151
|
The functions and potential roles of extracellular vesicle noncoding RNAs in gynecological malignancies. Cell Death Dis 2021; 7:258. [PMID: 34552067 PMCID: PMC8458395 DOI: 10.1038/s41420-021-00645-3] [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: 05/08/2021] [Revised: 08/18/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Abstract
Extracellular vesicles (EVs) are small membranous vesicles secreted by multiple kinds of cells and are widely present in human body fluids. EVs containing various constituents can transfer functional molecules from donor cells to recipient cells, thereby mediating intercellular communication. Noncoding RNAs (ncRNAs) are a type of RNA transcript with limited protein-coding capacity, that have been confirmed to be enriched in EVs in recent years. EV ncRNAs have become a hot topic because of their crucial regulating effect in disease progression, especially in cancer development. In this review, we summarized the biological functions of EV ncRNAs in the occurrence and progression of gynecological malignancies. In addition, we reviewed their potential applications in the diagnosis and treatment of gynecological malignancies.
Collapse
|
152
|
Scull KE, Pandey K, Ramarathinam SH, Purcell AW. Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome. Mol Cell Proteomics 2021; 20:100143. [PMID: 34509645 PMCID: PMC8724885 DOI: 10.1016/j.mcpro.2021.100143] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 01/08/2023] Open
Abstract
Human leukocyte antigen (HLA) molecules are cell-surface glycoproteins that present peptide antigens on the cell surface for surveillance by T lymphocytes, which contemporaneously seek signs of disease. Mass spectrometric analysis allows us to identify large numbers of these peptides (the immunopeptidome) following affinity purification of solubilized HLA-peptide complexes. However, in recent years, there has been a growing awareness of the "dark side" of the immunopeptidome: unconventional peptide epitopes, including neoepitopes, which elude detection by conventional search methods because their sequences are not present in reference protein databases (DBs). Here, we establish a bioinformatics workflow to aid identification of peptides generated by noncanonical translation of mRNA or by genome variants. The workflow incorporates both standard transcriptomics software and novel computer programs to produce cell line-specific protein DBs based on three-frame translation of the transcriptome. The final protein DB also includes sequences resulting from variants determined by variant calling on the same RNA-Seq data. We then searched our experimental data against both transcriptome-based and standard DBs using PEAKS Studio (Bioinformatics Solutions, Inc). Finally, further novel software helps to compare the various result sets arising for each sample, pinpoint putative genomic origins for unconventional sequences, and highlight potential neoepitopes. We applied the workflow to study the immunopeptidome of the acute myeloid leukemia cell line THP-1, using RNA-Seq and immunopeptidome data. We confidently identified over 14,000 peptides from three replicates of purified HLA peptides derived from THP-1 cells using the conventional UniProt human proteome. Using the transcriptome-based DB generated using our workflow, we recapitulated >85% of these and also identified 1029 unconventional peptides not explained by UniProt, including 16 sequences caused by nonsynonymous variants. Our workflow, which we term "immunopeptidogenomics," can provide DBs, which include pertinent unconventional sequences and allow neoepitope discovery, without becoming too large to search. Immunopeptidogenomics is a step toward unbiased search approaches that are needed to illuminate the dark side of the immunopeptidome.
Collapse
Affiliation(s)
- Katherine E Scull
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
153
|
Ranjan S, Jain S, Bhargava A, Shandilya R, Srivastava RK, Mishra PK. Lateral flow assay-based detection of long non-coding RNAs: A point-of-care platform for cancer diagnosis. J Pharm Biomed Anal 2021; 204:114285. [PMID: 34333453 DOI: 10.1016/j.jpba.2021.114285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Lateral flow assay (LFA) is a flexible, simple, low-costpoint-of-care platform for rapid detection of disease-specific biomarkers. Importantly, the ability of the assay to capture the circulating bio-molecules has gained significant attention, as it offers a potential minimal invasive system for early disease diagnosis and prognosis. In the present article, we review an innovative concept of LFA-based detection of circulating long non-coding RNAs (lncRNAs), one of the key regulators of fundamental biological processes. In addition, their disease-specific expression pattern and presence in biological fluids at differential levels make them excellent biomarker candidates for cancer detection. Our article also provides an update on the requirements for developing and improving such systems and discusses the key aspects of material selection, operational concepts, principles and conceptual design. We assume that the reviewed points will be helpful to improve the diagnostic applicability of LFA based lncRNA detection in cancer diagnosis.
Collapse
Affiliation(s)
- Shashi Ranjan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Surbhi Jain
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| |
Collapse
|
154
|
He Y, Xu Y, Yu X, Sun Z, Guo W. The Vital Roles of LINC00662 in Human Cancers. Front Cell Dev Biol 2021; 9:711352. [PMID: 34354995 PMCID: PMC8329443 DOI: 10.3389/fcell.2021.711352] [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: 05/18/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in many human diseases, particularly in tumorigenicity and progression. Although lncRNA research studies are increasing rapidly, our understanding of lncRNA mechanisms is still incomplete. The long intergenic non-protein coding RNA 662 (LINC00662) is a novel lncRNA, and accumulating evidence suggests that it is related to a variety of tumors in multiple systems, including the respiratory, reproductive, nervous, and digestive systems. LINC00662 has been shown to be upregulated in malignant tumors and has been confirmed to promote the development of malignant tumors. LINC00662 has also been reported to facilitate a variety of cellular events, such as tumor-cell proliferation, invasion, and migration, and its expression has been correlated to clinicopathological characteristics in patients with tumors. In terms of mechanisms, LINC00662 regulates gene expression by interacting with both proteins and with RNAs, so it may be a potential biomarker for cancer diagnosis, prognosis, and treatment. This article reviews the expression patterns, biological functions, and underlying molecular mechanisms of LINC00662 in tumors.
Collapse
Affiliation(s)
- Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Yating Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Zongzong Sun
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| |
Collapse
|
155
|
Dai H, Hu F, Yang X, Hu P, Chu Y, Bu S. Hsa_circ_0054633 association of C peptide is related to IL-17 and TNF-α in patients with diabetes mellitus receiving insulin treatment. J Clin Lab Anal 2021; 35:e23856. [PMID: 34272768 PMCID: PMC8373319 DOI: 10.1002/jcla.23856] [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: 03/10/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/29/2022] Open
Abstract
Background Chronic inflammation damaged the islet and resulted in dysfunction of T2D. Circular RNA is stable and better for biomarker in many diseases. Here, we aimed to identify potential circular RNA hsa_circ_0054633 that can be a biomarkers for the effects of insulin therapy in T2D. Methods In this retrospective case‐control study, patients were from Li Huili Hospital, Ningbo, China, from February 10, 2019, to August 15, 2019. We included 47 healthy adults, 46 new‐onset T2D with insulin resistance, and 51 patients with insulin therapy. Serum inflammation factors were tested by ELISA assays. We selected hsa_circ_0054633 as a candidate biomarker and measured its concentration in serum by qRT‐PCR. The Pearson correlation test was used to evaluate the correlation between this circRNA and clinical variables. Results Clinical data indicated that serum C peptide was increased in T2D treatment with insulin. Serum hsa_circ_0054633 was decreased in insulin treatment group. Hsa_circ_0054633 was negative correlated with C peptide (r = −0.2841, p = 0.0433,). IL‐1 and IL‐6, IL‐17, and TNF‐α were higher in T2D patients and decreased after insulin treatment, only IL‐17 and TNF‐α showed a positive correlation to hsa_circ_0054633 (r = 0.4825, p < 0.0001, and r = 0.6190, p < 0.0001). The area under ROC curve was 0.7432, 0.5839, and 0.7573 for Hsa_circ_0054633, C peptide, and their combination. Conclusion Hsa_circ_0054633 level was lower in T2D with insulin treatment than untreated and was a negative correlation with C peptide, and positively correlated with IL‐17 and TNF‐α, suggesting that hsa_circ_0054633 may be a potential early indicator of insulin treatment effect to improve inflammation condition.
Collapse
Affiliation(s)
- Huixue Dai
- Department of endocrinology, Ninghai Chengguan Hospital, Ningbo, China
| | - Fei Hu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, China.,Cixi Biomedical Research Institute, Wenzhou Medical University, Cixi, China
| | - Xiangwei Yang
- Department of endocrinology, Ninghai Chengguan Hospital, Ningbo, China
| | - Peng Hu
- Department of endocrinology, Ninghai Chengguan Hospital, Ningbo, China
| | - Yudong Chu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China.,Department of Nephrology, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Shizhong Bu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| |
Collapse
|
156
|
Gong L, Zhou X, Sun J. Circular RNAs Interaction with MiRNAs: Emerging Roles in Breast Cancer. Int J Med Sci 2021; 18:3182-3196. [PMID: 34400888 PMCID: PMC8364445 DOI: 10.7150/ijms.62219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 12/24/2022] Open
Abstract
Despite significant advances in cancer therapy strategies, breast cancer is one of the most common and lethal malignancies worldwide. Characterization of a new class of RNAs using next-generation sequencing opened new doors toward uncovering etiopathogenesis mechanisms of breast cancer as well as prognostic and diagnostic biomarkers. Circular RNAs (circRNAs) are a novel class of RNA with covalently closed and highly stable structures generated primarily from the back-splicing of precursor mRNAs. Although circRNAs exert their function through various mechanisms, acting as a sponge for miRNAs is their primary mechanism of function. Furthermore, growing evidence has shown that aberrant expression of circRNAs is involved in the various hallmarks of cancers. This paper reviews the biogenesis, characteristics, and mechanism of functions of circRNAs and their deregulation in various cancers. Finally, we focused on the circRNAs roles as a sponge for miRNAs in the development, metastasis, angiogenesis, drug resistance, apoptosis, and immune responses of breast cancer.
