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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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Fischer AD, Veronese Paniagua DA, Swaminathan S, Kashima H, Rubin DC, Madison BB. The oncogenic function of PLAGL2 is mediated via ASCL2 and IGF2 and a Wnt-independent mechanism in colorectal cancer. Am J Physiol Gastrointest Liver Physiol 2023; 325:G196-G211. [PMID: 37310750 PMCID: PMC10396286 DOI: 10.1152/ajpgi.00058.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Colorectal cancer (CRC) tumorigenesis and progression are linked to common oncogenic mutations, especially in the tumor suppressor APC, whose loss triggers the deregulation of TCF4/β-Catenin activity. CRC tumorigenesis is also driven by multiple epimutational modifiers such as transcriptional regulators. We describe the common (and near-universal) activation of the zinc finger transcription factor and Let-7 target PLAGL2 in CRC and find that it is a key driver of intestinal epithelial transformation. PLAGL2 drives proliferation, cell cycle progression, and anchorage-independent growth in CRC cell lines and nontransformed intestinal cells. Investigating effects of PLAGL2 on downstream pathways revealed very modest effects on canonical Wnt signaling. Alternatively, we find pronounced effects on the direct PLAGL2 target genes IGF2, a fetal growth factor, and ASCL2, an intestinal stem cell-specific bHLH transcription factor. Inactivation of PLAGL2 in CRC cell lines has pronounced effects on ASCL2 reporter activity. Furthermore, ASCL2 expression can partially rescue deficits of proliferation and cell cycle progression caused by depletion of PLAGL2 in CRC cell lines. Thus, the oncogenic effects of PLAGL2 appear to be mediated via core stem cell and onco-fetal pathways, with minimal effects on downstream Wnt signaling.NEW & NOTEWORTHY A Let-7 target called PLAGL2 drives oncogenic transformation via Wnt-independent pathways. This work illustrates the robust effects of this zinc finger transcription factor in colorectal cancer (CRC) cell lines and nontransformed intestinal epithelium, with effects mediated, in part, via the direct target genes ASCL2 and IGF2. This has implications for the role of PLAGL2 in activation of onco-fetal and onco-stem cell pathways, contributing to immature and highly proliferative phenotypes in CRC.
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Affiliation(s)
- Anthony D Fischer
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Daniel A Veronese Paniagua
- Washington University School of Medicine, Saint Louis, Missouri, United States
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, United States
| | - Shriya Swaminathan
- Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Hajime Kashima
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
| | - Blair B Madison
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States
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Lloyd DT, Skinner HG, Maguire R, Murphy SK, Motsinger-Reif AA, Hoyo C, House JS. Clomifene and Assisted Reproductive Technology in Humans Are Associated with Sex-Specific Offspring Epigenetic Alterations in Imprinted Control Regions. Int J Mol Sci 2022; 23:10450. [PMID: 36142363 PMCID: PMC9499479 DOI: 10.3390/ijms231810450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/04/2022] Open
Abstract
Children conceived with assisted reproductive technology (ART) have an increased risk of adverse outcomes, including congenital malformations and imprinted gene disorders. In a retrospective North Carolina-based-birth-cohort, we examined the effect of ovulation drugs and ART on CpG methylation in differentially methylated CpGs in known imprint control regions (ICRs). Nine ICRs containing 48 CpGs were assessed for methylation status by pyrosequencing in mixed leukocytes from cord blood. After restricting to non-smoking, college-educated participants who agreed to follow-up, ART-exposed (n = 27), clomifene-only-exposed (n = 22), and non-exposed (n = 516) groups were defined. Associations of clomifene and ART with ICR CpG methylation were assessed with linear regression and stratifying by offspring sex. In males, ART was associated with hypomethylation of the PEG3 ICR [β(95% CI) = -1.46 (-2.81, -0.12)] and hypermethylation of the MEG3 ICR [3.71 (0.01, 7.40)]; clomifene-only was associated with hypomethylation of the NNAT ICR [-5.25 (-10.12, -0.38)]. In female offspring, ART was associated with hypomethylation of the IGF2 ICR [-3.67 (-6.79, -0.55)]. Aberrant methylation of these ICRs has been associated with cardiovascular disease and metabolic and behavioral outcomes in children. The results suggest that the increased risk of adverse outcomes in offspring conceived through ART may be due in part to altered methylation of ICRs. Larger studies utilizing epigenome-wide interrogation are warranted.
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Affiliation(s)
- Dillon T. Lloyd
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Harlyn G. Skinner
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Rachel Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Duke University, Durham, NC 27701, USA
| | - Alison A. Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - John S. House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
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4
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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5
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Lee EY, Song JM, Kim HJ, Park HR. Hypomethylation of lncRNA H19 as a potential prognostic biomarker for oral squamous cell carcinoma. Arch Oral Biol 2021; 129:105214. [PMID: 34333230 DOI: 10.1016/j.archoralbio.2021.105214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Dysregulated DNA methylation is common in cancers and is considered one of the most important triggers in cancer development and progression. The expression and promoter methylation status of long non-coding RNA (lncRNA) H19 play a key role in several cancers, but its role is unclear in oral cancer. The aim of this study was to evaluate the potential of lncRNA H19 as a prognostic biomarker for oral cancer. DESIGNS The transcript levels and the methylation status of lncRNA H19 in OSCC cell lines and OSCC patient tissues were investigated by quantitative real-time RT-PCR (qRT-PCR) and methylation-specific PCR (MSP). Methylation ratio (%) were calculated from the intensity of the MSP in the gel image and Kaplan-Meier survival analysis of OSCC patient survival was performed for patients grouped according to the lncRNA H19 promoter methylation ratio. RESULTS lncRNA H19 was highly expressed and its promoter region was hypomethylated in OSSC cell lines as compared to normal control. Almost all OSCC patients tissues (63 out of 65, 97 %) showed hypomethylation of lncRNA H19 compared to normal oral mucosa tissues. There was a significant correlation between methylation ratio and tumor histopathologic grade. OSCC patients with hypomethylation of lncRNA H19 had a significantly lower 5-year survival rate. CONCLUSIONS Hypomethylation of lncRNA H19 may serve as a potential prognostic biomarker for oral cancer.
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Affiliation(s)
- Eun Young Lee
- Department of Oral Pathology, and BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea; Periodontal Disease Signaling Network Research Center (MRC), School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Jae Min Song
- Department of Oral and Maxillofacial Surgery, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea; Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea
| | - Hye Jung Kim
- Periodontal Disease Signaling Network Research Center (MRC), School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea.
| | - Hae Ryoun Park
- Department of Oral Pathology, and BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea; Periodontal Disease Signaling Network Research Center (MRC), School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea; Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, Gyeongsangnam-do, Republic of Korea.
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6
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Ni W, Mo H, Liu Y, Xu Y, Qin C, Zhou Y, Li Y, Li Y, Zhou A, Yao S, Zhou R, Huo J, Che L, Li J. Targeting cholesterol biosynthesis promotes anti-tumor immunity by inhibiting long noncoding RNA SNHG29-mediated YAP activation. Mol Ther 2021; 29:2995-3010. [PMID: 33992804 DOI: 10.1016/j.ymthe.2021.05.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/10/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022] Open
Abstract
Anti-tumor immunity through checkpoint inhibitors, specifically anti-programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) interaction, is a promising approach for cancer therapy. However, as early clinical trials indicate that colorectal cancers (CRCs) do not respond well to immune-checkpoint therapies, new effective immunotherapy approaches to CRC warrant further study. Simvastatin is an inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A (CoA) reductase (HMGCR), the rate-limiting enzyme of the mevalonate (MVA) pathway for the cholesterol biosynthesis. However, little is known about the functions of simvastatin in the regulation of immune checkpoints or long noncoding RNA (lncRNA)-mediated immunoregulation in cancer. Here, we found that simvastatin inhibited PD-L1 expression and promoted anti-tumor immunity via suppressing the expression of lncRNA SNHG29. Interestingly, SNHG29 interacted with YAP and inhibited phosphorylation and ubiquitination-mediated protein degradation of YAP, thereby facilitating downregulation of PD-L1 transcriptionally. Patient-derived tumor xenograft (PDX) models and the clinicopathological analysis in samples from CRC patients further supported the role of the lncRNA SNHG29-mediated PD-L1 signaling axis in tumor microenvironment reprogramming. Collectively, our study uncovers simvastatin as a potential therapeutic drug for immunotherapy in CRC, which suppresses lncRNA SNHG29-mediated YAP activation and promotes anti-tumor immunity by inhibiting PD-L1 expression.
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Affiliation(s)
- Wen Ni
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Hui Mo
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuanyuan Liu
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuanyuan Xu
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Chao Qin
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yunxia Zhou
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuhui Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuqing Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Aijun Zhou
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Su Yao
- Department of Pathology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Rong Zhou
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianping Huo
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Liheng Che
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianming Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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7
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Ruan T, Lu S, Xu J, Zhou JY. lncRNA LINC00460 Functions as a Competing Endogenous RNA and Regulates Expression of BGN by Sponging miR-149-5p in Colorectal Cancer. Technol Cancer Res Treat 2021; 20:1533033820964238. [PMID: 33472555 PMCID: PMC7829460 DOI: 10.1177/1533033820964238] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background and Aim: There are an increasing number of studies indicating the important roles
served by long non-coding RNAs (lncRNAs) in the development of different
types of cancer. LINC00460 is a novel identified lncRNA that was found to be
upregulated in colorectal cancer. However, the biological roles of LINC00460
in colorectal cancer have yet to be fully elucidated. This study was aimed
to investigate the functions and molecular mechanisms of LINC00460 on
colorectal cancer metastasis. Methods: Expression of LINC00460 and biglycan (BGN) in colorectal
cancer tissues and cell lines were quantified by real time PCR or western
blotting assay. Cell migration and invasion assays were performed to
determine the effect of LINC00460 on tumor metastasis in vitro. The binding
interaction between microRNA-149-5p and LINC00460 was revealed by luciferase
reporter assay. Results: In the present study, lncRNA LINC00460 was shown to be upregulated in
colorectal cancer tissues, and overexpression of LINC00460 significantly
promoted metastasis of colorectal cancer in vitro. Furthermore, miR-149-5p
interacted with LINC00460, and they negatively regulated expression of each
other. Transfection of miR-149-5p mimics partially counteracted the tumor
metastasis-promoting effects induced by LINC00460 overexpression. Finally,
overexpression of LINC00460 upregulated the expression levels of
biglycan, a target gene of miR-149-5p, which has also
been identified as an oncogenic driver in colorectal cancer. Conclusion: Taken together, the present study demonstrated that LINC00460 promoted
metastasis of CRC by sponging miR-149-5p and thereby affecting
biglycan expression levels.
