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Xie G, Li D, Lin Z, Gu G, Li W, Chen R, Liu Z. HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization. J Chem Inf Model 2024. [PMID: 39058598 DOI: 10.1021/acs.jcim.4c01070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Existing matrix factorization methods face challenges, including the cold start problem and global nonlinear data loss during similarity learning, particularly in predicting associations between long noncoding RNAs (LncRNAs) and diseases. To overcome these issues, we introduce HPTRMF, a matrix factorization approach incorporating high-order perturbation and flexible trifactor regularization. HPTRMF constructs a high-order correlation matrix utilizing the known association matrix, leveraging high-order perturbation to effectively address the cold start problem caused by data sparsity. Additionally, HPTRMF incorporates a flexible trifactor regularization term to capture similarity information on LncRNAs and diseases, enabling the effective handling of global nonlinear data loss by capturing such data in the similarity matrix. Experimental results demonstrate the superiority of HPTRMF over nine state-of-the-art algorithms in Leave-One-Out Cross-Validation (LOOCV) and Five-Fold Cross-Validation (5-Fold CV) on three data sets.HPTRMF and data sets are available in https://github.com/Llvvvv/HPTRMF.
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Affiliation(s)
- Guobo Xie
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Dayin Li
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhiyi Lin
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Guosheng Gu
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Weijun Li
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Ruibin Chen
- School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhenguo Liu
- 2MD Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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Liu Z, Xia G, Liang X, Li B, Deng J. DNA methylation-mediated suppression of TUSC1 expression regulates the malignant progression of esophagogastric junction cancer. Clin Epigenetics 2024; 16:97. [PMID: 39044262 PMCID: PMC11267789 DOI: 10.1186/s13148-024-01689-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/28/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Esophagogastric junction cancer (EJC) refers to malignant tumors that develop at the junction between the stomach and the esophagus. TUSC1 is a recently identified tumor suppressor gene known for its involvement in various types of cancer. The objective of this investigation was to elucidate the regulatory influence of DNA methylation on TUSC1 expression and its role in the progression of EJC. METHODS Bioinformatics software was utilized to analyze the expression of TUSC1, enriched pathways, and highly methylated sites in the promoter region. TUSC1 expression in EJC was assessed using quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blot (WB), and immunohistochemistry. Methylation-specific PCR was employed to detect the methylation level of TUSC1. To analyze the effects of TUSC1 and 5-AZA-2 on tumor cell proliferation, migration, invasion, cell cycle, and apoptosis, several assays including CCK-8, colony formation, transwell, and flow cytometry were conducted. The expression of MDM2 was assessed using qRT-PCR and WB. WB detected the expression of p53, and p-p53, markers for EJC cell proliferation, epithelial-mesenchymal transition, and apoptosis. The role of TUSC1 in tumor occurrence in vivo was examined using a xenograft mouse model. RESULTS TUSC1 expression was significantly downregulated in EJC. Overexpression of TUSC1 and treatment with 5-AZA-2 inhibited the malignant progression of EJC cells. In EJC, low methylation levels promoted the expression of TUSC1. Upregulation of TUSC1 suppressed the expression of MDM2 and activated the p53 signaling pathway. Inactivation of this pathway attenuated the inhibitory effect of TUSC1 overexpression on EJC cell proliferation, migration, invasion, and other behaviors. Animal experiments demonstrated that TUSC1 overexpression inhibited EJC tumor growth and metastasis in vivo. CONCLUSION TUSC1 was commonly downregulated in EJC and regulated by methylation. It repressed the malignant progression of EJC tumors by mediating the p53 pathway, suggesting its potential as a diagnostic and therapeutic target for EJC.
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Affiliation(s)
- Zhiqiang Liu
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and Therapy, TianjinTianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Department of Gastric Surgery, Anyang Tumor Hospital, Anyang, 455000, China
| | - Ganshu Xia
- Department of Gastric Surgery, Anyang Tumor Hospital, Anyang, 455000, China
| | - Xiaolong Liang
- Department of Gastric Surgery, Anyang Tumor Hospital, Anyang, 455000, China
| | - Baozhong Li
- Department of Gastric Surgery, Anyang Tumor Hospital, Anyang, 455000, China.
| | - Jingyu Deng
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and Therapy, TianjinTianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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Li Z, Wang W, Yu X, Zhao P, Li W, Zhang X, Peng M, Li S, Ruan M. Integrated analysis of DNA methylome and transcriptome revealing epigenetic regulation of CRIR1-promoted cold tolerance. BMC PLANT BIOLOGY 2024; 24:631. [PMID: 38965467 PMCID: PMC11225538 DOI: 10.1186/s12870-024-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND DNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance. RESULTS In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance. CONCLUSIONS In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.
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Affiliation(s)
- Zhibo Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Wenjuan Wang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
- College of Tropical Crops, Hainan University, Haikou, 570228, P.R. China
| | - Xiaoling Yu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Pingjuan Zhao
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Wenbin Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Xiuchun Zhang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Ming Peng
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Shuxia Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China.
| | - Mengbin Ruan
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China.
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Yu Y, Li L, Luo B, Chen D, Yin C, Jian C, You Q, Wang J, Fang L, Cai D, Sun J. Predicting potential therapeutic targets and small molecule drugs for early-stage lung adenocarcinoma. Biomed Pharmacother 2024; 174:116528. [PMID: 38555814 DOI: 10.1016/j.biopha.2024.116528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Lung cancer is a leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) constituting the majority, and its main subtype being lung adenocarcinoma (LUAD). Despite substantial advances in LUAD diagnosis and treatment, early diagnostic biomarkers inadequately fulfill clinical requirements. Thus, we conducted bioinformatics analysis to identify potential biomarkers and corresponding therapeutic drugs for early-stage LUAD patients. Here we identified a total of 10 differentially expressed genes (DEGs) with survival significance through the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Subsequently, we identified a promising small molecule drug, Aminopurvalanol A, based on the 10 key genes using the L1000FWD application, which was validated by molecular docking followed by in vivo and in vitro experiments. The results highlighted TOP2A, CDH3, ASPM, CENPF, SLC2A1, and PRC1 as potential detection biomarkers for early LUAD. We confirmed the efficacy and safety of Aminopurvalanol A, providing valuable insights for the clinical management of LUAD.
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Affiliation(s)
- Yongxin Yu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Lingchen Li
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Bangyu Luo
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Diangang Chen
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Chenrui Yin
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Chunli Jian
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Qiai You
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jianmin Wang
- Department of Oncology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, China
| | - Ling Fang
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Dingqin Cai
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jianguo Sun
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China.
