1
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Huang Q, Liang Z, Huang Q, Li X, Xia J, Huang L, Huang LB, Ou C. Involvement of lncRNAs in the regulation of aerobic glycolysis in hepatocellular carcinoma: Main functions, regulatory mechanisms and potential therapeutic implications (Review). Oncol Rep 2024; 51:84. [PMID: 38666534 PMCID: PMC11082637 DOI: 10.3892/or.2024.8743] [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: 12/02/2023] [Accepted: 04/11/2024] [Indexed: 05/04/2024] Open
Abstract
Even under aerobic conditions, tumor cells can reprogram their metabolism to preferentially metabolize glucose into lactic acid. This abnormal metabolic pattern, known as the 'Warburg' effect or aerobic glycolysis, promotes cancer progression. Long non‑coding RNAs (lncRNAs) are RNAs that are >200 nucleotides in length and do not have protein‑coding capabilities. However, these RNAs play a key role in tumor development. There is increasing evidence to indicate that lncRNAs regulate glucose metabolism in tumor cells by affecting metabolic enzymes and some signaling pathways, thereby regulating the occurrence and progression of hepatocellular carcinoma (HCC). Therefore, it is crucial to understand which lncRNAs play a regulatory role in HCC glycolysis and to determine the related molecular mechanisms. The present review summarized and discussed the functions of lncRNAs, focusing on the regulatory mechanisms of lncRNAs in the process of glycolysis in HCC. In addition, the present review suggests the importance of lncRNAs as future therapeutic targets for antitumor cell metabolism.
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Affiliation(s)
- Qiongqing Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Zhengui Liang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Qiqi Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Xueyu Li
- Experimental Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Jingjing Xia
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Lining Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Lin Bing Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
| | - Chao Ou
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, P.R. China
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2
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Du P, Chen Y, Li Q, Gai Z, Bai H, Zhang L, Liu Y, Cao Y, Zhai Y, Jin W. CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer. Database (Oxford) 2024; 2024:baae029. [PMID: 38613826 PMCID: PMC11015892 DOI: 10.1093/database/baae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
The discovery of key epigenetic modifications in cancer is of great significance for the study of disease biomarkers. Through the mining of epigenetic modification data relevant to cancer, some researches on epigenetic modifications are accumulating. In order to make it easier to integrate the effects of key epigenetic modifications on the related cancers, we established CancerMHL (http://www.positionprediction.cn/), which provide key DNA methylation, histone modifications and lncRNAs as well as the effect of these key epigenetic modifications on gene expression in several cancers. To facilitate data retrieval, CancerMHL offers flexible query options and filters, allowing users to access specific key epigenetic modifications according to their own needs. In addition, based on the epigenetic modification data, three online prediction tools had been offered in CancerMHL for users. CancerMHL will be a useful resource platform for further exploring novel and potential biomarkers and therapeutic targets in cancer. Database URL: http://www.positionprediction.cn/.
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Affiliation(s)
- Pengyu Du
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yingli Chen
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Qianzhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Zhimin Gai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Hui Bai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Luqiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yuxian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yanni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Yuanyuan Zhai
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
| | - Wen Jin
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, 235 West Daxue Road, Hohhot 010021, China
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3
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Gong HY, Zhou PC, Zhang HY, Chen LM, Zhou YM, Liu ZG. Transcriptional regulation of Glis2 in hepatic fibrosis. Exp Mol Med 2023:10.1038/s12276-023-01031-y. [PMID: 37394585 PMCID: PMC10393978 DOI: 10.1038/s12276-023-01031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/21/2023] [Accepted: 04/12/2023] [Indexed: 07/04/2023] Open
Abstract
The role of Gli-similar 2 (Glis2) in hepatic fibrosis (HF) is controversial. In this study, we focused on the functional and molecular mechanisms involved in the Glis2-mediated activation of hepatic stellate cells (HSCs)-a milestone event leading to HF. The expression levels of Glis2 mRNA and protein were significantly decreased in the liver tissues of patients with severe HF and in mouse fibrotic liver tissues as well as HSCs activated by TGFβ1. Functional studies indicated that upregulated Glis2 significantly inhibited HSC activation and alleviated BDL-induced HF in mice. Downregulation of Glis2 was found to correlate significantly with DNA methylation of the Glis2 promoter mediated by methyltransferase 1 (DNMT1), which restricted the binding of hepatic nuclear factor 1-α (HNF1-α), a liver-specific transcription factor, to Glis2 promoters. In addition, the enrichment of DNMT1 in the Glis2 promoter region was mediated by metastasis-associated lung adenocarcinoma transcriptor-1 (MALAT1) lncRNA, leading to transcriptional silencing of Glis2 and activation of HSCs. In conclusion, our findings reveal that the upregulation of Glis2 can maintain the resting state of HSCs. The decreased expression of Glis2 under pathological conditions may lead to the occurrence and development of HF with the expression silencing of DNA methylation mediated by MALAT1 and DNMT1.
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Affiliation(s)
- Huan-Yu Gong
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Peng-Cheng Zhou
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China
| | - Hao-Ye Zhang
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Li-Min Chen
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Yang-Mei Zhou
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China
| | - Zhen-Guo Liu
- Department of Infectious Disease, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, PR China.
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China.
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4
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Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:bioengineering9080406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [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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Yang K, Liang X, Wen K. Long non‑coding RNAs interact with RNA‑binding proteins to regulate genomic instability in cancer cells (Review). Oncol Rep 2022; 48:175. [PMID: 36004472 PMCID: PMC9478986 DOI: 10.3892/or.2022.8390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022] Open
Abstract
Genomic instability, a feature of most cancers, contributes to malignant cell transformation and cancer progression due to the accumulation of genetic alterations. Genomic instability is reflected at numerous levels, from single nucleotide to the chromosome levels. However, the exact molecular mechanisms and regulators of genomic instability in cancer remain unclear. Growing evidence indicates that the binding of long non-coding RNAs (lncRNAs) to protein chaperones confers a variety of regulatory functions, including managing of genomic instability. The aim of the present review was to examine the roles of mitosis, telomeres, DNA repair, and epigenetics in genomic instability, and the mechanisms by which lncRNAs regulate them by binding proteins in cancer cells. This review contributes to our understanding of the role of lncRNAs and genomic instability in cancer and can potentially provide entry points and molecular targets for cancer therapies.