Collapse
Affiliation(s)
- Liu Gong
- Department of Medical Oncology, Hangzhou Xiasha Hospital, Hangzhou, Zhejiang Province, China
| | | | | |
Collapse
|
157
|
Zeng L, Liu YM, Yang N, Zhang T, Xie H. Hsa_circRNA_100146 Promotes Prostate Cancer Progression by Upregulating TRIP13 via Sponging miR-615-5p. Front Mol Biosci 2021; 8:693477. [PMID: 34307457 PMCID: PMC8292639 DOI: 10.3389/fmolb.2021.693477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 01/13/2023] Open
Abstract
Objective: This study was conducted for investigating the functions of circular RNA circRNA_100146 (circRNA_100146) in the development of prostate cancer (PCa) and identifying the underlying mechanisms of the circRNA_100146/miR-615-5p/TRIP13 axis. Materials and Methods: Under the support of RT-PCR, the expression of circRNA_100146 in PCa cells was examined. Cell Counting Kit-8 (CCK-8) assays and clone formation assays were applied to the assessment of cell proliferation. We then determined cell invasion and migration through transwell assays and wound healing assays. RNA pull-down assays and luciferase reporter assays were performed for the exploration of the regulatory effects of potential molecules on the expressions of the targeting genes. In addition, a nude mouse xenograft model was applied to demonstrate the oncogenic roles of circRNA_100146 in PCa. Results: CircRNA_100146 expression was distinctly upregulated in PCa cells. Silencing of circRNA_100146 suppressed PCa cells' invasion, migration, and proliferation. CircRNA_100146 sponged miR-615-5p to suppress its expressions, while miR-615-5p targeted the 3'-UTR of TRIP13 to repress the expression of TRIP13. In addition, we observed that knockdown of miR-615-5p reversed the suppression of circRNA_100146 silence on the proliferation and invasion of PCa cells. In addition, the tumor growth was also suppressed by silencing circRNA_100146 in vivo. Conclusion: CircRNA_100146 is a tumor promoter in PCa, which promoted progression by mediating the miR-615-5p/TRIP13. CircRNA_100146 can be a potential candidate for targeted therapy of PCa.
Collapse
Affiliation(s)
- Liang Zeng
- Emergency Department, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Yi-Min Liu
- Department of Anesthesiology, The Affiliated Nanhua Hospital, University of South China, Engyang, China
| | - Ning Yang
- Department of Urology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Tao Zhang
- Department of Urology, The Second Affiliated Hospital of University of South China, Hengyang, China
| | - Huang Xie
- Department of Urology, The Second Affiliated Hospital of University of South China, Hengyang, China
| |
Collapse
|
158
|
Subcellular Localization of miRNAs and Implications in Cellular Homeostasis. Genes (Basel) 2021; 12:genes12060856. [PMID: 34199614 PMCID: PMC8226975 DOI: 10.3390/genes12060856] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are thought to act as post-transcriptional regulators in the cytoplasm by either dampening translation or stimulating degradation of target mRNAs. With the increasing resolution and scope of RNA mapping, recent studies have revealed novel insights into the subcellular localization of miRNAs. Based on miRNA subcellular localization, unconventional functions and mechanisms at the transcriptional and post-transcriptional levels have been identified. This minireview provides an overview of the subcellular localization of miRNAs and the mechanisms by which they regulate transcription and cellular homeostasis in mammals, with a particular focus on the roles of phase-separated biomolecular condensates.
Collapse
|
159
|
Jonaitis P, Kupcinskas L, Kupcinskas J. Molecular Alterations in Gastric Intestinal Metaplasia. Int J Mol Sci 2021; 22:ijms22115758. [PMID: 34071181 PMCID: PMC8199079 DOI: 10.3390/ijms22115758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) remains one of the most common causes of mortality worldwide. Intestinal metaplasia (IM) is one of the preneoplastic gastric lesions and is considered an essential predisposing factor in GC development. Here we present a review of recent most relevant papers to summarize major findings on the molecular alterations in gastric IM. The latest progress in novel diagnostic methods allows scientists to identify various types of molecular alterations in IM, such as polymorphisms in various genes, changes in the expression of micro-RNAs and long noncoding RNAs, and altered microbiome profiles. The results have shown that some of these alterations have strong associations with IM and a potential to be used for screening, treatment, and prognostic purposes; however, one of the most important limiting factors is the inhomogeneity of the studies. Therefore, further large-scale studies and clinical trials with standardized methods designed by multicenter consortiums are needed. As of today, various molecular alterations in IM could become a part of personalized medicine in the near future, which would help us deliver a personalized approach for each patient and identify those at risk of progression to GC.
Collapse
|
160
|
Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:67-82. [PMID: 34188972 PMCID: PMC8217334 DOI: 10.1016/j.omtn.2021.04.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As next-generation sequencing (NGS) is leaping forward, more than 160 covalent RNA modification processes have been reported, and they are widely present in every organism and overall RNA type. Many modification processes of RNA introduce a new layer to the gene regulation process, resulting in novel RNA epigenetics. The commonest RNA modification includes pseudouridine (Ψ), N 7-methylguanosine (m7G), 5-hydroxymethylcytosine (hm5C), 5-methylcytosine (m5C), N 1-methyladenosine (m1A), N 6-methyladenosine (m6A), and others. In this study, we focus on non-coding RNAs (ncRNAs) to summarize the epigenetic consequences of RNA modifications, and the pathogenesis of cancer, as diagnostic markers and therapeutic targets for cancer, as well as the mechanisms affecting the immune environment of cancer. In addition, we summarize the current status of epigenetic drugs for tumor therapy based on ncRNA modifications and the progress of bioinformatics methods in elucidating RNA modifications in recent years.
Collapse
|
161
|
Zhang DD, Shi Y, Liu JB, Yang XL, Xin R, Wang HM, Wang PY, Jia CY, Zhang WJ, Ma YS, Fu D. Construction of a Myc-associated ceRNA network reveals a prognostic signature in hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:1033-1050. [PMID: 34141458 PMCID: PMC8167205 DOI: 10.1016/j.omtn.2021.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) remains an extremely lethal disease worldwide. High-throughput methods have revealed global transcriptome dysregulation; however, a comprehensive investigation of the complexity and behavioral characteristics of the competing endogenous RNA (ceRNA) network in HCC is lacking. In this study, we extracted the transcriptome (RNA) sequencing data of 371 HCC patients from The Cancer Genome Atlas platform. With the comparison of the high Myc expression (Mychigh) tumor and low Myc expression (Myclow) tumor groups in HCC, we identified 1,125 differentially expressed (DE) mRNAs, 589 long non-coding RNAs (lncRNAs), and 93 microRNAs (miRNAs). DE RNAs predicted the interactions necessary to construct an associated Myc ceRNA network, including 19 DE lncRNAs, 5 miRNAs, and 72 mRNAs. We identified a significant signature (long intergenic non-protein-coding [LINC] RNA 2691 [LINC02691] and LINC02499) that effectively predicted overall survival and had protective effects. The target genes of microRNA (miR)-212-3p predicted to intersect with DE mRNAs included SEC14-like protein 2 (SEC14L2) and solute carrier family 6 member 1 (SLC6A1), which were strongly correlated with survival and prognosis. With the use of the lncRNA-miRNA-mRNA axis, we constructed a ceRNA network containing four lncRNAs (LINC02691, LINC02499, LINC01354, and NAV2 antisense RNA 4), one miRNA (miR-212-3p), and two mRNAs (SEC14L2 and SLC6A1). Overall, we successfully constructed a mutually regulated ceRNA network and identified potential precision-targeted therapies and prognostic biomarkers.
Collapse
Affiliation(s)
- Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China.,Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yi Shi
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wen-Jie Zhang
- Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China.,The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yu-Shui Ma
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai 200433, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| |
Collapse
|
162
|
Abstract
Cancer accounted for 16% of all death worldwide in 2018. Significant progress has been made in understanding tumor occurrence, progression, diagnosis, treatment, and prognosis at the molecular level. However, genomics changes cannot truly reflect the state of protein activity in the body due to the poor correlation between genes and proteins. Quantitative proteomics, capable of quantifying the relatively different protein abundance in cancer patients, has been increasingly adopted in cancer research. Quantitative proteomics has great application potentials, including cancer diagnosis, personalized therapeutic drug selection, real-time therapeutic effects and toxicity evaluation, prognosis and drug resistance evaluation, and new therapeutic target discovery. In this review, the development, testing samples, and detection methods of quantitative proteomics are introduced. The biomarkers identified by quantitative proteomics for clinical diagnosis, prognosis, and drug resistance are reviewed. The challenges and prospects of quantitative proteomics for personalized medicine are also discussed.
Collapse
|
163
|
Immarigeon C, Frei Y, Delbare SYN, Gligorov D, Machado Almeida P, Grey J, Fabbro L, Nagoshi E, Billeter JC, Wolfner MF, Karch F, Maeda RK. Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. Proc Natl Acad Sci U S A 2021; 118:e2001897118. [PMID: 33876742 PMCID: PMC8053986 DOI: 10.1073/pnas.2001897118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Even in well-characterized genomes, many transcripts are considered noncoding RNAs (ncRNAs) simply due to the absence of large open reading frames (ORFs). However, it is now becoming clear that many small ORFs (smORFs) produce peptides with important biological functions. In the process of characterizing the ribosome-bound transcriptome of an important cell type of the seminal fluid-producing accessory gland of Drosophila melanogaster, we detected an RNA, previously thought to be noncoding, called male-specific abdominal (msa). Notably, msa is nested in the HOX gene cluster of the Bithorax complex and is known to contain a micro-RNA within one of its introns. We find that this RNA encodes a "micropeptide" (9 or 20 amino acids, MSAmiP) that is expressed exclusively in the secondary cells of the male accessory gland, where it seems to accumulate in nuclei. Importantly, loss of function of this micropeptide causes defects in sperm competition. In addition to bringing insights into the biology of a rare cell type, this work underlines the importance of small peptides, a class of molecules that is now emerging as important actors in complex biological processes.