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Pokorná M, Černá M, Boussios S, Ovsepian SV, O’Leary VB. lncRNA Biomarkers of Glioblastoma Multiforme. Biomedicines 2024; 12:932. [PMID: 38790894 PMCID: PMC11117901 DOI: 10.3390/biomedicines12050932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules of 200 nucleotides or more in length that are not translated into proteins. Their expression is tissue-specific, with the vast majority involved in the regulation of cellular processes and functions. Many human diseases, including cancer, have been shown to be associated with deregulated lncRNAs, rendering them potential therapeutic targets and biomarkers for differential diagnosis. The expression of lncRNAs in the nervous system varies in different cell types, implicated in mechanisms of neurons and glia, with effects on the development and functioning of the brain. Reports have also shown a link between changes in lncRNA molecules and the etiopathogenesis of brain neoplasia, including glioblastoma multiforme (GBM). GBM is an aggressive variant of brain cancer with an unfavourable prognosis and a median survival of 14-16 months. It is considered a brain-specific disease with the highly invasive malignant cells spreading throughout the neural tissue, impeding the complete resection, and leading to post-surgery recurrences, which are the prime cause of mortality. The early diagnosis of GBM could improve the treatment and extend survival, with the lncRNA profiling of biological fluids promising the detection of neoplastic changes at their initial stages and more effective therapeutic interventions. This review presents a systematic overview of GBM-associated deregulation of lncRNAs with a focus on lncRNA fingerprints in patients' blood.
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Affiliation(s)
- Markéta Pokorná
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK;
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury CT2 7PB, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
| | - Saak V. Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK;
- Faculty of Medicine, Tbilisi State University, Tbilisi 0177, Georgia
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
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Sinha B, Choudhury Y. Revisiting edible insects as sources of therapeutics and drug delivery systems for cancer therapy. Front Pharmacol 2024; 15:1345281. [PMID: 38370484 PMCID: PMC10869617 DOI: 10.3389/fphar.2024.1345281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Cancer has been medicine's most formidable foe for long, and the rising incidence of the disease globally has made effective cancer therapy a significant challenge. Drug discovery is targeted at identifying efficacious compounds with minimal side effects and developments in nanotechnology and immunotherapy have shown promise in the fight against this complicated illness. Since ancient times, insects and insect-derived products have played a significant role in traditional medicine across several communities worldwide. The aim of this study was to inspect the traditional use of edible insects in various cultures and to explore their modern use in cancer therapy. Edible insects are sources of nutrients and a variety of beneficial substances with anticancer and immunomodulatory potential. Recently, insect derived bioactive-components have also been used as nanoparticles either in combination with chemotherapeutics or as a nano-cargo for the enhanced delivery of chemotherapeutic drugs due to their high biocompatibility, low bio-toxicity, and their antioxidant and anticancer effects. The crude extracts of different edible insects and their active components such as sericin, cecropin, solenopsin, melittin, antimicrobial peptides and fibroin produce anti-cancer and immunomodulatory effects by various mechanisms which have been discussed in this review.
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Rehman SU, Ullah N, Zhang Z, Zhen Y, Din AU, Cui H, Wang M. Recent insights into the functions and mechanisms of antisense RNA: emerging applications in cancer therapy and precision medicine. Front Chem 2024; 11:1335330. [PMID: 38274897 PMCID: PMC10809404 DOI: 10.3389/fchem.2023.1335330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The antisense RNA molecule is a unique DNA transcript consisting of 19-23 nucleotides, characterized by its complementary nature to mRNA. These antisense RNAs play a crucial role in regulating gene expression at various stages, including replication, transcription, and translation. Additionally, artificial antisense RNAs have demonstrated their ability to effectively modulate gene expression in host cells. Consequently, there has been a substantial increase in research dedicated to investigating the roles of antisense RNAs. These molecules have been found to be influential in various cellular processes, such as X-chromosome inactivation and imprinted silencing in healthy cells. However, it is important to recognize that in cancer cells; aberrantly expressed antisense RNAs can trigger the epigenetic silencing of tumor suppressor genes. Moreover, the presence of deletion-induced aberrant antisense RNAs can lead to the development of diseases through epigenetic silencing. One area of drug development worth mentioning is antisense oligonucleotides (ASOs), and a prime example of an oncogenic trans-acting long noncoding RNA (lncRNA) is HOTAIR (HOX transcript antisense RNA). NATs (noncoding antisense transcripts) are dysregulated in many cancers, and researchers are just beginning to unravel their roles as crucial regulators of cancer's hallmarks, as well as their potential for cancer therapy. In this review, we summarize the emerging roles and mechanisms of antisense RNA and explore their application in cancer therapy.
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Affiliation(s)
- Shahab Ur Rehman
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Numan Ullah
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Zhenbin Zhang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Yongkang Zhen
- College of Animals Nutrition Yangzhou University, Yangzhou, China
| | - Aziz-Ud Din
- Department of Human Genetics, Hazara University Mansehra, Mansehra, Pakistan
| | - Hengmi Cui
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics Yangzhou University, College of Animal Nutrition Yangzhou University, Yangzhou, China
| | - Mengzhi Wang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- College of Animals Nutrition Yangzhou University, Yangzhou, China
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Ahuja P, Yadav R, Goyal S, Yadav C, Ranga S, Kadian L. Targeting epigenetic deregulations for the management of esophageal carcinoma: recent advances and emerging approaches. Cell Biol Toxicol 2023; 39:2437-2465. [PMID: 37338772 DOI: 10.1007/s10565-023-09818-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Ranking from seventh in incidence to sixth in mortality, esophageal carcinoma is considered a severe malignancy of food pipe. Later-stage diagnosis, drug resistance, and a high mortality rate contribute to its lethality. Esophageal squamous cell carcinoma and esophageal adenocarcinoma are the two main histological subtypes of esophageal carcinoma, with squamous cell carcinoma alone accounting for more than eighty percent of its cases. While genetic anomalies are well known in esophageal cancer, accountability of epigenetic deregulations is also being explored for the recent two decades. DNA methylation, histone modifications, and functional non-coding RNAs are the crucial epigenetic players involved in the modulation of different malignancies, including esophageal carcinoma. Targeting these epigenetic aberrations will provide new insights into the development of biomarker tools for risk stratification, early diagnosis, and effective therapeutic intervention. This review discusses different epigenetic alterations, emphasizing the most significant developments in esophageal cancer epigenetics and their potential implication for the detection, prognosis, and treatment of esophageal carcinoma. Further, the preclinical and clinical status of various epigenetic drugs has also been reviewed.