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Affiliation(s)
- Kai Yang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xiaoxiang Liang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Kunming Wen
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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6
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Z-Guggulsterone Is a Potential Lead Molecule of Dawa-ul-Kurkum against Hepatocellular Carcinoma. Molecules 2022; 27:molecules27165104. [PMID: 36014345 PMCID: PMC9413334 DOI: 10.3390/molecules27165104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
An ancient saffron-based polyherbal formulation, Dawa-ul-Kurkum (DuK), has been used to treat liver ailments and other diseases and was recently evaluated for its anticancer potential against hepatocellular carcinoma (HCC) by our research team. To gain further insight into the lead molecule of DuK, we selected ten active constituents belonging to its seven herbal constituents (crocin, crocetin, safranal, jatamansone, isovaleric acid, cinnamaldehyde, coumaric acid, citral, guggulsterone and dehydrocostus lactone). We docked them with 32 prominent proteins that play important roles in the development, progression and suppression of HCC and those involved in endoplasmic reticulum (ER) stress to identify the binding interactions between them. Three reference drugs for HCC (sorafenib, regorafenib, and nivolumab) were also examined for comparison. The in silico studies revealed that, out of the ten compounds, three of them—viz., Z-guggulsterone, dehydrocostus lactone and crocin—showed good binding efficiency with the HCC and ER stress proteins. Comparison of binding affinity with standard drugs was followed by preliminary in vitro screening of these selected compounds in human liver cancer cell lines. The results provided the basis for selecting Z-guggulsterone as the best-acting phytoconstituent amongst the 10 studied. Further validation of the binding efficiency of Z-guggulsterone was undertaking using molecular dynamics (MD) simulation studies. The effects of Z-guggulsterone on clone formation and cell cycle progression were also assessed. The anti-oxidant potential of Z-guggulsterone was analyzed through DPPH and FRAP assays. qRTPCR was utilized to check the results at the in vitro level. These results indicate that Z-guggulsterone should be considered as the main constituent of DuK instead of the crocin in saffron, as previously hypothesized.
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7
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Pathania AS, Prathipati P, Pandey MK, Byrareddy SN, Coulter DW, Gupta SC, Challagundla KB. The emerging role of non-coding RNAs in the epigenetic regulation of pediatric cancers. Semin Cancer Biol 2022; 83:227-241. [PMID: 33910063 DOI: 10.1016/j.semcancer.2021.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/09/2023]
Abstract
Epigenetics is a process that involves the regulation of gene expression without altering the sequence of DNA. Numerous studies have documented that epigenetic mechanisms play a critical role in cell growth, differentiation, and cancer over the past decade. The well-known epigenetic modifications are either on DNA or at the histone proteins. Although several studies have focused on regulating gene expression by non-coding RNAs, the current understanding of their biological functions in various human diseases, particularly in cancers, is inadequate. Only about two percent of DNA is involved in coding the protein-coding genes, and leaving the rest 98 percent is non-coding and the scientific community regarded as junk or noise with no known purpose. Most non-coding RNAs are derived from such junk DNA and are known to be involved in various signaling pathways involving cancer initiation, progression, and the development of therapy resistance in many human cancer types. Recent studies have suggested that non-coding RNAs, especially microRNAs, piwi-interactingRNAs, and long non-coding RNAs, play a significant role in controlling epigenetic mechanism(s), indicating the potential effect of epigenetic modulation of non-coding RNAs on cancer progression. In this review article, we briefly presented epigenetic marks' characteristics, crosstalk between epigenetic modifications and microRNAs, piwi-interactingRNAs, and long non-coding RNAs to uncover the effect on the phenotype of pediatric cancers. Further, current knowledge on understanding the RNA epigenetics will help design novel therapeutics that target epigenetic regulatory networks to benefit cancer patients in the clinic.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Philip Prathipati
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Manoj K Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Siddappa N Byrareddy
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Don W Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Subash C Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Children's Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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8
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Jin H, Du W, Huang W, Yan J, Tang Q, Chen Y, Zou Z. lncRNA and breast cancer: Progress from identifying mechanisms to challenges and opportunities of clinical treatment. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:613-637. [PMID: 34589282 PMCID: PMC8463317 DOI: 10.1016/j.omtn.2021.08.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Breast cancer is a malignant tumor that has a high mortality rate and mostly occurs in women. Although significant progress has been made in the implementation of personalized treatment strategies for molecular subtypes in breast cancer, the therapeutic response is often not satisfactory. Studies have reported that long non-coding RNAs (lncRNAs) are abnormally expressed in breast cancer and closely related to the occurrence and development of breast cancer. In addition, the high tissue and cell-type specificity makes lncRNAs particularly attractive as diagnostic biomarkers, prognostic factors, and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in breast cancer is essential for developing new treatment strategies. In this review, we systematically elucidate the general characteristics, potential mechanisms, and targeted therapy of lncRNAs and discuss the emerging functions of lncRNAs in breast cancer. Additionally, we also highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets for drug resistance in breast cancer and present future perspectives in clinical practice.
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Affiliation(s)
- Huan Jin
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China.,MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Wei Du
- Department of Neurosurgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Wentao Huang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Jiajing Yan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Qing Tang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Zhengzhi Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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9
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Xia M, Duan LJ, Lu BN, Pang YZ, Pang ZR. LncRNA AFAP1-AS1/miR-27b-3p/VEGF-C axis modulates stemness characteristics in cervical cancer cells. Chin Med J (Engl) 2021; 134:2091-2101. [PMID: 34334630 PMCID: PMC8440026 DOI: 10.1097/cm9.0000000000001665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: Long non-coding RNA (lncRNA) actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) functions as a competing endogenous RNA to regulate target genes expression by sponging microRNAs (miRs) to play cancer-promoting roles in cancer stem cells. However, the regulatory mechanism of AFAP1-AS1 in cervical cancer (CC) stem cells is unknown. The present study aimed to provide a new therapeutic target for the clinical treatment of CC. Methods: Hyaluronic acid receptor cluster of differentiation 44 variant exon 6 (CD44v6)(+) CC cells were isolated by flow cytometry (FCM). Small interfering RNAs of AFAP1-AS1 (siAFAP1-AS1) were transfected into the (CD44v6)(+) cells. The levels of AFAP1-AS1 were measured by quantitative real-time PCR (qRT-PCR). Sphere formation assay, cell cycle analysis, and Western blotting were used to detect the effect of siAFAP1-AS1. RNA pull-down and luciferase reporter assay were used to verify the relationship between miR-27b-3p and AFAP1-AS1 or vascular endothelial growth factor (VEGF)-C. Results: CD44v6(+) CC cells had remarkable stemness and a high level of AFAP1-AS1. However, AFAP1-AS1 knockdown with siAFAP1-AS1 suppressed the cell cycle transition of G(1)/S phase and inhibited self-renewal of CD44v6(+) CC cells, the levels of the stemness markers octamer-binding transcription factor 4 (OCT4), osteopontin (OPN), and cluster of differentiation 133 (CD133), and the epithelial-mesenchymal transition (EMT)-related proteins Twist1, matrix metalloprotease (MMP)-9, and VEGF-C. In the mechanism study, miR-27b-3p/VEGF-C signaling was demonstrated to be a key downstream of AFAP1-AS1 in the CD44v6(+) CC cells. Conclusions: LncRNA AFAP1-AS1 knockdown inhibits the CC cell stemness by upregulating miR-27b-3p to suppress VEGF-C.