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Affiliation(s)
- Tingyan Ruan
- Department of Radiation Oncology, 74566The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu People's Republic of China
| | - Shourong Lu
- Department of Geriatrics, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China
| | - Junying Xu
- Department of Radiation Oncology, 74566The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Ju-Ying Zhou
- Department of Radiation Oncology, 74566The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu People's Republic of China
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8
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Zhou Q, Meng QR, Meng TG, He QL, Zhao ZH, Li QN, Lei WL, Liu SZ, Schatten H, Wang ZB, Sun QY. Deletion of BAF250a affects oocyte epigenetic modifications and embryonic development. Mol Reprod Dev 2020; 87:550-564. [PMID: 32215983 DOI: 10.1002/mrd.23339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 11/10/2022]
Abstract
BRG1-associated factor 250a (BAF250a) is a component of the SWI/SNF adenosine triphosphate-dependent chromatin remodeling complex, which has been shown to control chromatin structure and transcription. BAF250a was reported to be a key component of the gene regulatory machinery in embryonic stem cells controlling self-renewal, differentiation, and cell lineage decisions. Here we constructed Baf250aF/F ;Gdf9-cre (Baf250aCKO ) mice to specifically delete BAF250a in oocytes to investigate the role of maternal BAF250a in female germ cells and embryo development. Our results showed that BAF250a deletion did not affect folliculogenesis, ovulation, and fertilization, but it caused late embryonic death. RNA sequencing analysis showed that the expression of genes involved in cell proliferation and differentiation, tissue morphogenesis, histone modification, and nucleosome remodeling were perturbed in Baf250aCKO MII oocytes. We showed that covalent histone modifications such as H3K27me3 and H3K27ac were also significantly affected in oocytes, which may reduce oocyte quality and lead to birth defects. In addition, the DNA methylation level of Igf2r, Snrpn, and Peg3 differentially methylated regions was decreased in Baf250aCKO oocytes. Quantitative real-time polymerase chain reaction analysis showed that the relative messenger RNA (mRNA) expression levels of Igf2r and Snrpn were significantly increased. The mRNA expression level of Dnmt1, Dnmt3a, Dnmt3l, and Uhrf1 was decreased, and the protein expression in these genes was also reduced, which might be the cause for impaired imprinting establishment. In conclusion, our results demonstrate that BAF250a plays an important role in oocyte transcription regulation, epigenetic modifications, and embryo development.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Ren Meng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Long He
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zheng-Hui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qian-Nan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Long Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Zhen Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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9
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The IGF-II-Insulin Receptor Isoform-A Autocrine Signal in Cancer: Actionable Perspectives. Cancers (Basel) 2020; 12:cancers12020366. [PMID: 32033443 PMCID: PMC7072655 DOI: 10.3390/cancers12020366] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/18/2022] Open
Abstract
Insulin receptor overexpression is a common event in human cancer. Its overexpression is associated with a relative increase in the expression of its isoform A (IRA), a shorter variant lacking 11 aa in the extracellular domain, conferring high affinity for the binding of IGF-II along with added intracellular signaling specificity for this ligand. Since IGF-II is secreted by the vast majority of malignant solid cancers, where it establishes autocrine stimuli, the co-expression of IGF-II and IRA in cancer provides specific advantages such as apoptosis escape, growth, and proliferation to those cancers bearing such a co-expression pattern. However, little is known about the exact role of this autocrine ligand–receptor system in sustaining cancer malignant features such as angiogenesis, invasion, and metastasis. The recent finding that the overexpression of angiogenic receptor kinase EphB4 along with VEGF-A is tightly dependent on the IGF-II/IRA autocrine system independently of IGFIR provided new perspectives for all malignant IGF2omas (those aggressive solid cancers secreting IGF-II). The present review provides an updated view of the IGF system in cancer, focusing on the biology of the autocrine IGF-II/IRA ligand–receptor axis and supporting its underscored role as a malignant-switch checkpoint target.
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10
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Yu TX, Chung HK, Xiao L, Piao JJ, Lan S, Jaladanki SK, Turner DJ, Raufman JP, Gorospe M, Wang JY. Long Noncoding RNA H19 Impairs the Intestinal Barrier by Suppressing Autophagy and Lowering Paneth and Goblet Cell Function. Cell Mol Gastroenterol Hepatol 2019; 9:611-625. [PMID: 31862317 PMCID: PMC7078540 DOI: 10.1016/j.jcmgh.2019.12.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The protective intestinal mucosal barrier consists of multiple elements including mucus and epithelial layers and immune defense; nonetheless, barrier dysfunction is common in various disorders. The imprinted and developmentally regulated long noncoding RNA H19 is involved in many cell processes and diseases. Here, we investigated the role of H19 in regulating Paneth and goblet cells and autophagy, and its impact on intestinal barrier dysfunction induced by septic stress. METHODS Studies were conducted in H19-deficient (H19-/-) mice, mucosal tissues from patients with sepsis, primary enterocytes, and Caco-2 cells. Septic stress was induced by cecal ligation and puncture (CLP), and gut permeability was detected by tracer fluorescein isothiocyanate-dextran assays. The function of Paneth and goblet cells was examined by immunostaining for lysozyme and mucin 2, respectively, and autophagy was examined by microtubule-associated proteins 1A/1B light chain 3 II immunostaining and Western blot analysis. Intestinal organoids were isolated from H19-/- and control littermate mice and treated with lipopolysaccharide (LPS). RESULTS Intestinal mucosal tissues in mice 24 hours after exposure to CLP and in patients with sepsis showed high H19 levels, associated with intestinal barrier dysfunction. Targeted deletion of the H19 gene in mice enhanced the function of Paneth and goblet cells and promoted autophagy in the small intestinal mucosa. Knockout of H19 protected Paneth and goblet cells against septic stress, preserved autophagy activation, and promoted gut barrier function after exposure to CLP. Compared with organoids from control littermate mice, intestinal organoids isolated from H19-/- mice had increased numbers of lysozyme- and mucin 2-positive cells and showed increased tolerance to LPS. Conversely, ectopic overexpression of H19 in cultured intestinal epithelial cells prevented rapamycin-induced autophagy and abolished the rapamycin-induced protection of the epithelial barrier against LPS. CONCLUSIONS In investigations of mice, human tissues, primary organoids, and intestinal epithelial cells, we found that increased H19 inhibited the function of Paneth and goblet cells and suppressed autophagy, thus potentially contributing to barrier dysfunction in intestinal pathologies.
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Affiliation(s)
- Ting-Xi Yu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Hee K Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jun-Jie Piao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Shaoyang Lan
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Suraj K Jaladanki
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Douglas J Turner
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland
| | - Jean-Pierre Raufman
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland; Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland; Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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11
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Holly JMP, Biernacka K, Perks CM. The Neglected Insulin: IGF-II, a Metabolic Regulator with Implications for Diabetes, Obesity, and Cancer. Cells 2019; 8:cells8101207. [PMID: 31590432 PMCID: PMC6829378 DOI: 10.3390/cells8101207] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023] Open
Abstract
When originally discovered, one of the initial observations was that, when all of the insulin peptide was depleted from serum, the vast majority of the insulin activity remained and this was due to a single additional peptide, IGF-II. The IGF-II gene is adjacent to the insulin gene, which is a result of gene duplication, but has evolved to be considerably more complicated. It was one of the first genes recognised to be imprinted and expressed in a parent-of-origin specific manner. The gene codes for IGF-II mRNA, but, in addition, also codes for antisense RNA, long non-coding RNA, and several micro RNA. Recent evidence suggests that each of these have important independent roles in metabolic regulation. It has also become clear that an alternatively spliced form of the insulin receptor may be the principle IGF-II receptor. These recent discoveries have important implications for metabolic disorders and also for cancer, for which there is renewed acknowledgement of the importance of metabolic reprogramming.
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Affiliation(s)
- Jeff M P Holly
- Department of Translational Health Science, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Learning & Research Building, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Kalina Biernacka
- Department of Translational Health Science, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Learning & Research Building, Southmead Hospital, Bristol, BS10 5NB, UK
| | - Claire M Perks
- Department of Translational Health Science, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Learning & Research Building, Southmead Hospital, Bristol, BS10 5NB, UK
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12
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Kasprzak A, Adamek A. Insulin-Like Growth Factor 2 (IGF2) Signaling in Colorectal Cancer-From Basic Research to Potential Clinical Applications. Int J Mol Sci 2019; 20:ijms20194915. [PMID: 31623387 PMCID: PMC6801528 DOI: 10.3390/ijms20194915] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers in men and women worldwide as well as is the leading cause of death in the western world. Almost a third of the patients has or will develop liver metastases. While genetic as well as epigenetic mechanisms are important in CRC pathogenesis, the basis of the most cases of cancer is unknown. High spatial and inter-patient variability of the molecular alterations qualifies this cancer in the group of highly heterogeneous tumors, which makes it harder to elucidate the mechanisms underlying CRC progression. Determination of highly sensitive and specific early diagnosis markers and understanding the cellular and molecular mechanism(s) of cancer progression are still a challenge of the current era in oncology of solid tumors. One of the accepted risk factors for CRC development is overexpression of insulin-like growth factor 2 (IGF2), a 7.5-kDa peptide produced by liver and many other tissues. IGF2 is the first gene discovered to be parentally imprinted. Loss of imprinting (LOI) or aberrant imprinting of IGF2 could lead to IGF2 overexpression, increased cell proliferation, and CRC development. IGF2 as a mitogen is associated with increased risk of developing colorectal neoplasia. Higher serum IGF2 concentration as well as its tissue overexpression in CRC compared to control are associated with metastasis. IGF2 protein was one of the three candidates for a selective marker of CRC progression and staging. Recent research indicates dysregulation of different micro- and long non-coding RNAs (miRNAs and lncRNAs, respectively) embedded within the IGF2 gene in CRC carcinogenesis, with some of them indicated as potential diagnostic and prognostic CRC biomarkers. This review systematises the knowledge on the role of genetic and epigenetic instabilities of IGF2 gene, free (active form of IGF2) and IGF-binding protein (IGFBP) bound (inactive form), paracrine/autocrine secretion of IGF2, as well as mechanisms of inducing dysplasia in vitro and tumorigenicity in vivo. We have tried to answer which molecular changes of the IGF2 gene and its regulatory mechanisms have the most significance in initiation, progression (including liver metastasis), prognosis, and potential anti-IGF2 therapy in CRC patients.