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Affiliation(s)
- Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India.
| | - Sandeep Goyal
- Department of Internal Medicine, Pt. B.D, Sharma University of Health Sciences, (Haryana), Rohtak, 124001, India
| | - Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Lokesh Kadian
- Department of Dermatology, School of Medicine, Indiana University, Indianapolis, Indiana, 46202, USA
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Huang F, Wang X, Zhong J, Chen H, Song D, Xu T, Tian K, Sun P, Sun N, Qin J, Song Y, Ma W, Liu Y, Yu D, Meng X, Jiang C, Xuan H, Qian D, Cai J. Using integrated analysis from multicentre studies to identify RNA methylation-related lncRNA risk stratification systems for glioma. Cancer Cell Int 2023; 23:156. [PMID: 37542290 PMCID: PMC10403900 DOI: 10.1186/s12935-023-03001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A) are the main RNA methylation modifications involved in the progression of cancer. However, it is still unclear whether RNA methylation-related long noncoding RNAs (lncRNAs) affect the prognosis of glioma. METHODS We summarized 32 m6A/m5C/m1A-related genes and downloaded RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify differentially expressed (DE-) RNA methylation-related lncRNAs in order to construct a prognostic signature of glioma and in order to determine their correlation with immune function, immune therapy and drug sensitivity. In vitro and in vivo assays were performed to elucidate the effects of RNA methylation-related lncRNAs on glioma. RESULTS A total of ten RNA methylation-related lncRNAs were used to construct a survival and prognosis signature, which had good independent prediction ability for patients. It was found that the high-risk group had worse overall survival (OS) than the low-risk group in all cohorts. In addition, the risk group informed the immune function, immunotherapy response and drug sensitivity of patients with glioma in different subgroups. Knockdown of RP11-98I9.4 and RP11-752G15.8 induced a more invasive phenotype, accelerated cell growth and apparent resistance to temozolomide (TMZ) both in vitro and in vivo. We observed significantly elevated global RNA m5C and m6A levels in glioma cells. CONCLUSION Our study determined the prognostic implication of RNA methylation-related lncRNAs in gliomas, established an RNA methylation-related lncRNA prognostic model, and elucidated that RP11-98I9.4 and RP11-752G15.8 could suppress glioma proliferation, migration and TMZ resistance. In the future, these RNA methylation-related lncRNAs may become a new choice for immunotherapy of glioma.
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Affiliation(s)
- Fanxuan Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Xinyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Junzhe Zhong
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Hao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Dan Song
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Tianye Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Kaifu Tian
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Penggang Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Nan Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Jie Qin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Yu Song
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Wenbin Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Yuxiang Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Daohan Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Xiangqi Meng
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Chuanlu Jiang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
| | - Hanwen Xuan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086 China
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu No. 1 People’s Hospital, Changshu, 215500 Jiangsu Province China
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150086 China
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Al-Imam MJ, Hussein UAR, Sead FF, Faqri AMA, Mekkey SM, Khazel AJ, Almashhadani HA. The interactions between DNA methylation machinery and long non-coding RNAs in tumor progression and drug resistance. DNA Repair (Amst) 2023; 128:103526. [PMID: 37406581 DOI: 10.1016/j.dnarep.2023.103526] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
DNA methylation is one of the main epigenetic mechanisms in cancer development and progression. Aberrant DNA methylation of CpG islands within promoter regions contributes to the dysregulation of various tumor suppressors and oncogenes; this leads to the appearance of malignant features, including rapid proliferation, metastasis, stemness, and drug resistance. The discovery of two important protein families, DNA methyltransferases (DNMTs) and Ten-eleven translocation (TET) dioxygenases, respectively, which are responsible for deregulated transcription of genes that play pivotal roles in tumorigenesis, led to further understanding of DNA methylation-related pathways. But how these enzymes can target specific genes in different malignancies; recent studies have highlighted the considerable role of Long Non-coding RNAs (LncRNAs). LncRNAs recruit these enzymes to promoter regions of genes and mediate their functions, showing great potential as therapeutic agents targeting the epigenetic regulation of various genes. Considering the importance of combining the current treatment methods, especially chemotherapies, with DNA methylation inhibitors in improving patients' outcomes, this review aimed to summarize the recent findings about the interaction between DNA methylation machinery and LncRNAs in regulating genes involved in tumorigenesis and drug resistance. So, these studies could provide insights toward developing novel strategies for cancer-targeted therapy.
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Affiliation(s)
- Mokhtar Jawad Al-Imam
- Department of Experimental Therapy, Iraqi Center for Cancer and Medical Genetics Research, Almustansiriyah University, Baghdad, Iraq
| | | | | | | | - Shereen M Mekkey
- Pharmacy Department, Al-Mustaqbal University College, 51001 Hilla, Babylon, Iraq
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11
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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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12
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A review on the role of ADAMTS9-AS2 in different disorders. Pathol Res Pract 2023; 243:154346. [PMID: 36746036 DOI: 10.1016/j.prp.2023.154346] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recent decade has seen a tremendous progress in identification of the role of different long non-coding RNAs (lncRNAs) in human pathologies. ADAMTS9-AS2 is an example of lncRNAs with different roles in human disorders. It is mostly acknowledged as a tumor suppressor lncRNA in different types of cancers. However, it has been reported to be up-regulated in tongue squamous cell carcinoma, salivary adenoid cystic carcinoma and glioblastoma. Moreover, ADAMTS9-AS2 is possibly involved in the pathoetiology of pulpitis, acute ischemic stroke, type 2 diabetes and its complications. This lncRNA sponges miR-196b-5p, miR-223-3p, miR-130a-5p, miR-600, miR-223-3p, miR-27a-3p, miR-32, miR-143-3p, miR-143-3p and miR-182-5p in order to regulate downstream mRNAs. This review aims at summarization of the role of ADAMTS9-AS2 in different disorders with a particular focus on its diagnostic and prognostic values.
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13
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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Khan A, Zhang X. Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common and serious type of primary liver cancer. HCC patients have a high death rate and poor prognosis due to the lack of clear signs and inadequate treatment interventions. However, the molecular pathways that underpin HCC pathogenesis remain unclear. Long non-coding RNAs (lncRNAs), a new type of RNAs, have been found to play important roles in HCC. LncRNAs have the ability to influence gene expression and protein activity. Dysregulation of lncRNAs has been linked to a growing number of liver disorders, including HCC. As a result, improved understanding of lncRNAs could lead to new insights into HCC etiology, as well as new approaches for the early detection and treatment of HCC. The latest results with respect to the role of lncRNAs in controlling multiple pathways of HCC were summarized in this study. The processes by which lncRNAs influence HCC advancement by interacting with chromatin, RNAs, and proteins at the epigenetic, transcriptional, and post-transcriptional levels were examined. This critical review also highlights recent breakthroughs in lncRNA signaling pathways in HCC progression, shedding light on the potential applications of lncRNAs for HCC diagnosis and therapy.