Collapse
Affiliation(s)
- Clément Immarigeon
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
| | - Yohan Frei
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sofie Y N Delbare
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Dragan Gligorov
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Pedro Machado Almeida
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jasmine Grey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Léa Fabbro
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Emi Nagoshi
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jean-Christophe Billeter
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9700 CC, The Netherlands
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - François Karch
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Robert K Maeda
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
| |
Collapse
|
164
|
Du T, Gao Q, Zhao Y, Gao J, Li J, Wang L, Li P, Wang Y, Du L, Wang C. Long Non-coding RNA LINC02474 Affects Metastasis and Apoptosis of Colorectal Cancer by Inhibiting the Expression of GZMB. Front Oncol 2021; 11:651796. [PMID: 33898319 PMCID: PMC8063044 DOI: 10.3389/fonc.2021.651796] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most frequently diagnosed malignancies. Metastasis is the main event that impedes the therapeutic effect on CRC, and its underlying mechanisms remain largely unclear. LINC02474 is a novel long noncoding RNA (lncRNA) associated with metastasis of CRC, while little is known about how LINC02474 regulates these malignant characteristics. Methods Expressions of LINC02474 and granzyme B (GZMB) were assessed by quantitative real-time polymerase chain reaction (qRT-PCR) or Western blotting analysis. Cell metastasis was detected by transwell assay and metastatic nude mouse model, and apoptosis was determined by Western blotting analysis and flow cytometry. Besides, the interaction between LINC02474 and GZMB was detected by dual-luciferase reporter assays. Results The expression of LINC02474 was significantly up-regulated in CRC tissues. Moreover, depletion of LINC02474 damaged the metastatic abilities of CRC cells in vivo and in vitro while boosting apoptosis. Besides, up-regulation of LINC02474 could promote migration and invasion, while apoptosis was inhibited in CRC cells. Besides, down-regulation of LINC02474 promoted the expression of GZMB, and interference of GZMB could increase the metastatic abilities of CRC cells while reducing apoptosis. Furthermore, LINC02474 was related to the transcriptional repression of GZMB in CRC cells determined by the dual-luciferase reporter assay. Conclusions The findings revealed that a novel lncRNA, LINC02474, as an oncogene, could promote metastasis, but limit apoptosis partly by impeding GZMB expression in CRC. Besides, LINC02474 had the potential to be used as a biomarker in the prognosis of CRC.
Collapse
Affiliation(s)
- Tiantian Du
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qinglun Gao
- Department of Hepatobiliary Surgery, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Gao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lili Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Engineering & Technology Research Center for Tumor Marker Detection, The Second Hospital of Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Engineering & Technology Research Center for Tumor Marker Detection, The Second Hospital of Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| |
Collapse
|
165
|
Liu B, Zhao N, Zhou Y, Lu Y, Chen W, Huang Z, Wang D, Xu Y, Wai Ping Yam J, Cui Y. Circular RNA circ_ABCB10 in cancer. Clin Chim Acta 2021; 518:93-100. [PMID: 33746018 DOI: 10.1016/j.cca.2021.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 02/07/2023]
Abstract
Circular RNA (circRNA), a newly discovered type of endogenous noncoding RNA, has become a focus and hotspot in biological research in recent years. It exists widely and possesses a stable structure, is highly conserved and has cell-specific expression. circRNA is associated with disease occurence in general and cancer specifically due to its role in cell differentiation, proliferation, invasion and metastasis. Recently, circ_ABCB10, an increasingly studied member of the annular RNA family, has attracted considerable attention due to the fact that its expression is upregulated in various tumors, ie, esophageal cancer, breast cancer, lung cancer, and glioma, and may be of prognostic value. Molecular regulation and mechanism of circ_ABCB10 action in cancer are reviewed and its potential as a molecular marker and novel target for diagnosis and treatment are explored..
Collapse
Affiliation(s)
- Bowen Liu
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Na Zhao
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Yuanshi Zhou
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Yuxuan Lu
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Wangming Chen
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Ziyue Huang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Dongsheng Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China
| | - Yi Xu
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China; Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Block T, Queen Mary Hospital, Pokfulam 999077, China.
| | - Judy Wai Ping Yam
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Block T, Queen Mary Hospital, Pokfulam 999077, China.
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin 150086, China.
| |
Collapse
|
166
|
Gao YJ, Zhang RJ, Liu Q, Sun SG, Qi MY, Wang Y, Geng DD, Wang L. Functional predication of differentially expressed circRNAs/lncRNAs in the prefrontal cortex of Nrf2-knockout mice. Aging (Albany NY) 2021; 13:8797-8816. [PMID: 33714958 PMCID: PMC8034947 DOI: 10.18632/aging.202688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/01/2021] [Indexed: 12/25/2022]
Abstract
In the central nervous system, nuclear factor erythroid-2-related factor 2 (Nrf2) protects neurons from oxidant injury, thereby ameliorating neurodegeneration. We explored the key circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) involved in Nrf2-induced neuroprotection. We used microarrays to examine the circRNAs (DEcircRNAs), lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) differentially expressed between Nrf2 (+/+) and Nrf2 (-/-) mice and identified DEcircRNA/DElncRNA-miRNA-DEmRNA interaction networks. In total, 197 DEcircRNAs, 685 DElncRNAs and 356 DEmRNAs were identified in prefrontal cortical tissues from Nrf2 (-/-) mice. The expression patterns of selected DEcircRNAs (except for mmu_circ_0003404) and DElncRNAs in qRT-PCR analyses were generally consistent with the microarray analysis results. Functional annotation of the DEmRNAs in the DEcircRNA/DElncRNA-miRNA-DEmRNA networks indicated that five non-coding RNAs (mmu_circ_0000233, ENSMUST00000204847, NONMMUT024778, NONMMUT132160 and NONMMUT132168) may contribute to Nrf2 activity, with the help of mmu_circ_0015035 and NONMMUT127961. The results also revealed that four non-coding RNAs (cicRNA.20127, mmu_circ_0012936, ENSMUST00000194077 and NONMMUT109267) may influence glutathione metabolism. Additionally, 44 DEcircRNAs and 7 DElncRNAs were found to possess coding potential. These findings provide clues to the molecular pathways through which Nrf2 protects neurons.
Collapse
Affiliation(s)
- Yan-Jing Gao
- Department of Human Anatomy, Institute of Medicine and Health, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Run-Jiao Zhang
- Department of Human Anatomy, Institute of Medicine and Health, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Qing Liu
- Department of Human Anatomy, Institute of Medicine and Health, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Shao-Guang Sun
- Department of Biochemistry and Molecular Biology, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Mao-Yang Qi
- School of Basic Medicine, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Yue Wang
- School of Basic Medicine, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Dan-Dan Geng
- Department of Human Anatomy, Institute of Medicine and Health, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| | - Lei Wang
- Department of Human Anatomy, Institute of Medicine and Health, Hebei Medical University, Shijiazhuang 050017, Hebei, China
| |
Collapse
|
167
|
Yan Y, Tang R, Li B, Cheng L, Ye S, Yang T, Han YC, Liu C, Dong Y, Qu LH, Lui KO, Yang JH, Huang ZP. The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy. Mol Ther 2021; 29:2253-2267. [PMID: 33677093 PMCID: PMC8261087 DOI: 10.1016/j.ymthe.2021.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/11/2020] [Accepted: 03/02/2021] [Indexed: 11/27/2022] Open
Abstract
Hypertrophic growth of cardiomyocytes is one of the major compensatory responses in the heart after physiological or pathological stimulation. Protein synthesis enhancement, which is mediated by the translation of messenger RNAs, is one of the main features of cardiomyocyte hypertrophy. Although the transcriptome shift caused by cardiac hypertrophy induced by different stimuli has been extensively investigated, translatome dynamics in this cellular process has been less studied. Here, we generated a nucleotide-resolution translatome as well as transcriptome data from isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORFs) were detected from the deep sequencing of ribosome-protected fragments (Ribo-seq), which orchestrated the shift of the translatome in hypertrophied cardiomyocytes. Our data suggest that rather than increase the translational rate of ribosomes, the increased efficiency of protein synthesis in cardiomyocyte hypertrophy was attributable to an increased quantity of ribosomes. In addition, more than 100 uncharacterized short ORFs (sORFs) were detected in long noncoding RNA genes from Ribo-seq with potential of micropeptide coding. In a random test of 15 candidates, the coding potential of 11 sORFs was experimentally supported. Three micropeptides were identified to regulate cardiomyocyte hypertrophy by modulating the activities of oxidative phosphorylation, the calcium signaling pathway, and the mitogen-activated protein kinase (MAPK) pathway. Our study provides a genome-wide overview of the translational controls behind cardiomyocyte hypertrophy and demonstrates an unrecognized role of micropeptides in cardiomyocyte biology.
