beta value of cg13960339, as well as the expression of 4 microRNAs, negatively correlated with PEG3 mRNA level and were correlated with the prognosis of colon cancer patients. Moreover, the expression of PEG3 mRNA in colon cancer is significantly lower, but PEG3 protein expression is significantly higher compared to that in normal tissues. Conclusion PEG3 is likely associated with the progression and prognosis of colon cancer.
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Affiliation(s)
- Ting Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
| | - Wei Lin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Qiongni Zhu
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Helen Renaud
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Ruidong Li
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California, Riverside, CA 92507, USA
| | - Cui Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
| | - Chong Ma
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
| | - Tai Rao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
| | - Zhirong Tan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
| | - Ying Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China.,Human Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha, Hunan 410008, People's Republic of China
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12
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Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis. Int J Genomics 2019; 2019:1287671. [PMID: 31093489 PMCID: PMC6481143 DOI: 10.1155/2019/1287671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/26/2022] Open
Abstract
Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes. The results of this initial analysis were extended and validated in a set of 89 paired normal mucosa and CRC samples. We found that 14% of genes showed ASE in one or more cell lines and identified allelic switching of the potential cell survival genes DLX5, GRB10, and SVOPL on chromosome 7, whereby the most abundantly expressed allele in the normal tissue is the lowest expressed allele in the tumor and vice versa. We established that this allelic switch does not result from loss of imprinting. The allelic switching of SVOPL may be a result of transcriptional downregulation, while the exact mechanisms resulting in the allelic switching of DLX5 and GRB10 remain to be elucidated. In conclusion, our results show that profound changes take place in allelic transcriptional regulation during the tumorigenesis of CRC.
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13
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Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
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Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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14
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Perrera V, Martello G. How Does Reprogramming to Pluripotency Affect Genomic Imprinting? Front Cell Dev Biol 2019; 7:76. [PMID: 31143763 PMCID: PMC6521591 DOI: 10.3389/fcell.2019.00076] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/18/2019] [Indexed: 01/14/2023] Open
Abstract
Human induced Pluripotent Stem Cells (hiPSCs) have the capacity to generate a wide range of somatic cells, thus representing an ideal tool for regenerative medicine. Patient-derived hiPSCs are also used for in vitro disease modeling and drug screenings. Several studies focused on the identification of DNA mutations generated, or selected, during the derivation of hiPSCs, some of which are known to drive cancer formation. Avoiding such stable genomic aberrations is paramount for successful use of hiPSCs, but it is equally important to ensure that their epigenetic information is correct, given the critical role of epigenetics in transcriptional regulation and its involvement in a plethora of pathologic conditions. In this review we will focus on genomic imprinting, a prototypical epigenetic mechanism whereby a gene is expressed in a parent-of-origin specific manner, thanks to the differential methylation of specific DNA sequences. Conventional hiPSCs are thought to be in a pluripotent state primed for differentiation. They display a hypermethylated genome with an unexpected loss of DNA methylation at imprinted loci. Several groups recently reported the generation of hiPSCs in a more primitive developmental stage, called naïve pluripotency. Naïve hiPSCs share several features with early human embryos, such as a global genome hypomethylation, which is also accompanied by a widespread loss of DNA methylation at imprinted loci. Given that loss of imprinting has been observed in genetic developmental disorders as well as in a wide range of cancers, it is fundamental to make sure that hiPSCs do not show such epigenetic aberrations. We will discuss what specific imprinted genes, associated with human pathologies, have been found commonly misregulated in hiPSCs and suggest strategies to effectively detect and avoid such undesirable epigenetic abnormalities.
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Affiliation(s)
- Valentina Perrera
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
| | - Graziano Martello
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
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15
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Loukinov D. Targeting CTCFL/BORIS for the immunotherapy of cancer. Cancer Immunol Immunother 2018; 67:1955-1965. [PMID: 30390146 PMCID: PMC11028242 DOI: 10.1007/s00262-018-2251-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 07/13/2018] [Indexed: 10/27/2022]
Abstract
Cancer vaccines have great potential in the fight against metastatic malignancies. Current anti-tumor immunotherapy is hindered by existing tolerance to tumor-associated antigens (TAA) and tumor escape using various mechanisms, highlighting the need for improved targets for immunotherapy. The cancer-testis antigen CTCFL/BORIS was discovered 16 years ago and possesses all features necessary for an ideal TAA. Recently CTCFL/BORIS has received additional attention as a target expressed in cancer stem cells (CSC). These cells drive tumor growth recurrence, metastasis, and treatment resistance. CTCFL/BORIS silencing leads to senescence and death of CSC. Therefore, an immunotherapeutic strategy that targets CTCFL/BORIS may lead to the selective destruction of CSC and potential eradication of metastatic disease. The high immunotherapeutic potential of CTCFL/BORIS antigen was shown in a stringent 4T1 mouse model of breast cancer. Using these highly metastatic, poorly immunogenic carcinoma cells inoculated into T-helper2 prone mice, we showed that DC fed with recombinant CTCFL/BORIS as an immunogen inhibited tumor growth and reduced the number of metastases in distant organs. About 20% of CTCFL/BORIS immunized animals were tumor free. 50% of animals remained metastasis free. Those having metastasis showed at least tenfold fewer metastases compared to controls. In a rat model of breast cancer, we showed that alphavirus-based CTCFL/BORIS immunotherapy was capable of cancer elimination as we were able to cure 50% of animals. Based on the above data, we believe that translation of CTCFL/BORIS-targeting immunotherapeutic strategies to the clinic will provide new avenues for improving survival of breast cancer patients with advanced metastatic disease.
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Affiliation(s)
- Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, NIAID/NIH, Twinbrook 1, Room 1329, 5640 Fishers Lane, Rockville, MD, 20852, USA.
