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Li Z, Yan H, Wang B, Wang H, Chen A, Zhu T, Liu J, Yu G, Kang M. High methylation of the same promoter of lncRNA ZNF582-AS1/ ZNF582 promotes malignant progression of esophageal cancer. Epigenomics 2024:1-20. [PMID: 38869483 DOI: 10.1080/17501911.2024.2342229] [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: 11/13/2023] [Accepted: 04/09/2024] [Indexed: 06/14/2024] Open
Abstract
Aim: This study aimed to investigate the functions of ZNF582-AS1 and ZNF582 in esophageal cancer (EC). Materials & methods: Bioinformatics analysis, qRT-PCR and western blot were used to analyze the expression levels. Biological functions were evaluated using cell-counting kit 8, colony formation, Transwell assays and flow cytometry. FISH was used to detect subcellular localization, and methylation-specific PCR determined gene methylation levels. Animal experiments validated the impact on tumor progression. Results: ZNF582-AS1 and ZNF582 were highly methylated and downregulated in EC. Overexpression of ZNF582-AS1 up-regulated the expression of ZNF582, thereby inhibiting EC cell viability and metastasis, promoting apoptosis and inhibiting tumor growth. Conclusion: Low expression of ZNF582-AS1/ZNF582 mediated by DNA hypermethylation facilitates the malignant progression of EC.
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Affiliation(s)
- Zhupeng Li
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Hefang Yan
- Department of Endocrinology, Rheumatology & immunology, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Bin Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Haiyong Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Aixia Chen
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Ting Zhu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Jianjiang Liu
- Department of Radiotherapy, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Guangmao Yu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Mingqiang Kang
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
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2
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Fu H, Zhang M, Liu X, Yang Y, Xing Y. Abnormal methylation mediated upregulation of LINC00857 boosts malignant progression of lung adenocarcinoma by modulating the miR-486-5p/NEK2 axis. THE CLINICAL RESPIRATORY JOURNAL 2024; 18:e13765. [PMID: 38721812 PMCID: PMC11079885 DOI: 10.1111/crj.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/29/2023] [Accepted: 03/12/2024] [Indexed: 05/12/2024]
Abstract
LINC00857 is frequently dysregulated in varying cancers, which in turn exerts carcinogenic effects; however, its DNA methylation status in promoter region and molecular mechanisms underlying the progression of lung adenocarcinoma (LUAD) remain rarely understood. Through bioinformatics analysis, we examined the expression state and methylation site of LINC00857 in LUAD and further investigated the properties of LINC00857 as a competitive endogenous RNA in the cancer progression. The current study revealed that the overexpression of LINC00857 in LUAD tissue and cells was mainly caused by the hypomethylation of the promoter region. LINC00857 knockdown prominently reduced cell proliferation, impeded cell migration and invasion, and restrained lymph node metastasis, with enhancing radiosensitivity. The effects of LINC00857 on tumor growth were also investigated in nude mice models. Subsequently, the downstream factors, miR-486-5p and NEK2, were screened, and the putative regulatory axis was examined. Overall, the regulatory effect of methylation-mediated LINC00857 overexpression on miR-486-5p/NEK2 axis may be a new mechanism for LUAD progression.
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Affiliation(s)
- Haoyu Fu
- Department of Radiation OncologyTangshan People's HospitalTangshanChina
| | - Mingming Zhang
- Department of Thoracic SurgeryTangshan People's HospitalTangshanChina
| | - Xiaohui Liu
- Department of Thoracic SurgeryTangshan People's HospitalTangshanChina
| | - Yiming Yang
- Department of Breast SurgeryTangshan People's HospitalTangshanChina
| | - Ying Xing
- Department of Radiation OncologyTangshan People's HospitalTangshanChina
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3
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Ranjbar M, Heydarzadeh S, Shekari Khaniani M, Foruzandeh Z, Seif F, Pornour M, Rahmanpour D, Tarhriz V, Alivand M. Mutual interaction of lncRNAs and epigenetics: focusing on cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-023-00404-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
AbstractLong noncoding RNAs are characterized as noncoding transcripts longer than 200 nucleotides in response to a variety of functions within the cells. They are involved in almost all cellular mechanisms so as epigenetics. Given that epigenetics is an important phenomenon, which participates in the biology of complex diseases, many valuable studies have been performed to demonstrate the control status of lncRNAs and epigenetics. DNA methylation and histone modifications as epigenetic mechanisms can regulate the expression of lncRNAs by affecting their coding genes. Reciprocally, the three-dimensional structure of lncRNAs could mechanistically control the activity of epigenetic-related enzymes. Dysregulation in the mutual interaction between epigenetics and lncRNAs is one of the hallmarks of cancer. These mechanisms are either directly or indirectly involved in various cancer properties such as proliferation, apoptosis, invasion, and metastasis. For instance, lncRNA HOTAIR plays a role in regulating the expression of many genes by interacting with epigenetic factors such as DNA methyltransferases and EZH2, and thus plays a role in the initiation and progression of various cancers. Conversely, the expression of this lncRNA is also controlled by epigenetic factors. Therefore, focusing on this reciprocated interaction can apply to cancer management and the identification of prognostic, diagnostic, and druggable targets. In the current review, we discuss the reciprocal relationship between lncRNAs and epigenetic mechanisms to promote or prevent cancer progression and find new potent biomarkers and targets for cancer diagnosis and therapy.
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Zafari N, Bathaei P, Velayati M, Khojasteh-Leylakoohi F, Khazaei M, Fiuji H, Nassiri M, Hassanian SM, Ferns GA, Nazari E, Avan A. Integrated analysis of multi-omics data for the discovery of biomarkers and therapeutic targets for colorectal cancer. Comput Biol Med 2023; 155:106639. [PMID: 36805214 DOI: 10.1016/j.compbiomed.2023.106639] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
The considerable burden of colorectal cancer and the rising trend in young adults emphasize the necessity of understanding its underlying mechanisms, providing new diagnostic and prognostic markers, and improving therapeutic approaches. Precision medicine is a new trend all over the world and identification of novel biomarkers and therapeutic targets is a step forward towards this trend. In this context, multi-omics data and integrated analysis are being investigated to develop personalized medicine in the management of colorectal cancer. Given the large amount of data from multi-omics approach, data integration and analysis is a great challenge. In this Review, we summarize how statistical and machine learning techniques are applied to analyze multi-omics data and how it contributes to the discovery of useful diagnostic and prognostic biomarkers and therapeutic targets. Moreover, we discuss the importance of these biomarkers and therapeutic targets in the clinical management of colorectal cancer in the future. Taken together, integrated analysis of multi-omics data has great potential for finding novel diagnostic and prognostic biomarkers and therapeutic targets, however, there are still challenges to overcome in future studies.