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Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland.
| | - Agnieszka Adamek
- Department of Infectious Diseases, Hepatology and Acquired Immunodeficiencies, University of Medical Sciences, Szwajcarska Street 3, 61-285 Poznan, Poland.
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13
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LncRNA H19 promotes lung cancer proliferation and metastasis by inhibiting miR-200a function. Mol Cell Biochem 2019; 460:1-8. [PMID: 31187349 DOI: 10.1007/s11010-019-03564-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/27/2019] [Indexed: 12/24/2022]
Abstract
Lung cancer is the major cause leading to cancer mortality, and the 5-year survival rate for patients with lung cancer still remains low. It is urgent to fully understand the development and progression of lung cancer to discover new therapeutic targets and develop new therapeutic approaches. H19 was documented to be upregulated in lung cancer and related to cell proliferation. However, it is still unclear if H19 has other functions in lung cancer. The mRNA levels of genes were detected by qRT-PCR, and the cell proliferation rate and cell viability were measured through cell count assay and MTT assay. Transwell assays were applied to detect cell abilities to migration and invasion, while luciferase reporter assay and RNA pull-down assay were used to examine interaction between H19 and miR-200a. H19 expression was elevated in the lung cancer tissues and cell lines, while H19 overexpression promoted the lung cancer cell growth, cell migration and invasion, as well as the epithelial mesenchymal transition (EMT). Meantime, RNA pull-down assay showed that H19 interacted with miR-200a, and miR-200a inhibited the activity of H19-fused luciferase. Furthermore, H19 overexpression inhibited miR-200a function and thereby upregulated miR-200a target genes, ZEB1 and ZEB2.H19 sponged and inhibited miR-200a to de-repress expression of ZEB1 and ZEB2, and thereby enhanced lung cancer proliferation and metastasis.
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14
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Fu Y, Tessneer KL, Li C, Gaffney PM. From association to mechanism in complex disease genetics: the role of the 3D genome. Arthritis Res Ther 2018; 20:216. [PMID: 30268153 PMCID: PMC6162955 DOI: 10.1186/s13075-018-1721-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies (GWAS) and fine mapping studies in autoimmune diseases have identified thousands of genetic variants, the majority of which are located in non-protein-coding enhancer regions. Enhancers function within the context of the three-dimensional (3D) genome to form long-range DNA looping events with target gene promoters that spatially and temporally regulate gene expression. Investigating the functional significance of GWAS variants in the context of the 3D genome is essential for mechanistic understanding of these variants and how they influence disease pathology by altering DNA looping between enhancers and the target gene promoters they regulate. In this review, we discuss the functional complexity of the 3D genome and the technological approaches used to characterize DNA looping events. We then highlight examples from the literature that illustrate how functional mapping of the 3D genome can assist in defining mechanisms that influence pathogenic gene expression. We conclude by highlighting future advances necessary to fully integrate 3D genome analyses into the functional workup of GWAS variants in the continuing effort to improve the health of patients with autoimmune diseases.
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Affiliation(s)
- Yao Fu
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
| | - Kandice L Tessneer
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
| | - Chuang Li
- School of Electrical and Computer Engineering, University of Oklahoma, Devan Energy Hall 150, 110 West Boyd Street, Norman, OK 73019 USA
| | - Patrick M Gaffney
- Division of Genomics and Data Sciences, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104 USA
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15
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Imprinting defects at human 14q32 locus alters gene expression and is associated with the pathobiology of osteosarcoma. Oncotarget 2018; 7:21298-314. [PMID: 26802029 PMCID: PMC5008286 DOI: 10.18632/oncotarget.6965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/25/2015] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma is the most common primary bone malignancy affecting children and adolescents. Although several genetic predisposing conditions have been associated with osteosarcoma, our understanding of its pathobiology is rather limited. Here we show that, first, an imprinting defect at human 14q32-locus is highly prevalent (87%) and specifically associated with osteosarcoma patients < 30 years of age. Second, the average demethylation at differentially methylated regions (DMRs) in the 14q32-locus varied significantly compared to genome-wide demethylation. Third, the 14q32-locus was enriched in both H3K4-me3 and H3K27-me3 histone modifications that affected expression of all imprinted genes and miRNAs in this region. Fourth, imprinting defects at 14q32 - DMRs are present in triad DNA samples from affected children and their biological parents. Finally, imprinting defects at 14q32-DMRs were also observed at higher frequencies in an Rb1/Trp53 mutation-induced osteosarcoma mouse model. Further analysis of normal and tumor tissues from a Sleeping Beauty mouse model of spontaneous osteosarcoma supported the notion that these imprinting defects may be a key factor in osteosarcoma pathobiology. In conclusion, we demonstrate that imprinting defects at the 14q32 locus significantly alter gene expression, may contribute to the pathogenesis of osteosarcoma, and could be predictive of survival outcomes.
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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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Yang Y, Du Y, Liu X, Cho WC. Involvement of Non-coding RNAs in the Signaling Pathways of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:19-51. [PMID: 27573893 DOI: 10.1007/978-3-319-42059-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most common diagnosed cancers worldwide. The metastasis and development of resistance to anti-cancer treatment are major challenges in the treatment of CRC. Understanding mechanisms underpinning the pathogenesis is therefore critical in developing novel agents for CRC treatments. A large number of evidence has demonstrated that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs have functional roles in both the physiological and pathological processes by regulating the expression of their target genes. These molecules are engaged in the pathobiology of neoplastic diseases and are targets for the diagnosis, prognosis and therapy of a variety of cancers, including CRC. In this regard, ncRNAs have emerged as one of the hallmarks of CRC pathogenesis and they also play key roles in metastasis, drug resistance and the stemness of CRC stem cell by regulating various signaling networks. Therefore, a better understanding the ncRNAs involved in the signaling pathways of CRC may lead to the development of novel strategy for diagnosis, prognosis and treatment of CRC. In this chapter, we summarize the latest findings on ncRNAs, with a focus on miRNAs and lncRNAs involving in signaling networks and in the regulation of pathogenic signaling pathways in CRC.
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Affiliation(s)
- Yinxue Yang
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yong Du
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Xiaoming Liu
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China.
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18
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Wu K, Zhao Z, Liu K, Zhang J, Li G, Wang L. Long noncoding RNA lnc-sox5 modulates CRC tumorigenesis by unbalancing tumor microenvironment. Cell Cycle 2017. [PMID: 28632999 DOI: 10.1080/15384101.2017.1317416] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) have been recently regarded as systemic regulators in multiple biologic processes including tumorigenesis. In this study, we observed the expression of lncRNA lnc-sox5 was significantly increased in colorectal cancer (CRC). Despite the CRC cell growth, cell cycle and cell apoptosis was not affected by lnc-sox5 knock-down, lnc-sox5 knock-down suppressed CRC cell migration and invasion. In addition, xenograft animal model suggested that lnc-sox5 knock-down significantly suppressed the CRC tumorigenesis. Our results also showed that the expression of indoleamine 2,3-dioxygenase 1 (IDO1) was significantly reduced by lnc-sox5 knock-down and therefore modulated the infiltration and cytotoxicity of CD3+CD8+T cells. Taken together, these results suggested that lnc-sox5 unbalances tumor microenvironment to regulate colorectal cancer progression.
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Affiliation(s)
- Kaiming Wu
- a Gastrointestinal Surgery Center , 1st Affiliated Hospital of Sun Yat-Sen University , Guangzhou , Guangdong , P.R. China
| | - Zhenxian Zhao
- b Department of Pancreato-Biliary Surgery , 1st Affiliated Hospital of Sun Yat-Sen University , Guangzhou , Guangdong , P.R. China
| | - Kuanzhi Liu
- c Department of Anaesthesiology , 1st Affiliated Hospital of Sun Yat-Sen Univesity , Guangzhou , Guangdong , P.R. China
| | - Jian Zhang
- d Gastrointestinal Surgery Center , 1st Affiliated Hospital of Sun Yat-Sen University , Guangzhou , Guangdong , P.R. China
| | - Guanghua Li
- d Gastrointestinal Surgery Center , 1st Affiliated Hospital of Sun Yat-Sen University , Guangzhou , Guangdong , P.R. China
| | - Liang Wang
- d Gastrointestinal Surgery Center , 1st Affiliated Hospital of Sun Yat-Sen University , Guangzhou , Guangdong , P.R. China
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19
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The Interplay of LncRNA-H19 and Its Binding Partners in Physiological Process and Gastric Carcinogenesis. Int J Mol Sci 2017; 18:ijms18020450. [PMID: 28230721 PMCID: PMC5343984 DOI: 10.3390/ijms18020450] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 02/12/2017] [Accepted: 02/16/2017] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNA (lncRNA), a novel and effective modulator in carcinogenesis, has become a study hotspot in recent years. The imprinted oncofetal lncRNA H19 is one of the first identified imprinted lncRNAs with a high expression level in embryogenesis but is barely detectable in most tissues after birth. Aberrant alterations of H19 expression have been demonstrated in various tumors, including gastric cancer (GC), implicating a crucial role of H19 in cancer progression. As one of the top malignancies in the world, GC has already become a serious concern to public health with poor prognosis. The regulatory roles of H19 in gastric carcinogenesis have been explored by various research groups, which leads to the development of GC therapy. This review comprehensively summarizes the current knowledge of H19 in tumorigenesis, especially in GC pathogenesis, with emphasis on the underneath molecular mechanisms depicted from its functional partners. Furthermore, the accumulated knowledge of H19 will provide better understanding on targeted therapy of GC.