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16
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Küffer S, Gutting T, Belharazem D, Sauer C, Michel MS, Marx A, Trojan L, Ströbel P. Insulin-like growth factor 2 expression in prostate cancer is regulated by promoter-specific methylation. Mol Oncol 2018; 12:256-266. [PMID: 29239100 PMCID: PMC5792735 DOI: 10.1002/1878-0261.12164] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/16/2017] [Accepted: 11/25/2017] [Indexed: 12/12/2022] Open
Abstract
Deregulation of the insulin-like growth factor (IGF) axis and dysbalance of components of the IGF system as potential therapeutic targets have been described in different tumor types. IGF2 is a major embryonic growth factor and an important activator of IGF signaling. It is regulated by imprinting in a development- and tissue-dependent manner and has been implicated in a broad range of malignancies including prostate cancer (PCa). Loss of imprinting (LOI) usually results in bi-allelic gene expression and increased levels of IGF2. However, the regulatory mechanisms and the pathophysiological impact of altered IGF2 expression in PCa remain elusive. Here, we show that in contrast to many other tumors, IGF2 mRNA and protein levels were decreased in 80% of PCa in comparison with non-neoplastic adjacent prostate and were independent of LOI status. Instead, IGF2 expression in both tumors and adjacent prostate depended on preferential usage of the IGF2 promoters P3 and P4. Decreased IGF2 expression in tumors was strongly related to hypermethylation of these two promoters. Methylation of the A region in promoter P4 correlated specifically with IGF2 expression in the 20% of PCa where IGF2 was higher in tumors than in adjacent prostate. We conclude that IGF2 is downregulated in most PCa and may be particularly relevant during early stages of tumor development or during chemotherapy and androgen deprivation. PCa differs from other tumors in that IGF2 expression is mainly regulated through methylation of promoter-specific and not by imprinting. Targeting of promoter-specific regions may have relevance for the adjuvant treatment of PCa.
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Affiliation(s)
- Stefan Küffer
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Germany
| | - Tobias Gutting
- Institute of Pathology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany.,Department of Medicine II, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Djeda Belharazem
- Institute of Pathology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christian Sauer
- Institute of Pathology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maurice S Michel
- Department of Urology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Alexander Marx
- Institute of Pathology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lutz Trojan
- Department of Urology, University Medical Center Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Germany
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17
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Lopez SJ, Dunaway K, Islam MS, Mordaunt C, Vogel Ciernia A, Meguro-Horike M, Horike SI, Segal DJ, LaSalle JM. UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons. Epigenetics 2017; 12:982-990. [PMID: 28925810 PMCID: PMC5788436 DOI: 10.1080/15592294.2017.1376151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.
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Affiliation(s)
- S Jesse Lopez
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - Keith Dunaway
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - M Saharul Islam
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Charles Mordaunt
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Annie Vogel Ciernia
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Makiko Meguro-Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - Shin-Ichi Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - David J Segal
- b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA.,e Biochemistry and Molecular Medicine , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
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18
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19
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Bretz CL, Langohr IM, Kim J. Epigenetic response of imprinted domains during carcinogenesis. Clin Epigenetics 2017; 9:90. [PMID: 28855972 PMCID: PMC5572065 DOI: 10.1186/s13148-017-0393-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/16/2017] [Indexed: 11/25/2022] Open
Abstract
Background Imprinted domains have been identified as targets for aberrant DNA methylation during carcinogenesis, but it remains unclear when these epigenetic alterations occur and how they contribute to tumor progression. Epigenetic instability at key cis-regulatory elements within imprinted domains can concomitantly activate proto-oncogenes and turn off tumor suppressor genes. Thus, to further characterize the epigenetic response of imprinted domains during carcinogenesis, we compared the stability of DNA methylation at a variety of cis-regulatory elements within imprinted domains in two fundamentally different mouse tumors, benign and malignant, induced by the KrasG12D mutation. Results We report that imprinted domains remain stable in benign processes but are highly susceptible to epigenetic alterations in infiltrative lesions. The preservation of DNA methylation within imprinted domains in benign tumors throughout their duration suggests that imprinted genes are not involved with the initiation of carcinogenesis or the growth of tumors. However, the frequent detection of DNA methylation changes at imprinting control regions in infiltrative lesions suggest that imprinted genes are associated with tumor cells gaining the ability to defy tissue boundaries. Conclusion Overall, this study demonstrates that imprinted domains are targeted for DNA hypermethylation when benign tumor cells transition to malignant. Thus, monitoring DNA methylation within imprinted domains may be useful in evaluating the progression of neoplasms. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0393-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Corey L Bretz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Ingeborg M Langohr
- Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA 70803 USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
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20
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Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J. SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res 2017; 45:e36. [PMID: 27899585 PMCID: PMC5389478 DOI: 10.1093/nar/gkw1110] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 10/31/2016] [Indexed: 01/22/2023] Open
Abstract
Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.
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Affiliation(s)
- Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Erika Manlig
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Per Wahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
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21
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Buzby JS, Williams SA, Schaffer L, Head SR, Nugent DJ. Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome. Cancer Genet 2017; 211:9-17. [PMID: 28279309 DOI: 10.1016/j.cancergen.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/14/2016] [Accepted: 01/06/2017] [Indexed: 01/01/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is passed from parent to child. Tumor protein p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Paradoxically, some mutant TP53 carriers remain unaffected, while their children develop cancer within the first few years of life. To address this paradox, response to UV stress was compared in dermal fibroblasts (dFb) from an affected LFS patient vs. their unaffected carrier parent. UV induction of CDKN1A/p21, a regulatory target of p53, in LFS patient dFb was significantly reduced compared to the unaffected parent. UV exposure also induced significantly greater p53[Ser15]-phosphorylation in LFS patient dFb, a reported property of some mutant p53 variants. Taken together, these results suggested that unaffected parental dFb may express an increased proportion of wild-type vs. mutant p53. Indeed, a significantly increased ratio of wild-type to mutant TP53 allele-specific expression in the unaffected parent dFb was confirmed by RT-PCR-RFLP and RNA-seq analysis. Hence, allele-specific expression of wild-type TP53 may allow an unaffected parent to mount a response to genotoxic stress more characteristic of homozygous wild-type TP53 individuals than their affected offspring, providing protection from the oncogenesis associated with LFS.