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Affiliation(s)
- Nima Zafari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parsa Bathaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Velayati
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Elham Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Wang J, Katsaros D, Biglia N, Fu Y, Benedetto C, Loo L, Wang Z, Yu H. LncRNA ZNF582-AS1 Expression and Methylation in Breast Cancer and Its Biological and Clinical Implications. Cancers (Basel) 2022; 14:2788. [PMID: 35681777 PMCID: PMC9179509 DOI: 10.3390/cancers14112788] [Citation(s) in RCA: 4] [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: 04/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs) play an important role in cellular activities and functions, but our understanding of their involvement in cancer is limited. Methods: TCGA data on RNA expression and DNA methylation were analyzed for lncRNAs' association with breast cancer survival, using the Cox proportional hazard regression model. Fresh tumor samples and clinical information from 361 breast cancer patients in our study were used to confirm the TCGA finding on ZNF582-AS1. A RT-qPCR method was developed to measure ZNF582-AS1 expression. Survival associations with ZNF582-AS1 were verified with a meta-analysis. In silico predictions of molecular targets and cellular functions of ZNF582-AS1 were performed based on its molecular signatures and nucleotide sequences. Results:ZNF582-AS1 expression was lower in breast tumors than adjacent normal tissues. Low ZNF582-AS1 was associated with high-grade or ER-negative tumors. Patients with high ZNF582-AS1 had a lower risk of relapse and death. These survival associations were confirmed in a meta-analysis and remained significant after adjustment for tumor grade, disease stage, patient age, and hormone receptor status. Correlation analysis indicated the possible suppression of ZNF582-AS1 expression by promoter methylation. Bioinformatics interrogation of molecular signatures suggested that ZNF582-AS1 could suppress tumor cell proliferation via downregulating the HER2-mediated signaling pathway. Analysis of online data also suggested that HIF-1-related transcription factors could suppress ZNF582-AS1 expression, and the lncRNA might bind to hsa-miR-940, a known oncogenic miRNA in breast cancer. Conclusions: ZNF582-AS1 may play a role in suppressing breast cancer progression. Elucidating the lncRNA's function and regulation may improve our understanding of the disease.
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Affiliation(s)
- Junlong Wang
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Dionyssios Katsaros
- Department of Surgical Sciences, Gynecology, AOU Città della Salute, University of Torino School of Medicine, 10124 Turin, Italy; (D.K.); (C.B.)
| | - Nicoletta Biglia
- Department of Surgical Sciences, Division of Obstetrics and Gynecology, University of Torino School of Medicine, Mauriziano Hospital, 10124 Turin, Italy;
| | - Yuanyuan Fu
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Chiara Benedetto
- Department of Surgical Sciences, Gynecology, AOU Città della Salute, University of Torino School of Medicine, 10124 Turin, Italy; (D.K.); (C.B.)
| | - Lenora Loo
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
| | - Zhanwei Wang
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
| | - Herbert Yu
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
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6
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Yue M, Liu T, Yan G, Luo X, Wang L. LINC01605, regulated by the EP300-SMYD2 complex, potentiates the binding between METTL3 and SPTBN2 in colorectal cancer. Cancer Cell Int 2021; 21:504. [PMID: 34544413 PMCID: PMC8451128 DOI: 10.1186/s12935-021-02180-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
Background Colorectal cancer (CC) is one of the major contributors to tumor-related death worldwide, and its main cause of death is distant metastasis. Dysregulation of long non-coding RNA (lncRNA) LINC01605 has been implicated in CC. However, its role in metastasis of CC remains elusive. The goal of the study is to uncover the biological function and molecular mechanism of LINC01605 in CC. Methods The differentially expressed lncRNAs were first screened from GSE97300, GSE84983, GSE110715, GSE70880, and GSE75970 microarrays. The correlation between the expression of LINC01605 and the clinical phenotypes of enrolled CC patients (n = 134) was subsequently analyzed. The upstream and downstream regulatory mechanisms of LINC01605 in CC were identified through bioinformatics and RNA-seq analyses. Finally, the effects of related factors on CC cell growth and metastasis were confirmed through functional validation experiments. Results LINC01605, significantly highly expressed in CC, was a prognostic factor for patients with CC. Functional experiments revealed that LINC01605 knockdown inhibited the proliferatory and metastatic potential of CC cells in vitro and in vivo. Moreover, LINC01605 was regulated by SMYD2-EP300-mediated modifications of histone H3K4me3 as well as H3K27ac. LINC01605 was found to bind to METTL3 and promote the m6A modification of SPTBN2 mRNA, thereby facilitating the translation of SPTBN2. Conclusions Overexpression of LINC01605, regulated by SMYD2-EP300-mediated H3K27ac and H3K4me3 modifications, bound to METTL3 protein to promote m6A modification of SPTBN2 mRNA, leading to the development of CC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02180-8.
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Affiliation(s)
- Meng Yue
- Department of Colorecal and Anal Surgery, The First Hospital of Jilin University, No. 71, Xinmin Street, Chaoyang District, Changchun, 130021, Jilin, People's Republic of China
| | - Tao Liu
- Department of Colorecal and Anal Surgery, The First Hospital of Jilin University, No. 71, Xinmin Street, Chaoyang District, Changchun, 130021, Jilin, People's Republic of China
| | - Guoqiang Yan
- Department of Colorecal and Anal Surgery, The First Hospital of Jilin University, No. 71, Xinmin Street, Chaoyang District, Changchun, 130021, Jilin, People's Republic of China
| | - Xiaofan Luo
- Department of Colorecal and Anal Surgery, The First Hospital of Jilin University, No. 71, Xinmin Street, Chaoyang District, Changchun, 130021, Jilin, People's Republic of China
| | - Lei Wang
- Department of Colorecal and Anal Surgery, The First Hospital of Jilin University, No. 71, Xinmin Street, Chaoyang District, Changchun, 130021, Jilin, People's Republic of China.
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7
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Wang Y, Yan K, Wang L, Bi J. Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology. BMC Cancer 2021; 21:727. [PMID: 34167490 PMCID: PMC8229419 DOI: 10.1186/s12885-021-08356-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/29/2021] [Indexed: 12/04/2022] Open
Abstract
Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. “GSVA” package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. “Survival” package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model. Results In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model’s genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. Conclusion subsections These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08356-9.