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Affiliation(s)
- Meng Xia
- School of Pharmacy, Minzu University of China, Beijing 100081, China Department of Orthopedics, Bayannaoer City Hospital, Bayannaoer, Inner Mongolia 015000, China Guangxi Zhuang Yao Medicine Center of Engineering and Technology, Guangxi University of Chinese Medicine, Nanning, Guangxi 530200, China Key Laboratory of Ethnomedicine of Ministry of Education, Minzu University of China, Beijing 100081, China
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Ramasamy D, Deva Magendhra Rao AK, Rajkumar T, Mani S. Non-CpG methylation-a key epigenetic modification in cancer. Brief Funct Genomics 2021; 20:304-311. [PMID: 34318313 DOI: 10.1093/bfgp/elab035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
The methylation of cytosine residues that precede adenine/thymine or other cytosine nucleotides instead of guanine in DNA is known as non-CpG methylation. It is a pronounced epigenetic modification with a central role in gene regulation similar to CpG methylation. Due to technological limitations, the locus-specific role of non-CpG methylation was scarcely understood. At present, high-throughput analyses and improved enrichment methods can elucidate the role of genome-wide non-CpG methylation distributions. Although the functional basis of non-CpG methylation in regulating gene expression control is known, its role in cancer development is yet to be ascertained. This review sheds light on the possible mechanism of non-CpG methylation in embryos and developed tissues with a special focus on cancer development and progression. In particular, the maintenance and alteration of non-CpG methylation levels and the crucial factors that determine this level of non-CpG methylation and its functional role in cancer are discussed.
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11
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Li S, Zhu Y, Li R, Huang J, You K, Yuan Y, Zhuang S. LncRNA Lnc-APUE is Repressed by HNF4 α and Promotes G1/S Phase Transition and Tumor Growth by Regulating MiR-20b/E2F1 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003094. [PMID: 33854885 PMCID: PMC8025008 DOI: 10.1002/advs.202003094] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/07/2020] [Indexed: 06/07/2023]
Abstract
Many long noncoding RNAs (lncRNAs) have been annotated, but their functions remain unknown. The authors found a novel lnc-APUE (lncRNA accelerating proliferation by upregulating E2F1) that is upregulated in different cancer types, including hepatocellular carcinoma (HCC), and high lnc-APUE level is associated with short recurrence-free survival (RFS) of HCC patients. Gain- and loss-of-function analyses showed that lnc-APUE accelerated G1/S transition and tumor cell growth in vitro and allows hepatoma xenografts to grow faster in vivo. Mechanistically, lnc-APUE binds to miR-20b and relieves its repression on E2F1 expression, resulting in increased E2F1 level and accelerated G1/S phase transition and cell proliferation. Consistently, lnc-APUE level is positively associated with the expression of E2F1 and its downstream target genes in HCC tissues. Further investigations disclose that hepatocyte nuclear factor 4 alpha (HNF4α) binds to the lnc-APUE promoter, represses lnc-APUE transcription, then diminishes E2F1 expression and cell proliferation. HNF4α expression is reduced in HCC tissues and low HNF4α level is correlated with high lnc-APUE expression. Collectively, a HNF4α/lnc-APUE/miR-20b/E2F1 axis in which HNF4α represses lnc-APUE expression and keeps E2F1 at a low level is identified. In tumor cells, HNF4α downregulation leads to lnc-APUE upregulation, which prevents the inhibition of miR-20b on E2F1 expression and thereby promotes cell cycle progression and tumor growth.
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Affiliation(s)
- Song‐Yang Li
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Ruo‐Nan Li
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Jia‐Hui Huang
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Kai You
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Yun‐Fei Yuan
- Department of Hepatobilliary OncologyCancer CenterSun Yat‐sen UniversityGuangzhou510060China
| | - Shi‐Mei Zhuang
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
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Zhanghuang C, Chen S, Li L, Yang Z, Xie Y, Li J, Tang H, He X, Dong L, Yan B. Clinical and Molecular Differentiation Between Malignant Rhabdoid Tumor of the Kidney and Normal Tissue: A Two-Case Report. Front Oncol 2021; 11:659709. [PMID: 33859949 PMCID: PMC8042314 DOI: 10.3389/fonc.2021.659709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Malignant rhabdoid tumor of the kidney (MRTK) is a rare type of tumor that lacks typical clinical manifestations. Herein, we presented clinical data of 2 children with MRTK. In addition, we used a high-throughput RNA-sequencing (RNA-seq), GO analysis, and KEGG signaling pathway analysis to examine gene expression differences at the transcripts level between 2 patients with MRTK and 3 patients with non-tumor diseases without other symptoms. CASE REPORT Preoperative B-scan ultrasonography and computed tomography (CT) examination in 2 cases suggested nephroblastoma. Both patients were treated with radical nephrectomy. After the operation, MRTK was confirmed by pathological examination. Child 1 and Child 2 then received 7 courses and 12 courses of regular chemotherapy, respectively. Child 1 was followed up for 2 years, and Child 2 for 3.1 years without showing symptoms. RNA-seq results showed 2203 differential genes (DEGs) in the kidney tissue of children with MRTK compared to normal tissue (p <0.01). GO analysis suggested that most DEGs participate in protein binding. KEGG results showed that the DEGs were mainly involved in the PI3K-Akt signaling pathway and microRNA-related proteins. CONCLUSION The PI3K-Akt signaling pathway and microRNA-related proteins as targets have extremely high potential value for the diagnosis and treatment of MRTK.
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Affiliation(s)
| | - Shuo Chen
- Department of Pharmacology, Anhui Medical University, Hefei, China
| | - Li Li
- Yunnan Key Laboratory of Children’s Major Disease Research Kunming Children’s Hospital, Kunming, China
| | - Zhen Yang
- Department of Oncology, Kunming Children’s Hospital, Kunming, China
| | - Yucheng Xie
- Department of Pathology, Kunming Children’s Hospital, Kunming, China
| | - Jiwei Li
- Department of Pathology, Kunming Children’s Hospital, Kunming, China
| | - Haoyu Tang
- Department of Urology, Kunming Children’s Hospital, Kunming, China
| | - Xiaoli He
- Yunnan Key Laboratory of Children’s Major Disease Research Kunming Children’s Hospital, Kunming, China
| | - Liuyi Dong
- Department of Pharmacology, Anhui Medical University, Hefei, China
| | - Bing Yan
- Department of Urology, Kunming Children’s Hospital, Kunming, China
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13
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Deng T, Ye Q, Jin C, Wu M, Chen K, Yang J, Chen Z, Yu X, Chen G, Wang Y. Identification and validation of a glycolysis-associated multiomics prognostic model for hepatocellular carcinoma. Aging (Albany NY) 2021; 13:7481-7498. [PMID: 33686959 PMCID: PMC7993684 DOI: 10.18632/aging.202613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Abstract
Increased glycolysis has been reported as a major metabolic hallmark in many cancers, and is closely related to malignant behavior of tumors. However, the potential mechanism of glycolysis in hepatocellular carcinoma (HCC) and its prognostic value are not well understood. To address this, we investigated glycolysis-related gene expression data of patients with HCC from TCGA and ICGC. Patients were categorized into three different glycolysis-associated subgroups: Glycolysis-M, Glycolysis-H, and Glycolysis-L. We found that Glycolysis-H combined with Glycolysis-M (Glycolysis-H+M) subgroup was associated with poor overall survival and distinct cancer stem cell characteristics and immune infiltrate patterns. Additionally, multiomics-based analyses were conducted to evaluate genomic patterns of glycolysis subgroups, including their gene mutations, copy number variations, and RNA-sequencing data. Finally, a glycolysis-associated multiomics prognostic model (GMPM) consisting of 19 glycolysis-associated genes was developed. The capability of GMPM in categorizing patients with HCC into high- and low-risk groups was validated with independent HCC datasets. Finally, GMPM was confirmed as an independent risk factor for the prognosis of patients with HCC. We believe that our findings provide new insights into the mechanism of glycolysis and highlight the potential clinical value of GMPM in predicting the prognosis of patients with HCC.