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Affiliation(s)
- Jeffrey S Buzby
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA.
| | - Shirley A Williams
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA
| | - Lana Schaffer
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Diane J Nugent
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Hematology, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Pediatric Hematology, School of Medicine, University of California at Irvine, Orange, CA, USA
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Kowluru RA, Mishra M. Epigenetic regulation of redox signaling in diabetic retinopathy: Role of Nrf2. Free Radic Biol Med 2017; 103:155-164. [PMID: 28012783 PMCID: PMC5258851 DOI: 10.1016/j.freeradbiomed.2016.12.030] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Diabetic retinopathy is a major vision threatening disease among working age adults, and increased oxidative stress is one of the prime causative factors in its pathogenesis. Increased reactive oxygen species (ROS) in the cytosol damage mitochondria, and due to compromised antioxidant signaling system and dysfunctional mitochondria with damaged mitochondrial DNA, ROS continue to pile up, accelerating capillary cell loss. In addition to other cellular and enzymatic defense systems, the retina is also equipped with the nuclear erythroid-2-p45-related factor-2 (Nrf2) antioxidant response element signaling pathway, which controls the expression of genes important in detoxification and elimination of ROS. However, in diabetes, its transcriptional activity is impaired, further exacerbating and exposing the retina to elevated stress. Diabetic milieu also alters epigenetic factors responsible for chromatin modifications and gene regulation, and kelch-like ECH-associated protein 1 (Keap1), important in regulating Nrf2-antioxidant signaling axis, is epigenetically modified, impeding nuclear translocation of Nrf2, and this inhibits the transcription of genes with Antioxidant Response Element. This review discusses antioxidant signaling, especially the role of Nrf2, in diabetic retinopathy, and possible involvement of epigenetic modifications in antioxidant signaling and Nrf2 transcriptional activity. Therapies targeting Nrf2 activation, including epigenetic modifications, have potentional to prevent mitochondrial damage and inhibit the development, and progression of this sight-threatening disease which most of the patients get after 20-25 years of diabetes.
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Affiliation(s)
- Renu A Kowluru
- Kresge Eye Institute, Wayne State University, Detroit, MI, United States.
| | - Manish Mishra
- Kresge Eye Institute, Wayne State University, Detroit, MI, United States
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23
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Villacis RAR, Basso TR, Canto LM, Nóbrega AF, Achatz MI, Rogatto SR. Germline large genomic alterations on 7q in patients with multiple primary cancers. Sci Rep 2017; 7:41677. [PMID: 28139749 PMCID: PMC5282589 DOI: 10.1038/srep41677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/29/2016] [Indexed: 11/11/2022] Open
Abstract
Patients with multiple primary cancers (MPCs) are suspected to have a hereditary cancer syndrome. However, only a small proportion may be explained by mutations in high-penetrance genes. We investigate two unrelated MPC patients that met Hereditary Breast and Ovaria Cancer criteria, both presenting triple negative breast tumors and no mutations in BRCA1, BRCA2 and TP53 genes. Germline rearrangements on chromosome 7q, involving over 40 Mb of the same region, were found in both patients: one with mosaic loss (80% of cells) and the other with cnLOH (copy-neutral loss of heterozygosity) secondary to maternal allele duplication. Five children tested had no alterations on 7q. The patients shared 330 genes in common on 7q22.1-q34, including several tumor suppressor genes (TSGs) previously related to breast cancer risk and imprinted genes. The analysis of the triple negative BC from one patient revealed a mosaic gain of 7q translated for over-expressed cancer-related genes. The involvement of TSGs and imprinted genes, mapped on 7q, has the potential of being associated to MPC risk, as well as cancer progression. To our knowledge, this is the first description of patients with MPCs that harbor constitutive large alterations on 7q.
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Affiliation(s)
- R. A. R. Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília - UnB, Brasília, DF, Brazil
| | - T. R. Basso
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - L. M. Canto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - A. F. Nóbrega
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - M. I. Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - S. R. Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital, DK and University of Southern Denmark, Denmark
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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24
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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25
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Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
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Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
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Bretz CL, Langohr IM, Lee S, Kim J. Epigenetic instability at imprinting control regions in a Kras(G12D)-induced T-cell neoplasm. Epigenetics 2016; 10:1111-20. [PMID: 26507119 DOI: 10.1080/15592294.2015.1110672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Although aberrant DNA methylation within imprinted domains has been reported in a variety of neoplastic diseases, it remains largely uncharacterized in the context of carcinogenesis. In this study, we induced T-cell lymphoma in mice by employing a breeding scheme involving mouse strains, LSL-Kras(G12D) and MMTV-Cre. We then systematically surveyed imprinted domains for DNA methylation changes during tumor progression using combined bisulfite restriction analysis and NGS-based bisulfite sequencing. We detected hyper- or hypo-methylation at the imprinting control regions (ICRs) of the Dlk1, Peg10, Peg3, Grb10, and Gnas domains. These DNA methylation changes at ICRs were more prevalent and consistent than those observed at the promoter regions of well-known tumor suppressors, such as Mgmt, Fhit, and Mlh1. Thus, the changes observed at these imprinted domains are the outcome of isolated incidents affecting DNA methylation settings. Within imprinted domains, DNA methylation changes tend to be restricted to ICRs as nearby somatic differentially methylated regions and promoter regions experience no change. Furthermore, detailed analyses revealed that small cis-regulatory elements within ICRs tend to be resistant to DNA methylation changes, suggesting potential protection by unknown trans-factors. Overall, this study demonstrates that DNA methylation changes at ICRs are dynamic during carcinogenesis and advocates that detection of aberrant DNA methylation at ICRs may serve as a biomarker to enhance diagnostic procedures.