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Affiliation(s)
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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15
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Chen Z, Tang W, Ye W, Song L, Chen Z. ADAMTS9-AS2 regulates PPP1R12B by adsorbing miR-196b-5p and affects cell cycle-related signaling pathways inhibiting the malignant process of esophageal cancer. Cell Cycle 2022; 21:1710-1725. [PMID: 35503407 PMCID: PMC9302527 DOI: 10.1080/15384101.2022.2067675] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
This study explored the mechanism that ADAMTS9-AS2/miR-196b-5p/PPP1R12B/cell cycle pathway axis in inhibiting the malignant progression of esophageal cancer (EC), providing a new idea for targeted molecular therapy of EC. The expression data of EC tissue were acquired from TCGA database. The target lncRNA, downstream miRNA and its target gene were determined by bioinformatics analysis. ADAMTS9-AS2, miR-196b-5p and PPP1R12B levels in EC tissue and cells were assayed through qRT-PCR. Western blot was applied to assess protein level of PPP1R12B in cells and tissues, as well as protein expression of CDK1, cyclin A2, cyclin B1 and Plk1 in EC cells. Cell proliferation was assayed via CCK-8 assay. Cell cycle distribution was analyzed by flow cytometry. Cell migratory and invasive abilities were measured through scratch healing and transwell assays. Pearson correlation analysis was utilized to analyze relationship among ADAMTS9-AS2, miR-196b-5p and PPP1R12B. RIP was introduced to assess binding among the three. Dual-luciferase assay was utilized to verify targeted binding sites. The tumor formation in nude mice assay was utilized to detect tumorigenesis of EC cells in vivo. ADAMTS9-AS2 was significantly lowly expressed while miR-196b-5p was increased in EC tissue and cells. ADAMTS9-AS2 bound to miR-196b-5p and constrained its expression. Overexpressed ADAMTS9-AS2 inhibited EC cell malignant progression via downregulating miR-196b-5p, while overexpressed miR-196b-5p reversed this inhibitory effect. ADAMTS9-AS2 modulated PPP1R12B level by competitively inhibiting miR-196b-5p. PPP1R12B played a modulatory role in EC by inhibiting cell cycle pathway. Overexpressed ADAMTS9-AS2 regulated the tumor-forming ability of EC cells in vivo through miR-196b-5p/PPP1R12B/cell cycle signaling pathway axis. ADAMTS9-AS2 downregulated PPP1R12B by adsorbing miR-196b-5p, so as to regulate the cell cycle signaling pathway to inhibit EC malignant progression.
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Affiliation(s)
- Zhao Chen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weijian Tang
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weiwen Ye
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Lijiang Song
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhoumiao Chen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
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16
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Yang C, Chen K. Long Non-Coding RNA in Esophageal Cancer: A Review of Research Progress. Pathol Oncol Res 2022; 28:1610140. [PMID: 35241975 PMCID: PMC8885534 DOI: 10.3389/pore.2022.1610140] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022]
Abstract
In recent years, there has been significant progress in the diagnosis and treatment of esophageal cancer. However, owing to the lack of early diagnosis strategies and treatment targets, the prognosis of patients with esophageal cancer remains unsatisfactory. There is an urgent need to identify novel biomarkers and treatment targets for esophageal cancer. With the development of genomics, long-chain non-coding RNAs (LncRNAs), which were once considered transcriptional “noise,” are being identified and characterized rapidly in large numbers. Recent research shows that LncRNAs are closely related to a series of steps in tumor development and play an important regulatory role in DNA replication, transcription, and post-transcriptional regulation. The abnormal expression of LncRNAs leads to tumor cell proliferation, migration, invasion, and treatment resistance. This review focuses on the latest progress in research on the abnormal expression and functional mechanisms of LncRNAs in esophageal cancer. Further, it discusses the potential applications of these findings towards achieving an early diagnosis, improving treatment efficacy, and evaluating the prognosis of esophageal cancer.
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Affiliation(s)
- Chenbo Yang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, China
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, China
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LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond. J Exp Clin Cancer Res 2022; 41:100. [PMID: 35292092 PMCID: PMC8922926 DOI: 10.1186/s13046-022-02319-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms to regulate gene expression, which is highly dynamic during development and specifically maintained in somatic cells. Aberrant DNA methylation patterns are strongly associated with human diseases including cancer. How are the cell-specific DNA methylation patterns established or disturbed is a pivotal question in developmental biology and cancer epigenetics. Currently, compelling evidence has emerged that long non-coding RNA (lncRNA) mediates DNA methylation in both physiological and pathological conditions. In this review, we provide an overview of the current understanding of lncRNA-mediated DNA methylation, with emphasis on the roles of this mechanism in cancer, which to the best of our knowledge, has not been systematically summarized. In addition, we also discuss the potential clinical applications of this mechanism in RNA-targeting drug development.
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ADAMTS9-AS2 Promotes Angiogenesis of Brain Microvascular Endothelial Cells Through Regulating miR-185-5p/IGFBP-2 Axis in Ischemic Stroke. Mol Neurobiol 2022; 59:2593-2604. [DOI: 10.1007/s12035-021-02641-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/07/2021] [Indexed: 12/21/2022]
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19
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Yusuf IH, Garrett A, MacLaren RE, Issa PC. Retinal cadherins and the retinal cadherinopathies: Current concepts and future directions. Prog Retin Eye Res 2022; 90:101038. [DOI: 10.1016/j.preteyeres.2021.101038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022]
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Corrigendum. Mol Carcinog 2021; 61:435-436. [PMID: 34935185 DOI: 10.1002/mc.23387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Lin Z, Huang W, Yi Y, Li D, Xie Z, Li Z, Ye M. LncRNA ADAMTS9-AS2 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Lung Adenocarcinoma. Int J Gen Med 2021; 14:8541-8555. [PMID: 34849000 PMCID: PMC8626860 DOI: 10.2147/ijgm.s340683] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background The role of long noncoding RNA (LncRNA) ADAMTS9 antisense RNA 2 (ADAMTS9-AS2) is unclear in lung adenocarcinoma (LUAD). The aim of this study was to explore the relationship between ADAMTS9-AS2 and LUAD, based on The Cancer Genome Atlas (TCGA) database and bioinformatics analysis. Methods Various statistical methods, Kaplan–Meier method, Cox regression analysis, GSEA, and immune infiltration analysis were used to evaluate the relationship between clinical features and ADAMTS9-AS2 expression, prognostic factors, and the significant involvement of ADAMTS9-AS2 in function. Results In LUAD patients, low expression of ADAMTS9-AS2 was associated with N stage (P=0.011), gender (P=0.002), number of packs smoked (P=0.024) and smoker (P<0.001). Low ADAMTS9-AS2 expression predicted a poorer overall survival (OS) (HR: 0.68; 95% CI: 0.51–0.91; P=0.01). And ADAMTS9-AS2 expression (HR: 0.626; 95% CI: 0.397–0.986; P=0.043) was independently correlated with OS in LUAD patients. Unwinding of DNA, extrinsic pathway, polo-like kinase-mediated events, cori cycle, MCM pathway, proteasome pathway, lagging strand synthesis and PCNA-dependent long patch base excision repair were differentially enriched in ADAMTS9-AS2 high expression phenotype. ADAMTS9-AS2 expression was correlated with certain immune infiltrating cells. Conclusion In LUAD patients, ADAMTS9-AS2 expression was significantly associated with poor survival and immune infiltration. ADAMTS9-AS2 may be a promising biomarker of prognosis and response to immunotherapy for LUAD.