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20
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Chen L, Zhang YH, Lu G, Huang T, Cai YD. Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways. Artif Intell Med 2017; 76:27-36. [PMID: 28363286 DOI: 10.1016/j.artmed.2017.02.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/31/2017] [Accepted: 02/05/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cancer is a disease that involves abnormal cell growth and can invade or metastasize to other tissues. It is known that several factors are related to its initiation, proliferation, and invasiveness. Recently, it has been reported that long non-coding RNAs (lncRNAs) can participate in specific functional pathways and further regulate the biological function of cancer cells. Studies on lncRNAs are therefore helpful for uncovering the underlying mechanisms of cancer biological processes. METHODS We investigated cancer-related lncRNAs using gene ontology (GO) terms and KEGG pathway enrichment scores of neighboring genes that are co-expressed with the lncRNAs by extracting important GO terms and KEGG pathways that can help us identify cancer-related lncRNAs. The enrichment theory of GO terms and KEGG pathways was adopted to encode each lncRNA. Then, feature selection methods were employed to analyze these features and obtain the key GO terms and KEGG pathways. RESULTS The analysis indicated that the extracted GO terms and KEGG pathways are closely related to several cancer associated processes, such as hormone associated pathways, energy associated pathways, and ribosome associated pathways. And they can accurately predict cancer-related lncRNAs. CONCLUSIONS This study provided novel insight of how lncRNAs may affect tumorigenesis and which pathways may play important roles during it. These results could help understanding the biological mechanisms of lncRNAs and treating cancer.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China; College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Guohui Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China.
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.
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Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities? Adv Cancer Res 2017; 133:129-156. [PMID: 28052819 DOI: 10.1016/bs.acr.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Screening for uterine cervical intraepithelial neoplasia (CIN) followed by aggressive treatment has reduced invasive cervical cancer (ICC) incidence and mortality. However, ICC cases and carcinoma in situ (CIS) continue to be diagnosed annually in the United States, with minorities bearing the brunt of this burden. Because ICC peak incidence and mortality are 10-15 years earlier than other solid cancers, the number of potential years of life lost to this cancer is substantial. Screening for early signs of CIN is still the mainstay of many cervical cancer control programs. However, the accuracy of existing screening tests remains suboptimal. Changes in epigenetic patterns that occur as a result of human papillomavirus infection contribute to CIN progression to cancer, and can be harnessed to improve existing screening tests. However, this requires a concerted effort to identify the epigenomic landscape that is reliably altered by HPV infection specific to ICC, distinct from transient changes.
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22
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Tan D, Wu Y, Hu L, He P, Xiong G, Bai Y, Yang K. Long noncoding RNA H19 is up-regulated in esophageal squamous cell carcinoma and promotes cell proliferation and metastasis. Dis Esophagus 2017; 30:1-9. [PMID: 27247022 DOI: 10.1111/dote.12481] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play various roles in tumorigenesis, among which lncRNA H19 has been revealed as an ambivalent factor that acts as both an oncogene and a tumor suppressor in carcinogenesis. However, the exact biological role of H19 in esophageal squamous cell carcinoma (ESCC) remains to be determined. The aim of this study was to examine the expression pattern of H19 in ESCC and evaluate its biological role and clinical significance in the progression of ESCC. Expression of H19 was analyzed in 64 ESCC tissues and four ESCC cell lines by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Proliferation, cell cycle, migration, and invasion assays were performed in ESCC cell lines following knockdown of H19 to determine the biological function of H19 in the progression of ESCC both in vitro and in vivo. Western blot analysis was also performed to identify the potential mechanisms involved. H19 was highly expressed both in ESCC samples and cell lines compared with corresponding normal counterparts. The up-regulation of of H19 was significantly correlated with ESCC clinical stage and lymph node metastasis. Knockdown of H19 not only exerted inhibitory effect on tumor proliferation in vitro and in vivo, but also repressed the migratory and invasive capacity. G0/G1 phase arrest was also found in H19 knockdown cell lines. In addition, silencing of H19 up-regulated epithelial marker E-cadherin while down-regulating mesenchymal marker vimentin and metastasis-associated protein such as MMP-9. These findings indicate that H19 acts as an oncogene and promotes ESCC cell proliferation and metastasis, which may infer H19 as a marker of poor prognosis and, thus, a potential therapeutic target for treating ESCC patients.
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Affiliation(s)
- Deli Tan
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Yuanyuan Wu
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Chongqing, China
| | - Liwen Hu
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Ping He
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Gang Xiong
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Chongqing, China
| | - Kang Yang
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
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Carcinoma of the colon and rectum with deregulation of insulin-like growth factor 2 signaling: clinical and molecular implications. J Gastroenterol 2016; 51:971-84. [PMID: 26984550 DOI: 10.1007/s00535-016-1181-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/02/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Loss of imprinting (LOI) of the insulin-like growth factor 2 (IGF2) is an early event in the development of colorectal cancer (CRC). Whether LOI of IGF2 denotes a molecular or clinical cancer subgroup is currently unknown. METHODS Tumor biopsies and paired normal mucosa from 399 patients with extensive clinical annotations were analyzed for LOI and IGF2 expression. LOI status in 140 informative cases was correlated with clinicopathologic parameters and outcome. RESULTS LOI was frequent in normal mucosa and tumors and occurred throughout the large intestine. LOI was unrelated to microsatellite instability, KRAS mutation status, stage, and survival. However, CRC with LOI showed increased IGF2 protein levels and activation of AKT1. Gene expression analysis of tumors with and without LOI and knockdown of IGF2 in cell lines revealed that IGF2 induced distinct sets of activated and repressed genes, including Wnt5a, CEACAM6, IGF2BP3, KPN2A, BRCA2, and CDK1. Inhibition of AKT1 in IGF2-stimulated cells showed that the downstream effects of IGF2 on cell proliferation and gene expression were strictly AKT1-dependent. CONCLUSIONS LOI of IGF2 is a frequent and early event in CRC that occurs both in the adenomatous polyposis coli (APC) gene-mutated and serrated route of carcinogenesis. LOI leads to overexpression of IGF2, activates IGF1R and AKT1, and is a powerful driver of cell proliferation. Moreover, our results suggest that IGF2 via AKT1 also contributes to non-canonical wnt signaling. Although LOI had no significant impact on major clinical parameters and outcome, its potential as a target for preventive and therapeutic interventions merits further investigation.
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Jia P, Cai H, Liu X, Chen J, Ma J, Wang P, Liu Y, Zheng J, Xue Y. Long non-coding RNA H19 regulates glioma angiogenesis and the biological behavior of glioma-associated endothelial cells by inhibiting microRNA-29a. Cancer Lett 2016; 381:359-69. [PMID: 27543358 DOI: 10.1016/j.canlet.2016.08.009] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in the development and progression of glioma. Previous studies indicated that lncRNA H19 regulated tumor carcinogenesis, angiogenesis and metastasis. This study aimed to investigate its functional role in glioma-induced endothelial cell proliferation, migration and tube formation as well as its possible molecular mechanisms. H19 was up-regulated in microvessels from glioma tissues and glioma-associated endothelial cells (GEC) cultured in glioma conditioned medium. Knockdown of H19 suppressed glioma-induced endothelial cell proliferation, migration and tube formation in vitro and meanwhile up-regulated the expression of miR-29a. Bioinformatics analysis and luciferase reporter assay defined that H19 mediated the above effects via directly binding to miR-29a. In addition, miR-29a targeted 3'-UTR region of vasohibin 2 (VASH2) and decreased its expression. VASH2 has been identified as an angiogenic factor. Knockdown of H19 also decreased the VASH2 expression by up-regulating miR-29a. In conclusion, the results indicated that knockdown of H19 suppressed glioma induced angiogenesis by inhibiting microRNA-29a, which may modulate the onset of glioma by regulating biological behaviors of glioma vascular endothelial cells.
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Affiliation(s)
- Peng Jia
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, People's Republic of China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China
| | - Jiajia Chen
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, People's Republic of China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, People's Republic of China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, People's Republic of China.
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Overproduction of IGF-2 drives a subset of colorectal cancer cells, which specifically respond to an anti-IGF therapeutic antibody and combination therapies. Oncogene 2016; 36:797-806. [PMID: 27399333 DOI: 10.1038/onc.2016.248] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 04/15/2016] [Accepted: 05/24/2016] [Indexed: 12/28/2022]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with a broad spectrum of genetic and epigenetic changes. A comprehensive molecular characterization of CRC by The Cancer Genome Atlas Network detected the overexpression of the insulin-like growth factor 2 (IGF2) gene, encoding a ligand for the insulin-like growth factor 1 receptor (IGF-1R), in a subset of CRC tumors. In this study, we investigated the oncogenic potential of IGF-2 in IGF2-overexpressing CRC models and the efficacy of MEDI-573, an IGF-1/2-neutralizing antibody. We found that a subset of CRC cell lines express high IGF-2 levels owing to an increased DNA copy number and hypermethylation in the H19 promoter of the IGF2 gene. MEDI-573 efficiently neutralized IGF-2 and induced apoptosis, which resulted in significant tumor growth inhibition in CRC mouse models that express high levels of IGF-2. These effects were specific to CRCs overexpressing IGF-2, as MEDI-573 did not affect the growth CRC cell lines with normal levels. Moreover, blockade of IGF-2 by MEDI-573 modulated other signaling pathways, suggesting combination therapies with inhibitors of these pathways. Indeed, in vivo efficacy was significantly enhanced when MEDI-573 was used in combination with trastuzumab, AZD2014 (dual mTORC1/2i), AZD5363 (AKTi) and selumetinib (AZD6244/ARRY-142886, MEK1/2i) or cetuximab. These results demonstrate that overexpressed IGF-2 is the major tumorigenic driver in a subset of CRCs and encourage testing of MEDI-573, alone and in combinations, in IGF2-overexpressing CRC patients.
