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Liao W, Du J, Wang Z, Feng Q, Liao M, Liu H, Yuan K, Zeng Y. The role and mechanism of noncoding RNAs in regulation of metabolic reprogramming in hepatocellular carcinoma. Int J Cancer 2022; 151:337-347. [PMID: 35460073 PMCID: PMC9325518 DOI: 10.1002/ijc.34040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Metabolic reprogramming is considered to be an important hallmark of cancer. Emerging studies have demonstrated that noncoding RNAs (ncRNAs) are closely associated with metabolic reprogramming of HCC. NcRNAs can directly regulate the expressions or functions of metabolic enzymes or indirectly regulate the metabolism of HCC cells through some vital signaling pathways. Until now, the mechanisms of HCC development and progression remain largely unclear, and understanding the regulatory mechanism of ncRNAs on metabolic reprogramming of HCC may provide an important basis for breakthrough progress in the treatment of HCC. In this review, we summarize the ncRNAs involved in regulating metabolic reprogramming of HCC. Specifically, the regulatory roles of ncRNAs in glucose, lipid and amino acid metabolism are elaborated. In addition, we discuss the molecular mechanism of ncRNAs in regulation of metabolic reprogramming and possible therapeutic strategies that target the metabolism of cancer cells by modulating the expressions of specific ncRNAs.
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Affiliation(s)
- Wenwei Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jinpeng Du
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zhen Wang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qingbo Feng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Mingheng Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Huixian Liu
- Department of Postanesthesia Care Unit & Surgical Anesthesia Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
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Miao Q, Ni B, Tang J. Coding potential of circRNAs: new discoveries and challenges. PeerJ 2021; 9:e10718. [PMID: 33552732 PMCID: PMC7819118 DOI: 10.7717/peerj.10718] [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: 07/10/2019] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
The circular (circ)RNAs are a newly recognized group of noncoding (nc)RNAs. Research to characterize the functional features of circRNAs has uncovered distinctive profiles of conservation, stability, specificity and complexity. However, a new line of evidence has indicated that although circRNAs can function as ncRNAs, such as in the role of miRNA sponges, they are also capable of coding proteins. This discovery is no accident. In the last century, scientist detected the ability of translate in some virus and artificial circRNAs. Artificial circRNA translation products are usually nonfunctional, whereas natural circRNA translation products are completely different. Those new proteins have various functions, which greatly broadens the new ideas and research direction for our research. These series findings also raise questions about whether circRNA is still classified as non-coding RNA. Here, we summarize the evidence concerning translation potential of circRNAs, including synthetic and endogenous circRNA translation ability, and discuss the mechanisms of circRNA translation.
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Affiliation(s)
- Qingqing Miao
- Dermatology Department of The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.,Department of Dermatology, the 901th Hospital of the Joint Logistics Support Force of PLA Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Bing Ni
- Department of Pathophysiology, Third Military Medical University, Chongqing, China
| | - Jun Tang
- Dermatology Department of The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.,Department of Dermatology, the 901th Hospital of the Joint Logistics Support Force of PLA Affiliated to Anhui Medical University, Hefei, Anhui, China
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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Noncoding RNAs in Regulation of Cancer Metabolic Reprogramming. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:191-215. [PMID: 27376736 DOI: 10.1007/978-981-10-1498-7_7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the description of the Warburg effect 90 years ago, metabolic reprogramming has been gradually recognized as a major hallmark of cancer cells. Mounting evidence now indicates that cancer is a kind of metabolic disease, quite distinct from conventional perception. While metabolic alterations in cancer cells have been extensively observed in glucose, lipid, and amino acid metabolisms, its underlying regulatory mechanisms are still poorly understood. Noncoding RNA, also known as the "dark matter in life," functions through various mechanisms at RNA level regulating different biological pathways. The last two decades have witnessed the booming of noncoding RNA study on microRNA (miRNA), long noncoding RNA (lncRNA), circular RNA (circRNA), PIWI-interacting RNA (piRNA), etc. In this chapter, we will discuss the regulatory roles of noncoding RNAs on cancer metabolism.