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Affiliation(s)
- Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Yongsheng Yi
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Dongbing Li
- MyGene Diagnostics Co., Ltd., Guangzhou, 510000, Guangdong, People's Republic of China
| | - Zehua Xie
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Zumei Li
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
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22
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Li Z, Xue H, Tan G, Xu Z. Effects of miRNAs, lncRNAs and circRNAs on osteoporosis as regulatory factors of bone homeostasis (Review). Mol Med Rep 2021; 24:788. [PMID: 34505632 PMCID: PMC8441966 DOI: 10.3892/mmr.2021.12428] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/25/2021] [Indexed: 01/03/2023] Open
Abstract
Osteoporosis is a common metabolic bone disorder typically characterized by decreased bone mass and an increased risk of fracture. At present, the detailed molecular mechanism underlying the development of osteoporosis remains to be elucidated. Accumulating evidence shows that non-coding (nc)RNAs, such as microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), play significant roles in osteoporosis through the post-transcriptional regulation of gene expression as regulatory factors. Previous studies have demonstrated that ncRNAs participate in maintaining bone homeostasis by regulating physiological and developmental processes in osteoblasts, osteoclasts and bone marrow stromal cells. In the present review, the latest research investigating the involvement of miRNAs, lncRNAs and circRNAs in regulating the differentiation, proliferation, apoptosis and autophagy of cells that maintain the bone microenvironment in osteoporosis is summarized. Deeper insight into the aspects of osteoporosis pathogenesis involving the deregulation of ncRNAs could facilitate the development of therapeutic approaches for osteoporosis.
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Affiliation(s)
- Zhichao Li
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250011, P.R. China
| | - Haipeng Xue
- Department of Orthopaedics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250011, P.R. China
| | - Guoqing Tan
- Department of Orthopaedics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250011, P.R. China
| | - Zhanwang Xu
- Department of Orthopaedics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250011, P.R. China
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Liu B, Xiang W, Liu J, Tang J, Wang J, Liu B, Long Z, Wang L, Yin G, Liu J. The regulatory role of antisense lncRNAs in cancer. Cancer Cell Int 2021; 21:459. [PMID: 34461912 PMCID: PMC8404292 DOI: 10.1186/s12935-021-02168-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
Antisense long non-coding RNAs (antisense lncRNAs), transcribed from the opposite strand of genes with either protein coding or non-coding function, were reported recently to play a crucial role in the process of tumor onset and development. Functionally, antisense lncRNAs either promote or suppress cancer cell proliferation, migration, invasion, and chemoradiosensitivity. Mechanistically, they exert their regulatory functions through epigenetic, transcriptional, post-transcriptional, and translational modulations. Simultaneously, because of nucleotide sequence complementarity, antisense lncRNAs have a special role on its corresponding sense gene. We highlight the functions and molecular mechanisms of antisense lncRNAs in cancer tumorigenesis and progression. We also discuss the potential of antisense lncRNAs to become cancer diagnostic biomarkers and targets for tumor treatment.
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Affiliation(s)
- Biao Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Wei Xiang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jiahao Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jinrong Wang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Bin Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Zhi Long
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Guangming Yin
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jianye Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China.
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Identification of a glycolysis-related lncRNA prognostic signature for clear cell renal cell carcinoma. Biosci Rep 2021; 41:229592. [PMID: 34402862 PMCID: PMC8403747 DOI: 10.1042/bsr20211451] [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: 06/16/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background: The present study investigated the independent prognostic value of glycolysis-related long noncoding (lnc)RNAs in clear cell renal cell carcinoma (ccRCC). Methods: A coexpression analysis of glycolysis-related mRNAs–long noncoding RNAs (lncRNAs) in ccRCC from The Cancer Genome Atlas (TCGA) was carried out. Clinical samples were randomly divided into training and validation sets. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were performed to establish a glycolysis risk model with prognostic value for ccRCC, which was validated in the training and validation sets and in the whole cohort by Kaplan–Meier, univariate and multivariate Cox regression, and receiver operating characteristic (ROC) curve analyses. Principal component analysis (PCA) and functional annotation by gene set enrichment analysis (GSEA) were performed to evaluate the risk model. Results: We identified 297 glycolysis-associated lncRNAs in ccRCC; of these, 7 were found to have prognostic value in ccRCC patients by Kaplan–Meier, univariate and multivariate Cox regression, and ROC curve analyses. The results of the GSEA suggested a close association between the 7-lncRNA signature and glycolysis-related biological processes and pathways. Conclusion: The seven identified glycolysis-related lncRNAs constitute an lncRNA signature with prognostic value for ccRCC and provide potential therapeutic targets for the treatment of ccRCC patients.
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Zhao Y, Ma S, Cui Z, Li S, Chen Y, Yin Y, Yin Z. The relationship between LncRNAs and lung adenocarcinoma as well as their ceRNA network. Cancer Biomark 2021; 31:165-176. [PMID: 33896828 DOI: 10.3233/cbm-203078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND More and more studies have shown that long non-coding RNA (LncRNA) as a competing endogenous RNA (ceRNA) plays an important role in lung cancer. Therefore, we analyzed the RNA expression profiles of 82 lung cancer patients which were all from Gene Expression Omnibus (GEO). METHODS Firstly, we used BLASTN (evalue = 1e-10) to annotate the gene sets, performed in-group correction and batched normalization of the three data sets with R. Secondly, we used the limma and sva packages to compare tumor tissues with normal tissues. Then through WGCNA, we obtained the 4 gene modules most related to the trait. RESULTS We intersected the genes of above 4 modules with the differential expression genes: 28 LncRNAs (up: 5, down: 23) and 265 mRNAs (up:11, down: 254). Based on these genes, we picked up 6 LncRNAs (CCDC39, FAM182A, SRGAP3-AS2, ADAMTS9-AS2, AC020907.2, SFTA1P), then set and visualized the LncRNA-miRNA-mRNA ceRNA network with 12 miRNAs related to 12 mRNAs. Finally, we performed downstream analysis of 265 mRNAs by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network. CONCLUSION After analyzing, we think this study provides a new direction for basic and clinical research related to LAD, and is expected to provide new targets for early diagnosis, prognostic evaluation and clinical treatment of lung cancer.