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Affiliation(s)
- Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Linhui Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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8
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Xu D, Wang L, Pang S, Cao M, Wang W, Yu X, Xu Z, Xu J, Wang H, Lu J, Li K. The Functional Characterization of Epigenetically Related lncRNAs Involved in Dysregulated CeRNA-CeRNA Networks Across Eight Cancer Types. Front Cell Dev Biol 2021; 9:649755. [PMID: 34222227 PMCID: PMC8247484 DOI: 10.3389/fcell.2021.649755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Numerous studies have demonstrated that lncRNAs could compete with other RNAs to bind miRNAs, as competing endogenous RNAs (ceRNAs), to regulate each other. On the other hand, ceRNAs were found to be recurrently dysregulated in cancer status. However, limited studies considered the upstream epigenetic regulatory factors that disrupted the normal competing mechanism. In the present study, we constructed the lncRNA-associated dysregulated ceRNA networks across eight cancer types. lncRNAs in the individual dysregulated network and pan-cancer core dysregulated ceRNA subnetwork were found to play more important roles than mRNAs. Integrating lncRNA methylation profiles, we identified 49 epigenetically related (ER) lncRNAs involved in the dysregulated ceRNA networks, including 18 epigenetically activated (EA) lncRNAs, 18 epigenetically silenced (ES) lncRNAs, and 13 rewired ER lncRNAs across eight cancer types. Furthermore, we evaluated the epigenetic regulating patterns of these lncRNAs and screened nine pan-cancer ER lncRNAs (six EA and three ES lncRNAs). The nine lncRNAs were found to regulate the cancer hallmarks by competing with mRNAs. Moreover, we found that integrating the expression and methylation profiles of the nine lncRNAs could predict cancer incidence in eight cancer types robustly and the cancer outcome of several cancer types. These results provide an improved understanding of methylation regulation to ceRNA and offer novel potential molecular therapeutic targets for the diagnosis and prognosis across different cancer types.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Liqiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sainan Pang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Meng Cao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenxiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaorong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhizhou Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Jiankai Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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9
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Multi-omics annotation of human long non-coding RNAs. Biochem Soc Trans 2021; 48:1545-1556. [PMID: 32756901 DOI: 10.1042/bst20191063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and also extensively involved in a variety of essential biological processes and human diseases. The comprehensive annotation of human lncRNAs is of great significance in navigating the functional landscape of the human genome and deepening the understanding of the multi-featured RNA world. However, the unique characteristics of lncRNAs as well as their enormous quantity have complicated and challenged the annotation of lncRNAs. Advances in high-throughput sequencing technologies give rise to a large volume of omics data that are generated at an unprecedented rate and scale, providing possibilities in the identification, characterization and functional annotation of lncRNAs. Here, we review the recent important discoveries of human lncRNAs through analysis of various omics data and summarize specialized lncRNA database resources. Moreover, we highlight the multi-omics integrative analysis as a powerful strategy to efficiently discover and characterize the functional lncRNAs and elucidate their potential molecular mechanisms.
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10
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Yang W, Zhang K, Li L, Xu Y, Ma K, Xie H, Zhou J, Cai L, Gong Y, Gong K. Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:92. [PMID: 33691743 PMCID: PMC7945252 DOI: 10.1186/s13046-021-01889-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/21/2021] [Indexed: 12/24/2022]
Abstract
Background Emerging evidence confirms that lncRNAs (long non-coding RNAs) are potential biomarkers that play vital roles in tumors. ZNF582-AS1 is a novel lncRNA that serves as a potential prognostic marker of cancers. However, the specific clinical significance and molecular mechanism of ZNF582-AS1 in ccRCC (clear cell renal cell carcinoma) are unclear. Methods Expression level and clinical significance of ZNF582-AS1 were determined by TCGA-KIRC data and qRT-PCR results of 62 ccRCCs. DNA methylation status of ZNF582-AS1 promoter was examined by MSP, MassARRAY methylation and demethylation analysis. Gain-of-function experiments were conducted to investigate the biological roles of ZNF582-AS1 in the phenotype of ccRCC. The subcellular localization of ZNF582-AS1 was detected by RNA FISH. iTRAQ, RNA pull-down and RIP-qRT-PCR were used to identify the downstream targets of ZNF582-AS1. rRNA MeRIP-seq and MeRIP-qRT-PCR were utilized to examine the N(6)-methyladenosine modification status. Western blot and immunohistochemistry assays were used to determine the protein expression level. Results ZNF582-AS1 was downregulated in ccRCC, and decreased ZNF582-AS1 expression was significantly correlated with advanced tumor stage, higher pathological stage, distant metastasis and poor prognosis. Decreased ZNF582-AS1 expression was caused by DNA methylation at the CpG islands within its promoter. ZNF582-AS1 overexpression inhibited cell proliferative, migratory and invasive ability, and increased cell apoptotic rate in vitro and in vivo. Mechanistically, we found that ZNF582-AS1 overexpression suppressed the N(6)-methyladenosine modification of MT-RNR1 by reducing rRNA adenine N(6)-methyltransferase A8K0B9 protein level, resulting in the decrease of MT-RNR1 expression, followed by the inhibition of MT-CO2 protein expression. Furthermore, MT-RNR1 overexpression reversed the decreased MT-CO2 expression and phenotype inhibition of ccRCC induced by increased ZNF582-AS1 expression. Conclusions This study demonstrates for the first time that ZNF582-AS1 functions as a tumor suppressor gene in ccRCC and ZNF582-AS1 may serve as a potential biomarker and therapeutic target of ccRCC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01889-8.
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Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Lei Li
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Yawei Xu
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Kaifang Ma
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Lin Cai
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, P. R. China.,National Urological Cancer Center, Beijing, 100034, P. R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, P. R. China. .,National Urological Cancer Center, Beijing, 100034, P. R. China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, P. R. China. .,National Urological Cancer Center, Beijing, 100034, P. R. China.
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11
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Long non-coding RNA levels can be modulated by 5-azacytidine in Schistosoma mansoni. Sci Rep 2020; 10:21565. [PMID: 33299037 PMCID: PMC7725772 DOI: 10.1038/s41598-020-78669-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects more than 200 million people worldwide. There is only one drug indicated for treatment, praziquantel, which may lead to parasite resistance emergence. The ribonucleoside analogue 5-azacytidine (5-AzaC) is an epigenetic drug that inhibits S. mansoni oviposition and ovarian development through interference with parasite transcription, translation and stem cell activities. Therefore, studying the downstream pathways affected by 5-AzaC in S. mansoni may contribute to the discovery of new drug targets. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein coding potential that have been involved in reproduction, stem cell maintenance and drug resistance. We have recently published a catalog of lncRNAs expressed in S. mansoni life-cycle stages, tissues and single cells. However, it remains largely unknown if lncRNAs are responsive to epigenetic drugs in parasites. Here, we show by RNA-Seq re-analyses that hundreds of lncRNAs are differentially expressed after in vitro 5-AzaC treatment of S. mansoni females, including intergenic, antisense and sense lncRNAs. Many of these lncRNAs belong to co-expression network modules related to male metabolism and are also differentially expressed in unpaired compared with paired females and ovaries. Half of these lncRNAs possess histone marks at their genomic loci, indicating regulation by histone modification. Among a selected set of 8 lncRNAs, half of them were validated by RT-qPCR as differentially expressed in females, and some of them also in males. Interestingly, these lncRNAs are also expressed in other life-cycle stages. This study demonstrates that many lncRNAs potentially involved with S. mansoni reproductive biology are modulated by 5-AzaC and sheds light on the relevance of exploring lncRNAs in response to drug treatments in parasites.
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12
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Poursheikhani A, Abbaszadegan MR, Kerachian MA. Mechanisms of long non-coding RNA function in colorectal cancer tumorigenesis. Asia Pac J Clin Oncol 2020; 17:7-23. [PMID: 32970938 DOI: 10.1111/ajco.13452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) is one of the most common cancers globally. Although a variety of CRC screening methods have been developed, many patients are diagnosed at advanced stages of CRC with tumor invasion and distance metastasis. Several studies have suggested the long noncoding RNAs (lncRNAs) as one of the main contributors in CRC tumorigenesis, although the exact underlying mechanism of lncRNAs in CRC is still unknown. Numerous studies have indicated aberrant expression of lncRNAs in CRC through different modes of action such as cell proliferation, apoptosis, cell cycle, DNA repair response, drug-resistance, migration, and metastasis. Furthermore, lncRNA polymorphisms can influence the risk of CRC development. Accordingly, lncRNAs can be served as promising diagnostic or prognostic biomarkers and also desired therapeutic targets affecting the outcome of patients with CRC. In this review, we summarized the updated and novel evidence that identifies different roles of lncRNAs in the tumorigenesis of CRC.