Collapse
Affiliation(s)
- Youchen Yan
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Tang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Bin Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liangping Cheng
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Shangmei Ye
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Tiqun Yang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan-Chuang Han
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Chen Liu
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yugang Dong
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR 999077, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, Guangzhou 510080, China.
| |
Collapse
|
168
|
Xiang X, Fu Y, Zhao K, Miao R, Zhang X, Ma X, Liu C, Zhang N, Qu K. Cellular senescence in hepatocellular carcinoma induced by a long non-coding RNA-encoded peptide PINT87aa by blocking FOXM1-mediated PHB2. Theranostics 2021; 11:4929-4944. [PMID: 33754036 PMCID: PMC7978318 DOI: 10.7150/thno.55672] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Rationale: Recently, long non-coding RNAs (lncRNAs), known to be involved in human cancer progression, have been shown to encode peptides with biological functions, but the role of lncRNA-encoded peptides in cellular senescence is largely unexplored. We previously reported the tumor-suppressive role of PINT87aa, a peptide encoded by the long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT). Here, we investigated PINT87aa's role in hepatocellular carcinoma (HCC) cellular senescence. Methods: We examined PINT87aa and truncated PINT87aa functions in vitro by monitoring cell proliferation and performed flow cytometry, senescence-associated β-galactosidase staining, JC-1 staining indicative of mitochondrial membrane potential, the ratio of the overlapping area of light chain 3 beta (LC3B) and mitochondrial probes and the ratio of lysosomal associated membrane protein 1 (LAMP1) overlapping with cytochrome c oxidase subunit 4I1 (COXIV) denoting mitophagy. PINT87aa and truncated PINT87aa functions in vivo were verified by subcutaneously transplanted tumors in nude mice. The possible binding between PINT87aa and forkhead box M1 (FOXM1) was predicted through structural analysis and verified by co-immunoprecipitation and immunofluorescence co-localization. Rescue experiments were performed in vivo and in vitro following FOXM1 overexpression. Further, chromatin immunoprecipitation, polymerase chain reaction, and dual-luciferase reporter gene assay were conducted to validate FOXM1 binding to the prohibitin 2 (PHB2) promoter. Results: PINT87aa was significantly increased in the hydrogen peroxide-induced HCC cell senescence model. Overexpression of PINT87aa induced growth inhibition, cellular senescence, and decreased mitophagy in vitro and in vivo. In contrast, FOXM1 gain-of-function could partially reduce the proportion of senescent HCC cells and enhance mitophagy. PINT87aa overexpression did not affect the expression of FOXM1 itself but reduced that of its target genes involved in cell cycle and proliferation, especially PHB2, which was involved in mitophagy and transcribed by FOXM1. Structural analysis indicated that PINT87aa could bind to the DNA-binding domain of FOXM1, which was confirmed by co-immunoprecipitation and immunofluorescence co-localization. Furthermore, we demonstrated that the 2 to 39 amino acid truncated form of the peptide exerted effects similarly to the full form. Conclusion: Our study established the role of PINT87aa as a novel biomarker and a key regulator of cellular senescence in HCC and identified PINT87aa as a potential therapeutic target for HCC.
Collapse
Affiliation(s)
- Xiaohong Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yunong Fu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Kun Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, PR China
| | - Runchen Miao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xing Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xiaohua Ma
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Chang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, PR China
| | - Kai Qu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| |
Collapse
|
169
|
Rong R, Wang M, You M, Li H, Xia X, Ji D. Pathogenesis and prospects for therapeutic clinical application of noncoding RNAs in glaucoma: Systematic perspectives. J Cell Physiol 2021; 236:7097-7116. [PMID: 33634475 PMCID: PMC8451868 DOI: 10.1002/jcp.30347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
Noncoding ribonucleic acids (ncRNAs) are an increasingly studied class of RNA molecules with extensive biological activities, including important roles in human development, health, and disease. Glaucoma is a neurodegenerative disease of the retina, and one of the leading causes of blindness worldwide. However, the specific roles of ncRNAs in the development and progression of glaucoma are unclear, and related reports are fragmented. An in‐depth understanding of ncRNAs participating in the pathogenesis and progression of glaucoma would be helpful for opening up new avenues to facilitate the early diagnosis and clinical treatment. Therefore, in this review, we aimed to discuss the current research progress, the potentialfuture clinical applications and the research limitations of three critical classes of ncRNAs in glaucoma, namely microRNAs, long noncoding RNAs, and circular RNAs.
Collapse
Affiliation(s)
- Rong Rong
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengxiao Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengling You
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Haibo Li
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Dan Ji
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| |
Collapse
|
170
|
Tang L, Jiang B, Zhu H, Gao T, Zhou Y, Gong F, He R, Xie L, Li Y. The Biogenesis and Functions of circRNAs and Their Roles in Breast Cancer. Front Oncol 2021; 11:605988. [PMID: 33718157 PMCID: PMC7947672 DOI: 10.3389/fonc.2021.605988] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Recent statistics show that breast cancer is among the most frequent cancers in clinical practice. It is also the second-leading cause of cancer-related deaths among women worldwide. CircRNAs are a new class of endogenous regulatory RNA molecules whose 5’ end and 3’ end are connected together to form a covalently closed single-stranded loop by back-splicing. CircRNAs present the advantages of disease-specific expression and excellent expression stability, and they can modulate gene expression at posttranscriptional and transcriptional levels. CircRNAs are abnormally expressed in multiple cancers, such as breast cancer, and drive the initiation and progression of cancer. In this review, we describe current knowledge about the functions of circRNAs and generalize their roles in various aspects of breast cancer, including cell proliferation, cell cycle, apoptosis, invasion and metastasis, autophagy, angiogenesis, drug resistance, and tumor immunity, and their prognostic and diagnostic value. This may add to a better understanding of the functions and roles of circRNAs in breast cancer, which may become new diagnostic and predictive biomarkers of breast cancer.
Collapse
Affiliation(s)
- Liting Tang
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Baohong Jiang
- Department of Pharmacy, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Hongbo Zhu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Ting Gao
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yu Zhou
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Fuqiang Gong
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Rongfang He
- Department of Pathology The First Affiliated Hospital, University of South China, Hengyang, China
| | - Liming Xie
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yuehua Li
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China.,Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang, China
| |
Collapse
|
171
|
Thomas PB, Jeffery P, Gahete MD, Whiteside E, Walpole C, Maugham M, Jovanovic L, Gunter J, Williams E, Nelson C, Herington A, Luque RM, Veedu R, Chopin LK, Seim I. The long non-coding RNA GHSROS reprograms prostate cancer cell lines toward a more aggressive phenotype. PeerJ 2021; 9:e10280. [PMID: 33585078 PMCID: PMC7860111 DOI: 10.7717/peerj.10280] [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: 07/05/2019] [Accepted: 10/09/2020] [Indexed: 12/27/2022] Open
Abstract
It is now appreciated that long non-coding RNAs (lncRNAs) are important players in orchestrating cancer progression. In this study we characterized GHSROS, a human lncRNA gene on the opposite DNA strand (antisense) to the ghrelin receptor gene, in prostate cancer. The lncRNA was upregulated by prostate tumors from different clinical datasets. Transcriptome data revealed that GHSROS alters the expression of cancer-associated genes. Functional analyses in vitro showed that GHSROS mediates tumor growth, migration and survival, and resistance to the cytotoxic drug docetaxel. Increased cellular proliferation of GHSROS-overexpressing PC3, DU145, and LNCaP prostate cancer cell lines in vitro was recapitulated in a subcutaneous xenograft model. Conversely, in vitro antisense oligonucleotide inhibition of the lncRNA reciprocally regulated cell growth and migration, and gene expression. Notably, GHSROS modulates the expression of PPP2R2C, the loss of which may drive androgen receptor pathway-independent prostate tumor progression in a subset of prostate cancers. Collectively, our findings suggest that GHSROS can reprogram prostate cancer cells toward a more aggressive phenotype and that this lncRNA may represent a potential therapeutic target.
Collapse
Affiliation(s)
- Patrick B. Thomas
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Comparative and Endocrine Biology Laboratory, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Penny Jeffery
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Comparative and Endocrine Biology Laboratory, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Manuel D. Gahete
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, Spain
- Hospital Universitario Reina Sofía (HURS), Cordoba, Spain
- Campus de Excelencia Internacional Agroalimentario (ceiA3), Cordoba, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Cordoba, Spain
| | - Eliza Whiteside
- Centre for Health Research, University of Southern Queensland, Toowoomba, Queensland, Australia
- Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Carina Walpole
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michelle Maugham
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Comparative and Endocrine Biology Laboratory, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lidija Jovanovic
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jennifer Gunter
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Elizabeth Williams
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Colleen Nelson
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Adrian Herington
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Raul M. Luque
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, Spain
- Hospital Universitario Reina Sofía (HURS), Cordoba, Spain
- Campus de Excelencia Internacional Agroalimentario (ceiA3), Cordoba, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Cordoba, Spain
| | - Rakesh Veedu
- Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, Australia
| | - Lisa K. Chopin
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Comparative and Endocrine Biology Laboratory, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Inge Seim
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Comparative and Endocrine Biology Laboratory, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Brisbane, Queensland, Australia
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
172
|
Zong T, Yang Y, Zhao H, Li L, Liu M, Fu X, Tang G, Zhou H, Aung LHH, Li P, Wang J, Wang Z, Yu T. tsRNAs: Novel small molecules from cell function and regulatory mechanism to therapeutic targets. Cell Prolif 2021; 54:e12977. [PMID: 33507586 PMCID: PMC7941233 DOI: 10.1111/cpr.12977] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
tsRNAs are small fragments of RNAs with specific lengths that are generated by particular ribonucleases, such as dicer and angiogenin (ANG), clipping on the rings of transfer RNAs (tRNAs) in specific cells and tissues under specific conditions. Depending on where the splicing site is, tsRNAs can be segmented into two main types, tRNA‐derived stress‐induced RNAs (tiRNAs) and tRNA‐derived fragments (tRFs). Many studies have shown that tsRNAs are functional molecules, not the random degradative products of tRNAs. Notably, due to their regulatory mechanism in regulating mRNA stability, transcription, ribosomal RNA (rRNA) synthesis and RNA reverse transcription, tsRNAs are significantly involved in the cell function, such as cell proliferation, migration, cycle and apoptosis, as well as the occurrence and development of a variety of diseases. In addition, tsRNAs may represent a new generation of clinical biomarkers or therapeutic targets because of their stable structures, high conservation and widely distribution, particularly in the peripheral tissues, bodily fluids and exosomes. In this review, we describe the generation, function and mechanism of tsRNAs and illustrate the current research progress of tsRNAs in various diseases, highlight their potentials as biomarkers and therapeutic targets in clinical application. Although our understanding of tsRNAs is still in infancy, the application prospects shown in this field deserve further exploration.