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Affiliation(s)
- Corey L Bretz
- a Department of Biological Sciences ; Louisiana State University ; Baton Rouge ; LA , USA
| | - Ingeborg M Langohr
- b Louisiana State University School of Veterinary Medicine ; Department of Pathobiological Sciences ; Baton Rouge ; LA , USA
| | - Suman Lee
- a Department of Biological Sciences ; Louisiana State University ; Baton Rouge ; LA , USA
| | - Joomyeong Kim
- a Department of Biological Sciences ; Louisiana State University ; Baton Rouge ; LA , USA
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Boot A, Oosting J, de Miranda NFCC, Zhang Y, Corver WE, van de Water B, Morreau H, van Wezel T. Imprinted survival genes preclude loss of heterozygosity of chromosome 7 in cancer cells. J Pathol 2016; 240:72-83. [DOI: 10.1002/path.4756] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/21/2016] [Accepted: 05/24/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Arnoud Boot
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Jan Oosting
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Noel FCC de Miranda
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Yinghui Zhang
- Division of Toxicology, Leiden Academic Center for Drug Research; Leiden University; The Netherlands
| | - Willem E Corver
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Center for Drug Research; Leiden University; The Netherlands
| | - Hans Morreau
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Tom van Wezel
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
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Anwar SL, Krech T, Hasemeier B, Schipper E, Schweitzer N, Vogel A, Kreipe H, Lehmann U. Loss of DNA methylation at imprinted loci is a frequent event in hepatocellular carcinoma and identifies patients with shortened survival. Clin Epigenetics 2015; 7:110. [PMID: 26473022 PMCID: PMC4606497 DOI: 10.1186/s13148-015-0145-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 02/07/2023] Open
Abstract
Background Aberrant DNA methylation at imprinted loci is an important molecular mechanism contributing to several developmental and pathological disorders including cancer. However, knowledge about imprinting defects due to DNA methylation changes is relatively limited in hepatocellular carcinoma (HCC), the third leading cause of cancer death worldwide. Therefore, comprehensive quantitative DNA methylation analysis at imprinted loci showing ~50 % methylation in healthy liver tissues was performed in primary HCC specimens and the peritumoural liver tissues. Results We found frequent and extensive DNA methylation aberrations at many imprinted loci in HCC. Unsupervised cluster analysis of DNA methylation patterns at imprinted loci revealed subgroups of HCCs with moderate and severe loss of methylation. Hypomethylation at imprinted loci correlated significantly with poor overall survival (log-rank test, p = 0.02). Demethylation at imprinted loci was accompanied by loss of methylation at LINE-1, a commonly used marker for global DNA methylation levels (p < 0.001). In addition, we found that loss of methylation at imprinted loci correlated with the presence of a CTNNB1 mutation (Fisher’s exact test p = 0.03). Re-analysis of publically available genome-wide methylation data sets confirmed our findings. The analysis of benign liver tumours (hepatocellular adenoma (HCA) and focal nodular hyperplasia (FNH)), the corresponding adjacent liver tissues, and healthy liver tissues showed that aberrant DNA methylation at imprinted loci is specific for HCC. Conclusions Our analyses demonstrate frequent and widespread DNA methylation aberrations at imprinted loci in human HCC and identified a hypomethylated subgroup of patients with shorter overall survival. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0145-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sumadi Lukman Anwar
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany ; Present address: Department of Surgery, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, 55281 Indonesia
| | - Till Krech
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Britta Hasemeier
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Elisa Schipper
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Nora Schweitzer
- Department of Gastroenterology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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29
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Harrison K, Hoad G, Scott P, Simpson L, Horgan GW, Smyth E, Heys SD, Haggarty P. Breast cancer risk and imprinting methylation in blood. Clin Epigenetics 2015; 7:92. [PMID: 26347357 PMCID: PMC4560070 DOI: 10.1186/s13148-015-0125-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 08/17/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Altered DNA methylation of imprinted genes has been implicated in a range of cancers. Imprinting is established early in development, and some are maintained throughout the life course in multiple tissues, providing a plausible mechanism linking known early life factors to cancer risk. This study investigated methylation status of seven imprinted differentially methylated regions-PLAGL1/ZAC1, H19-ICR1, IGF2-DMR2, KvDMR-ICR2, RB1, SNRPN-DMR1 and PEG3-in blood samples from 189 women with the most common type of invasive breast cancer (invasive ductal carcinoma-IDC), 41 women with in situ breast cancer (ductal carcinoma in situ-DCIS) and 363 matched disease-free controls. RESULTS There was no evidence that imprinted gene methylation levels varied with age (between 25 and 87 years old), weight or height. Higher PEG3 methylation was associated with an elevated risk of IDC (odds ratio (OR) 1.065; 95 % confidence interval (CI) 1.002, 1.132; p = 0.042) and DCIS (OR 1.139; 95 % CI 1.027, 1.263; p = 0.013). The effect was stronger when in situ and invasive breast cancer were combined (OR 1.079; 95 % CI 1.020, 1.142; p = 0.008). DCIS breast cancer risk increased with higher KvDMR-ICR2 methylation (OR 1.395; 95 % CI 1.190, 1.635; p < 0.001) and lower PLAGL1/ZAC1 methylation (OR 0.905; 95 % CI 0.833, 0.982; p = 0.017). In a combined model, only KvDMR-ICR2 methylation remained significantly associated. CONCLUSIONS These findings may help to improve our understanding of the aetiology of breast cancer and the importance of early life factors in particular. Imprinting methylation status also has the potential to contribute to the development of improved screening and treatment strategies for women with, or at risk of, breast cancer.
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Affiliation(s)
- Kristina Harrison
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Gwen Hoad
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Paula Scott
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Louise Simpson
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, University Medical Buildings, Foresterhill, Aberdeen, UK
| | | | - Elizabeth Smyth
- Aberdeen Royal Infirmary, Ward 308, Foresterhill, Aberdeen, UK
| | - Steven D Heys
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, University Medical Buildings, Foresterhill, Aberdeen, UK
| | - Paul Haggarty
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
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Kim J, Bretz CL, Lee S. Epigenetic instability of imprinted genes in human cancers. Nucleic Acids Res 2015; 43:10689-99. [PMID: 26338779 PMCID: PMC4678850 DOI: 10.1093/nar/gkv867] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022] Open
Abstract
Many imprinted genes are often epigenetically affected in human cancers due to their functional linkage to insulin and insulin-like growth factor signaling pathways. Thus, the current study systematically characterized the epigenetic instability of imprinted genes in multiple human cancers. First, the survey results from TCGA (The Cancer Genome Atlas) revealed that the expression levels of the majority of imprinted genes are downregulated in primary tumors compared to normal cells. These changes are also accompanied by DNA methylation level changes in several imprinted domains, such as the PEG3, MEST and GNAS domains. Second, these DNA methylation level changes were further confirmed manually using several sets of cancer DNA. According to the results, the Imprinting Control Regions of the PEG3, MEST and GNAS domains are indeed affected in breast, lung and ovarian cancers. This DNA methylation survey also revealed that evolutionarily conserved cis-regulatory elements within these imprinted domains are very variable in both normal and cancer cells. Overall, this study highlights the epigenetic instability of imprinted domains in human cancers and further suggests its potential use as cancer biomarkers.