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Affiliation(s)
- Tuo Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qian Ye
- Department of Clinical Laboratory, Wenzhou People's Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Chen Jin
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mingliang Wu
- Department of Oncology, The First School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kaiyu Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinhuan Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ziyan Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - XiXiang Yu
- Department of Oncology, The First School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Gang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
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14
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Zhang C, Wang L, Jin C, Zhou J, Peng C, Wang Y, Xu Z, Zhang D, Huang Y, Zhang Y, Ji D, Peng W, Jin K, Tang J, Feng Y, Sun Y. Long non-coding RNA Lnc-LALC facilitates colorectal cancer liver metastasis via epigenetically silencing LZTS1. Cell Death Dis 2021; 12:224. [PMID: 33637680 PMCID: PMC7910484 DOI: 10.1038/s41419-021-03461-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 01/17/2023]
Abstract
Colorectal cancer (CRC) is one of the most common cancers around the world and endangers human health seriously. Liver metastasis is an important factor affecting the long-term prognosis of CRC and the specific mechanism of CRLM (colorectal cancer with liver metastasis) is not fully understood. LZTS1 has been found dysregulated in many cancers, especially in CRC. Theories suggested that hypermethylation of the promoter regions of LZTS1 was responsible for LZTS1 abnormal expression in multiple malignant tumors. Although the role of LZTS1 in CRC cell proliferation has been reported, its role in CRLM remains unclear. Numerous studies reported Long non-coding RNA (lncRNA) could regulate the gene expression level by regulating gene methylation status in many tumors. However, whether there were lncRNAs could change the methylation status of LZTS1 or not in CRLM was unknown. In this study, we aimed to investigate whether there are lncRNAs can regulate the expression of LZTS1 through affecting DNA methylation in CRLM. We found that upregulated Lnc-LALC in CRC was negatively correlated with LZTS1 expression, and Lnc-LALC could regulate LZTS1 expression in both mRNA and protein level in our study. Functionally, Lnc-LALC enhanced the CRC cells metastasis ability in vitro and vivo through inhibiting the expression of LZTS1. Furthermore, the precise mechanisms exploration showed that lnc-LALC could recruit DNA methyltransferases (DNMTs) to the LZTS1 promoter by combining with Enhancer of zeste homolog 2(EZH2) and then altered the expression of LZTS1 via DNMTs-mediated DNA methylation. Collectively, our data demonstrated the important role of Lnc-LALC/ LZTS1 axis in CRLM development.
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Affiliation(s)
- Chuan Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Lu Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Chi Jin
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Jiahui Zhou
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Chaofan Peng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yong Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Ziwei Xu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Dongsheng Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yuanjian Huang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yue Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Dongjian Ji
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Wen Peng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Kangpeng Jin
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Junwei Tang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China.
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Yifei Feng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China.
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Yueming Sun
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, PR China.
- Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
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15
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The paradoxical functions of long noncoding RNAs in hepatocellular carcinoma: Implications in therapeutic opportunities and precision medicine. Genes Dis 2020; 9:358-369. [PMID: 35224152 PMCID: PMC8843871 DOI: 10.1016/j.gendis.2020.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most aggressive and lethal diseases with poor prognosis, worldwide. However, the mechanisms underlying HCC have not been comprehensively elucidated. With the recent application of high-throughput sequencing techniques, a diverse catalogue of differentially expressed long non-coding RNAs (lncRNA) in cancer have been shown to participate in HCC. Rather than being “transcriptional noise,” they are emerging as important regulators of many biological processes, including chromatin remodelling, transcription, alternative splicing, translational and post-translational modification. Moreover, lncRNAs have dual effects in the development and progression of HCC, including oncogenic and tumour-suppressive roles. Collectively, recently data point to lncRNAs as novel diagnostic and prognostic biomarkers with satisfactory sensitivity and specificity, as well as being therapeutic targets for HCC patients. In this review, we highlight recent progress of the molecular patterns of lncRNAs and discuss their potential clinical application in human HCC.
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16
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Raizis AM, Racher HM, Foucal A, Dimaras H, Gallie BL, George PM. DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the RB1 gene promoter. Epigenetics 2020; 16:940-954. [PMID: 33258708 DOI: 10.1080/15592294.2020.1834911] [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: 12/30/2022] Open
Abstract
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1 gene (RB-/-). RB1 encodes a tumour suppressing, cell cycle regulating transcription factor (pRB) that binds and regulates the RB1 core and other E2F responsive promoters with epigenetic functions that include recruitment of histone deacetylases (HDACs). Evidence suggests that bi-allelic epigenetic inactivation/hypermethylation of the RB1 core promoter (PrE-/E-), is specific to sporadic retinoblastomas (frequency~10%), whereas heritable RB1 promoter variants (Pr-/+, frequency~1-2%) are not associated with known epigenetic phenomena. We report heritable Pr-/- retinoblastomas with the expected loss of pRB expression, in which hypermethylation consistent with distal boundary displacement (BD) relative to normal peripheral blood DNAs was detected in 4/4 cases. In contrast, proximal BD was identified in 16/16 RB-/- retinoblastomas while multiple boundaries distal of the core promoter was further identified in PrE-/E-and PrE-/E+ retinoblastomas. However, weak or no DNA hypermethylation/BD in peripheral blood DNA was detected in 8/9 Pr-/+ patients, with the exception, a carrier of a microdeletion encompassing several RB1 promoter elements. These findings suggest that loss of boundary control may be a critical step leading to epigenetic inactivation of the RB1 gene and that novel DNA methylation boundaries/profiles identified in the RB1 promoter of Pr-/- retinoblastomas, may be the result of epigenetic phenomena associated with epimutation in conjunction with loss of pRB expression/binding and/or RB1 promoter interactions with boundary control elements.