Collapse
Affiliation(s)
- Tingyu Zong
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Hui Zhao
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Li
- Department of Vascular surgery, Qingdao Hiser Medical Center, Qingdao, China
| | - Meixin Liu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiuxiu Fu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guozhang Tang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hong Zhou
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lynn Htet Htet Aung
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jianxun Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zhibin Wang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tao Yu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.,Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
173
|
Circular RNA 100146 Promotes Colorectal Cancer Progression by the MicroRNA 149/HMGA2 Axis. Mol Cell Biol 2021; 41:MCB.00445-20. [PMID: 33257506 PMCID: PMC8093498 DOI: 10.1128/mcb.00445-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) has developed into the third leading cause of cancer-associated death worldwide. Studies have confirmed that circular RNAs (circRNAs) absorb microRNAs (miRNAs) to regulate the function of downstream genes. This study aimed to explore the underlying mechanism of circRNA 100146 in CRC. The expression of circRNA 100146, miRNA 149 (miR-149), and high mobility group AT-Hook 2 (HMGA2) was detected by quantitative real-time PCR (RT-qPCR). A series of biofunctional effects (cell viability, apoptosis, migration/invasion) were evaluated by the use of methyl thiazolyl tetrazolium (MTT), flow cytometry, and transwell assays. Protein levels were measured by Western blot assay. A xenograft model was established for in vivo experiments. The interactions among circRNA 100146, miR-149, and HMGA2 were evaluated by dual-luciferase reporter assay, RNA immunoprecipitation assays, or RNA pulldown assay. circRNA 100146 was upregulated in CRC tissues and cells. circRNA 100146 knockdown inhibited cell proliferation, promoted apoptosis, and suppressed migration and invasion in vitro and impeded tumor growth in vivo Also, miR-149 was negatively regulated by circRNA 100146 and was targeted to HMGA2 and mediated its expression. Moreover, miR-149 interference abrogated the activities of silenced circRNA 100146 in proliferation, apoptosis, migration, and invasion. Furthermore, HMGA2 overexpression abated the effects described above caused by circRNA 100146 silencing, while the mutations on miR-149 binding sites in the 3' untranslated region (3'-UTR) of HMGA2 led to its loss of this ability. circRNA 100146 knockdown repressed proliferation, enhanced apoptosis, and hindered migration and invasion in SW620 and SW480 cells through targeting the miR-149/HMGA2 axis.
Collapse
|
174
|
Erady C, Boxall A, Puntambekar S, Suhas Jagannathan N, Chauhan R, Chong D, Meena N, Kulkarni A, Kasabe B, Prathivadi Bhayankaram K, Umrania Y, Andreani A, Nel J, Wayland MT, Pina C, Lilley KS, Prabakaran S. Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. NPJ Genom Med 2021; 6:4. [PMID: 33495453 PMCID: PMC7835362 DOI: 10.1038/s41525-020-00167-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.
Collapse
Affiliation(s)
- Chaitanya Erady
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Adam Boxall
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Shraddha Puntambekar
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - N Suhas Jagannathan
- Cancer and Stem Cell Biology Programme, and Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Ruchi Chauhan
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - David Chong
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Narendra Meena
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Apurv Kulkarni
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Bhagyashri Kasabe
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | | | - Yagnesh Umrania
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Adam Andreani
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Jean Nel
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Matthew T Wayland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Cristina Pina
- Department of Haematology, Cambridge Biomedical Campus, Cambridge, CB2 0PT, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
| |
Collapse
|
175
|
Zhang S, Chen Y, Wang Y, Zhang P, Chen G, Zhou Y. Insights Into Translatomics in the Nervous System. Front Genet 2021; 11:599548. [PMID: 33408739 PMCID: PMC7779767 DOI: 10.3389/fgene.2020.599548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Most neurological disorders are caused by abnormal gene translation. Generally, dysregulation of elements involved in the translational process disrupts homeostasis in neurons and neuroglia. Better understanding of how the gene translation process occurs requires detailed analysis of transcriptomic and proteomic profile data. However, a lack of strictly direct correlations between mRNA and protein levels limits translational investigation by combining transcriptomic and proteomic profiling. The much better correlation between proteins and translated mRNAs than total mRNAs in abundance and insufficiently sensitive proteomics approach promote the requirement of advances in translatomics technology. Translatomics which capture and sequence the mRNAs associated with ribosomes has been effective in identifying translational changes by genetics or projections, ribosome stalling, local translation, and transcript isoforms in the nervous system. Here, we place emphasis on the main three translatomics methods currently used to profile mRNAs attached to ribosome-nascent chain complex (RNC-mRNA). Their prominent applications in neurological diseases including glioma, neuropathic pain, depression, fragile X syndrome (FXS), neurodegenerative disorders are outlined. The content reviewed here expands our understanding on the contributions of aberrant translation to neurological disease development.
Collapse
Affiliation(s)
- Shuxia Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeru Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjie Wang
- Key Laboratory of Elemene Anti-Cancer Medicine of Zhejiang Province and Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China
| | - Piao Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Gang Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Youfa Zhou
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
176
|
An epithelial-mesenchymal transition-related long noncoding RNA signature correlates with the prognosis and progression in patients with bladder cancer. Biosci Rep 2021; 41:227198. [PMID: 33289830 PMCID: PMC7786330 DOI: 10.1042/bsr20203944] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/22/2022] Open
Abstract
Bladder cancer is a common malignant tumour worldwide. Epithelial-mesenchymal transition (EMT)-related biomarkers can be used for early diagnosis and prognosis of cancer patients. To explore, accurate prediction models are essential to the diagnosis and treatment for bladder cancer. In the present study, an EMT-related long noncoding RNA (lncRNA) model was developed to predict the prognosis of patients with bladder cancer. Firstly, the EMT-related lncRNAs were identified by Pearson correlation analysis, and a prognostic EMT-related lncRNA signature was constructed through univariate and multivariate Cox regression analyses. Then, the diagnostic efficacy and the clinically predictive capacity of the signature were assessed. Finally, Gene set enrichment analysis (GSEA) and functional enrichment analysis were carried out with bioinformatics. An EMT-related lncRNA signature consisting of TTC28-AS1, LINC02446, AL662844.4, AC105942.1, AL049840.3, SNHG26, USP30-AS1, PSMB8-AS1, AL031775.1, AC073534.1, U62317.2, C5orf56, AJ271736.1, and AL139385.1 was constructed. The diagnostic efficacy of the signature was evaluated by the time-dependent receiver-operating characteristic (ROC) curves, in which all the values of the area under the ROC (AUC) were more than 0.73. A nomogram established by integrating clinical variables and the risk score confirmed that the signature had a good clinically predict capacity. GSEA analysis revealed that some cancer-related and EMT-related pathways were enriched in high-risk groups, while immune-related pathways were enriched in low-risk groups. Functional enrichment analysis showed that EMT was associated with abundant GO terms or signaling pathways. In short, our research showed that the 14 EMT-related lncRNA signature may predict the prognosis and progression of patients with bladder cancer.
Collapse
|
177
|
RP11-323N12.5 promotes the malignancy and immunosuppression of human gastric cancer by increasing YAP1 transcription. Gastric Cancer 2021; 24:85-102. [PMID: 32623586 DOI: 10.1007/s10120-020-01099-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND YAP1 is a core protein of the Hippo signaling pathway and is associated with malignancy and immunosuppression. In the present study, we discovered a novel lncRNA, RP11-323N12.5, with tumor promotion and immunosuppression activities through enhancing transcription of YAP1. METHODS RP11-323N12.5 was identified using GEPIA. Its expression levels and their relationship with clinical features were investigated using clinical samples. The regulation of YAP1 transcription by RP11-323N12.5 was investigated in both GC and T cells, the tumor and immunosuppression promotion roles of RP11-323N12.5 were explored in vitro and in vivo. RESULTS RP11-323N12.5 was the most up-regulated lncRNA in human GC, based on data from the TCGA database. Its transcription was significantly positively correlated with YAP1 transcription, YAP1 downstream gene expression which contribute to tumor growth and immunosuppression. RP11-323N12.5 promoted YAP1 transcription by binding to c-MYC in the YAP1 promoter region. Meanwhile, transcription of RP11-323N12.5 was also regulated by YAP1/TAZ/TEADs activation in GC cells. RP11-323N12.5 had tumor- and immnosuppression-promoting effects by enhancing YAP1 downstream genes in GC cells. Excessive RP11-323N12.5 was also observed in tumor-infiltrating leukocytes (TILs), which may be exosome-derived and also be related to enhanced Treg differentiation as a result YAP1 up-regulation. Moreover, RP11-323N12.5 promoted tumor growth and immunosuppression via YAP1 up-regulation in vivo. CONCLUSIONS RP11-323N12.5 was the most up-regulated lncRNA in human GC and it promoted YAP1 transcription by binding to c-MYC within the YAP1 promoter in both GC and T cells. RP11-323N12.5 is an ideal therapeutic target in human GC due to its tumor-promoting and immunosuppression characteristics.
Collapse
|
178
|
Liu Y, Zhang B, Cao WB, Wang HY, Niu L, Zhang GZ. Study on Clinical Significance of LncRNA EGOT Expression in Colon Cancer and Its Effect on Autophagy of Colon Cancer Cells. Cancer Manag Res 2020; 12:13501-13512. [PMID: 33408522 PMCID: PMC7781029 DOI: 10.2147/cmar.s285254] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Colon cancer (CC) is a common digestive tract tumor, and the increase of new and dead patients every year still puzzles clinical workers. LncRNA eosinophil granule ontogeny transcript (EGOT), as a newly discovered long-chain noncoding RNA (lncRNA), is differentially expressed in other tumors, but there are fewer studies of it in colon cancer. Methods The relative expression and diagnostic value of EGOT in CC were detected and analyzed by starBase online website and qRT-PCR. The patients were followed-up for five years, and Cox regression was used to analyze the independent prognostic factors of CC. The effects of EGOT overexpression (pcDNA-RGOT) on CC cell function were detected by CCK-8, transwell and flow cytometry. WB was applied to detect autophagy. The influence of knocking out EGOT (sh-EGOT) on tumor growth was observed by tumor allogeneic inhibition. The microRNA (miR) and mRNA in the downstream of EGOT were predicted and the ceRNA network map was drawn. Results The online database and qRT-PCR detection showed that EGOT was highly expression in patients with CC and had good diagnostic value. The five-year survival rate of patients with high expression of EGOT decreased. EGOT and TNM staging were independent prognostic factors of patients with CC. Functional analysis revealed that the growth and invasion abilities of cells increased, and the apoptosis rate decreased after overexpression. Upregulation of EGOT inhibited autophagy of CC cells and promoted cell growth. However, the tumor in nude mice was significantly lessened after knockout of EGOT. Bioinformatic analysis showed that microRNA-33a-5p and microRNA-33b-5p had targeted binding sites with EGOT. Conclusion EGOT is highly expressed in CC and has high diagnostic value. In addition, inhibition of EGOT can promote autophagy of CC cells and inhibit cell growth and metastasis, which is expected to be a potential therapeutic index.