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Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Corey L Bretz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Suman Lee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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31
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Zhao H, Lai X, Xu X, Sui K, Bu X, Ma W, Li D, Guo K, Xu J, Yao L, Li W, Su J. Histochemical analysis of testis specific gene 13 in human normal and malignant tissues. Cell Tissue Res 2015; 362:653-63. [PMID: 26111495 DOI: 10.1007/s00441-015-2227-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 05/20/2015] [Indexed: 11/25/2022]
Abstract
Testis-specific gene 13 (TSGA13) is abundantly expressed in testis. As previous studies of TSGA13 expression pattern have all been based on mRNA analysis, it is imperative to investigate its actual protein expression. Here, we first examined TSGA13 gene tree and protein homology among species, and found that TSGA13 is relatively well conserved. Next, we detected its protein expression in normal human tissues as well as in a limited number of malignant tumors by immunohistochemistry (IHC). It was demonstrated that, in addition to testis, high expression of TSGA13 could also be observed in multiple normal tissues, including stomach, larynx, spleen, bladder, tonsil, liver and thyroid. Notably, most types of human carcinoma tissues displayed reduced expression of TSGA13 rather than their adjacent normal tissues except glioblastoma and lung cancer. Hence, the data from the current study strongly suggest the association between TSGA13 and tumor malignancy.
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Affiliation(s)
- Hu Zhao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Xiaofeng Lai
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Xinyuan Xu
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Ke Sui
- Department of Stomatology, Air Force General Hospital, Beijing, 100142, China
| | - Xin Bu
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Wenqiang Ma
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Di Li
- Department of Stomatology, Air Force General Hospital, Beijing, 100142, China
| | - Kai Guo
- Department of Orthopedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Jinke Xu
- Department of Oral and Maxillofacial Surgery, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Libo Yao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China
| | - Wei Li
- Department of Human Anatomy, Histology, and Embryology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Jin Su
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, 169 Changle Western Road, Xi'an, 710032, China.
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32
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Contribution of epigenetics in diabetic retinopathy. SCIENCE CHINA-LIFE SCIENCES 2015; 58:556-63. [PMID: 26025281 DOI: 10.1007/s11427-015-4853-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/04/2015] [Indexed: 12/22/2022]
Abstract
Diabetes has become the epidemic of the 21st century, and with over 90% patients with diabetes becoming at a risk of developing retinopathy, diabetic retinopathy has emerged as a major public health concern. In spite of cutting edge research in the field, how retina and its vasculature are damaged by the diabetic milieu remains ambiguous. The environmental factors, life style or disease process can also bring in modifications in the DNA, and these epigenetic modifications either silence or activate a gene without altering the DNA sequence. Diabetic environment up- or downregulates a number of genes in the retina, and emerging research has shown that it also facilitates epigenetic modifications. In the pathogenesis of diabetic retinopathy, the genes associated with important enzymes (e.g., mitochondrial superoxide dismutase, matrix metalloproteinase-9 and thioredoxin interacting protein) and transcriptional factors are epigenetically modified, the enzymes responsible for these epigenetic modifications are either activated or inhibited, and the levels of microRNAs are altered. With epigenetic modifications taking an important place in diabetic retinopathy, it is now becoming critical to evaluate these modifications, and understand their impact on this slow progressing blinding disease.
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Keller RB, El Demellawy D, Quaglia A, Finegold M, Kapur RP. Methylation status of the chromosome arm 19q MicroRNA cluster in sporadic and androgenetic-Biparental mosaicism-associated hepatic mesenchymal hamartoma. Pediatr Dev Pathol 2015; 18:218-27. [PMID: 25751191 DOI: 10.2350/15-01-1600-oa.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The C19MC gene on chromosome band 19q13.4 encodes a cluster of 46 microRNAs; those microRNAs are normally only expressed from the paternal allele and in the placenta. Placental expression correlates with selective demethylation of the paternal C19MC promoter, in contrast to methylation of both maternal and paternal alleles in nonplacental tissues. Prior investigations demonstrated "ectopic" activation of this gene in most hepatic mesenchymal hamartomas, including sporadic tumors and others with androgenetic-biparental mosaicism (subset of cells are diploid, but contain only paternally derived chromosomes). In the present investigation of C19MC promoter methylation status in a series of 14 mesenchymal hamartomas, a demethylated allele was identified in 6 tumors, including all 4 with androgenetic-biparental mosaicism. Conversely, only methylated alleles were cloned from sporadic hamartomas, including 3 tumors with chromosomal rearrangements thought likely to activate C19MC expression independent of the native promoter. In conjunction with published data, the findings suggest multiple molecular mechanisms for C19MC activation in hepatic mesenchymal hamartoma, including the existence of a normal placental imprinting pattern in mesenchymal cells in a subset of cases. Some or all of the latter hamartomas may result from placental "grafting," a hypothesis supported by endothelial expression of the placental vascular marker, glucose transporter-1, in 1 of the 6 cases with a demethylated allele.
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Affiliation(s)
- Rachel B. Keller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Dina El Demellawy
- Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alberto Quaglia
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Milton Finegold
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Raj P. Kapur
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
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Cheong CY, Chng K, Ng S, Chew SB, Chan L, Ferguson-Smith AC. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. Genome Res 2015; 25:611-23. [PMID: 25862382 PMCID: PMC4417110 DOI: 10.1101/gr.183301.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.
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Affiliation(s)
- Clara Y Cheong
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Keefe Chng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Shilen Ng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Siew Boom Chew
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Louiza Chan
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Anne C Ferguson-Smith
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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35
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de Araújo E, Vasques L, Stabellini R, Krepischi A, Pereira L. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line. Braz J Med Biol Res 2014; 47:1029-35. [PMID: 25387668 PMCID: PMC4244667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/27/2014] [Indexed: 12/16/2023] Open
Abstract
DNA methylation is essential in X chromosome inactivation and genomic imprinting, maintaining repression of XIST in the active X chromosome and monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase genes DNMT1 and DNMT3B in the HCT116 cell line (DKO cells) leads to global DNA hypomethylation and biallelic expression of the imprinted gene IGF2 but does not lead to reactivation of XIST expression, suggesting that XIST repression is due to a more stable epigenetic mark than imprinting. To test this hypothesis, we induced acute hypomethylation in HCT116 cells by 5-aza-2'-deoxycytidine (5-aza-CdR) treatment (HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by microarray and monitoring the expression of XIST and imprinted genes IGF2, H19, and PEG10. Whereas imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the XIST locus was hypomethylated and weakly expressed only under acute hypomethylation conditions, indicating the importance of XIST repression in the active X to cell survival. Given that DNMT3A is the only active DNMT in DKO cells, it may be responsible for ensuring the repression of XIST in those cells. Taken together, our data suggest that XIST repression is more tightly controlled than genomic imprinting and, at least in part, is due to DNMT3A.