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Affiliation(s)
- A M Raizis
- C/o Dept. of Molecular Pathology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - H M Racher
- Department of Genetics, c/o Impact Genetics, Bowmanville, Ontario, Canada
| | - A Foucal
- Universit#xE9; de Nantes, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - H Dimaras
- Departments of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada.,Division of Clinical Public Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Child Health Evaluative Sciences, SickKids Research Institute, Toronto, Canada
| | - B L Gallie
- Departments of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada.,Department of Pediatrics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Departments of Molecular Genetics and Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - P M George
- Department of Pathology, University of Otago, Christchurch, New Zealand
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17
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Pérez-Molina R, Arzate-Mejía RG, Ayala-Ortega E, Guerrero G, Meier K, Suaste-Olmos F, Recillas-Targa F. An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines. Front Genet 2020; 11:928. [PMID: 33061937 PMCID: PMC7489498 DOI: 10.3389/fgene.2020.00928] [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: 06/06/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Alu elements are primate-specific repeats and represent the most abundant type of transposable elements (TE) in the human genome. Genome-wide analysis of the enrichment of histone post-translational modifications suggests that human Alu sequences could function as transcriptional enhancers; however, no functional experiments have evaluated the role of Alu sequences in the control of transcription in situ. The present study analyses the regulatory activity of a human Alu sequence from the AluSx family located in the second intron of the long intergenic non-coding RNA Linc00441, found in divergent orientation to the RB1 gene. We observed that the Alu sequence acts as an enhancer element based on reporter gene assays while CRISPR-Cas9 deletions of the Alu sequence in K562 cells resulted in a marked transcriptional upregulation of Linc00441 and a decrease in proliferation. Our results suggest that an intragenic Alu sequence with enhancer activity can act as a transcriptional attenuator of its host lincRNA.
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Affiliation(s)
- Rosario Pérez-Molina
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Erandi Ayala-Ortega
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Georgina Guerrero
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Karin Meier
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Fernando Suaste-Olmos
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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18
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Yang P, Li J, Peng C, Tan Y, Chen R, Peng W, Gu Q, Zhou J, Wang L, Tang J, Feng Y, Sun Y. TCONS_00012883 promotes proliferation and metastasis via DDX3/YY1/MMP1/PI3K-AKT axis in colorectal cancer. Clin Transl Med 2020; 10:e211. [PMID: 33135346 PMCID: PMC7568852 DOI: 10.1002/ctm2.211] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 01/07/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have emerged as key regulators in multiple cancers, including colorectal cancer (CRC). However, the biological functions and molecular mechanisms underlying most lncRNAs in CRC remain largely unknown. Methods A novel lncRNA (TCONS_00012883) was identified using RNA sequencing. The level of TCONS_00012883 expression in CRC was analyzed by qRT‐PCR. The biological functions of TCONS_00012883 in CRC were investigated by a series of in vitro and in vivo experiments: CCK8, colony formation, EdU, flow cytometric assays, transwell assays, and mouse xenograft. The molecular mechanisms of TCONS_00012883 were demonstrated by RNA pulldown, mass spectrometry analysis, RIP, coimmunoprecipitation, RNA sequencing, chromatin immunoprecipitation, and rescue experiments. Results Elevated expression of TCONS_00012883 was confirmed in CRC and positively associated with a poor prognosis. Functionally, gain‐ and loss‐of‐function assays indicated that TCONS_00012883 promoted proliferation and metastasis of CRC cell lines in vitro and in vivo. Mechanistically, RNA pulldown and mass spectrometry analysis showed that DEAD‐box helicase 3 (DDX3) was the protein partner of TCONS_00012883. Furthermore, RNA sequencing assay revealed that matrix metallopeptidase 1 (MMP1) was the downstream of TCONS_00012883. Intriguingly, we found that transcription factor (YY1) could serve as a bridge between TCONS_00012883, DDX3, and MMP1. Conclusions TCONS_00012883 significantly promoted CRC progression via the DDX3/YY1/MMP1 axis, and thus, may act as a major role in diagnosis and therapy of CRC.
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Affiliation(s)
- Peng Yang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jie Li
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chaofan Peng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqian Tan
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ranran Chen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Peng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiou Gu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiahui Zhou
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junwei Tang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifei Feng
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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19
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The roles of long noncoding RNAs in breast cancer metastasis. Cell Death Dis 2020; 11:749. [PMID: 32929060 PMCID: PMC7490374 DOI: 10.1038/s41419-020-02954-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most significant threat to female health. Breast cancer metastasis is the major cause of mortality in breast cancer patients. To fully unravel the molecular mechanisms that underlie the breast cancer cell metastasis is critical for developing strategies to improve survival and prognosis in breast cancer patients. Recent studies have revealed that the long noncoding RNAs (lncRNAs) are involved in breast cancer metastasis through a variety of molecule mechanisms, though the precise functional details of these lncRNAs are yet to be clarified. In the present review, we focus on the functions of lncRNAs in breast cancer invasion and metastasis, with particular emphasis on the functional properties, the regulatory factors, the therapeutic promise, as well as the future challenges in studying these lncRNA.
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20
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LncRNA KCNQ1OT1 regulates the invasion and migration of hepatocellular carcinoma by acting on S1PR1 through miR-149. Cancer Gene Ther 2020; 28:850-863. [PMID: 32753631 DOI: 10.1038/s41417-020-0203-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023]
Abstract
The aim of this study was to investigate the effect of lncRNA KCNQ1OT1 on HCC and to explore the possible underlying mechanisms. The expression levels of KCNQ1OT1, miR-149 and S1PR1 were detected by qRT-PCR assay. A dual luciferase reporter assay was used to detect the interaction between KCNQ1OT1 and miR-149, as well as miR-149 and S1PR1. The interaction between KCNQ1OT1 and miR-149 was further investigated by RNA pull-down assay. Wound healing assays and Transwell assays were carried out to determine cell migration and invasion. A xenograft tumour assay was used to validate the role of KCNQ1OT1 in vivo. KCNQ1OT1 and S1PR1 were significantly increased, but miR-149 was decreased in HCC cells. Luciferase reporter assays and RNA pull-down assays revealed that KCNQ1OT1 directly targeted miR-149. In addition, miR-149 bound to the 3'-UTR of S1PR1. Knockdown of KCNQ1OT1 or overexpression of miR-149 inhibited the invasion and migration of HCC cells. However, suppression of miR-149 could abrogate the effect of KCNQ1OT1 knockdown on the invasion and migration abilities of HCC cells. In vivo assays showed that KCNQ1OT1 knockdown suppressed tumour growth. This work suggests that lncRNA KCNQ1OT1 might act as a potential therapeutic target in HCC.