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Bohne F, Langer D, Martiné U, Eider CS, Cencic R, Begemann M, Elbracht M, Bülow L, Eggermann T, Zechner U, Pelletier J, Zabel BU, Enklaar T, Prawitt D. Kaiso mediates human ICR1 methylation maintenance and H19 transcriptional fine regulation. Clin Epigenetics 2016; 8:47. [PMID: 27152123 PMCID: PMC4857248 DOI: 10.1186/s13148-016-0215-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022] Open
Abstract
Background Genomic imprinting evolved in a common ancestor to marsupials and eutherian mammals and ensured the transcription of developmentally important genes from defined parental alleles. The regulation of imprinted genes is often mediated by differentially methylated imprinting control regions (ICRs) that are bound by different proteins in an allele-specific manner, thus forming unique chromatin loops regulating enhancer-promoter interactions. Factors that maintain the allele-specific methylation therefore are essential for the proper transcriptional regulation of imprinted genes. Binding of CCCTC-binding factor (CTCF) to the IGF2/H19-ICR1 is thought to be the key regulator of maternal ICR1 function. Disturbances of the allele-specific CTCF binding are causative for imprinting disorders like the Silver-Russell syndrome (SRS) or the Beckwith-Wiedemann syndrome (BWS), the latter one being associated with a dramatically increased risk to develop nephroblastomas. Methods Kaiso binding to the human ICR1 was detected and analyzed by chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA). The role of Kaiso-ICR1 binding on DNA methylation was tested by lentiviral Kaiso knockdown and CRISPR/Cas9 mediated editing of a Kaiso binding site. Results We find that another protein, Kaiso (ZBTB33), characterized as binding to methylated CpG repeats as well as to unmethylated consensus sequences, specifically binds to the human ICR1 and its unmethylated Kaiso binding site (KBS) within the ICR1. Depletion of Kaiso transcription as well as deletion of the ICR1-KBS by CRISPR/Cas9 genome editing results in reduced methylation of the paternal ICR1. Additionally, Kaiso affects transcription of the lncRNA H19 and specifies a role for ICR1 in the transcriptional regulation of this imprinted gene. Conclusions Kaiso binding to unmethylated KBS in the human ICR1 is necessary for ICR1 methylation maintenance and affects transcription rates of the lncRNA H19. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0215-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Bohne
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - David Langer
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Ursula Martiné
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Claudia S Eider
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Regina Cencic
- Department of Biochemistry and the Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Matthias Begemann
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Luzie Bülow
- Institute of Human Genetics, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Ulrich Zechner
- Institute of Human Genetics, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Jerry Pelletier
- Department of Biochemistry and the Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Bernhard Ulrich Zabel
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Mathildenstr. 1, 79106 Freiburg, Germany
| | - Thorsten Enklaar
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Dirk Prawitt
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany.,Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Obere Zahlbacher Str. 63, 55131 Mainz, Germany
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Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. Lead Exposure during Early Human Development and DNA Methylation of Imprinted Gene Regulatory Elements in Adulthood. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:666-73. [PMID: 26115033 PMCID: PMC4858407 DOI: 10.1289/ehp.1408577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Lead exposure during early development causes neurodevelopmental disorders by unknown mechanisms. Epidemiologic studies have focused recently on determining associations between lead exposure and global DNA methylation; however, such approaches preclude the identification of loci that may alter human disease risk. OBJECTIVES The objective of this study was to determine whether maternal, postnatal, and early childhood lead exposure can alter the differentially methylated regions (DMRs) that control the monoallelic expression of imprinted genes involved in metabolism, growth, and development. METHODS Questionnaire data and serial blood lead levels were obtained from 105 participants (64 females, 41 males) of the Cincinnati Lead Study from birth to 78 months. When participants were adults, we used Sequenom EpiTYPER assays to test peripheral blood DNA to quantify CpG methylation in peripheral blood leukocytes at DMRs of 22 human imprinted genes. Statistical analyses were conducted using linear regression. RESULTS Mean blood lead concentration from birth to 78 months was associated with a significant decrease in PEG3 DMR methylation (β = -0.0014; 95% CI: -0.0023, -0.0005, p = 0.002), stronger in males (β = -0.0024; 95% CI: -0.0038, -0.0009, p = 0.003) than in females (β = -0.0009; 95% CI: -0.0020, 0.0003, p = 0.1). Elevated mean childhood blood lead concentration was also associated with a significant decrease in IGF2/H19 (β = -0.0013; 95% CI: -0.0023, -0.0003, p = 0.01) DMR methylation, but primarily in females, (β = -0.0017; 95% CI: -0.0029, -0.0006, p = 0.005) rather than in males, (β = -0.0004; 95% CI: -0.0023, 0.0015, p = 0.7). Elevated blood lead concentration during the neonatal period was associated with higher PLAGL1/HYMAI DMR methylation regardless of sex (β = 0.0075; 95% CI: 0.0018, 0.0132, p = 0.01). The magnitude of associations between cumulative lead exposure and CpG methylation remained unaltered from 30 to 78 months. CONCLUSIONS Our findings provide evidence that early childhood lead exposure results in sex-dependent and gene-specific DNA methylation differences in the DMRs of PEG3, IGF2/H19, and PLAGL1/HYMAI in adulthood. CITATION Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. 2016. Lead exposure during early human development and DNA methylation of imprinted gene regulatory elements in adulthood. Environ Health Perspect 124:666-673; http://dx.doi.org/10.1289/ehp.1408577.
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Affiliation(s)
- Yue Li
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Changchun Xie
- Division of Epidemiology and Biostatistics, Department of Environmental Health, Center for Clinical and Translational Science and Training, University of Cincinnati (UC), Cincinnati, Ohio, USA
| | - Susan K. Murphy
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - David Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Monica Nye
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adriana C. Vidal
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Kim M. Cecil
- Cincinnati Children’s Environmental Health Center, Cincinnati Children’s Hospital Medical Center, UC College of Medicine, Cincinnati, Ohio, USA
- Department of Radiology,
- Department of Pediatrics,
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Kim N. Dietrich
- Division of Epidemiology and Biostatistics, UC College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Randy L. Jirtle
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Sport and Exercise Sciences, Institute of Sport and Physical Activity Research, University of Bedfordshire, Bedford, Bedfordshire, United Kingdom
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
| | - Cathrine Hoyo
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
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Chen X, Fan S, Song E. Noncoding RNAs: New Players in Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:1-47. [PMID: 27376730 DOI: 10.1007/978-981-10-1498-7_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The world of noncoding RNAs (ncRNAs) has gained widespread attention in recent years due to their novel and crucial potency of biological regulation. Noncoding RNAs play essential regulatory roles in a broad range of developmental processes and diseases, notably human cancers. Regulatory ncRNAs represent multiple levels of structurally and functionally distinct RNAs, including the best-known microRNAs (miRNAs), the complicated long ncRNAs (lncRNAs), and the newly identified circular RNAs (circRNAs). However, the mechanisms by which they act remain elusive. In this chapter, we will review the current knowledge of the ncRNA field, discussing the genomic context, biological functions, and mechanisms of action of miRNAs, lncRNAs, and circRNAs. We also highlight the implications of the biogenesis and gene expression dysregulation of different ncRNA subtypes in the initiation and development of human malignancies.
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Affiliation(s)
- Xueman Chen
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Siting Fan
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Erwei Song
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China.
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Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 2015; 5:13186. [PMID: 26278472 PMCID: PMC4538606 DOI: 10.1038/srep13186] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/22/2015] [Indexed: 12/16/2022] Open
Abstract
Accumulating experimental studies have indicated that lncRNAs play important roles in various critical biological process and their alterations and dysregulations have been associated with many important complex diseases. Developing effective computational models to predict potential disease-lncRNA association could benefit not only the understanding of disease mechanism at lncRNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis and prevention. However, known experimentally confirmed disease-lncRNA associations are still very limited. In this study, a novel model of HyperGeometric distribution for LncRNA-Disease Association inference (HGLDA) was developed to predict lncRNA-disease associations by integrating miRNA-disease associations and lncRNA-miRNA interactions. Although HGLDA didn't rely on any known disease-lncRNA associations, it still obtained an AUC of 0.7621 in the leave-one-out cross validation. Furthermore, 19 predicted associations for breast cancer, lung cancer, and colorectal cancer were verified by biological experimental studies. Furthermore, the model of LncRNA Functional Similarity Calculation based on the information of MiRNA (LFSCM) was developed to calculate lncRNA functional similarity on a large scale by integrating disease semantic similarity, miRNA-disease associations, and miRNA-lncRNA interactions. It is anticipated that HGLDA and LFSCM could be effective biological tools for biomedical research.
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Affiliation(s)
- Xing Chen
- National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
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30
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Wang H, Liang L, Fang JY, Xu J. Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers. Oncogene 2015; 35:2011-9. [PMID: 26257062 DOI: 10.1038/onc.2015.304] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/07/2015] [Accepted: 07/12/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) results from the accumulation of genetic alterations, and somatic copy number alterations (CNAs) are crucial for the development of CRC. Genome-wide survey of CNAs provides opportunities for identifying cancer driver genes in an unbiased manner. The detection of aberrant CNAs may provide novel markers for the early diagnosis and personalized treatment of CRC. A major challenge in array-based profiling of CNAs is to distinguish the alterations that play causative roles from the random alterations that accumulate during colorectal carcinogenesis. In this view, we systematically discuss the frequent CNAs in CRC, focusing on functional genes that have potential diagnostic, prognostic and therapeutic significance.
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Affiliation(s)
- H Wang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - L Liang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J-Y Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J Xu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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Zia A, Bhatti A, John P, Kiani AK. Data interpretation: deciphering the biological function of Type 2 diabetes associated risk loci. Acta Diabetol 2015; 52:789-800. [PMID: 25585593 DOI: 10.1007/s00592-014-0700-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
AIMS Type 2 diabetes (T2D) is a complex multifactorial disorder with more than 40 loci associated with disease susceptibility. Most of these genome-wide significant loci reside in noncoding regions, it is important to decipher the potential regulatory function of these variants and to differentiate between true and tag signals. Nowadays, databases are being developed to study and predict the function of these associated variants, and RegulomeDB is one such database. METHODS We used RegulomeDB to analyze the potential function of the associated variants reported in five genome-wide association studies (GWAS) of T2D. RESULTS We investigated the 1,567 single nucleotide polymorphisms (SNPs) with 989 SNPs with a score of 1-6. Of those 989 SNPs, only 64 returned with RegulomeDB score <3 (evidence of regulatory function), and only four of these were GWAS significant SNPs (THADA/rs10203174, score = 1b; UBE2E2/rs7612463, score = 2a; ARAP1/rs1552224 and TP53INP1/rs8996852, score = 2b). But only 63 % of the annotated SNPs showed regulatory function that is an important limitation of the RegulomeDB as this database only provides information of few regulatory elements. CONCLUSION This study further supports that some of the noncoding GWAS variants are the true associations and not the tag ones. This study also proves the utility and importance of the RegulomeDB and other such databases. Although it is an extensive database of regulatory elements but has certain limitation due to utilization of only few types of regulatory elements and pathways.