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Affiliation(s)
- E.S.S. de Araújo
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - L.R. Vasques
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
| | - R. Stabellini
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - A.C.V. Krepischi
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - L.V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
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36
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de Araújo E, Vasques L, Stabellini R, Krepischi A, Pereira L. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line. Braz J Med Biol Res 2014. [PMID: 25387668 PMCID: PMC4244667 DOI: 10.1590/1414-431x20144058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA methylation is essential in X chromosome inactivation and genomic imprinting,
maintaining repression of XIST in the active X chromosome and
monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase
genes DNMT1 and DNMT3B in the HCT116 cell line (DKO
cells) leads to global DNA hypomethylation and biallelic expression of the imprinted
gene IGF2 but does not lead to reactivation of XIST
expression, suggesting that XIST repression is due to a more stable
epigenetic mark than imprinting. To test this hypothesis, we induced acute
hypomethylation in HCT116 cells by 5-aza-2′-deoxycytidine (5-aza-CdR) treatment
(HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by
microarray and monitoring the expression of XIST and imprinted genes
IGF2, H19, and PEG10. Whereas
imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the
XIST locus was hypomethylated and weakly expressed only under
acute hypomethylation conditions, indicating the importance of XIST
repression in the active X to cell survival. Given that DNMT3A is the only active
DNMT in DKO cells, it may be responsible for ensuring the repression of
XIST in those cells. Taken together, our data suggest that
XIST repression is more tightly controlled than genomic
imprinting and, at least in part, is due to DNMT3A.
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Affiliation(s)
- E.S.S. de Araújo
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
| | | | - R. Stabellini
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
| | - A.C.V. Krepischi
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
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Kuhtz J, Romero S, De Vos M, Smitz J, Haaf T, Anckaert E. Human in vitro oocyte maturation is not associated with increased imprinting error rates at LIT1, SNRPN, PEG3 and GTL2. Hum Reprod 2014; 29:1995-2005. [PMID: 24963167 DOI: 10.1093/humrep/deu155] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
STUDY QUESTION Does in vitro maturation (IVM) of cumulus-enclosed germinal vesicle (GV) stage oocytes retrieved from small antral follicles in minimally stimulated cycles without an ovulatory hCG dose induce imprinting errors at LIT1, SNRPN, PEG3 and GTL2 in human oocytes? SUMMARY ANSWER There is no significant increase in imprinting mutations at LIT1, SNRPN, PEG3 and GTL2 after IVM of cumulus-enclosed GV oocytes from small antral follicles in minimally stimulated cycles without hCG priming. WHAT IS KNOWN ALREADY Animal models have generally demonstrated correct methylation imprint establishment for in vitro grown and matured oocytes. For human IVM, well-designed studies allowing conclusions on imprint establishment are currently not available. STUDY DESIGN, SIZE, DURATION Immature oocyte-cumulus complexes from 2 to 9 mm follicles were retrieved in polycystic ovary syndrome (PCOS) subjects in minimally stimulated cycles without hCG priming and matured in vitro. In vivo grown oocytes were retrieved after conventional ovarian stimulation for IVF/ICSI or after ovulation induction. Imprinting error rates at three maternally methylated (LIT1, SNRPN and PEG3) and one paternally methylated (GTL2) imprinted genes were compared in 71 in vitro and 38 in vivo matured oocytes. PARTICIPANTS/MATERIALS, SETTING, METHODS The limiting dilution bisulfite sequencing technique was applied, allowing increased sensitivity based on multiplex PCR for the imprinted genes and the inclusion of non-imprinted marker genes for cumulus cell DNA contamination. MAIN RESULTS AND THE ROLE OF CHANCE In vitro as well as in vivo matured oocytes showed only a few abnormal alleles, consistent with epimutations. The abnormalities were more frequent in immature than in mature oocytes for both groups, although no significant difference was reached. There was no statistically significant increase in imprinting errors in IVM oocytes. LIMITATIONS, REASONS FOR CAUTION This single cell methylation analysis was restricted to a number of well-selected imprinted genes. Genome-wide methylation analysis of single human oocytes is currently not possible. WIDER IMPLICATIONS OF THE FINDINGS IVM is a patient-friendly alternative to conventional ovarian stimulation in PCOS patients and is associated with reduced gonadotrophin costs and avoidance of OHSS. The results of this study show for the first time that optimized human IVM procedures have no significant effects on the establishment of maternal DNA methylation patterns at LIT1, SNRPN, PEG3 and GTL2. STUDY FUNDING/COMPETING INTERESTS This study was supported by research funds from Agentschap voor Innovatie door Wetenschap en Technologie (IWT-TBM 110680), Wetenschappelijk Fonds Willy Gepts (WFWG 2011) and German Research Foundation (HA 1374/12-2). There are no competing interests.
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Affiliation(s)
- J Kuhtz
- Institute of Human Genetics, University of Wuerzburg, Wuerzburg 97074, Germany
| | - S Romero
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
| | - M De Vos
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
| | - J Smitz
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
| | - T Haaf
- Institute of Human Genetics, University of Wuerzburg, Wuerzburg 97074, Germany
| | - E Anckaert
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
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Anwar SL, Krech T, Hasemeier B, Schipper E, Schweitzer N, Vogel A, Kreipe H, Lehmann U. Deregulation of RB1 expression by loss of imprinting in human hepatocellular carcinoma. J Pathol 2014; 233:392-401. [PMID: 24838394 DOI: 10.1002/path.4376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/30/2014] [Accepted: 05/11/2014] [Indexed: 12/19/2022]
Abstract
The tumour suppressor gene RB1 is frequently silenced in many different types of human cancer, including hepatocellular carcinoma (HCC). However, mutations of the RB1 gene are relatively rare in HCC. A systematic screen for the identification of imprinted genes deregulated in human HCC revealed that RB1 shows imprint abnormalities in a high proportion of primary patient samples. Altogether, 40% of the HCC specimens (16/40) showed hyper- or hypomethylation at the CpG island in intron 2 of the RB1 gene. Re-analysis of publicly available genome-wide DNA methylation data confirmed these findings in two independent HCC cohorts. Loss of correct DNA methylation patterns at the RB1 locus leads to the aberrant expression of an alternative RB1-E2B transcript, as measured by quantitative real-time PCR. Demethylation at the intron 2 CpG island by DNMT1 knock-down or aza-deoxycytidine (DAC) treatment stimulated expression of the RB1-E2B transcript, accompanied by diminished RB1 main transcript expression. No aberrant DNA methylation was found at the RB1 locus in hepatocellular adenoma (HCA, n = 10), focal nodular hyperplasia (FNH, n = 5) and their corresponding adjacent liver tissue specimens. Deregulated RB1 expression due to hyper- or hypomethylation in intron 2 of the RB1 gene is found in tumours without loss of heterozygosity and is associated with a decrease in overall survival (p = 0.032) if caused by hypermethylation of CpG85. This unequivocally demonstrates that loss of imprinting represents an important additional mechanism for RB1 pathway inactivation in human HCC, complementing well-described molecular defects.