Collapse
Affiliation(s)
- Yang Liu
- Department of General Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan City, Hebei Province 063000, People's Republic of China
| | - Bo Zhang
- Department of General Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan City, Hebei Province 063000, People's Republic of China
| | - Wen-Bin Cao
- Department of General Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan City, Hebei Province 063000, People's Republic of China
| | - Hai-Yan Wang
- Department of Oncology, The 982 Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Tangshan City, Hebei Province 063000, People's Republic of China
| | - Lei Niu
- Department of Respiratory Medicine, Tangshan Hong Ci Hospital Co. Ltd, Tangshan City, Hebei Province 063000, People's Republic of China
| | - Guo-Zhi Zhang
- Department of General Surgery, North China University of Science and Technology Affiliated Hospital, Tangshan City, Hebei Province 063000, People's Republic of China
| |
Collapse
|
179
|
Identification of the ceRNA networks in α-MSH-induced melanogenesis of melanocytes. Aging (Albany NY) 2020; 13:2700-2726. [PMID: 33318297 PMCID: PMC7880406 DOI: 10.18632/aging.202320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022]
Abstract
α-MSH is known for melanogenesis stimulation, and ceRNA is a new method involved in physiological regulation. However, whether ceRNA participates in α-MSH-induced melanogenesis remains unknown. We used ceRNA array to detect the expression profiles of lncRNAs, circRNAs, and mRNAs in melanocytes after α-MSH treatment. Moreover, the melanogenesis-related ceRNA regulatory networks were screened and validated. The expression profile analysis showed that 20 lncRNAs and 49 circRNAs changed five-fold after α-MSH treatment, while 933 mRNAs changed two-fold. Based on differentially expressed genes, GO and KEGG analysis were conducted and revealed that 14 genes were enriched in melanogenesis. Then, multiple lncRNA or circRNA-miRNA-mRNA ceRNA networks and lncRNA/circRNA-miRNA-mRNA quaternary ceRNA networks were identified. Thereinto, ENST00000606533, circ_0091223, and TYR expression were upregulated in α-MSH-treated melanocytes, while their complementary miR-1291 was decreased. Dual-luciferase reporter assay further verified that ENST00000606533 and circ_0091223 could bind to miR-1291. ENST00000606533 and circ_0091223 siRNAs decreased circ_0091223, ENST00000606533, and TYR expression, but increased miR-1291 expression. Conversely, miR-1291 mimics inhibited ENST00000606533, circ_0091223, and TYR expression. Moreover, miR-1291 inhibitor could reverse the inhibitory effect of the two siRNAs on TYR expression. Hence, the "ENST00000606533/circ_0091223-miR-1291-TYR" ceRNA network is involved in α-MSH-induced melanogenesis, and ceRNA networks may be potential therapeutic targets for skin pigmentation disorders.
Collapse
|
180
|
Tao X, Zhang Y, Li J, Ni Z, Tao Z, You Q, He Z, Huang D, Zheng S. Low expression of long non-coding RNA ARAP1-AS1 can inhibit lung cancer proliferation by inducing G0/G1 cell cycle organization. J Thorac Dis 2020; 12:7326-7336. [PMID: 33447422 PMCID: PMC7797826 DOI: 10.21037/jtd-20-3378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background This paper examines the expression, function, and molecular mechanism of long non-coding ribonucleic acid (lncRNA) ARAP1 antisense RNA 1 (ARAP1-AS1) in lung cancer. Specifically, it aims to clarify the molecular mechanism of lncRNA ARAP1-AS1 that affects the occurrence and development of lung cancer, and provide a theoretical basis and molecular targets for targeted therapy or early diagnosis of lung cancer. Methods Fluorescence quantitative detection of lncRNA ARAP1-AS1 expression in lung cancer tissues and cell lines, and methylthiazolyldiphenyl-tetrazolium (MTT), plate cloning experiment, and flow cytometry were used to detect the effect of knockdown of lncRNA ARAP1-AS1 on cell proliferation, clone formation, and the cell cycle, respectively. Western blotting was used to detect the expression of cell cycle-related proteins as well as the effect of knockdown of lncRNA ARAP1-AS1 on lung cancer. Cell proliferation was assessed by a nude mouse subcutaneous tumor formation experiment. Results LncRNA ARAP1-AS1 is highly expressed in lung cancer tissues and cells. Knockdown of LncRNA ARAP1-AS1 can significantly inhibit the proliferation and clonal formation of lung cancer cells and induce G0/G1 cell cycle arrest. Knockdown of ARAP1-AS1 can markedly inhibit the expression of cell cycle-related protein cyclin D1, but has no significant effect on the expression of cyclin-dependent kinase (CDK)4 and CDK6. Furthermore, knockdown of ARAP1-AS1 can also notably inhibit the growth of lung cancer cells and substantially reduce the expression of Ki-67 in tumor-bearing tissues in nude mice. Conclusions LncRNA ARAP1-AS1 is highly expressed in lung cancer. Knocking down of this gene can significantly inhibit cell proliferation in vitro and in vivo, and can also cause G0/G1 cell cycle arrest by inhibiting the expression of cyclin D1.
Collapse
Affiliation(s)
- Xinlu Tao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Yan Zhang
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Jiaping Li
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Zhengzheng Ni
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Zheng Tao
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Qi You
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Zhijie He
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Dengjun Huang
- Department of Thoracic Surgery, Yijishan Hospital, First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Shiying Zheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
181
|
Cardon T, Fournier I, Salzet M. Shedding Light on the Ghost Proteome. Trends Biochem Sci 2020; 46:239-250. [PMID: 33246829 DOI: 10.1016/j.tibs.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023]
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.
Collapse
Affiliation(s)
- Tristan Cardon
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| |
Collapse
|
182
|
Chen Y, Ho L, Tergaonkar V. sORF-Encoded MicroPeptides: New players in inflammation, metabolism, and precision medicine. Cancer Lett 2020; 500:263-270. [PMID: 33157158 DOI: 10.1016/j.canlet.2020.10.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/30/2022]
Abstract
Significant technological advances have enabled the discovery and identification of a new class of molecules, micropeptides or small ORF encoded peptides (SEPs) within non-coding RNAs (ncRNAs). As ncRNAs are well known to be transcriptionally silent, the discovery of SEPs implies that many ncRNAs are misannotated or play both coding and non-coding functions. SEPs have reportedly diverse regulatory roles in embryogenesis, myogenesis, inflammation, diseases, and cancer. SEPs appearing in different subcellular compartments show distinct functions. In this review, we summarized the functions of SEPs that have been characterized thus far. As SEPs are amenable to therapeutic development as biologics, understanding their underlying functions will provide novel targets for the treatment of inflammatory or metabolic disorders.
Collapse
Affiliation(s)
- Ying Chen
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore.
| | - Lena Ho
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore; Cardiovascular Metabolic Disorders Program, Duke-NUS Graduate School, Singapore; Institute of Medical Biology, A*STAR, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117597, Singapore.
| |
Collapse
|
183
|
Circular RNA circ-CCAC1 Facilitates Adrenocortical Carcinoma Cell Proliferation, Migration, and Invasion through Regulating the miR-514a-5p/C22orf46 Axis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3501451. [PMID: 33195693 PMCID: PMC7641692 DOI: 10.1155/2020/3501451] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 01/02/2023]
Abstract
Adrenocortical carcinoma (ACC) is a rare but clinically aggressive endocrine malignancy. Circular RNAs (circRNAs) were found to play key roles in tumorigenesis. In the current study, we aimed to investigate the functions and mechanisms of a novel circRNA, circ-CCAC1, in ACC cells. circ-CCAC1 expression levels in ACC tissue specimens and cell lines were evaluated by RT-qPCR. Kaplan-Meier analysis was applied to explore the relationship between circ-CCAC1 and patients' prognosis. Cell counting kit-8 (CCK-8), colony formation, acridine orange/ethidium bromide (AO/EB) double fluorescence staining, and Transwell assays were performed to evaluate the functions of circ-CCAC1 in ACC cells. Bioinformatics analysis and a dual-luciferase reporter assay were utilized to explore the mechanisms of circ-CCAC1. As a result, circ-CCAC1 was overexpressed in ACC tissue samples and cell lines and correlated with poor prognosis. Gain- and loss-of-function tests demonstrated that circ-CCAC1 acted as an oncogene in ACC. What is more, circ-CCAC1 enhanced C22orf46 expression by sponging miR-514a-5p in ACC cells. A rescue assay illustrated that circ-CCAC1 facilitated ACC progression through miR-514a-5p/C22orf46 signaling. To sum up, we identified a novel circRNA, circ-CCAC1, which may be used as a potential therapeutic target for ACC.
Collapse
|
184
|
Ye M, Zhang J, Wei M, Liu B, Dong K. Emerging role of long noncoding RNA-encoded micropeptides in cancer. Cancer Cell Int 2020; 20:506. [PMID: 33088214 PMCID: PMC7565808 DOI: 10.1186/s12935-020-01589-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/19/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.