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Affiliation(s)
- Asima Zia
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
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Valo S, Kaur S, Ristimäki A, Renkonen-Sinisalo L, Järvinen H, Mecklin JP, Nyström M, Peltomäki P. DNA hypermethylation appears early and shows increased frequency with dysplasia in Lynch syndrome-associated colorectal adenomas and carcinomas. Clin Epigenetics 2015. [PMID: 26203307 PMCID: PMC4511034 DOI: 10.1186/s13148-015-0102-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is associated with germline mutations in DNA mismatch repair (MMR) genes. The first "hit" to inactivate one allele of the predisposing MMR gene is present in every cell, contributing to accelerated tumorigenesis. Less information is available of the nature, timing, and order of other molecular "hits" required for tumor development. To this end, MMR protein expression and coordinated promoter methylation were examined in colorectal specimens prospectively collected from LS mutation carriers (n = 55) during colonoscopy surveillance (10/2011-5/2013), supplemented with retrospective specimens. RESULTS Loss of MMR protein corresponding to the gene mutated in the germline increased with dysplasia, with frequency of 0 % in normal mucosa, 50-68 % in low-grade dysplasia adenomas, and 100 % in high-grade dysplasia adenomas and carcinomas. Promoter methylation as a putative "second hit" occurred in 1/56 (2 %) of tumors with silenced MMR protein. A general hypermethylation tendency was evaluated by two gene sets, eight CpG island methylator phenotype (CIMP) genes, and seven candidate tumor suppressor genes linked to colorectal carcinoma (CRC). Hypermethylation followed the same trend as MMR protein loss and was present in some low-grade dysplasia adenomas that still expressed MMR protein suggesting the absence of a "second hit." To assess prospectively collected normal mucosa for carcinogenic "fields," the specimen donors were stratified according to age at biopsy (50 years or below vs. above 50 years) and further according to the absence vs. presence of a (previous or concurrent) diagnosis of CRC. In mutation carriers over 50 years old, two markers from the candidate gene panel (SFRP1 and SLC5A8) revealed a significantly elevated average degree of methylation in individuals with CRC diagnosis vs. those without. CONCLUSIONS Our findings emphasize the importance and early appearance of epigenetic alterations in LS-associated tumorigenesis. The results serve early detection and assessment of progression of CRC.
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Affiliation(s)
- Satu Valo
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland ; Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sippy Kaur
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland ; Department of Pathology, HUSLAB, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal and General Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Heikki Järvinen
- Department of Gastrointestinal and General Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Minna Nyström
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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Zeng S, Xiao YF, Tang B, Hu CJ, Xie R, Yang SM, Li BS. Long Noncoding RNA in Digestive Tract Cancers: Function, Mechanism, and Potential Biomarker. Oncologist 2015; 20:898-906. [PMID: 26156325 DOI: 10.1634/theoncologist.2014-0475] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/07/2015] [Indexed: 01/06/2023] Open
Abstract
Digestive tract cancers (DTCs) are a leading cause of cancer-related death worldwide. Current therapeutic tools for advanced stage DTCs have limitations, and patients with early stage DTCs frequently have a missed diagnosis due to shortage of efficient biomarkers. Consequently, it is necessary to develop novel biomarkers for early diagnosis and novel therapeutic targets for treatment of DTCs. In recent years, long noncoding RNAs (lncRNAs), a class of noncoding RNAs with >200 nucleotides, have been shown to be aberrantly expressed in DTCs and to have an important role in DTC development: the expression profiles of lncRNAs strongly correlated with poor survival of patients with DTCs, and lncRNAs acted as oncogenes or tumor suppressor genes in DTC progression. In this review, we summarized the functional lncRNAs and expounded on their regulatory mechanisms in DTCs.
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Affiliation(s)
- Shuo Zeng
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Rei Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Bo-Sheng Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
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Long noncoding RNAs: Novel players in colorectal cancer. Cancer Lett 2015; 361:13-21. [DOI: 10.1016/j.canlet.2015.03.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 12/18/2022]
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Lambert MP, Ancey PB, Esposti DD, Cros MP, Sklias A, Scoazec JY, Durantel D, Hernandez-Vargas H, Herceg Z. Aberrant DNA methylation of imprinted loci in hepatocellular carcinoma and after in vitro exposure to common risk factors. Clin Epigenetics 2015; 7:15. [PMID: 25755686 PMCID: PMC4353474 DOI: 10.1186/s13148-015-0053-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/06/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is among the most frequent human malignancies and a major cause of cancer-related death worldwide. It is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be one of the molecular mechanisms leading to hepatocarcinogenesis. Previous studies from our group revealed that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression. Imprinted genes are mono-allelically expressed in a parent-of-origin-dependent manner and have been suggested to be more susceptible to deregulation in cancer. To test this notion, we performed a targeted analysis of DNA methylation in known imprinted genes, using HCC samples and in vitro models of carcinogenic exposure. RESULTS Analysis of HCC DNA methylation in two independent datasets showed that differentially methylated loci are significantly enriched in imprinted genes. Most of the promoters of imprinted genes were found hypomethylated in HCC tumors compared to surrounding tissues, contrasting with the frequent promoter hypermethylation observed in tumors. We next investigated the status of methylation of the imprinting control region (ICR) of different imprinted clusters and found that the 15q11-13 ICR was significantly hypomethylated in tumors relative to their surrounding tissues. In addition, expression of imprinted genes within this cluster was frequently deregulated in a gene-specific manner, suggesting distinct mechanisms of regulation in this region. Finally, primary human hepatocytes and hepatocyte-like HepaRG cells displayed higher methylation variability in certain imprinted loci after natural hepatitis B virus (HBV) infection and after lipid accumulation, respectively. CONCLUSION The methylation status of a large panel of imprinted genes was found deregulated in HCC, suggesting a major role of this mechanism during hepatocarcinogenesis. In vitro models support the hypothesis of imprinted gene methylation as a potential marker of environmental exposures.
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Affiliation(s)
- Marie-Pierre Lambert
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
- />Current address: Epissage alternatif et progression tumorale, Centre de Recherche en Cancérologie de Lyon (CRCL), 28 rue Laennec, 69008 Lyon, France
| | - Pierre-Benoit Ancey
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Davide Degli Esposti
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Marie-Pierre Cros
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Athena Sklias
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Jean-Yves Scoazec
- />Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - David Durantel
- />INSERM U871, Molecular physiopathology and new treatments of viral hepatitis, Centre de recherche en cancérologie (CRCL), 151 Cours Albert-Thomas, 69008 Lyon, France
| | - Hector Hernandez-Vargas
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Zdenko Herceg
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
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SUN HUILING, PAN YUQIN, HE BANGSHUN, DENG QIWEN, LI RUI, XU YEQIONG, CHEN JIE, GAO TIANYI, YING HOUQUN, WANG FENG, LIU XIAN, WANG SHUKUI. Gene therapy for human colorectal cancer cell lines with recombinant adenovirus 5 based on loss of the insulin-like growth factor 2 imprinting. Int J Oncol 2015; 46:1759-67. [DOI: 10.3892/ijo.2015.2852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/29/2014] [Indexed: 11/06/2022] Open
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Ye LEC, Zhu DEX, Qiu JJ, Xu J, Wei Y. Involvement of long non-coding RNA in colorectal cancer: From benchtop to bedside (Review). Oncol Lett 2015; 9:1039-1045. [PMID: 25663854 PMCID: PMC4315074 DOI: 10.3892/ol.2015.2846] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/12/2014] [Indexed: 01/30/2023] Open
Abstract
Colorectal cancer (CRC) is one of the greatest threats to public health. Recent advances in whole-genome transcriptome analyses have enabled the identification of numerous members of a novel class of non-coding (nc)RNA, long ncRNA (lncRNA), which is broadly defined as RNA molecules that are >200 nt in length and lacking an open reading frame. In the present review, all lncRNAs associated with CRC are briefly summarized, with a particular focus on their potential roles as clinical biomarkers. CRC-associated lncRNAs involved in the underlying mechanisms of CRC progression are also initially included. This should benefit the development of novel markers and effective therapeutic targets for patients with CRC.
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Affiliation(s)
- LE-Chi Ye
- Department of Oncological Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, P.R. China
| | - DE-Xiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Jun-Jun Qiu
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P.R. China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
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Danielsen SA, Eide PW, Nesbakken A, Guren T, Leithe E, Lothe RA. Portrait of the PI3K/AKT pathway in colorectal cancer. Biochim Biophys Acta Rev Cancer 2014; 1855:104-21. [PMID: 25450577 DOI: 10.1016/j.bbcan.2014.09.008] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/07/2014] [Indexed: 12/16/2022]
Abstract
PI3K/AKT signaling leads to reduced apoptosis, stimulates cell growth and increases proliferation. Under normal conditions, PI3K/AKT activation is tightly controlled and dependent on both extracellular growth signals and the availability of amino acids and glucose. Genetic aberrations leading to PI3K/AKT hyper-activation are observed at considerable frequency in all major nodes in most tumors. In colorectal cancer the most commonly observed pathway changes are IGF2 overexpression, PIK3CA mutations and PTEN mutations and deletions. Combined, these alterations are found in about 40% of large bowel tumors. In addition, but not mutually exclusive to these, KRAS mutations are observed at a similar frequency. There are however additional, less frequent and more poorly understood events that may also push the PI3K/AKT pathway into overdrive and thus promote malignant growth. Here we discuss aberrations of components at the genetic, epigenetic, transcriptional, post-transcriptional, translational and post-translational level where perturbations may drive excessive PI3K/AKT signaling. Integrating multiple molecular levels will advance our understanding of this cancer critical circuit and more importantly, improve our ability to pharmacologically target the pathway in view of clonal development, tumor heterogeneity and drug resistance mechanisms. In this review, we revisit the PI3K/AKT pathway cancer susceptibility syndromes, summarize the known aberrations at the different regulatory levels and the prognostic and predictive values of these alterations in colorectal cancer.