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Edfeldt K, Ahmad T, Åkerström G, Janson ET, Hellman P, Stålberg P, Björklund P, Westin G. TCEB3C a putative tumor suppressor gene of small intestinal neuroendocrine tumors. Endocr Relat Cancer 2014; 21:275-84. [PMID: 24351681 DOI: 10.1530/erc-13-0419] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small intestinal neuroendocrine tumors (SI-NETs), formerly known as midgut carcinoids, are rare and slow-growing neoplasms. Frequent loss of one copy of chromosome 18 in primary tumors and metastases has been observed. The aim of the study was to investigate a possible role of TCEB3C (Elongin A3), currently the only imprinted gene on chromosome 18, as a tumor suppressor gene in SI-NETs, and whether its expression is epigenetically regulated. Primary tumors, metastases, the human SI-NET cell line CNDT2.5, and two other cell lines were included. Immunohistochemistry, gene copy number determination by PCR, colony formation assay, western blotting, real-time quantitative RT-PCR, RNA interference, and quantitative CpG methylation analysis by pyrosequencing were performed. A large majority of tumors (33/43) showed very low to undetectable Elongin A3 expression and as expected 89% (40/45) displayed one gene copy of TCEB3C. The DNA hypomethylating agent 5-aza-2'-deoxycytidine induced TCEB3C expression in CNDT2.5 cells, in primary SI-NET cells prepared directly after surgery, but not in two other cell lines. Also siRNA to DNMT1 and treatment with the general histone methyltransferase inhibitor 3-deazaneplanocin A induced TCEB3C expression in a cell type-specific way. CpG methylation at the TCEB3C promoter was observed in all analyzed tissues and thus not related to expression. Overexpression of TCEB3C resulted in a 50% decrease in clonogenic survival of CNDT2.5 cells, but not of control cells. The results support a putative role of TCEB3C as a tumor suppressor gene in SI-NETs. Epigenetic repression of TCEB3C seems to be tumor cell type-specific and involves both DNA and histone methylation.
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Affiliation(s)
- Katarina Edfeldt
- Departments of Surgical Sciences Medical Sciences, Uppsala University Hospital, Uppsala University, Entrance 70, 3 tr, SE-75185 Uppsala, Sweden
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40
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Ribarska T, Goering W, Droop J, Bastian KM, Ingenwerth M, Schulz WA. Deregulation of an imprinted gene network in prostate cancer. Epigenetics 2014; 9:704-17. [PMID: 24513574 DOI: 10.4161/epi.28006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Multiple epigenetic alterations contribute to prostate cancer progression by deregulating gene expression. Epigenetic mechanisms, especially differential DNA methylation at imprinting control regions (termed DMRs), normally ensure the exclusive expression of imprinted genes from one specific parental allele. We therefore wondered to which extent imprinted genes become deregulated in prostate cancer and, if so, whether deregulation is due to altered DNA methylation at DMRs. Therefore, we selected presumptive deregulated imprinted genes from a previously conducted in silico analysis and from the literature and analyzed their expression in prostate cancer tissues by qRT-PCR. We found significantly diminished expression of PLAGL1/ZAC1, MEG3, NDN, CDKN1C, IGF2, and H19, while LIT1 was significantly overexpressed. The PPP1R9A gene, which is imprinted in selected tissues only, was strongly overexpressed, but was expressed biallelically in benign and cancerous prostatic tissues. Expression of many of these genes was strongly correlated, suggesting co-regulation, as in an imprinted gene network (IGN) reported in mice. Deregulation of the network genes also correlated with EZH2 and HOXC6 overexpression. Pyrosequencing analysis of all relevant DMRs revealed generally stable DNA methylation between benign and cancerous prostatic tissues, but frequent hypo- and hyper-methylation was observed at the H19 DMR in both benign and cancerous tissues. Re-expression of the ZAC1 transcription factor induced H19, CDKN1C and IGF2, supporting its function as a nodal regulator of the IGN. Our results indicate that a group of imprinted genes are coordinately deregulated in prostate cancers, independently of DNA methylation changes.
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Affiliation(s)
- Teodora Ribarska
- Department of Urology; Heinrich Heine University; Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Urology; Heinrich Heine University; Düsseldorf, Germany
| | - Johanna Droop
- Department of Urology; Heinrich Heine University; Düsseldorf, Germany
| | | | - Marc Ingenwerth
- Department of Urology; Heinrich Heine University; Düsseldorf, Germany; Institute for Anatomy II; Heinrich Heine University; Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology; Heinrich Heine University; Düsseldorf, Germany
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41
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Horsthemke B. In brief: genomic imprinting and imprinting diseases. J Pathol 2014; 232:485-7. [PMID: 24395592 DOI: 10.1002/path.4326] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 12/19/2013] [Accepted: 12/27/2013] [Indexed: 11/07/2022]
Abstract
Genomic imprinting is an epigenetic process by which the male and the female germline confer different DNA methylation marks and histone modifications onto specific gene regions, so that one allele of an imprinted gene is active and the other one is silent. Since the dosage of imprinted genes is important for normal development, growth and behaviour, the loss or duplication of the active allele can cause disease.