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21
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Han H, Shao Q, Liu X. LINC00441 promotes cervical cancer progression by modulating miR-450b-5p/RAB10 axis. Cancer Cell Int 2020; 20:368. [PMID: 32774162 PMCID: PMC7409438 DOI: 10.1186/s12935-020-01400-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Background As one of the most common gynaecological malignant tumors, cervical cancer (CC) has become an important public health issue. Emerging evidence has revealed long non-coding RNAs (lncRNAs) are crucial regulators of biological functions in cancers, including CC. And the oncogenic role of LINC00441 has been verified in hepatocellular carcinoma (HCC). But the molecular mechanism and biological functions of LINC00441 in CC remain unknown. Methods qRT-PCR analysis detected the expression of genes in CC tissues or cells. CCK-8, colony formation, flow cytometry, transwell, western blot assays as well as animal studies were conducted to analyze the function of LINC00441 in CC. Luciferase reporter, RIP and RNA pull down assays were applied to verify the binding relations among the indicated genes. Results LINC00441 was upregulated in CC tissues and cells. Further, LINC00441 depletion repressed cell proliferation and motility in vitro as well as tumor growth in vivo. LINC00441 could sponge miR-450b-5p to upregulate RAB10 expression. Finally, miR-450b-5p inhibitor or RAB10 upregulation counteracted LINC00441 knockdown-mediated function on the development of CC. Conclusions LINC00441 drives CC progression by targeting miR-450b-5p/RAB10 axis, which might provide new idea for researching CC-related molecular mechanism.
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Affiliation(s)
- Haiyan Han
- Reproductive Center, Affiliated Hospital of Weifang Medical College, No. 2428 Yuhe Road, Kuiwen District, Weifang, 261031 Shandong China
| | - Qingchun Shao
- Obstetrical Department 1, Affiliated Hospital of Weifang Medical College, No. 2428 Yuhe Road, Kuiwen District, Weifang, 261031 Shandong China
| | - Xuejie Liu
- Reproductive Center, Affiliated Hospital of Weifang Medical College, No. 2428 Yuhe Road, Kuiwen District, Weifang, 261031 Shandong China
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22
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Liu A, Wu Q, Peng D, Ares I, Anadón A, Lopez-Torres B, Martínez-Larrañaga MR, Wang X, Martínez MA. A novel strategy for the diagnosis, prognosis, treatment, and chemoresistance of hepatocellular carcinoma: DNA methylation. Med Res Rev 2020; 40:1973-2018. [PMID: 32525219 DOI: 10.1002/med.21696] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/29/2020] [Accepted: 05/17/2020] [Indexed: 12/11/2022]
Abstract
The cancer mortality rate of hepatocellular carcinoma (HCC) is the second highest in the world and the therapeutic options are limited. The incidence of this deadly cancer is rising at an alarming rate because of the high degree of resistance to chemo- and radiotherapy, lack of proper, and adequate vaccination to hepatitis B, and lack of consciousness and knowledge about the disease itself and the lifestyle of the people. DNA methylation and DNA methylation-induced epigenetic alterations, due to their potential reversibility, open the access to develop novel biomarkers and therapeutics for HCC. The contribution to these epigenetic changes in HCC development still has not been thoroughly summarized. Thus, it is necessary to better understand the new molecular targets of HCC epigenetics in HCC diagnosis, prevention, and treatment. This review elaborates on recent key findings regarding molecular biomarkers for HCC early diagnosis, prognosis, and treatment. Currently emerging epigenetic drugs for the treatment of HCC are summarized. In addition, combining epigenetic drugs with nonepigenetic drugs for HCC treatment is also mentioned. The molecular mechanisms of DNA methylation-mediated HCC resistance are reviewed, providing some insights into the difficulty of treating liver cancer and anticancer drug development.
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Affiliation(s)
- Aimei Liu
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China
| | - Qinghua Wu
- College of Life Science, Yangtze University, Jingzhou, China.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China
| | - Irma Ares
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Arturo Anadón
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Bernardo Lopez-Torres
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - María-Rosa Martínez-Larrañaga
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University (HZAU), Wuhan, China.,Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - María-Aránzazu Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Research Institute Hospital 12 de Octubre (i+12), Universidad Complutense de Madrid (UCM), Madrid, Spain
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23
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Abstract
Hepatocellular carcinoma (HCC) is the most frequent subtype of primary liver cancer and one of the leading causes of cancer-related death worldwide. However, the molecular mechanisms underlying HCC pathogenesis have not been fully understood. Emerging evidences have recently suggested the crucial role of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of HCC. Various HCC-related lncRNAs have been shown to possess aberrant expression and participate in cancerous phenotypes (e.g. persistent proliferation, evading apoptosis, accelerated vessel formation and gain of invasive capability) through their binding with DNA, RNA or proteins, or encoding small peptides. Thus, a deeper understanding of lncRNA dysregulation would provide new insights into HCC pathogenesis and novel tools for the early diagnosis and treatment of HCC. In this review, we summarize the dysregulation of lncRNAs expression in HCC and their tumor suppressive or oncogenic roles during HCC tumorigenesis. Moreover, we discuss the diagnostic and therapeutic potentials of lncRNAs in HCC.
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24
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Huang Y, Guo Q, Ding XP, Wang X. Mechanism of long noncoding RNAs as transcriptional regulators in cancer. RNA Biol 2020; 17:1680-1692. [PMID: 31888402 DOI: 10.1080/15476286.2019.1710405] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of gene expression, often interpreted by gene transcription as an endpoint response, is tightly associated with human cancer. Long noncoding RNAs (lncRNAs), derived from the noncoding elements in the genome and appeared no less than 200nt in length, have emerged as a novel class of pivotal regulatory component. Recently, great attention has been paid to the cancer-related lncRNAs and growing evidence have shown that lncRNAs act as key transcriptional regulators in cancer cells through diverse mechanisms. Here, we focus on the nucleus-expressed lncRNAs and summarize their molecular mechanisms in transcriptional control during tumorigenesis and cancer metastasis. Six major mechanisms will be discussed in this review: association with transcriptional factor, modulating DNA methylation or histone modification enzyme, influencing on chromatin remodelling complex, facilitating chromosomal looping, interaction with RNA polymerase and direct association with promoter.