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Affiliation(s)
- Arash Poursheikhani
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy, and Oncology Center, Mashhad, Iran
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13
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Zhang D, Wang Y, Hu X. Identification and Comprehensive Validation of a DNA Methylation-Driven Gene-Based Prognostic Model for Clear Cell Renal Cell Carcinoma. DNA Cell Biol 2020; 39:1799-1812. [PMID: 32716214 DOI: 10.1089/dna.2020.5601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent renal malignancy in adults with generally poor prognosis. This study aimed to establish a DNA methylation-driven gene-based prognostic model for ccRCC. We collected DNA methylation and gene expression profiles of over 1500 ccRCC samples from The Cancer Genome Atlas (TCGA) dataset, four Gene Expression Omnibus (GEO) datasets, the Genotype-Tissue Expression (GTEx) dataset, and cancer cell lines from Cancer Cell Line Encyclopedia database and performed comprehensive bioinformatics analysis. As a result, a total of 31 differentially expressed methylation-driven genes (DEMDGs) were identified. After univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analyses, four (NFE2L3, HHLA2, IFI16, and ZNF582) were finally selected to construct a risk score prognostic model. The high-risk group demonstrated significantly poor prognosis than the low-risk group did in TCGA training (hazard ratio [HR] = 3.533, p < 0.001), TCGA internal, and GEO external validation datasets. Furthermore, the nomogram, including the prognostic model and clinical factors, showed promising prognostic value (HR = 5.756, p < 0.001, and area under the curve at 1 year = 0.856). In addition, the model was found to be significantly associated with drug sensitivity of eight targeted agents. These findings provided a novel and reliable four DEMDG-based prognostic model for ccRCC.
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Affiliation(s)
- Di Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Yicun Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
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14
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Wen D, Huang Z, Li Z, Tang X, Wen X, Liu J, Li M. LINC02535 co-functions with PCBP2 to regulate DNA damage repair in cervical cancer by stabilizing RRM1 mRNA. J Cell Physiol 2020; 235:7592-7603. [PMID: 32324262 DOI: 10.1002/jcp.29667] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Cervical cancer (CC) is one of the commonest malignant cancers among women with high morbidity and mortality. Despite encouraging advances had been found in diagnostic and therapeutic strategies, effective therapeutic strategy and further exploration of the mechanism underlying in CC is still needed. We searched The Cancer Genome Atlas database and found that long noncoding RNA LINC02535 was highly expressed in CC. LINC02535 has not been studied in CC, and its molecular regulation mechanism remains unknown. Based on starBase database, LINC02535 could potentially bind poly (rC) binding protein 2 (PCBP2). In the present study, we discovered a significant increase of the LINC02535 and PCBP2 expression in CC tissues and cells as compared with the adjacent normal tissues and normal cervical epithelial cells. LINC02535 and PCBP2 can bind with each other and were colocated in cytoplasm. LINC02535 and PCBP2 promoted cell proliferation, migration, invasion, and suppressed apoptosis in CC. LINC02535 and PCBP2 facilitated the repair of DNA damage to promote CC progression. LINC02535 cooperated with PCBP2 to enhance the stability of RRM1 messenger RNA (mRNA). RRM1 promoted the repair of DNA damage and epithelial-to-mesenchymal transition (EMT) process in CC cells. LINC02535 regulated tumorigenesis in vivo. In conclusion, LINC02535 cooperated with PCBP2, regulated stability of RRM1 mRNA to promote cell proliferation and EMT process in CC cells by facilitating the repair of DNA damage, providing a potential biomarker for CC.
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Affiliation(s)
- Danxia Wen
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhong Huang
- The 3rd Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhouyu Li
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xi Tang
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaomin Wen
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinquan Liu
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mingyi Li
- The 5th Ward of Radiotherapy Department of Affiliated Cancer Hospital, Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
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15
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He Y, Zhang R, Chen J, Tan J, Wang M, Wu X. The ability of arsenic metabolism affected the expression of lncRNA PANDAR, DNA damage, or DNA methylation in peripheral blood lymphocytes of laborers. Hum Exp Toxicol 2019; 39:605-613. [DOI: 10.1177/0960327119897101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Arsenic has been associated with significant effects on human health. Exposure to inorganic arsenic has been associated with the changes in gene expression. Promoter of CDKN1A antisense DNA damage activated RNA (PANDAR) expression is induced by p53 protein and DNA damage response. Here, we investigated whether the ability of arsenic metabolism in individuals affected the expression of PANDAR, DNA damage, and DNA methylation. Levels of gene expression and DNA damage were examined by the quantitative polymerase chain reaction and DNA methylation was measured by the methylation-sensitive high-resolution melting curve. In our study, we demonstrated that arsenic exposure increased PANDAR expression and DNA damage among arsenic smelting plant laborers. The PANDAR expression and DNA damage were positively linked to monomethylarsonic acid % ( R = 0.25, p < 0.05 and R = 0.32, p < 0.01) and negatively linked to dimethylarsinic acid % ( R = −0.21, p < 0.05 and R = −0.31, p < 0.01). Subjects with low primary methylation index had increased levels of DNA damage (51.62 ± 2.96 vs. 60.93 ± 3.10, p < 0.05) and methylation (17.14 (15.88–18.51) vs. 15.83 (14.82–18.00), p < 0.05). Subjects with low secondary methylation index had increased levels of PANDAR expression (4.88 ± 0.29 vs. 4.07 ± 0.23, p < 0.01) and DNA damage (17.38 (15.88–19.29) vs. 15.83 (14.82–17.26), p < 0.01). DNA methylation of PANDAR gene was linked to the regulation of its expression in peripheral blood lymphocytes among laborers ( Y = −2.08 × X + 5.64, p < 0.05). These findings suggested arsenic metabolism ability and exposure affected the expression of PANDAR, DNA damage, and DNA methylation.
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Affiliation(s)
- Y He
- School of Public Health, Kunming Medical University, Kunming, China
| | - R Zhang
- School of Public Health, Kunming Medical University, Kunming, China
| | - J Chen
- School of Public Health, Kunming Medical University, Kunming, China
| | - J Tan
- School of Public Health, Kunming Medical University, Kunming, China
| | - M Wang
- School of Public Health, Kunming Medical University, Kunming, China
| | - X Wu
- School of Public Health, Kunming Medical University, Kunming, China
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16
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Cheng G, Liu D, Liang H, Yang H, Chen K, Zhang X. A cluster of long non-coding RNAs exhibit diagnostic and prognostic values in renal cell carcinoma. Aging (Albany NY) 2019; 11:9597-9615. [PMID: 31727869 PMCID: PMC6874440 DOI: 10.18632/aging.102407] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Kidney cancer ranked in the top 10 for both men and women in the estimated numbers of new cancer cases in the United States in 2018. Targeted therapies have recently been administered to patients with clear cell renal cell carcinoma (ccRCC), but the overall survival of patients at the terminal stage of the disease has not been as good as expected. It is therefore necessary to uncover efficient biomarkers for early diagnosis, and to clarify the molecular mechanisms underlying ccRCC progression and metastasis. Increased evidence has shown that long non-coding RNAs (lncRNAs) play important roles during tumor progression. In this study, 10 candidate lncRNAs with diagnostic and prognostic values in ccRCC were identified: IGFL2-AS1, AC023043.1, AP000439.2, AC124854.1, AL355102.4, TMEM246-AS1, AL133467.3, ZNF582-AS1, LINC01510 and PSMG3-AS1. Enrichment analysis revealed metabolic and functional pathways, which may be closely associated with kidney cancer tumorigenesis. Six representative processes were summarized, namely glycolysis, amino acid metabolism, lipid synthesis, reductive carboxylation, nucleotide metabolism, transmembrane transport and signal transduction. In combination, the present results provided prognostic and diagnostic biomarkers for ccRCC and might pave the way for targeted intervention and molecular therapies in the future.