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Affiliation(s)
- Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Germany
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42
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Autuoro JM, Pirnie SP, Carmichael GG. Long noncoding RNAs in imprinting and X chromosome inactivation. Biomolecules 2014; 4:76-100. [PMID: 24970206 PMCID: PMC4030979 DOI: 10.3390/biom4010076] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/18/2013] [Accepted: 12/27/2013] [Indexed: 12/11/2022] Open
Abstract
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Technological advancements and deep-sequencing of the transcriptome have facilitated the identification of numerous new lncRNAs, many with unusual properties, however, the function of most of these molecules is still largely unknown. Some evidence suggests that several of these lncRNAs may regulate their own transcription in cis, and that of nearby genes, by recruiting remodeling factors to local chromatin. Notably, lncRNAs are known to exist at many imprinted gene clusters. Genomic imprinting is a complex and highly regulated process resulting in the monoallelic silencing of certain genes, based on the parent-of-origin of the allele. It is thought that lncRNAs may regulate many imprinted loci, however, the mechanism by which they exert such influence is poorly understood. This review will discuss what is known about the lncRNAs of major imprinted loci, and the roles they play in the regulation of imprinting.
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Affiliation(s)
- Joseph M Autuoro
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
| | - Stephan P Pirnie
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
| | - Gordon G Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
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43
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Genomic Imprinting - der Kampf der Geschlechter auf molekularer Ebene. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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45
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Jurkowska RZ, Jeltsch A. Genomic Imprinting-The Struggle of the Genders at the Molecular Level. Angew Chem Int Ed Engl 2013; 52:13524-36. [DOI: 10.1002/anie.201307005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 11/10/2022]
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46
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Menigatti M, Staiano T, Manser CN, Bauerfeind P, Komljenovic A, Robinson M, Jiricny J, Buffoli F, Marra G. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis 2013; 2:e56. [PMID: 23857251 PMCID: PMC3740287 DOI: 10.1038/oncsis.2013.21] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022] Open
Abstract
Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of these tumors.
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Affiliation(s)
- M Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - T Staiano
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - C N Manser
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - P Bauerfeind
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - A Komljenovic
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - M Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - J Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - F Buffoli
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - G Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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47
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Ito Y, Nativio R, Murrell A. Induced DNA demethylation can reshape chromatin topology at the IGF2-H19 locus. Nucleic Acids Res 2013; 41:5290-302. [PMID: 23585276 PMCID: PMC3664821 DOI: 10.1093/nar/gkt240] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 11/15/2022] Open
Abstract
Choriocarcinomas are embryonal tumours with loss of imprinting and hypermethylation at the insulin-like growth factor 2 (IGF2)-H19 locus. The DNA methyltransferase inhibitor, 5-Aza-2'deoxycytidine (5-AzaCdR) is an approved epigenetic cancer therapy. However, it is not known to what extent 5-AzaCdR influences other epigenetic marks. In this study, we set out to determine whether 5-AzaCdR treatment can reprogram the epigenomic organization of the IGF2-H19 locus in a choriocarcinoma cancer cell line (JEG3). We found that localized DNA demethylation at the H19 imprinting control region (ICR) induced by 5-AzaCdR, reduced IGF2, increased H19 expression, increased CTCF and cohesin recruitment and changed histone modifications. Furthermore chromatin accessibility was increased locus-wide and chromatin looping topography was altered such that a CTCF site downstream of the H19 enhancers switched its association with the CTCF site upstream of the IGF2 promoters to associate with the ICR. We identified a stable chromatin looping domain, which forms independently of DNA methylation. This domain contains the IGF2 gene and is marked by a histone H3 lysine 27 trimethylation block between CTCF site upstream of the IGF2 promoters and the Centrally Conserved Domain upstream of the ICR. Together, these data provide new insights into the responsiveness of chromatin topography to DNA methylation changes.
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Affiliation(s)
- Yoko Ito
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
| | - Raffaella Nativio
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
| | - Adele Murrell
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
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Barault L, Ellsworth RE, Harris HR, Valente AL, Shriver CD, Michels KB. Leukocyte DNA as surrogate for the evaluation of imprinted Loci methylation in mammary tissue DNA. PLoS One 2013; 8:e55896. [PMID: 23409079 PMCID: PMC3567003 DOI: 10.1371/journal.pone.0055896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 01/04/2013] [Indexed: 01/01/2023] Open
Abstract
There is growing interest in identifying surrogate tissues to identify epimutations in cancer patients since primary target tissues are often difficult to obtain. Methylation patterns at imprinted loci are established during gametogenesis and post fertilization and their alterations have been associated with elevated risk of cancer. Methylation at several imprinted differentially methylated regions (GRB10 ICR, H19 ICR, KvDMR, SNRPN/SNURF ICR, IGF2 DMR0, and IGF2 DMR2) were analyzed in DNA from leukocytes and mammary tissue (normal, benign diseases, or malignant tumors) from 87 women with and without breast cancer (average age of cancer patients: 53; range: 31-77). Correlations between genomic variants and DNA methylation at the studied loci could not be assessed, making it impossible to exclude such effects. Methylation levels observed in leukocyte and mammary tissue DNA were close to the 50% expected for monoallellic methylation. While no correlation was observed between leukocyte and mammary tissue DNA methylation for most of the analyzed imprinted genes, Spearman's correlations were statistically significant for IGF2 DMR0 and IGF2 DMR2, although absolute methylation levels differed. Leukocyte DNA methylation levels of selected imprinted genes may therefore serve as surrogate markers of DNA methylation in cancer tissue.
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Affiliation(s)
- Ludovic Barault
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rachel E. Ellsworth
- Clinical Breast Care Project, Henry M. Jackson Foundation for the Advancement of Military Medicine, Windber, Pennsylvania, United States of America
| | - Holly R. Harris
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Allyson L. Valente
- Clinical Breast Care Project, Windber Research Institute, Windber, Pennsylvania, United States of America
| | - Craig D. Shriver
- Clinical Breast Care Project, Walter Reed Army Medical Center, Washington, District of Columbia, United States of America
| | - Karin B. Michels
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Epigenetics: How Genes and Environment Interact. ENVIRONMENTAL EPIGENOMICS IN HEALTH AND DISEASE 2013. [DOI: 10.1007/978-3-642-23380-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Anckaert E, De Rycke M, Smitz J. Culture of oocytes and risk of imprinting defects. Hum Reprod Update 2012; 19:52-66. [DOI: 10.1093/humupd/dms042] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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