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Affiliation(s)
- Yuxin Zhao
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Shuwen Ma
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Zhigang Cui
- School of Nursing, China Medical University, Shenyang, Liaoning, China
| | - Sixuan Li
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yao Chen
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Yu Yin
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Zhihua Yin
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang North New Area, Shenyang, Liaoning, China
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26
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Yang Z, Xu F, Wang H, Teschendorff AE, Xie F, He Y. Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation. EBioMedicine 2021; 68:103399. [PMID: 34044218 PMCID: PMC8245911 DOI: 10.1016/j.ebiom.2021.103399] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Disruption of DNA methylation (DNAm) is one of the key signatures of cancer, however, detailed mechanisms that alter the DNA methylome in cancer remain to be elucidated. METHODS Here we present a novel integrative analysis framework, called MeLncTRN (Methylation mediated LncRNA Transcriptional Regulatory Network), that integrates genome-wide transcriptome, DNA methylome and copy number variation profiles, to systematically identify the epigenetically-driven lncRNA-gene regulation circuits across 18 cancer types. FINDING We show that a significant fraction of the aberrant DNAm and gene expression landscape in cancer is associated with long noncoding RNAs (lncRNAs). We reveal distinct types of regulation between lncRNA modulators and target genes that are operative in either only specific cancers or across cancers. Functional studies identified a common theme of cancer hallmarks that lncRNA modulators may participate in. The coupled lncRNA gene interactions via DNAm also serve as markers for classifications of cancer subtypes with different prognoses. INTERPRETATION Our study reveals a vital layer of DNAm and associated expression regulation for many cancer-related genes and we also provide a valuable database resource for interrogating epigenetically mediated lncRNA-gene interactions in cancer. FUNDING National Natural Science Foundation of China [91959106, 31871255].
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Feng Xu
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Haizhou Wang
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Andrew E Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute for Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Feng Xie
- Soochow University, 8 Jixue Road, Suzhou 215131, Jiangsu Province, China
| | - Yungang He
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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27
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Fang X, Bai Y, Zhang L, Ding S. MicroRNA-665 regulates the proliferation, apoptosis and adhesion of gastric cancer cells by binding to cadherin 3. Oncol Lett 2021; 21:494. [PMID: 33968210 PMCID: PMC8100969 DOI: 10.3892/ol.2021.12755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Numerous studies have reported that abnormal cadherin 3 (CDH3) and microRNA (miRNA/miR)-665 expression can induce the progression of gastric cancer (GC). However, the mechanism of interaction between miR-665 and CDH3 in GC requires further investigation. The present study aimed to investigate the influence of miR-665 and CDH3 in GC development. The effect of miR-665 and CDH3 on GC tissues and cell lines was examined using reverse transcription-quantitative PCR. Subsequently, CDH3 protein expression in GC cell lines was detected using western blotting. To confirm the association between miR-665 and CDH3, a dual-luciferase reporter assay system was employed. Cell proliferation and adhesion were analyzed using BrdU ELISA, MTT and cell adhesion assays. Finally, caspase-3 activity assay kit and FITC apoptosis detection kit were used for the determination of apoptosis of GC cells. The current findings confirmed the upregulation of CDH3 expression in GC cell lines and tissues. Experimental results indicated that CDH3 overexpression increased cell proliferation and adhesion, but decreased the apoptosis level of the cells. Similarly, the miR-665 inhibitor enhanced cell proliferation and adhesion, but inhibited apoptosis of GC cells. Additionally, it was observed that CDH3 was a direct target of miR-665 in GC cells and that miR-665 inhibited CDH3 expression, thereby repressing the progression of GC. In conclusion, the present study suggested that by targeting CDH3, miR-665 suppressed the progression of GC. These findings may provide a significant theoretical basis for future GC clinical therapy.
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Affiliation(s)
- Xinhui Fang
- Department of Gastroenterology and Hepatology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Yangqiu Bai
- Department of Gastroenterology and Hepatology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Lida Zhang
- Department of Gastroenterology and Hepatology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Songze Ding
- Department of Gastroenterology and Hepatology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003, P.R. China
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28
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Wang A, Xu Q, Sha R, Bao T, Xi X, Guo G. MicroRNA-29a inhibits cell proliferation and arrests cell cycle by modulating p16 methylation in cervical cancer. Oncol Lett 2021; 21:272. [PMID: 33717269 PMCID: PMC7885157 DOI: 10.3892/ol.2021.12533] [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: 05/29/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer is the second most common gynecological malignancy. Accumulating evidence has suggested that microRNAs (miRNAs) are involved in the occurrence and development of cervical cancer. The present study aimed to investigate the function and underlying molecular mechanism of microRNA (miRNA/miR)-29a in cervical cancer. Reverse transcription-quantitative PCR and methylation-specific PCR were used to examine the expression of miR-29a and methylated status of p16 promoter, respectively. Cell Counting Kit-8 analysis and flow cytometry were performed to evaluate cell viability and cycle, respectively. Dual-luciferase reporter assay was performed to verify the interaction between miR-29a and its targets. Western blot analysis was performed to detect the protein levels of DNA methyltransferases (DNMT)3A and DNMT3B. The results demonstrated that miR-29a expression was downregulated in cervical cancer tissues and cells, and negatively correlated with p16 promoter hypermethylation. Furthermore, cell experiments confirmed that miR-29a suppressed cell proliferation and induced cell cycle arrest in HeLa and C-33A cells. Mechanically, miR-29a restored normal methylation pattern of the p16 gene by sponging DNMT3A and DNMT3B. Taken together, the results of the present study demonstrated the epigenetic regulation of tumor suppressor p16 by miR-29a as a unique mechanism, thus providing a rationale for the development of miRNA-based strategies in the treatment of cervical cancer.
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Affiliation(s)
- Anjin Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Qiying Xu
- Department of Gynecology, Affiliated Hospital of Qinghai University, Xining, Qinghai 810100, P.R. China
| | - Rengaowa Sha
- Department of Gynecology, Affiliated Hospital of Qinghai University, Xining, Qinghai 810100, P.R. China
| | - Tonghui Bao
- Department of Gynecology, Affiliated Hospital of Qinghai University, Xining, Qinghai 810100, P.R. China
| | - Xiaoli Xi
- Department of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Guilan Guo
- Department of Gynecology, Affiliated Hospital of Qinghai University, Xining, Qinghai 810100, P.R. China
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Chen B, Sun D, Qin X, Gao XH. Screening and identification of potential biomarkers and therapeutic drugs in melanoma via integrated bioinformatics analysis. Invest New Drugs 2021; 39:928-948. [PMID: 33501609 DOI: 10.1007/s10637-021-01072-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Melanoma is a highly aggressive malignant skin tumor with a high rate of metastasis and mortality. In this study, a comprehensive bioinformatics analysis was used to clarify the hub genes and potential drugs. Download the GSE3189, GSE22301, and GSE35388 microarray datasets from the Gene Expression Omnibus (GEO), which contains a total of 33 normal samples and 67 melanoma samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) approach analyze DEGs based on the DAVID. Use STRING to construct protein-protein interaction network, and use MCODE and cytoHubba plug-ins in Cytoscape to perform module analysis and identified hub genes. Use Gene Expression Profile Interactive Analysis (GEPIA) to assess the prognosis of genes in tumors. Finally, use the Drug-Gene Interaction Database (DGIdb) to screen targeted drugs related to hub genes. A total of 140 overlapping DEGs were identified from the three microarray datasets, including 59 up-regulated DEGs and 81 down-regulated DEGs. GO enrichment analysis showed that these DEGs are mainly involved in the biological process such as positive regulation of gene expression, positive regulation of cell proliferation, positive regulation of MAP kinase activity, cell migration, and negative regulation of the apoptotic process. The cellular components are concentrated in the membrane, dendritic spine, the perinuclear region of cytoplasm, extracellular exosome, and membrane raft. Molecular functions include protein homodimerization activity, calmodulin-binding, transcription factor binding, protein binding, and cytoskeletal protein binding. KEGG pathway analysis shows that these DEGs are mainly related to protein digestion and absorption, PPAR signaling pathway, signaling pathways regulating stem cells' pluripotency, and Retinol metabolism. The 23 most closely related DEGs were identified from the PPI network and combined with the GEPIA prognostic analysis, CDH3, ESRP1, FGF2, GBP2, KCNN4, KIT, SEMA4D, and ZEB1 were selected as hub genes, which are considered to be associated with poor prognosis of melanoma closely related. Besides, ten related drugs that may have therapeutic effects on melanoma were also screened. These newly discovered genes and drugs provide new ideas for further research on melanoma.