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Affiliation(s)
- Gong Cheng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Di Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Huageng Liang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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17
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Hua JT, Chen S, He HH. Landscape of Noncoding RNA in Prostate Cancer. Trends Genet 2019; 35:840-851. [DOI: 10.1016/j.tig.2019.08.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/09/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
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18
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Galamb O, Barták BK, Kalmár A, Nagy ZB, Szigeti KA, Tulassay Z, Igaz P, Molnár B. Diagnostic and prognostic potential of tissue and circulating long non-coding RNAs in colorectal tumors. World J Gastroenterol 2019; 25:5026-5048. [PMID: 31558855 PMCID: PMC6747286 DOI: 10.3748/wjg.v25.i34.5026] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are members of the non-protein coding RNA family longer than 200 nucleotides. They participate in the regulation of gene and protein expression influencing apoptosis, cell proliferation and immune responses, thereby playing a critical role in the development and progression of various cancers, including colorectal cancer (CRC). As CRC is one of the most frequently diagnosed malignancies worldwide with high mortality, its screening and early detection are crucial, so the identification of disease-specific biomarkers is necessary. LncRNAs are promising candidates as they are involved in carcinogenesis, and certain lncRNAs (e.g., CCAT1, CRNDE, CRCAL1-4) show altered expression in adenomas, making them potential early diagnostic markers. In addition to being useful as tissue-specific markers, analysis of circulating lncRNAs (e.g., CCAT1, CCAT2, BLACAT1, CRNDE, NEAT1, UCA1) in peripheral blood offers the possibility to establish minimally invasive, liquid biopsy-based diagnostic tests. This review article aims to describe the origin, structure, and functions of lncRNAs and to discuss their contribution to CRC development. Moreover, our purpose is to summarise lncRNAs showing altered expression levels during tumor formation in both colon tissue and plasma/serum samples and to demonstrate their clinical implications as diagnostic or prognostic biomarkers for CRC.
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Affiliation(s)
- Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Barbara K Barták
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Zsófia B Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Krisztina A Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Peter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
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19
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Yang F, Wu Q, Zhang L, Xie W, Sun X, Zhang Y, Wang L, Dai Q, Yu H, Chen Q, Sheng H, Qiu J, He X, Miao H, He F, Zhang K. The long noncoding RNA KCNQ1DN suppresses the survival of renal cell carcinoma cells through downregulating c-Myc. J Cancer 2019; 10:4662-4670. [PMID: 31528231 PMCID: PMC6746116 DOI: 10.7150/jca.29280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/28/2019] [Indexed: 01/29/2023] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have been demonstrated to play essential roles in renal cell carcinoma (RCC). However, the role of lncRNA KCNQ1DN in RCC remains unclear. Methods: The expression of KCNQ1DN in RCC and the corresponding adjacent tissues was measured by qPCR. RNA fluorescence in situ hybridization (FISH) assay, methylation analysis, reporter gene assays and functional tests were performed to reveal the effects of KCNQ1DN on RCC. Results: In the present study, we found that lncRNA KCNQ1DN was notably decreased in RCC tissues and cell lines. RNA FISH assay showed that KCNQ1DN mainly localized to the cytoplasm. Methylation analysis revealed that the proximal region of KCNQ1DN promoter was hypermethylated in RCC tissues relative to the adjacent normal ones. Functional studies clarified that KCNQ1DN repressed the RCC cell growth and cell cycle progression. Mechanistically, KCNQ1DN inhibited the expression of c-Myc, which might further upregulate cyclin D1 and suppress p27 at mRNA and protein levels in RCC cells. Reporter gene assays revealed that the transcriptional activity of c-Myc promoter was inhibited by KCNQ1DN. The in vivo experiments in nude mice showed that KCNQ1DN overexpression dramatically repressed the growth of xenograft tumors and the expression of corresponding c-Myc. Conclusion: These results indicated that KCNQ1DN inhibit the growth of RCC cells in vitro and in vivo through repressing the oncogene c-myc, suggesting that KCNQ1DN may serve as a novel target for the treatment of RCC.
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Affiliation(s)
- Fan Yang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China.,Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Qingjian Wu
- Department of Urology, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Le Zhang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Wei Xie
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Xiaoli Sun
- Nursing division, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Yan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Lei Wang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian Dai
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hua Yu
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian Chen
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Halei Sheng
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Jing Qiu
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Xiaomei He
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hongming Miao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Fengtian He
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Kebin Zhang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
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20
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Yeh SJ, Chang CA, Li CW, Wang LHC, Chen BS. Comparing progression molecular mechanisms between lung adenocarcinoma and lung squamous cell carcinoma based on genetic and epigenetic networks: big data mining and genome-wide systems identification. Oncotarget 2019; 10:3760-3806. [PMID: 31217907 PMCID: PMC6557199 DOI: 10.18632/oncotarget.26940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the predominant type of lung cancer in the world. Lung adenocarcinoma (LADC) and lung squamous cell carcinoma (LSCC) are subtypes of NSCLC. We usually regard them as different disease due to their unique molecular characteristics, distinct cells of origin and dissimilar clinical response. However, the differences of genetic and epigenetic progression mechanism between LADC and LSCC are complicated to analyze. Therefore, we applied systems biology approaches and big databases mining to construct genetic and epigenetic networks (GENs) with next-generation sequencing data of LADC and LSCC. In order to obtain the real GENs, system identification and system order detection are conducted on gene regulatory networks (GRNs) and protein-protein interaction networks (PPINs) for each stage of LADC and LSCC. The core GENs were extracted via principal network projection (PNP). Based on the ranking of projection values, we got the core pathways in respect of KEGG pathway. Compared with the core pathways, we found significant differences between microenvironments, dysregulations of miRNAs, epigenetic modifications on certain signaling transduction proteins and target genes in each stage of LADC and LSCC. Finally, we proposed six genetic and epigenetic multiple-molecule drugs to target essential biomarkers in each progression stage of LADC and LSCC, respectively.