Collapse
Affiliation(s)
- Mujie Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Jingjing Zhang
- Department of Medical Imaging, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210001 China
| | - Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| |
Collapse
|
185
|
Li J, Wu X, Cao W, Zhao J. Long non-coding RNA NCK1-AS1 promotes the proliferation, migration and invasion of non-small cell lung cancer cells by acting as a ceRNA of miR-137. Am J Transl Res 2020; 12:6908-6920. [PMID: 33194081 PMCID: PMC7653585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in carcinogenesis and progression. In this study, we mainly investigate the potential influence of lncRNA NCK1 antisense RNA 1 (NCK1-AS1) on the progression of non-small cell lung cancer (NSCLC). RT-PCR was performed to determine the expression of NCK1-AS1 and miR-137 in NSCLC specimens and cell lines. The clinical significance of NCK1-AS1 in 148 patients was analyzed statistically. The receiver operating characteristic (ROC) curve was performed to estimate the diagnostic value of NCK1-AS1 and miR-137. Regulatory effects of NCK1-AS1 on proliferative, colony formation abilities, metastasis and apoptosis of SK-MES-1 and H1299 cells were assessed through a series of functional experiments. RNA-pull down and Dual-Luciferase reporter assay was performed to verify the sponge effect of NCK1-AS1 on miR-137. We observed that NCK1-AS1 expression was upregulated, while miR-137 expression was down-regulated in NSCLC specimens and cell lines. Increased NCK1-AS1 expression was positively correlated with TNM stage and lymph node metastasis and poor clinical outcome. The diagnostic value of NCK1-AS1 and miR-137 expression was also confirmed. Functionally, knockdown of NCK1-AS1 suppressed the proliferation, migration and invasion of NSCLC cells, and promoted apoptosis. Moreover, NCK1-AS1 was able to adsorb miR-137 via a sponge effect. Overall, our findings suggested that NCK1-AS1 may be a candidate biomarker and a target for new therapies in NSCLC patients.
Collapse
Affiliation(s)
- Jianxin Li
- Department of Clinical Laboratory, Rizhao Hospital of Traditional Chinese MedicineRizhao City, Shandong Province, China
| | - Xinglong Wu
- Department of Clinical Laboratory, Lanling People’s HospitalLinyi City, Shandong Province, China
| | - Wenxia Cao
- Department of Clinical Laboratory, Anqiu Women and Children’s HospitalAnqiu City, Shandong Province, China
| | - Jianqiang Zhao
- Department of Clinical Laboratory, Weifang People’s HospitalWeifang City, Shandong Province, China
| |
Collapse
|
186
|
Dragomir MP, Manyam GC, Ott LF, Berland L, Knutsen E, Ivan C, Lipovich L, Broom BM, Calin GA. FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs. Noncoding RNA 2020; 6:E41. [PMID: 32977531 PMCID: PMC7712257 DOI: 10.3390/ncrna6040041] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs.
Collapse
Affiliation(s)
- Mihnea P. Dragomir
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.); (B.M.B.)
| | - Leonie Florence Ott
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Léa Berland
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
| | - Erik Knutsen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Cristina Ivan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Centre, Houston, TX 77054, USA
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA;
| | - Bradley M. Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.); (B.M.B.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Centre, Houston, TX 77054, USA
| |
Collapse
|
187
|
Zhang E, Zhang M, Shi C, Sun L, Shan L, Zhang H, Song Y. An overview of advances in multi-omics analysis in prostate cancer. Life Sci 2020; 260:118376. [PMID: 32898525 DOI: 10.1016/j.lfs.2020.118376] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 02/09/2023]
Abstract
Prostate cancer (PCa) is a deadly disease for men, and studies of all types of omics data are necessary to promote precision medicine. The maturity of sequencing technology, the improvements of computer processing power, and the progress achieved in omics analysis methods have improved research efficiency and saved research costs. The occurrence and development of PCa is due to multisystem and multilevel pathological changes. Although omics research at a single level is important, this approach often has limitations. In contrast, the combined analysis of multiple types of omics data can better analyze PCa changes as a whole, thus ensuring the validity of research results to the greatest extent. This paper introduces the applications of single omics in PCa and then summarizes research progress in the combined analysis of two or more types of omics data, so as to systematically and comprehensively analyze the necessity of combined analysis of multiple omics data in PCa.
Collapse
Affiliation(s)
- Enchong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Mo Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Changlong Shi
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Li Sun
- Department of Breast Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Liping Shan
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Hui Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
| | - Yongsheng Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China.
| |
Collapse
|
188
|
Protein-Related Circular RNAs in Human Pathologies. Cells 2020; 9:cells9081841. [PMID: 32781555 PMCID: PMC7463956 DOI: 10.3390/cells9081841] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are a distinct family of RNAs derived from alternative splicing which play a crucial role in regulating gene expression by acting as microRNA (miRNA) and RNA binding protein (RBP) sponges. However, recent studies have also reported the multifunctional potential of these particles. Under different conditions, circRNAs not only regulate protein synthesis, destination, and degradation but can serve as protein scaffolds or recruiters and are also able to produce short peptides with active biological functions. circRNAs are under ongoing investigation because of their close association with the development of diseases. Some circRNAs are reportedly expressed in a tissue- and development stage-specific manner. Furthermore, due to other features of circRNAs, including their stability, conservation, and high abundance in bodily fluids, they are believed to be potential biomarkers for various diseases, including cancers. In this review, we focus on providing a summary of the current knowledge on circRNA-protein interactions. We present the properties and functions of circRNAs, the possible mechanisms of their translation abilities, and the emerging functions of circRNA-derived peptides in human pathologies.
Collapse
|
189
|
Farooqi AA, Fayyaz S, Poltronieri P, Calin G, Mallardo M. Epigenetic deregulation in cancer: Enzyme players and non-coding RNAs. Semin Cancer Biol 2020; 83:197-207. [PMID: 32738290 DOI: 10.1016/j.semcancer.2020.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 02/08/2023]
Abstract
Data obtained from cutting-edge research have shown that deregulated epigenetic marks are critical hallmarks of cancer. Rapidly emerging scientific evidence has helped in developing a proper understanding of the mechanisms leading to control of cellular functions, from changes in chromatin accessibility, transcription and translation, and in post-translational modifications. Firstly, mechanisms of DNA methylation and demethylation are introduced, as well as modifications of DNA and RNA, with particular focus on N6-methyladenosine (m6A), discussing the effects of these modifications in normal cells and in malignancies. Then, chromatin modifying proteins and remodelling complexes are discussed. Many enzymes and accessory proteins in these complexes have been found mutated or have undergone differential splicing, leading to defective protein complexes. Epigenetic mechanisms acting on nucleosomes by polycomb repressive complexes and on chromatin by SWI/SNF complexes on nucleosome assembly/disassembly, as well as main mutated genes linked to cancers, are reviewed. Among enzymes acting on histones and other proteins erasing the reversible modifications are histone deacetylases (HDACs). Sirtuins are of interest since most of these enzymes not only deacylate histones and other proteins, but also post-translationally modify proteins adding a Mono-ADP-ribose (MAR) moiety. MAR can be read by MACRO-domain containing proteins such as histone MacroH2A1, with specific function in chromatin assembly. Finally, recent advances are presented on non-coding RNAs with a scaffold function, prospecting their role in assembly of chromatin modifying complexes, recruiting enzyme players to chromatin regions. Lastly, the imbalance in metabolites production due to mitochondrial dysfunction is presented, with the potential of these metabolites to inhibit enzymes, either writers, readers or erasers of epitranscriptome marks. In the perspectives, studies are overwied on drugs under development aiming to limit excessive enzyme activities and to reactivate chromatin modifying complexes, for therapeutic application. This knowledge may lead to novel drugs and personalised medicine for cancer patients.
Collapse
Affiliation(s)
- Ammad Ahmad Farooqi
- Department of Molecular Oncology, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan.
| | | | - Palmiro Poltronieri
- Institute of Sciences of Food Productions, National Research Council of Italy, via Monteroni Km 7, 73100 Lecce, Italy.
| | - George Calin
- Department of Experimental Therapeutics, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples, "Federico II" via Pansini 5, Napoli, Italy.
| |
Collapse
|
190
|
Zhang X, Wang L, Li H, Zhang L, Zheng X, Cheng W. Crosstalk between noncoding RNAs and ferroptosis: new dawn for overcoming cancer progression. Cell Death Dis 2020; 11:580. [PMID: 32709863 PMCID: PMC7381619 DOI: 10.1038/s41419-020-02772-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
Cancer progression including proliferation, metastasis, and chemoresistance has become a serious hindrance to cancer therapy. This phenomenon mainly derives from the innate insensitive or acquired resistance of cancer cells to apoptosis. Ferroptosis is a newly discovered mechanism of programmed cell death characterized by peroxidation of the lipid membrane induced by reactive oxygen species. Ferroptosis has been confirmed to eliminate cancer cells in an apoptosis-independent manner, however, the specific regulatory mechanism of ferroptosis is still unknown. The use of ferroptosis for overcoming cancer progression is limited. Noncoding RNAs have been found to play an important roles in cancer. They regulate gene expression to affect biological processes of cancer cells such as proliferation, cell cycle, and cell death. Thus far, the functions of ncRNAs in ferroptosis of cancer cells have been examined, and the specific mechanisms by which noncoding RNAs regulate ferroptosis have been partially discovered. However, there is no summary of ferroptosis associated noncoding RNAs and their functions in different cancer types. In this review, we discuss the roles of ferroptosis-associated noncoding RNAs in detail. Moreover, future work regarding the interaction between noncoding RNAs and ferroptosis is proposed, the possible obstacles are predicted and associated solutions are put forward. This review will deepen our understanding of the relationship between noncoding RNAs and ferroptosis, and provide new insights in targeting noncoding RNAs in ferroptosis associated therapeutic strategies.