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Affiliation(s)
- Bo Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Donghong Sun
- Department of Dermatology, The First Hospital of China Medical University, No. 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China
| | - Xiuni Qin
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, No. 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China.
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30
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Zhou S, Zhu Y, Li Z, Zhu Y, He Z, Zhang C. Exosome-derived long non-coding RNA ADAMTS9-AS2 suppresses progression of oral submucous fibrosis via AKT signalling pathway. J Cell Mol Med 2020; 25:2262-2273. [PMID: 33345447 PMCID: PMC7882956 DOI: 10.1111/jcmm.16219] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Oral submucosal fibrosis (OSF) is one of the pre‐cancerous lesions of oral squamous cell carcinoma (OSCC). Its malignant rate is increasing, but the mechanism of malignancy is not clear. We previously have elucidated the long non‐coding RNA (lncRNA) expression profile during OSF progression at the genome‐wide level. However, the role of lncRNA ADAMTS9‐AS2 in OSF progression via extracellular communication remains unclear. lncRNA ADAMTS9‐AS2 is down‐regulated in OSCC tissues compared with OSF and normal mucous tissues. Low ADAMTS9‐AS2 expression is associated with poor overall survival. ADAMTS9‐AS2 is frequently methylated in OSCC tissues, but not in normal oral mucous and OSF tissues, suggesting tumour‐specific methylation. Functional studies reveal that exosomal ADAMTS9‐AS2 suppresses OSCC cell growth, migration and invasion in vitro. Mechanistically, exosomal ADAMTS9‐AS2 inhibits AKT signalling pathway and regulates epithelial‐mesenchymal transition markers. Through profiling miRNA expression profile regulated by exosomal ADAMTS9‐AS2, significantly enriched pathways include metabolic pathway, PI3K‐Akt signalling pathway and pathways in cancer, indicating that exosomal ADAMTS9‐AS2 exerts its functions through interacting with miRNAs during OSF progression. Thus, our findings highlight the crucial role of ADAMTS9‐AS2 in the cell microenvironment during OSF carcinogenesis, which is expected to become a marker for early diagnosis of OSCC.
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Affiliation(s)
- Shanghui Zhou
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yun Zhu
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Zhenming Li
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yonggan Zhu
- Department of Nursing, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijing He
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chenping Zhang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
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31
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Tian S, Tang M, Li J, Wang C, Liu W. Identification of long non-coding RNA signatures for squamous cell carcinomas and adenocarcinomas. Aging (Albany NY) 2020; 13:2459-2479. [PMID: 33318305 PMCID: PMC7880362 DOI: 10.18632/aging.202278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/08/2020] [Indexed: 11/25/2022]
Abstract
Studies have demonstrated that both squamous cell carcinomas (SCCs) and adenocarcinomas (ACs) possess some common molecular characteristics. Evidence has accumulated to support the theory that long non-coding RNAs (lncRNAs) serve as novel biomarkers and therapeutic targets in complex diseases such as cancer. In this study, we aimed to identify pan lncRNA signatures that are common to squamous cell carcinomas or adenocarcinomas with different tissues of origin. With the aid of elastic-net regularized regression models, a 35-lncRNA pan discriminative signature and an 11-lncRNA pan prognostic signature were identified for squamous cell carcinomas, whereas a 6-lncRNA pan discriminative signature and a 5-lncRNA pan prognostic signature were identified for adenocarcinomas. Among them, many well-known cancer relevant genes such as MALAT1 and PVT1 were included. The identified pan lncRNA lists can help experimental biologists generate research hypotheses and adopt existing treatments for less prevalent cancers. Therefore, these signatures warrant further investigation.
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Affiliation(s)
- Suyan Tian
- Division of Clinical Research, First Hospital of Jilin University, Changchun 130021, Jilin, P.R. China
| | - Mingbo Tang
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Jialin Li
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Chi Wang
- Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Wei Liu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun 130021, Jilin, China
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32
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Shen FF, Zhang F, Yang HJ, Li JK, Su JF, Yu PT, Zhou FY, Che GW. ADAMTS9-AS2 and CADM2 expression and association with the prognosis in esophageal squamous cell carcinoma. Biomark Med 2020; 14:1415-1426. [PMID: 32892630 DOI: 10.2217/bmm-2020-0432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: We investigated whether ADAMTS9-AS2 and CADM2 were related to esophageal squamous cell carcinoma (ESCC). Methodology: ESCC microarray datasets and reverse transcriptase qualitative PCR were used to analyze ADAMTS9-AS2 and CADM2 expression. Results: The GSE120356 and GSE33810 datasets identified ADAMTS9-AS2 and CADM2 as the candidates and ADAMTS9-AS2 and CADM2 expression was downregulated in ESCC. ADAMTS9-AS2 and CADM2 were positively correlated with ESCC. ADAMTS9-AS2 and CADM2 expression could discriminate ESCC from normal tissue. Five-year overall survival was shorter in underexpressed ADAMTS9-AS2 patients, and CADM2 expression level was related to 5-year overall survival. ADAMTS9-AS2 and CADM2 expression were independent prognosis indicators in ESCC patients. Conclusion: Our findings shed new light on the clinical significance of ADAMTS9-AS2 and CADM2 in ESCC carcinogenesis.