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Geisler SJ, Paro R. Trithorax and Polycomb group-dependent regulation: a tale of opposing activities. Development 2015; 142:2876-2887. [DOI: 10.1242/dev.120030] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Intricate layers of regulation determine the unique gene expression profiles of a given cell and, therefore, underlie the immense phenotypic diversity observed among cell types. Understanding the mechanisms that govern which genes are expressed and which genes are silenced is a fundamental focus in biology. The Polycomb and Trithorax group chromatin proteins play important roles promoting the stable and heritable repression and activation of gene expression, respectively. These proteins, which are conserved across metazoans, modulate post-translational modifications on histone tails and regulate nucleosomal structures. Here, we review recent advances that have shed light on the mechanisms by which these two classes of proteins act to maintain epigenetic memory and allow dynamic switches in gene expression during development.
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Affiliation(s)
- Sarah J. Geisler
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
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MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun 2015. [PMID: 26205790 PMCID: PMC4525211 DOI: 10.1038/ncomms8743] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin,
but how they target chromatin remains poorly understood. We have used chromatin RNA
immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs
enriched in repressive chromatin from breast cancer cells. Using one of the
chromatin-interacting lncRNAs, MEG3, we explore the mechanisms by which
lncRNAs target chromatin. Here we show that MEG3 and EZH2 share common
target genes, including the TGF-β pathway genes. Genome-wide mapping of
MEG3 binding sites reveals that MEG3 modulates the activity of
TGF-β genes by binding to distal regulatory elements. MEG3 binding
sites have GA-rich sequences, which guide MEG3 to the chromatin through
RNA–DNA triplex formation. We have found that RNA–DNA triplex
structures are widespread and are present over the MEG3 binding sites
associated with the TGF-β pathway genes. Our findings suggest that
RNA–DNA triplex formation could be a general characteristic of target gene
recognition by the chromatin-interacting lncRNAs. Long noncoding RNAs (lncRNAs) regulate gene expression by association
with chromatin. Here, the authors show that lncRNA MEG3 regulates the
TGF-β pathway by bridging the interactions between polycomb repressive complex
2 and the distal regulatory elements of the TGF-β pathway genes via formation
of RNA–DNA triplexes.
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Havill JT, Bhatiya C, Johnson SM, Sheets JD, Thompson JS. A new approach for detecting riboswitches in DNA sequences. ACTA ACUST UNITED AC 2014; 30:3012-9. [PMID: 25015992 DOI: 10.1093/bioinformatics/btu479] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MOTIVATION Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression. RESULTS The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a 'heaviest path' problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼ 88-99% sensitivity and >99.99% specificity on 13 riboswitch families. AVAILABILITY AND IMPLEMENTATION DRD is available at http://drd.denison.edu.
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Affiliation(s)
- Jessen T Havill
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Chinmoy Bhatiya
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Steven M Johnson
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joseph D Sheets
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeffrey S Thompson
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
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Abstract
The study of long noncoding RNAs (lncRNAs) is still in its infancy with more putative RNAs identified than those with ascribed functions. Defined as transcripts that are longer than 200 nucleotides without a coding sequence, their numbers are on the rise and may well challenge protein coding transcripts in number and diversity. lncRNAs are often expressed at low levels and their sequences are frequently poorly conserved, making it unclear if they are transcriptional noise or bonafide effectors. Despite these limitations, inroads into their functions are being made and it is clear they make a contribution in regulating all aspects of biology. The early verdict on their activity, however, suggests the majority function as chromatin modifiers. A good proportion show a connection to disease highlighting their importance and the need to determine their function. The focus of this review is on lncRNAs which influence developmental processes which in itself covers a large range of known activities.
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Affiliation(s)
- Jamila I Horabin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W. Call St., Tallahassee, FL, 32306-4300, USA,
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