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Affiliation(s)
- Stine Aske Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Peter Wold Eide
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Tormod Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Edward Leithe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.
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Liyanage VRB, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR. DNA modifications: function and applications in normal and disease States. BIOLOGY 2014; 3:670-723. [PMID: 25340699 PMCID: PMC4280507 DOI: 10.3390/biology3040670] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
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Affiliation(s)
- Vichithra R B Liyanage
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Nanditha Murugeshan
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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Ozaki S, Kawahara E, Maenaka S, Hoang NV, Oyama T, Imai M, Oda M, Yano S. Distinct allelic expression patterns of imprinted IGF2 in adenocarcinoma and squamous cell carcinoma of the lung. Oncol Lett 2014; 8:2561-2564. [PMID: 25364428 PMCID: PMC4214443 DOI: 10.3892/ol.2014.2572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 08/22/2014] [Indexed: 11/30/2022] Open
Abstract
The insulin-like growth factor 2 gene (IGF2) is an imprinting gene, which mediates cell growth and apoptosis. The loss of imprinting (LOI) of IGF2 has been associated with the development of cancer. In the present study, loss LOI of IGF2 in lung cancer was analyzed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in combination with DNA sequencing of samples collected by laser capture microdissection. The status of each sample was assigned as imprinting when PCR-RFLP revealed only one band or sequence with a single peak; otherwise, the case was classified as LOI. LOI was identified in eight out of 13 adenocarcinoma cases (62%), but was not detected in any of the nine squamous cell carcinoma cases (0%). These results suggest that IGF2 LOI is involved in the molecular pathogenesis of lung adenocarcinoma, but not squamous cell carcinoma, and that LOI may be detected through increased IGF2 expression levels.
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Affiliation(s)
- Satoru Ozaki
- Department of Clinical Laboratory Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Ei Kawahara
- Department of Clinical Laboratory Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Shiori Maenaka
- Department of Clinical Laboratory Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Nguyen Viet Hoang
- Department of Clinical Laboratory Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Takeru Oyama
- Department of Pathology, Kanazawa University, Ishikawa 920-0942, Japan
| | - Miwa Imai
- Department of Health Science, Ishikawa Prefectural Nursing University, Ishikawa 929-1212, Japan
| | - Makoto Oda
- Department of Lung Surgery, Kanazawa University Hospital, Ishikawa 920-8641, Japan
| | - Seiji Yano
- Department of Internal Medicine, Kanazawa University Cancer Research Institute, Ishikawa 920-1192, Japan
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Bathe OF, Farshidfar F. From genotype to functional phenotype: unraveling the metabolomic features of colorectal cancer. Genes (Basel) 2014; 5:536-60. [PMID: 25055199 PMCID: PMC4198916 DOI: 10.3390/genes5030536] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/27/2014] [Accepted: 06/27/2014] [Indexed: 12/12/2022] Open
Abstract
Much effort in recent years has been expended in defining the genomic and epigenetic alterations that characterize colorectal adenocarcinoma and its subtypes. However, little is known about the functional ramifications related to various subtypes. Metabolomics, the study of small molecule intermediates in disease, provides a snapshot of the functional phenotype of colorectal cancer. Data, thus far, have characterized some of the metabolic perturbations that accompany colorectal cancer. However, further studies will be required to identify biologically meaningful metabolic subsets, including those corresponding to specific genetic aberrations. Moreover, further studies are necessary to distinguish changes due to tumor and the host response to tumor.
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Affiliation(s)
- Oliver F Bathe
- Department of Surgery, Tom Baker Cancer Center, University of Calgary, 1331 29th St NW, Calgary, AB T2N 4N2, Canada.
| | - Farshad Farshidfar
- Department of Surgery, Tom Baker Cancer Center, University of Calgary, 1331 29th St NW, Calgary, AB T2N 4N2, Canada.
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Downregulation of LncRNAH19 and MiR-675 promotes migration and invasion of human hepatocellular carcinoma cells through AKT/GSK-3β/Cdc25A signaling pathway. ACTA ACUST UNITED AC 2014; 34:363-369. [DOI: 10.1007/s11596-014-1284-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/24/2014] [Indexed: 12/14/2022]
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Cao Y, Lindström S, Schumacher F, Stevens VL, Albanes D, Berndt S, Boeing H, Bueno-de-Mesquita HB, Canzian F, Chamosa S, Chanock SJ, Diver WR, Gapstur SM, Gaziano JM, Giovannucci EL, Haiman CA, Henderson B, Johansson M, Le Marchand L, Palli D, Rosner B, Siddiq A, Stampfer M, Stram DO, Tamimi R, Travis RC, Trichopoulos D, Willett WC, Yeager M, Kraft P, Hsing AW, Pollak M, Lin X, Ma J. Insulin-like growth factor pathway genetic polymorphisms, circulating IGF1 and IGFBP3, and prostate cancer survival. J Natl Cancer Inst 2014; 106:dju085. [PMID: 24824313 PMCID: PMC4081624 DOI: 10.1093/jnci/dju085] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The insulin-like growth factor (IGF) signaling pathway has been implicated in prostate cancer (PCa) initiation, but its role in progression remains unknown. METHODS Among 5887 PCa patients (704 PCa deaths) of European ancestry from seven cohorts in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium, we conducted Cox kernel machine pathway analysis to evaluate whether 530 tagging single nucleotide polymorphisms (SNPs) in 26 IGF pathway-related genes were collectively associated with PCa mortality. We also conducted SNP-specific analysis using stratified Cox models adjusting for multiple testing. In 2424 patients (313 PCa deaths), we evaluated the association of prediagnostic circulating IGF1 and IGFBP3 levels and PCa mortality. All statistical tests were two-sided. RESULTS The IGF signaling pathway was associated with PCa mortality (P = .03), and IGF2-AS and SSTR2 were the main contributors (both P = .04). In SNP-specific analysis, 36 SNPs were associated with PCa mortality with P trend less than .05, but only three SNPs in the IGF2-AS remained statistically significant after gene-based corrections. Two were in linkage disequilibrium (r 2 = 1 for rs1004446 and rs3741211), whereas the third, rs4366464, was independent (r 2 = 0.03). The hazard ratios (HRs) per each additional risk allele were 1.19 (95% confidence interval [CI] = 1.06 to 1.34; P trend = .003) for rs3741211 and 1.44 (95% CI = 1.20 to 1.73; P trend < .001) for rs4366464. rs4366464 remained statistically significant after correction for all SNPs (P trend.corr = .04). Prediagnostic IGF1 (HRhighest vs lowest quartile = 0.71; 95% CI = 0.48 to 1.04) and IGFBP3 (HR = 0.93; 95% CI = 0.65 to 1.34) levels were not associated with PCa mortality. CONCLUSIONS The IGF signaling pathway, primarily IGF2-AS and SSTR2 genes, may be important in PCa survival.
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Hoyo C, Daltveit AK, Iversen E, Benjamin-Neelon SE, Fuemmeler B, Schildkraut J, Murtha AP, Overcash F, Vidal AC, Wang F, Huang Z, Kurtzberg J, Seewaldt V, Forman M, Jirtle RL, Murphy SK. Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort. Epigenetics 2014; 9:1120-30. [PMID: 24874916 DOI: 10.4161/epi.29332] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic mechanisms are proposed to link maternal concentrations of methyl group donor nutrients with the risk of low birth weight. However, empirical data are lacking. We have examined the association between maternal folate and birth weight and assessed the mediating role of DNA methylation at nine differentially methylated regions (DMRs) of genomically imprinted genes in these associations. Compared with newborns of women with folate levels in the lowest quartile, birth weight was higher in newborns of mothers in the second (β = 143.2, se = 63.2, P = 0.02), third (β = 117.3, se = 64.0, P = 0.07), and fourth (β = 133.9, se = 65.2, P = 0.04) quartiles, consistent with a threshold effect. This pattern of association did not vary by race/ethnicity but was more apparent in newborns of non-obese women. DNA methylation at the PLAGL1, SGCE, DLK1/MEG3 and IGF2/H19 DMRs was associated with maternal folate levels and also birth weight, suggestive of threshold effects. MEG3 DMR methylation mediated the association between maternal folate levels and birth weight (P =0.06). While the small sample size and partial scope of examined DMRs limit our conclusions, our data suggest that, with respect to birth weight, no additional benefits may be derived from increased maternal folate concentrations, especially in non-obese women. These data also support epigenetic plasticity as a key mechanistic response to folate availability during early fetal development.