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Affiliation(s)
- Yan Huang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, China
| | - Qi Guo
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, China
| | - Xi-Ping Ding
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, China
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25
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Zhang J, Sui S, Wu H, Zhang J, Zhang X, Xu S, Pang D. The transcriptional landscape of lncRNAs reveals the oncogenic function of LINC00511 in ER-negative breast cancer. Cell Death Dis 2019; 10:599. [PMID: 31395854 PMCID: PMC6687715 DOI: 10.1038/s41419-019-1835-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Advances in the molecular characteristics of cancers have facilitated the classification system from morphology to molecular characteristic-based subtypes. Cancer profiling has expanded in its focus from protein-coding genes to noncoding RNAs, with advances in the depth and quality of transcriptome sequencing. Here, we examined the profiles of long noncoding RNAs (lncRNAs) according to breast cancer subtype categories in The Cancer Genome Atlas (TCGA) database to identify a cohort of breast cancer- and oestrogen receptor (ER)-negative-associated lncRNAs. According to the prioritization of variation in ER-negative-associated lncRNAs, we identified and investigated the role of LINC00511 in breast cancer. We determined that high LINC00511 expression was an unfavourable prognostic factor for patients with breast cancer. Furthermore, LINC00511 promoted tumour growth by accelerating the G1/S transition and inhibiting apoptosis. At the transcriptional level, ER deficiency directly affected the expression of LINC00511 activated by transcription factor AP-2 (TFAP-2) in breast cancer cells. Moreover, mechanistic investigations demonstrated that ER-negative-associated LINC00511 interacted with enhancer of zeste homologue 2 (EZH2, the catalytic subunit of polycomb repressive complex 2, PRC2) and recruited PRC2 to mediate histone methylation, contributing to the repression of CDKN1B in the nucleus. This process resulted in altered ER-negative breast cancer cell biology. By highlighting the oncogenic function of LINC00511, we revealed the role of lncRNAs in regulating the network of cell cycle control in ER-negative breast cancer and suggested the exploitation of LINC00511 as an anticancer therapy in the future.
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Affiliation(s)
- Jian Zhang
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China
| | - Shiyao Sui
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China
| | - Hao Wu
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China
| | - Jinfeng Zhang
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China
| | - Xingda Zhang
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China
| | - Shouping Xu
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China.
| | - Da Pang
- Department of breast surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, 150081, Harbin, China. .,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, 150086, Harbin, China.
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26
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Epigenetic regulation of histone H3 in the process of hepatocellular tumorigenesis. Biosci Rep 2019; 39:BSR20191815. [PMID: 31320544 PMCID: PMC6680372 DOI: 10.1042/bsr20191815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022] Open
Abstract
Better understanding of epigenetic regulation of hepatocellular carcinoma (HCC) will help us to cure this most common malignant liver cancer worldwide. The underlying mechanisms of HCC tumorigenesis are genomic aberrations regulated by genetic and epigenetic modifications. Histone H3 lysine modifications regulate histone structure and modulate transcriptional factor binding with target gene promoters. Targetting genes include VASH2, fatty acids synthase, RIZ1, FBP1, MPP1/3, YAP, which affect tumorigenesis, metabolisms, angiogenesis, and metastasis. Signal pathway studies demonstrate that the HGF-MET-MLL axis, phosphatase and tensin homolog (PTEN)-PI3K-Akt axis; WNT-β-catenin signal pathway is involved in histone H3 modification. A variety of factors such as virus infection, reactive oxygen species, food-borne toxins, irradiation, or non-coding RNA cause hepatocellular DNA damage or modification. Dysfunctional DNA repair mechanisms, including those at the epigenetic level are also major causes of HCC tumorigenesis. The development of therapies based on epigenetic regulatory mechanisms has great potential to advance the care of HCC patients in the future.
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27
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Wang Y, Liu J, Yang J, Yu X, Chen Z, Chen Y, Kuang M, Zhu Y, Zhuang S. Lnc-UCID Promotes G1/S Transition and Hepatoma Growth by Preventing DHX9-Mediated CDK6 Down-regulation. Hepatology 2019; 70:259-275. [PMID: 30865310 PMCID: PMC6618099 DOI: 10.1002/hep.30613] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/10/2019] [Indexed: 12/22/2022]
Abstract
Although thousands of long noncoding RNAs (lncRNAs) have been annotated, only a limited number of them have been functionally characterized. Here, we identified an oncogenic lncRNA, named lnc-UCID (lncRNA up-regulating CDK6 by interacting with DHX9). Lnc-UCID was up-regulated in hepatocellular carcinoma (HCC), and a higher lnc-UCID level was correlated with shorter recurrence-free survival of HCC patients. Both gain-of-function and loss-of function studies revealed that lnc-UCID enhanced cyclin-dependent kinase 6 (CDK6) expression and thereby promoted G1/S transition and cell proliferation. Studies from mouse xenograft models revealed that tumors derived from lnc-UCID-silenced HCC cells had a much smaller size than those from control cells, and intratumoral injection of lnc-UCID small interfering RNA suppressed xenograft growth. Mechanistically, the 850-1030-nt domain of lnc-UCID interacted physically with DEAH (Asp-Glu-Ala-His) box helicase 9 (DHX9), an RNA helicase. On the other hand, DHX9 post-transcriptionally suppressed CDK6 expression by binding to the 3'-untranslated region (3'UTR) of CDK6 mRNA. Further investigation disclosed that lnc-UCID enhanced CDK6 expression by competitively binding to DHX9 and sequestering DHX9 from CDK6-3'UTR. In an attempt to explore the mechanisms responsible for lnc-UCID up-regulation in HCC, we found that the lnc-UCID gene was frequently amplified in HCC. Furthermore, miR-148a, whose down-regulation was associated with an increase of lnc-UCID in HCC, could bind lnc-UCID and inhibit its expression. Conclusion: Up-regulation of lnc-UCID, which may result from amplification of its gene locus and down-regulation of miR-148a, can promote HCC growth by preventing the interaction of DHX9 with CDK6 and subsequently enhancing CDK6 expression. These findings provide insights into the biological functions of lncRNAs, the regulatory network of cell cycle control, and the mechanisms of HCC development, which may be exploited for anticancer therapy.
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Affiliation(s)
- Yun‐Long Wang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jin‐Yu Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jin‐E Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina,Key Laboratory of Liver Disease of Guangdong ProvinceThe Third Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Xiao‐Man Yu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Zhan‐Li Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ya‐Jing Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ming Kuang
- Department of Liver SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Shi‐Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina,Key Laboratory of Liver Disease of Guangdong ProvinceThe Third Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
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28
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Mai H, Zhou B, Liu L, Yang F, Conran C, Ji Y, Hou J, Jiang D. Molecular pattern of lncRNAs in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:198. [PMID: 31097003 PMCID: PMC6524221 DOI: 10.1186/s13046-019-1213-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most notable lethal malignancies worldwide. However, the molecular mechanisms involved in the initiation and progression of this disease remain poorly understood. Over the past decade, many studies have demonstrated the important regulatory roles of long non-coding RNAs (lncRNAs) in HCC. Here, we comprehensively review recent discoveries regarding HCC-associated lncRNA functions, which we have classified and described according to their mechanism models.