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Affiliation(s)
- Fang-Fang Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,The Key Laboratory for Tumor Translational Medicine, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Fan Zhang
- The Key Laboratory for Tumor Translational Medicine, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Hai-Jun Yang
- Anyang key Laboratory for Esophageal Cancer Research, Anyang Tumor Hospital, Anyang, Henan, China
| | - Jun-Kuo Li
- Anyang key Laboratory for Esophageal Cancer Research, Anyang Tumor Hospital, Anyang, Henan, China
| | - Jing-Fen Su
- Anyang key Laboratory for Esophageal Cancer Research, Anyang Tumor Hospital, Anyang, Henan, China
| | - Pan-Ting Yu
- The Key Laboratory for Tumor Translational Medicine, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Fu-You Zhou
- Anyang key Laboratory for Esophageal Cancer Research, Anyang Tumor Hospital, Anyang, Henan, China
| | - Guo-Wei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Zhang Z, Jia JP, Zhang YJ, Liu G, Zhou F, Zhang BC. Long Noncoding RNA ADAMTS9-AS2 Inhibits the Proliferation, Migration, and Invasion in Bladder Tumor Cells. Onco Targets Ther 2020; 13:7089-7100. [PMID: 32801743 PMCID: PMC7382762 DOI: 10.2147/ott.s245826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/29/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Bladder tumor is the fifth most prevalent tumor in men, yet its pathogenesis remains to be fully identified. Albeit a host of long noncoding RNAs (lncRNA) are emerging as new players involved in bladder tumor, the functions of many lncRNAs are still enigmatic. Reports on the deluge of studies on lncRNA ADAMTS9-AS2 have been convincingly associated with various tumors, but without mention of its roles in bladder tumor. Therefore, the roles of ADAMTS9-AS2 in bladder tumor cells were explored in our study. MATERIALS AND METHODS Quantitative real-time PCR assays and bioinformatic tools were applied in bladder tumor cells to identify the ADAMTS9-AS2 and ADAMTS9 expression. Western blot assays were performed to obtain the protein levels of bladder tumor related key molecules. CCK8, clonogenic assay, scratch wound healing, and transwell assays were separately applied to identify the functional roles of ADAMTS9-AS2 on proliferation, migration, and invasion in bladder tumor cells. RESULTS First, ADAMTS9-AS2 downregulation in bladder tumor cells was identified. Overexpression and knockdown experiments showed that ADAMTS9-AS2 expression was positively related to ADAMTS9, which is in accordance with the results from GEO database. Second, ADAMTS9-AS2 contributed to the inhibition of proliferation, migration, and invasion in bladder tumor cells. Third, ADAMTS9-AS2 was linked with PI3K/AKT/mTOR pathway related-molecules, several key autophagy, and apoptotic proteins. CONCLUSION Conjointly, our findings suggested that ADAMTS9-AS2 might function as a tumor suppressor to restrain the proliferation, migration, and invasion in bladder tumor cells. The potential mechanism of ADAMTS9-AS2 related to PI3K/AKT/mTOR signal pathway was further identified. Of note, we found that ADAMTS9-AS2 has a significant effect on several key autophagy and apoptotic proteins. Therefore, these observations will provide supportive evidence to ADAMTS9-AS2 as a potential biomarker in patients with bladder tumor.
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Affiliation(s)
- Zhan Zhang
- Department of Rehabilitation Medicine, Changhai Hospital, Second Military Medical University, Shanghai200433, People’s Republic of China
| | - Jin-Peng Jia
- Department of Orthopaedics, General Hospital of Chinese People’s Liberation Army, Beijing100853, People’s Republic of China
| | - Yin-Jiang Zhang
- School of Pharmacy, Minzu University of China, Beijing100081, People’s Republic of China
| | - Gang Liu
- Department of Urology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi435000, Hubei, People’s Republic of China
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Hubei Polytechnic University, Huangshi435000, Hubei, People’s Republic of China
| | - Fan Zhou
- Department of Urology, Wuhan Fourth Hospital, Pu’ai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430033, Hubei, People’s Republic of China
| | - Bi-Cheng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan430060, Hubei, People’s Republic of China
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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35
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Nie K, Deng Z, Zheng Z, Wen Y, Pan J, Jiang X, Yan Y, Liu P, Liu F, Li P. Identification of a 14-lncRNA Signature and Construction of a Prognostic Nomogram Predicting Overall Survival of Gastric Cancer. DNA Cell Biol 2020; 39:1532-1544. [PMID: 32644844 DOI: 10.1089/dna.2020.5565] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence suggests that aberrant long noncoding (lnc) RNA expression plays a vital role in gastric cancer (GC) initiation and progression. Thus, we aimed to develop a lncRNA-based risk signature and nomogram to predict overall survival (OS) for patients with GC. Our primary cohort was composed of 341 patients with clinical and lncRNA expression data in The Cancer Genome Atlas stomach adenocarcinoma (TCGA STAD), the internal validation cohort was composed of 172 randomly assigned patients, and the external validation cohort was composed of 300 patients from GSE62254 dataset. A risk signature and nomogram were developed for the primary cohort and validated on the validation cohorts. Furthermore, gene set enrichment analysis (GSEA) was used to investigate the pathway enrichment for the risk signature. The expression patterns of several lncRNAs were also investigated in clinical samples from 10 GC patients. We identified and validated a 14-lncRNA signature highly associated with the OS of patients with GC, which performed well on evaluation with C-index, area under the curve, and calibration curves. In addition, univariate and multivariate Cox regression analyses indicated that the lncRNA signature was an independent predictive factor for GC patients. Therefore, a nomogram incorporating lncRNA signature and clinical factors was constructed to predict OS for patients with GC in primary cohort that suggested powerful predictive values for survival in the TCGA cohort and the other two validation cohorts. In addition, GSEA indicated that the identified lncRNAs may regulate the autophagy pathway, affecting tumorigenesis and prognosis of patients with GC. Experimental validation demonstrated that the expression of lncRNAs showed the same trend both in our clinical samples and STAD dataset. These results suggest that both risk signature and nomogram were effective prognostic indicators for patients with GC.
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Affiliation(s)
- Kechao Nie
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhitong Deng
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihua Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yi Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jinglin Pan
- Department of Gastroenterology, Hainan Provincial Hospital of Traditional Chinese Medicine, Haikou, Hainan, China
| | - Xiaotao Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yanhua Yan
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Peng Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Fengbin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Peiwu Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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36
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Wang D, Chen F, Zeng T, Tang Q, Chen B, Chen L, Dong Y, Li X. Comprehensive biological function analysis of lncRNAs in hepatocellular carcinoma. Genes Dis 2020; 8:157-167. [PMID: 33997162 PMCID: PMC8099694 DOI: 10.1016/j.gendis.2019.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/16/2019] [Accepted: 12/31/2019] [Indexed: 12/19/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been discovered in human genomes by gene chip, next-generation sequencing, and/or other methods in recent years, which represent a significant subset of the universal genes involved in a wide range of biological functions. An abnormal expression of lncRNAs is associated with the growth, invasion, and metastasis of various types of human cancers, including hepatocellular carcinoma (HCC), which is an aggressive, highly malignant, and invasive tumor, and a poor prognosis in China. With a more in-depth understanding of lncRNA research for HCC and the emergence of new molecular-targeted therapies, the diagnosis, treatment, and prognosis of HCC will be considerably improved. Therefore, this review is expected to provide recommendations and directions for future lncRNA research for HCC.
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Affiliation(s)
- Dan Wang
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China.,Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Fengjiao Chen
- Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Tao Zeng
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan Province, Chengdu, 611731, PR China
| | - Qingxia Tang
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China
| | - Bing Chen
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China
| | - Ling Chen
- Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yan Dong
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Xiaosong Li
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
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