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Affiliation(s)
- Shan-Ju Yeh
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-An Chang
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cheng-Wei Li
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Lily Hui-Ching Wang
- Department of Medical Science, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bor-Sen Chen
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Electrical Engineering, Yuan Ze University, Chungli 32003, Taiwan
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21
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Lei L, Xia S, Liu D, Li X, Feng J, Zhu Y, Hu J, Xia L, Guo L, Chen F, Cheng H, Chen K, Hu H, Chen X, Li F, Zhong S, Mittal N, Yang G, Qian Z, Han L, He C. Genome-wide characterization of lncRNAs in acute myeloid leukemia. Brief Bioinform 2019; 19:627-635. [PMID: 28203711 DOI: 10.1093/bib/bbx007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a large family of noncoding RNAs that play a critical role in various normal bioprocesses as well as tumorigenesis. However, the expression patterns and biological functions of lncRNAs in acute leukemia have not been well studied. Here, we performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) patient samples, along with non-leukemia control hematopoietic samples. We found that lncRNAs were differentially expressed in AML samples relative to control samples. Notably, we identified that lncRNAs upregulated in AML (relative to the control samples) are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2 and ELK-1 compared with those downregulated in AML. Moreover, an enrichment of H3K4me3 and a depletion of H3K27me3 were observed in upregulated lncRNAs in AML. Expression patterns of three types of lncRNAs (antisense, enhancer and intergenic lncRNAs) have previously been characterized. Of the identified lncRNAs, we found that high expression level lncRNA LOC285758 is associated with the poor prognosis in AML patients. Furthermore, we found that LOC285758 regulates proliferation of AML cell lines by enhancing the expression of HDAC2, a key factor in carcinogenesis. Collectively, our study depicts a landscape of important lncRNAs in AML and provides novel potential therapeutic targets and prognostic markers for AML treatment.
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Affiliation(s)
- Lijun Lei
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Siyu Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Dan Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoqing Li
- Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, China
| | - Jing Feng
- International School of Software, Wuhan University, Wuhan, China
| | - Yaqi Zhu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Linjian Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lieping Guo
- Physician in Eastern Hepatobiliary Hospital, Hospital of Second Military Medical University, Wuhan, Hubei, China
| | - Fei Chen
- Zhongnan hospital of Wuhan University, Wuhan, China
| | - Hui Cheng
- Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ke Chen
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Hanyang Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaohua Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | | | - Shan Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Nupur Mittal
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Guohua Yang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhijian Qian
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
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22
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Li N, He Y, Mi P, Hu Y. ZNF582 methylation as a potential biomarker to predict cervical intraepithelial neoplasia type III/worse: A meta-analysis of related studies in Chinese population. Medicine (Baltimore) 2019; 98:e14297. [PMID: 30732145 PMCID: PMC6380660 DOI: 10.1097/md.0000000000014297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 12/03/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE DNA methylation markers have been assessed as potential biomarkers for early cervical cancer detection. Herein, we evaluated the diagnostic performance of zinc finger protein 582 (ZNF582) methylation for cervical cancer detection. METHODS Eligible studies were systematically searched from the electronic databases. The quality of enrolled studies was evaluated using the second version of the check list for Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). The bivariate meta-analysis model was employed to plot the summary receiver operator characteristic (SROC) curve using Stata 14.0 software. Cochran's Q test and I statistics were applied to assess heterogeneity among studies. Publication bias was evaluated by the Deeks' funnel plot asymmetry test. RESULTS Seven studies composed of 1749 patients were eventually included. The pooled sensitivity of ZNF582 methylation was estimated to be 0.71 [95% confidence interval (CI): 0.67-0.75] in differentiating patients with cervical intraepithelial neoplasia type III/worse (CIN3+), corresponding to a specificity of 0.81 (95% CI: 0.79-0.83) and area under the curve (AUC) of 0.85. Our stratified analysis suggested that sequential combined of HPV DNA and ZNF582 methylation test (AUC, sensitivity, and specificity of 0.876, 0.75, and 0.87, respectively) achieved higher diagnostic accuracy than single HPV DNA testing test (AUC, sensitivity and specificity of 0.669, 0.96, and 0.41, respectively). CONCLUSIONS ZNF582 methylation has a prospect to be an auxiliary biomarker for cervical cancer screening. A new strategy of co-testing HPV DNA and ZNF582 methylation test in cervical scrapings confers an improved diagnostic accuracy than single HPV DNA testing.
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Affiliation(s)
- Na Li
- Department of Gynecologic Oncology, Tianjin Central Hospital of Gynecology Obstetrics, Nankai University Affiliated Hospital
| | | | - Peng Mi
- Department of Epidemiology, Tianjin Medical University, Tianjin, China
| | - Yuanjing Hu
- Department of Gynecologic Oncology, Tianjin Central Hospital of Gynecology Obstetrics, Nankai University Affiliated Hospital
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Ji D, Chen GF, Liu X, Zhu J, Sun JY, Zhang XY, Lu XJ. Identification of LINC01615 as potential metastasis-related long noncoding RNA in hepatocellular carcinoma. J Cell Physiol 2018; 234:12964-12970. [PMID: 30556902 DOI: 10.1002/jcp.27963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma is one of the most prevalent and fatal cancers. Studying the long noncoding RNA (lncRNA) alterations in hepatocellular carcinoma may lead to new therapeutic strategies. We checked whether there were correlations between The Cancer Genome Atlas expression profiles of the differentially expressed lncRNAs and their DNA methylation status or the copy number variations for hepatocellular carcinoma. We obtained 41 lncRNAs that were differentially expressed between tumor and normal samples, and their DNA methylation status was negatively correlated with the expression levels. We identified five lncRNAs that were recurrently amplified or deleted in tumor samples, but none of them were associated with the messenger RNA (mRNA) expression levels. To obtain the biological function of these lncRNAs, the coexpressed mRNAs in the hepatocellular carcinoma were figured out. A total of 10 lncRNAs were highly correlated with at least one gene. Six out of the ten lncRNAs were already known to be related with cancer previously. LINC01615 had 72 coexpressed genes, and we carried out the gene ontology (GO) term enrichment for these protein-coding genes. The results suggested that these lncRNAs were associated with extracellular matrix organization. To summarize, we identified 41 potentially cancer-related lncRNAs. In particular, we proposed that LINC01615 potentially affected the extracellular matrix and had further impacts on the metastasis of hepatocellular carcinoma.