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Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Li Liu
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China
| | - Carly Conran
- University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China. .,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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29
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Peng L, Yuan XQ, Zhang CY, Peng JY, Zhang YQ, Pan X, Li GC. The emergence of long non-coding RNAs in hepatocellular carcinoma: an update. J Cancer 2018; 9:2549-2558. [PMID: 30026854 PMCID: PMC6036883 DOI: 10.7150/jca.24560] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounting for roughly 90% of all primary liver neoplasms is the sixth most frequent neoplasm and the second prominent reason of tumor fatality worldwide. As regulators of diverse biological processes, long non-coding RNAs (lncRNAs) are involved in onset and development of neoplasms. With the continuous booming of well-featured lncRNAs in HCC from 2016 to now, we reviewed the newly-presented comprehension about the relationship between lncRNAs and HCC in this study. To be specific, we summarized the overview function and study tools of lncRNAs, elaborated the roles of lncRNAs in HCC, and sketched the molecule mechanisms of lncRNAs in HCC. In addition, the application of lncRNAs serving as biomarkers in early diagnosis and outcome prediction of HCC patients was highlighted.
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Affiliation(s)
- Li Peng
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Chao-Yang Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Jiang-Yun Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Ya-Qin Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Xi Pan
- Department of Oncology, the third Xiangya Hospital, Central South University, Changsha 410013, P.R. China
| | - Guan-Cheng Li
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
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30
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The Role of Long Non-Coding RNAs in Hepatocarcinogenesis. Int J Mol Sci 2018; 19:ijms19030682. [PMID: 29495592 PMCID: PMC5877543 DOI: 10.3390/ijms19030682] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 02/07/2023] Open
Abstract
Whole-transcriptome analyses have revealed that a large proportion of the human genome is transcribed in non-protein-coding transcripts, designated as long non-coding RNAs (lncRNAs). Rather than being “transcriptional noise”, increasing evidence indicates that lncRNAs are key players in the regulation of many biological processes, including transcription, post-translational modification and inhibition and chromatin remodeling. Indeed, lncRNAs are widely dysregulated in human cancers, including hepatocellular carcinoma (HCC). Functional studies are beginning to provide insights into the role of oncogenic and tumor suppressive lncRNAs in the regulation of cell proliferation and motility, as well as oncogenic and metastatic potential in HCC. A better understanding of the molecular mechanisms and the complex network of interactions in which lncRNAs are involved could reveal novel diagnostic and prognostic biomarkers. Crucially, it may provide novel therapeutic opportunities to add to the currently limited number of therapeutic options for HCC patients. In this review, we summarize the current status of the field, with a focus on the best characterized dysregulated lncRNAs in HCC.
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31
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Wu X, Zheng Y, Han B, Dong X. Long noncoding RNA BLACAT1 modulates ABCB1 to promote oxaliplatin resistance of gastric cancer via sponging miR-361. Biomed Pharmacother 2018; 99:832-838. [PMID: 29710482 DOI: 10.1016/j.biopha.2018.01.130] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/17/2018] [Accepted: 01/28/2018] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as novel gene regulators in multiple tumorigenesis and chemoresistance. However, their potential roles and molecular mechanisms in gastric cancer chemoresistance remain unclear. In present study, our team investigated the role and potential regulatory mechanism of lncRNA s bladder cancer associated transcript-1 (BLACAT1) in the gastric cancer chemoresistance. Results showed that BLACAT1 expression was up-regulated in the oxaliplatin (OXA) resistant gastric cancer tissue and cells compared with OXA-sensitive tissue and parental cell lines. In vitro, BLACAT1 knockdown decreased the expression levels of drug resistance related genes and ABCB1 protein. Besides, BLACAT1 knockdown significantly promoted apoptosis and down-regulated the invasion and the IC50 value of oxaliplatin. In vivo, BLACAT1 knockdown suppressed the tumor growth of gastric cancer cells. Bioinformatics tools and luciferase assay indicated that miR-361 both targeted 3?-UTR of BLACAT1 and ABCB1mRNA, suggesting the BLACAT1/miR-361/ABCB1 regulatory pathway. In summary, our results conclude that BLACAT1 accelerates the oxaliplatin-resistance of gastric cancer via promoting ABCB1 protein expression by targeting miR-361, providing a novel insight for the chemoresistance of gastric cancer.
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Affiliation(s)
- Xiao Wu
- Department of Gastrointestinal Surgery, People's Hospital of Yueqing, Wenzhou, Zhejiang, 325000, China
| | - Yuanzheng Zheng
- Department of Gastrointestinal Surgery, People's Hospital of Yueqing, Wenzhou, Zhejiang, 325000, China
| | - Bin Han
- Department of Nephrology, First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Xuefan Dong
- Department of Gastrointestinal Surgery, People's Hospital of Yueqing, Wenzhou, Zhejiang, 325000, China.
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32
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El Khodiry A, Afify M, El Tayebi HM. Behind the curtain of non-coding RNAs; long non-coding RNAs regulating hepatocarcinogenesis. World J Gastroenterol 2018; 24:549-572. [PMID: 29434445 PMCID: PMC5799857 DOI: 10.3748/wjg.v24.i5.549] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/17/2018] [Accepted: 01/23/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers worldwide. HCC is the fifth common malignancy in the world and the second leading cause of cancer death in Asia. Long non-coding RNAs (lncRNAs) are RNAs with a length greater than 200 nucleotides that do not encode proteins. lncRNAs can regulate gene expression and protein synthesis in several ways by interacting with DNA, RNA and proteins in a sequence specific manner. They could regulate cellular and developmental processes through either gene inhibition or gene activation. Many studies have shown that dysregulation of lncRNAs is related to many human diseases such as cardiovascular diseases, genetic disorders, neurological diseases, immune mediated disorders and cancers. However, the study of lncRNAs is challenging as they are poorly conserved between species, their expression levels aren’t as high as that of mRNAs and have great interpatient variations. The study of lncRNAs expression in cancers have been a breakthrough as it unveils potential biomarkers and drug targets for cancer therapy and helps understand the mechanism of pathogenesis. This review discusses many long non-coding RNAs and their contribution in HCC, their role in development, metastasis, and prognosis of HCC and how to regulate and target these lncRNAs as a therapeutic tool in HCC treatment in the future.
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Affiliation(s)
- Aya El Khodiry
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Menna Afify
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Hend M El Tayebi
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
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33
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LincRNa-p21: function and mechanism in cancer. Med Oncol 2017; 34:98. [PMID: 28425074 DOI: 10.1007/s12032-017-0959-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/12/2017] [Indexed: 12/29/2022]
Abstract
In view of the rapid development of gene chips and high-throughput sequencing technology, noncoding RNAs (ncRNas) form a high percentage of the mammalian genome. Two major subgroups of ncRNAs that have been identified are the long ncRNAs (lncRNas) and the microRNAs. A number of studies in the past few years have showed crucial functions for lncRNas in cancer. LincRNa-p21 as a p53-dependent transcriptional target gene and a potential diagnostic marker is involved in proliferation, cell cycle, metabolism and reprogramming. In addition, more researches revealed that lincRNa-p21 is associated with cancer progression and contributed to the treatment and prognosis of cancer. In this review, we briefly summarize the function and molecular mechanisms of lincRNa-p21 in cancer and its regulation for the genes expression .
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