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Affiliation(s)
- Cathrine Hoyo
- Department of Biological Sciences; North Carolina State University; Raleigh, NC USA; Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Anne Kjersti Daltveit
- Department of Global Public Health and Primary Care; University of Bergen; Bergen, Norway
| | - Edwin Iversen
- Department of Statistics; Duke University; Durham, NC USA
| | - Sara E Benjamin-Neelon
- Department of Community and Family Medicine; Duke University School of Medicine and Duke Global Health Institute; Durham, NC USA
| | - Bernard Fuemmeler
- Department of Community and Family Medicine; Duke University; Durham, NC USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Amy P Murtha
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; School of Medicine; Duke University; Durham, NC USA
| | - Francine Overcash
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Adriana C Vidal
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Frances Wang
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Joanne Kurtzberg
- Duke University Department of Pediatrics; Duke Cancer Institute; School of Medicine; Duke University; Durham, NC USA
| | - Victoria Seewaldt
- Department of Medicine; Division of Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Michele Forman
- Department of Nutritional Sciences; University of Texas; Austin, TX USA
| | - Randy L Jirtle
- Department of Oncology; McArdle Laboratory for Cancer Research; University of Wisconsin-Madison; Madison, WI USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
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Insulin-like Growth Factor Pathway Genetic Polymorphisms, Circulating IGF1 and IGFBP3, and Prostate Cancer Survival. J Natl Cancer Inst 2014; 106:dju218. [PMCID: PMC4111284 DOI: 10.1093/jnci/dju218] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 04/11/2024] Open
Abstract
Background The insulin-like growth factor (IGF) signaling pathway has been implicated in prostate cancer (PCa) initiation, but its role in progression remains unknown. Methods Among 5887 PCa patients (704 PCa deaths) of European ancestry from seven cohorts in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium, we conducted Cox kernel machine pathway analysis to evaluate whether 530 tagging single nucleotide polymorphisms (SNPs) in 26 IGF pathway-related genes were collectively associated with PCa mortality. We also conducted SNP-specific analysis using stratified Cox models adjusting for multiple testing. In 2424 patients (313 PCa deaths), we evaluated the association of prediagnostic circulating IGF1 and IGFBP3 levels and PCa mortality. All statistical tests were two-sided. Results The IGF signaling pathway was associated with PCa mortality (P = .03), and IGF2-AS and SSTR2 were the main contributors (both P = .04). In SNP-specific analysis, 36 SNPs were associated with PCa mortality with P trend less than .05, but only three SNPs in the IGF2-AS remained statistically significant after gene-based corrections. Two were in linkage disequilibrium (r 2 = 1 for rs1004446 and rs3741211), whereas the third, rs4366464, was independent (r 2 = 0.03). The hazard ratios (HRs) per each additional risk allele were 1.19 (95% confidence interval [CI] = 1.06 to 1.34; P trend = .003) for rs3741211 and 1.44 (95% CI = 1.20 to 1.73; P trend < .001) for rs4366464. rs4366464 remained statistically significant after correction for all SNPs (P trend.corr = .04). Prediagnostic IGF1 (HRhighest vs lowest quartile = 0.71; 95% CI = 0.48 to 1.04) and IGFBP3 (HR = 0.93; 95% CI = 0.65 to 1.34) levels were not associated with PCa mortality. Conclusions The IGF signaling pathway, primarily IGF2-AS and SSTR2 genes, may be important in PCa survival.
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Cesaroni M, Powell J, Sapienza C. Validation of methylation biomarkers that distinguish normal colon mucosa of cancer patients from normal colon mucosa of patients without cancer. Cancer Prev Res (Phila) 2014; 7:717-26. [PMID: 24806665 DOI: 10.1158/1940-6207.capr-13-0407] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have validated differences in DNA methylation levels of candidate genes previously reported to discriminate between normal colon mucosa of patients with colon cancer and normal colon mucosa of individuals without cancer. Here, we report that CpG sites in 16 of the 30 candidate genes selected show significant differences in mean methylation level in normal colon mucosa of 24 patients with cancer and 24 controls. A support vector machine trained on these data and data for an additional 66 CpGs yielded an 18-gene signature, composed of ten of the validated candidate genes plus eight additional candidates. This model exhibited 96% sensitivity and 100% specificity in a 40-sample training set and classified all eight samples in the test set correctly. Moreover, we found a moderate-strong correlation (Pearson coefficients r = 0.253-0.722) between methylation levels in colon mucosa and methylation levels in peripheral blood for seven of the 18 genes in the support vector model. These seven genes, alone, classified 44 of the 48 patients in the validation set correctly and five CpGs selected from only two of the seven genes classified 41 of the 48 patients in the discovery set correctly. These results suggest that methylation biomarkers may be developed that will, at minimum, serve as useful objective and quantitative diagnostic complements to colonoscopy as a cancer-screening tool. These data also suggest that it may be possible to monitor biomarker methylation levels in tissues collected much less invasively than by colonoscopy.
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Affiliation(s)
- Matteo Cesaroni
- Authors' Affiliations: Fels Institute for Cancer Research and Molecular Biology; and
| | - Jasmine Powell
- Authors' Affiliations: Fels Institute for Cancer Research and Molecular Biology; and
| | - Carmen Sapienza
- Authors' Affiliations: Fels Institute for Cancer Research and Molecular Biology; and Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania
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Tsui S, Dai W, Lu L. CCCTC-binding factor mediates effects of glucose on beta cell survival. Cell Prolif 2013; 47:28-37. [PMID: 24354619 DOI: 10.1111/cpr.12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Pancreatic islet β-cell survival is paramount for regulation of insulin activity and for maintaining glucose homeostasis. Recently, Pax6 has been shown to be essential for many vital functions in β-cells, although many molecular mechanisms of its homeostasis in β-cells remain unclear. The present study investigates novel effects of glucose- and insulin-induced CCCTC-binding factor (CTCF) activity on Pax6 gene expression as well as for subsequent effects of insulin-activated signalling pathways, on β-cell proliferation. MATERIALS AND METHODS Pancreatic β-TC-1-6 cells were cultured in DMEM and stimulated with high concentrations of glucose (5-125 mm); cell viability was assessed by MTT assay. Effects of CTCF on Pax6 were evaluated in the high glucose-induced environment and CTCF/Erk-suppressed cells, by promoter reporter and western blotting analyses. RESULTS Increases in glucose and insulin concentrations upregulated CTCF and consequently downregulated Pax6 in β-cell survival and proliferation. Knocking-down CTCF directly affected Pax6 transcription through CTCF binding and blocked the response to glucose. Altered Erk activity mediated effects of CTCF on controlling Pax6 expression, which partially regulated β-cell proliferation. CONCLUSIONS CTCF functioned as a molecular mediator between insulin-induced upstream Erk signalling and Pax6 expression in these pancreatic β-cells. This pathway may contribute to regulation of β-cell survival and proliferation.
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Affiliation(s)
- S Tsui
- Department of Medicine, David Geffen School of Medicine University of California Los Angeles, Torrance, CA, 90502, USA
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Murata A, Baba Y, Watanabe M, Shigaki H, Miyake K, Ishimoto T, Iwatsuki M, Iwagami S, Yoshida N, Oki E, Morita M, Nakao M, Baba H. IGF2 DMR0 methylation, loss of imprinting, and patient prognosis in esophageal squamous cell carcinoma. Ann Surg Oncol 2013; 21:1166-74. [PMID: 24318096 DOI: 10.1245/s10434-013-3414-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND Insulin like growth factor 2 gene (IGF2) is normally imprinted. Loss of imprinting (LOI) of IGF2 in humans is associated with an increased risk of cancer and is controlled by CpG-rich regions known as differentially methylated regions (DMRs). Specifically, the methylation level at IGF2 DMR0 is correlated with IGF2 LOI and is a suggested surrogate marker for IGF2 LOI. A relationship between IGF2 DMR0 hypomethylation and poor prognosis has been shown in colorectal cancer. However, to our knowledge, no study has examined the relationships among the IGF2 DMR0 methylation level, LOI, and clinical outcome in esophageal squamous cell carcinoma (ESCC). METHODS The IGF2 imprinting status was screened using ApaI polymorphism, and IGF2 protein expression was evaluated by immunohistochemistry with 30 ESCC tissue specimens. For survival analysis, IGF2 DMR0 methylation was measured using a bisulfite pyrosequencing assay with 216 ESCC tissue specimens. RESULTS Twelve (40 %) of 30 cases were informative (i.e., heterozygous for ApaI), and 5 (42 %) of 12 informative cases displayed IGF2 LOI. IGF2 LOI cases exhibited lower DMR0 methylation levels (mean 23 %) than IGF2 non-LOI cases (37 %). The IGF2 DMR0 methylation level was significantly associated with IGF2 protein expression. Among 202 patients eligible for survival analysis, IGF2 DMR0 hypomethylation was significantly associated with higher cancer-specific mortality. CONCLUSIONS The IGF2 DMR0 methylation level in ESCC was associated with IGF2 LOI and IGF2 protein expression. In addition, IGF2 DMR0 hypomethylation was associated with a shorter survival time, suggesting its potential role as a prognostic biomarker.
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Affiliation(s)
- Asuka Murata
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto City, Kumamoto, Japan
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Hubertus J, Zitzmann F, Trippel F, Müller-Höcker J, Stehr M, von Schweinitz D, Kappler R. Selective methylation of CpGs at regulatory binding sites controls NNAT expression in Wilms tumors. PLoS One 2013; 8:e67605. [PMID: 23825673 PMCID: PMC3692448 DOI: 10.1371/journal.pone.0067605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/20/2013] [Indexed: 11/18/2022] Open
Abstract
Aberrant expression of imprinted genes, such as those coding for the insulin-like growth factor 2 (IGF2) and neuronatin (NNAT), is a characteristic of a variety of embryonic neoplasms, including Wilms tumor (WT). In case of IGF2, it is generally accepted that loss of imprinting in a differentially methylated region of the IGF2/H19 locus results in biallelic expression and, thus, upregulation of the gene. In this study we examined methylation pattern at potential regulatory elements of the paternally expressed NNAT gene in a cohort of WT patients in order to further characterize the molecular mechanism causing overexpression of this regulatory gene. We demonstrate that transcriptional upregulation of NNAT in WT is grossly independent of the bladder cancer-associated protein (BLCAP) gene, an imprinted gene within the imprinted domain of the NNAT locus. However, expression of the BLCAP transcript isoform v2a formerly known to be selectively expressed from the paternal allele in brain was associated with high expression of NNAT. This contrasts the situation we found at the IGF2/H19 locus, which shows high overexpression of IGF2 and inversely correlated expression of the H19 gene in WT. An analysis of DNA methylation in two potential regulatory regions of the NNAT locus by pyrosequencing revealed significant hypomethylation of the tumors compared to normal kidney tissue. Interestingly, the difference in DNA methylation was highest at CpGs that were observed within three putative binding sites of the CCCTC-binding factor CTCF. Most importantly, hypomethylation of both NNAT regulatory regions is significantly associated with the upregulation of NNAT expression and the BLCAP_v2a transcript. Our data indicate that the methylation status of a not-yet-described regulatory element within the NNAT locus that contains four potential CTCF binding sites determines the expression level of NNAT and the nearby located BLCAP_v2a transcript, thereby suggesting a functional role in the aberrant upregulation of NNAT in WT.
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Affiliation(s)
- Jochen Hubertus
- Department of Pediatric Surgery, Research Laboratories, Ludwig-Maximilians-University, Munich, Germany.
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Hasanali Z, Stuart A, Yee N, Sharma K, Epner E. The Epigenetics of Gastrointestinal Malignancies. CURRENT COLORECTAL CANCER REPORTS 2012. [DOI: 10.1007/s11888-012-0147-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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