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Affiliation(s)
- Dong Ji
- Second Liver Cirrhosis Diagnosis and Treatment Center, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Guo-Feng Chen
- Second Liver Cirrhosis Diagnosis and Treatment Center, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaoliu Liu
- Medical Laboratory of Shenzhen LuoHu People's Hospital, Shenzhen, China
| | - Jing Zhu
- Sparkfire Scientific Research Group, Nanjing Medical University, Nanjing, China
| | - Jin-Yu Sun
- Sparkfire Scientific Research Group, Nanjing Medical University, Nanjing, China
| | - Xiao-Yu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Xiao-Jie Lu
- Department of General Surgery, Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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24
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Fang S, Shen Y, Chen B, Wu Y, Jia L, Li Y, Zhu Y, Yan Y, Li M, Chen R, Guo L, Chen X, Chen Q. H3K27me3 induces multidrug resistance in small cell lung cancer by affecting HOXA1 DNA methylation via regulation of the lncRNA HOTAIR. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:440. [PMID: 30596070 DOI: 10.21037/atm.2018.10.21] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Background The long non-coding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) serves as a powerful predictor of tumor progression and overall survival in patients. Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC). Moreover, H3 lysine 27 trimethylation (H3K27me3) is catalyzed by enhancer of zeste homolog 2 (EZH2) and plays a critical role in SCLC chemoresistance. However, it is not completely clear whether H3K27me3 affects HOXA1 DNA methylation or whether this effect is mediated by HOTAIR. Methods The levels of EZH2 and H3K27me3 were identified in SCLC tissues by immunohistochemical (IHC) staining and in SCLC multidrug-resistant cells by Western blotting. Cell counting kit-8 (CCK-8) and flow cytometry were used to detect and analyze the biological function of H3K27me3. Then, we assessed the role of HOTAIR in the regulation of EZH2 and H3K27me3 by using lentivirus and small interfering RNA. Further, bisulfite sequencing PCR was conducted to detect the methylation levels of HOXA1 DNA. Finally, Western blotting was performed to examine the regulatory role of H3K27me3 in controlling HOTAIR expression in SCLC. Results In this study, we found that EZH2 and H3K27me3 levels were markedly higher in SCLC tissues and multidrug-resistant SCLC cells. The results indicated that H3K27me3 was related to multidrug resistance. HOTAIR overexpression and knockdown showed that EZH2 and H3K27me3 were regulated by HOTAIR. Moreover, H3K27me3 affected HOXA1 DNA methylation levels. Strikingly, we found that H3K27me3 acted as a negative feedback regulator of HOTAIR. Conclusions Our study showed that H3K27me3 affects HOXA1 DNA methylation via HOTAIR regulation, indicating that H3K27me3 may be a potential therapy target for SCLC chemoresistance.
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Affiliation(s)
- Shun Fang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yefeng Shen
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Bin Chen
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuanzhou Wu
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Longfei Jia
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yaling Li
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yaru Zhu
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yusheng Yan
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Rui Chen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xin Chen
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Qunqing Chen
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
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25
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Yuan LY, Qin X, Li L, Zhou J, Zhou M, Li X, Xu Y, Wang XJ, Xing H. The transcriptome profiles and methylation status revealed the potential cancer-related lncRNAs in patients with cervical cancer. J Cell Physiol 2018; 234:9756-9763. [PMID: 30362566 DOI: 10.1002/jcp.27661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022]
Abstract
Cervical cancer continues to be a major public health problem. Although long noncoding RNAs (lncRNAs) were involved in the initiation and progression of cancer, few studies focus on the lncRNAs in the cervical cancer. Here, we systematically studied the clinical information, transcriptome profiling, and methylation array data of cervical squamous cell carcinoma and endocervical adenocarcinoma that retrieved from genomic data commons (GDC). Compared with protein-coding genes, the expression levels of pseudogenes and lncRNAs were much lower. A total of 190 differentially expressed lncRNAs and 2,326 protein-coding genes were identified. Meanwhile, 269 differentially methylation regions (DMRs), where 16 lncRNAs were located, were figured out. Only one lncRNA, LINC00592, which was located in the DMRs, was also found differentially expressed. Several transcriptional regulation genes, such as ZNF20, ZNF441, ZNF573, and TMF1, were highly correlated with the expression of LINC00592, which illustrated its possible function on the transcription. Two microRNAs, which were both associated with tumor progression, can bind to LINC00592. Moreover, LINC00592 were also differentially expressed in other tumors. We proposed, with the help of various databases, that LINC00592 is a potential cancer-related lncRNA in cervical cancer and might activate the cancer progression through the regulation of transcription or structural integrity.
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Affiliation(s)
- Li-Yun Yuan
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xiaomin Qin
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Lin Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jinting Zhou
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Min Zhou
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xianxian Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Ying Xu
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xiao-Jun Wang
- Nursing and Midwifery College, Jiangsu College of Nursing, Huai'an, Jiangsu, China
| | - Hui Xing
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
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26
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Adamopoulos PG, Raptis GD, Kontos CK, Scorilas A. Discovery and expression analysis of novel transcripts of the human SR-related CTD-associated factor 1 (SCAF1) gene in human cancer cells using Next-Generation Sequencing. Gene 2018; 670:155-165. [PMID: 29787824 DOI: 10.1016/j.gene.2018.05.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/13/2018] [Indexed: 02/07/2023]
Abstract
The human SR-related CTD associated factor 1 (SCAF1) gene is a new member of the human SR (Ser/Arg-rich) superfamily of pre-mRNA splicing factors, which has been discovered and cloned by members of our lab. SCAF1 interacts with the CTD domain of the RNA polymerase II polypeptide A and is firmly involved in pre-mRNA splicing. Although it was found to be expressed widely in multiple human tissues, its mRNA levels vary a lot. The significant relation of SCAF1 with cancer has been confirmed by many studies, since SCAF1 mRNA transcript was found to be overexpressed in breast and ovarian tumors, confirming its significant prognostic value as a cancer biomarker in both these human malignancies. In this study, we describe the discovery and cloning of fifteen novel transcripts of the human SCAF1 gene (SCAF1 v.2 - v.16), using nested PCR and NGS technology. In detail, extensive bioinformatic analysis revealed that these novel SCAF1 splice variants comprise a total of nine novel alternative splicing events between the annotated exons of the gene, thus producing seven novel SCAF1 transcripts with open-reading frames, which are predicted to encode novel SCAF1 isoforms and eight novel SCAF1 transcripts with premature termination codons that are likely long non-coding RNAs. Additionally, a novel 3' UTR was discovered and cloned using nested 3' RACE and was validated with Sanger sequencing. In order to validate the NGS findings as well as to investigate the expression profile of each novel transcript, RT-PCR experiments were carried out with the use of variant-specific primers. Since SCAF1 is implicated in many human malignancies, qualifying as a potential biomarker, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios D Raptis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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27
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Chen L, Zhang W, Li DY, Wang X, Tao Y, Zhang Y, Dong C, Zhao J, Zhang L, Zhang X, Guo J, Zhang X, Liao Q. Regulatory network analysis of LINC00472, a long noncoding RNA downregulated by DNA hypermethylation in colorectal cancer. Clin Genet 2018; 93:1189-1198. [PMID: 29488624 DOI: 10.1111/cge.13245] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the common malignant cancers in the world, is caused by accumulated alterations of genetic and epigenetic factors over a long period of time. Along with that protein-coding genes being identified as oncogenes or tumor suppressors in CRC, a number of lncRNAs have also been found to be associated with CRC. Considering the important regulatory role of lncRNAs, the first goal of this study was to identify CRC-associated lncRNAs from a public database. One such lncRNA, LINC00472, was verified to be downregulated in CRC cell lines and cancer tissues compared with adjacent tissues. In addition, the down-regulation of LINC00472 seemed to be caused by DNA hypermethylation at its promoter region. Furthermore, the expression of LINC00472 and DNA methylation of promoter were significantly correlated with clinicopathological features. And DNA hypermethylation of LINC00472 may serve as a better diagnostic biomarker than its expression for CRC. Finally, we predicted the functions of LINC00472 and constructed a regulatory network and found LINC00472 may be involved in cell cycle and cell proliferation processes. Our results may provide a clue to further research into the function and regulatory mechanism of LINC00472 in CRC.
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Affiliation(s)
- L Chen
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - W Zhang
- Department of Medical Image, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - D Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - X Wang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Y Tao
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Y Zhang
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - C Dong
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - J Zhao
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - L Zhang
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - X Zhang
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - J Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - X Zhang
- Department of Gastroenterology, The Affiliated Hospital of Ningbo University School of Medicine, Ningbo, China
| | - Q Liao
- Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Department of Preventative Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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28
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Interplay between regulation by methylation and noncoding RNAs in cancers. Eur J Cancer Prev 2018; 27:418-424. [PMID: 29557800 DOI: 10.1097/cej.0000000000000433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cancer is one of the most important health problems today; therefore, many researchers are focusing on exploring the mechanisms underlying its development and treatment. The field of cancer epigenetics has flourished in recent decades, and studies have shown that different epigenetic events, such as DNA methylation, histone modification, and noncoding RNA regulation, work together to influence cancer development and progression. In this short review, we summarize the interactions between methylation and noncoding RNAs that affect cancer development.
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29
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Luo J, Qu J, Wu DK, Lu ZL, Sun YS, Qu Q. Long non-coding RNAs: a rising biotarget in colorectal cancer. Oncotarget 2017; 8:22187-22202. [PMID: 28108736 PMCID: PMC5400657 DOI: 10.18632/oncotarget.14728] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a common gastrointestinal cancer, with a high incidence and high mortality. Long non-coding RNAs (lncRNAs) are involved in the development, invasion and metastasis, early diagnosis, prognosis, the chemoresistance and radioresistance of CRC through interference with mRNA activity, directly combining with proteins to regulate their activity or alter their localization, influencing downstream gene expression by inhibiting RNA polymerase and regulating gene expression as competing endogenous RNAs. Recent progress in next generation sequencing and transcriptome analysis has revealed that tissue and cancer-type specific lncRNAs could be useful prognostic markers. Here, the CRC-associated lncRNAs from recent studies until October 2016 are reviewed and multiple studies that have confirmed CRC-associated lncRNAs are summarized. This review may be helpful in understanding the overall relationships between the lncRNAs involved in CRC.
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Affiliation(s)
- Jian Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, P. R. China
| | - Dong-Kai Wu
- Department of Cardiothoracic Surgery, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Zhi-Li Lu
- Department of Pathology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, P. R. China
| | - Yue-Sheng Sun
- Department of General Surgery, The Third Clinical College of Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, P. R. China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P. R. China
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30
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Noncoding RNAs in the development, diagnosis, and prognosis of colorectal cancer. Transl Res 2017; 181:108-120. [PMID: 27810413 DOI: 10.1016/j.trsl.2016.10.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022]
Abstract
More than 90% of the human genome is actively transcribed, but less than 2% of the total genome encodes protein-coding RNA, and thus, noncoding RNA (ncRNA) is a major component of the human transcriptome. Recently, ncRNA was demonstrated to play important roles in multiple biological processes by directly or indirectly interfering with gene expression, and the dysregulation of ncRNA is associated with a variety of diseases, including cancer. In this review, we summarize the function and mechanism of miRNA, long intergenic ncRNA, and some other types of ncRNAs, such as small nucleolar RNA, circular ncRNA, pseudogene RNA, and even protein-coding mRNA, in the progression of colorectal cancer (CRC). We also presented their clinical application in the diagnosis and prognosis of CRC. The summary of the current state of ncRNA in CRC will contribute to our understanding of the complex processes of CRC initiation and development and will help in the discovery of novel biomarkers and therapeutic targets for CRC diagnosis and treatment.
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Feng N, Wang Y, Zheng M, Yu X, Lin H, Ma RN, Shi O, Zheng X, Gao M, Yu H, Garmire L, Qian B. Genome-wide analysis of DNA methylation and their associations with long noncoding RNA/mRNA expression in non-small-cell lung cancer. Epigenomics 2017; 9:137-153. [PMID: 28111977 DOI: 10.2217/epi-2016-0120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM The goal of this study is to identify differentially methylated (DM) loci associated with long noncoding RNA (lncRNA)/mRNA expression in non-small-cell lung cancer (NSCLC). MATERIALS & METHODS Microarrays were used to interrogate genome-wide methylation and expression of lncRNA/mRNA in NSCLC. RESULTS We identified 113,644 DM loci between tumors and adjacent tissues. Among them, 26,310 DM loci were associated with 1685 differentially expressed genes, and 839 genes had significant correlations between methylation and expression, of which 26 hypermethylated loci in transcription start site 200 were correlated with low gene expression. We validated the correlations between methylation and expression in five genes (CDO1, C2orf40, SCARF1, ZFP106 and IFFO1) using pyrosequencing and quantitative polymerase chain reaction. We also found significant correlations between lncRNAs and mRNAs, and validated four of the correlations with quantitative polymerase chain reaction. CONCLUSION Integrated analysis of genome-wide DNA methylation and lncRNA/mRNA expression allows us to identify new DM loci-correlated with gene expression in NSCLC.
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Affiliation(s)
- Nannan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Min Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongyan Lin
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rong-Na Ma
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Oumin Shi
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiangqian Zheng
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Ming Gao
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA
| | - Lana Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Hu Y, Sun X, Mao C, Guo G, Ye S, Xu J, Zou R, Chen J, Wang L, Duan P, Xue X. Upregulation of long noncoding RNA TUG1 promotes cervical cancer cell proliferation and migration. Cancer Med 2017; 6:471-482. [PMID: 28088836 PMCID: PMC5313648 DOI: 10.1002/cam4.994] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/09/2016] [Accepted: 11/19/2016] [Indexed: 01/22/2023] Open
Abstract
Long noncoding RNAs (lncRNAs), a novel class of transcripts that have critical roles in carcinogenesis and progression, have emerged as important gene expression modulators. Recent evidence indicates that lncRNA taurine‐upregulated gene 1 (TUG1) functions as an oncogene in numerous types of human cancers. However, its function in the development of cervical cancer remains unknown. The aim of this research was to investigate the clinical significance and biological functions of TUG1 in cervical cancer. TUG1 was found to be significantly upregulated in cervical cancer tissues and four cervical cancer cell lines by quantitative real‐time polymerase chain reaction (qRT‐PCR). Elevated TUG1 expression was correlated with larger tumor size, advanced international federation of gynecology and obstetrics (FIGO) stage, poor differentiation, and lymph node metastasis. Furthermore, knockdown of TUG1 suppressed cell proliferation with activation of apoptosis, in part by regulating the expression of Bcl‐2 and caspase‐3. Silencing of TUG1 inhibited cell migration and invasion via the progression of epithelial–mesenchymal transition (EMT). Taken together, our findings indicate that TUG1 acts as an oncogene in cervical cancer and may represent a novel therapeutic target.
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Affiliation(s)
- Yingying Hu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Xiangwei Sun
- Department of General Surgery, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Chenchen Mao
- Department of General Surgery, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Gangqiang Guo
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Sisi Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Jianfeng Xu
- Department of General Surgery, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Ruanmin Zou
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Jun Chen
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Ledan Wang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
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