Collapse
Affiliation(s)
- Xuefei Zhang
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China
| | - Lingling Wang
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China
| | - Haixia Li
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China
| | - Lei Zhang
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China.
| | - Xiulan Zheng
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China.
| | - Wen Cheng
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, 150 Haping Road, 150040, Harbin, China.
| |
Collapse
|
191
|
Wang L, Liang W, Wang S, Wang Z, Bai H, Jiang Y, Bi Y, Chen G, Chang G. Circular RNA expression profiling reveals that circ-PLXNA1 functions in duck adipocyte differentiation. PLoS One 2020; 15:e0236069. [PMID: 32692763 PMCID: PMC7373283 DOI: 10.1371/journal.pone.0236069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Adipocytes are derived from pluripotent mesenchymal stem cells through adipogenesis. Pre-adipocyte differentiation in poultry greatly influences fat deposition and meat quality. Circular RNAs (circRNAs) have an important function in cancer and some differentiation processes. Herein, high-throughput transcriptome sequencing was used to detect circRNAs present in cherry valley duck pre-adipocyte and adipocyte differentiation over 3 days. We identified 9,311 circRNAs and 141 differentially expressed circRNAs. Sequencing results were verified through qRT-PCR using seven randomly selected circRNAs, and competing endogenous RNA (ceRNA) networks were exhibited by ten important circRNAs in duck adipocyte differentiation. circRNA plexin A1 (circ-PLXNA1) was detected in duck adipocytes and mainly expressed in adipose, leg muscle and liver. Inhibition of circ-PLXNA1 limited the differentiation of duck adipocyte. There were four corresponding miRNAs for circ-PLXNA1 and 313 target genes for those miRNAs. CeRNA“circ-PLXNA1/miR-214/CTNNB1 axis” was focused and verified by a dual-luciferase reporter experiment. After co-transfection of cells with si-circ-PLXNA1 and miR-214 mimics, the expression level of CTNNB1 was down-regulated, triglyceride content and the adipogenic capacity of preadipocytes decreased. While there were no significant change after si-CTNNB1 transfection. All these results provide further insight into the circRNAs, especially for circ-PLXNA1 in duck adipocyte differentiation.
Collapse
Affiliation(s)
- Laidi Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Wenshuang Liang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Shasha Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
- * E-mail:
| |
Collapse
|
192
|
Fu D, Shi Y, Liu JB, Wu TM, Jia CY, Yang HQ, Zhang DD, Yang XL, Wang HM, Ma YS. Targeting Long Non-coding RNA to Therapeutically Regulate Gene Expression in Cancer. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:712-724. [PMID: 32771923 PMCID: PMC7412722 DOI: 10.1016/j.omtn.2020.07.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023]
Abstract
Long-chain non-coding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nt and no function of encoding proteins. lncRNAs play a precise regulatory function at different levels of transcription and post-transcription, and they interact with various regulatory factors to regulate gene expression, and then participate in cell growth, differentiation, apoptosis, and other life processes. In recent years, studies have shown that the abnormal expression of lncRNAs is closely related to the occurrence and development of tumors, which is expected to become an effective biomarker in tumor diagnosis. The sequencing analysis of mutations in the whole tumor genome suggests that mutations in non-coding regions may play an important role in the occurrence and development of tumors. Therefore, in-depth study of lncRNAs is helpful to clarify the molecular mechanism of tumor occurrence and development and to provide new targets for tumor diagnosis and treatment. This review introduces the molecular mechanism and clinical application prospect of lncRNAs affecting tumor development from the perspective of gene expression and regulation.
Collapse
Affiliation(s)
- Da Fu
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China; Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| | - Yi Shi
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Ting-Miao Wu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Qiong Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yu-Shui Ma
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China; Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| |
Collapse
|
193
|
Lv X, Chen W, Sun W, Hussain Z, Wang S, Wang J. Analysis of lncRNAs Expression Profiles in Hair Follicle of Hu Sheep Lambskin. Animals (Basel) 2020; 10:ani10061035. [PMID: 32549352 PMCID: PMC7341247 DOI: 10.3390/ani10061035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Lambskin of the Hu sheep exhibits high economic value due to its water-wave pattern. Wool curvature is the key factor of the pattern types and quality of lambskin, and it is formed by the interaction between dermal papilla cells and hair matrix cells in the hair follicle, which is regulated by various genes and signaling pathways. Herein, three full-sibling pairs of two-day-old healthy lambs (n = 6) were divided into a straight wool group (ST) and small waves group (SM) with three repetitions. RNA-seq was applied to determine the expression profile of mRNAs and lncRNAs in Hu sheep hair follicles. 25 differentially expressed mRNAs and 75 differentially expressed lncRNAs were found between SM and ST. FGF12, ATP1B4, and TCONS_00279168 were probably associated with hair follicle development. Then, Gene Ontology (GO) and KEGG enrichment analysis were implemented for the functional annotation of target genes of differentially expressed lncRNAs. The results showed that many genes, such as FGF12 and ATP1B4, were found enriched in PI3K-Akt signaling, MAPK signaling, and Ras signaling pathway associated with hair follicle growth and development. In addition, the interaction network of differentially expressed lncRNAs and mRNAs showed that a total of 6 differentially expressed lncRNAs were associated with 12 differentially expressed mRNAs, which may be as candidate mRNAs and lncRNAs. TCONS_00279168 may target ATP1B4 and FGF12 to regulate MAPK, PI3K-Akt, Ras signaling pathways involved in the sheep hair follicle development process. These results will provide the basis for exploring hair follicle development.
Collapse
Affiliation(s)
- Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.S.); (J.W.); Tel.: +86-0514-87979213 (W.S.)
| | - Zahid Hussain
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
- Correspondence: (W.S.); (J.W.); Tel.: +86-0514-87979213 (W.S.)
| |
Collapse
|
194
|
Zhao T, Zhang J, Ye C, Tian L, Li Y. lncRNA FOXD2-AS1 promotes hemangioma progression through the miR-324-3p/PDRG1 pathway. Cancer Cell Int 2020; 20:189. [PMID: 32489325 PMCID: PMC7247140 DOI: 10.1186/s12935-020-01277-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) are reported could function as tumor promoter in several cancers. However, its role in hemangioma was not reported to yet. Methods Expression level of FOXD2-AS1 in hemangioma tissues and cells was explored using quantitative reverse-time PCR. Cell counting kit-8 (CCK-8) assay, colony formation assay, wound-healing assay, and transwell invasion assay were conducted to measure the roles of FOXD2-AS1. In addition, the levels of markers for proliferation and Epithelial-Mesenchymal Transition were investigated. Connection of FOXD2-AS1 and mcroRNA-324-3p (miR-324-3p) or miR-324-3p and p53 and DNA damage regulated 1 (PDRG1) was analyzed with bioinformatic analysis method and dual-luciferase activity reporter assay. Results Here, we found that FOXD2-AS1 was highly expressed in proliferating-phase hemangioma tissues compared with the involuting-phase hemangioma tissues. Functionally, FOXD2-AS1 knockdown suppressed cell proliferation, colony formation, migration, and invasion in vitro. Conversely, overexpression of FOXD2-AS1 promoted tumor growth in vitro. Mechanistically, FOXD2-AS1 inversely regulated miR-324-3p abundance in hemangioma cells. We also found FOXD2-AS1 acted as a competing endogenous RNA (ceRNA) by directly sponging miR-324-3p to regulate PDRG1 expression. In addition, the knockdown of PDRG1 reversed the stimulation effects of FOXD2-AS1 overexpression on HA cells. Conclusion To conclude, our study sheds novel light on the biological roles of FOXD2-AS1 in hemangioma, which may help the development of targeted therapy method for cancer.
Collapse
Affiliation(s)
- Tiancheng Zhao
- Department of Endoscopic Center, The Third Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jiayu Zhang
- Department of Gastrointestinal Colorectal and Anal Surgery, The Third Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Cong Ye
- Department of Obstetrics and Gynecology, The Third Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Leilei Tian
- Operating Room, The Third Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Yezhou Li
- Department of Vascular Surgery, The Third Hospital of Jilin University, Changchun, 130000 Jilin China
| |
Collapse
|
195
|
Mechanisms of Long Non-Coding RNAs in Cancers and Their Dynamic Regulations. Cancers (Basel) 2020; 12:cancers12051245. [PMID: 32429086 PMCID: PMC7281179 DOI: 10.3390/cancers12051245] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA (lncRNA), which is a kind of noncoding RNA, is generally characterized as being more than 200 nucleotide transcripts in length. LncRNAs exhibit many biological activities, including, but not limited to, cancer development. In this review, a search of the PubMed database was performed to identify relevant studies published in English. The term "lncRNA or long non-coding RNA" was combined with a range of search terms related to the core focus of the review: mechanism, structure, regulation, and cancer. The eligibility of the retrieved studies was mainly based on the abstract. The decision as to whether or not the study was included in this review was made after a careful assessment of its content. The reference lists were also checked to identify any other study that could be relevant to this review. We first summarized the molecular mechanisms of lncRNAs in tumorigenesis, including competing endogenous RNA (ceRNA) mechanisms, epigenetic regulation, decoy and scaffold mechanisms, mRNA and protein stability regulation, transcriptional and translational regulation, miRNA processing regulation, and the architectural role of lncRNAs, which will help a broad audience better understand how lncRNAs work in cancer. Second, we introduced recent studies to elucidate the structure of lncRNAs, as there is a link between lncRNA structure and function and visualizing the architectural domains of lncRNAs is vital to understanding their function. Third, we explored emerging evidence for regulators of lncRNA expression, lncRNA turnover, and lncRNA modifications (including 5-methylcytidine, N6-methyladenosine, and adenosine to inosine editing), highlighting the dynamics of lncRNAs. Finally, we used autophagy in cancer as an example to interpret the diverse mechanisms of lncRNAs and introduced clinical trials of lncRNA-based cancer therapies.
Collapse
|
196
|
Tian Q, Yan X, Yang L, Liu Z, Yuan Z, Shen Z, Zhang Y. lncRNA NORAD promotes hepatocellular carcinoma progression via regulating miR-144-3p/SEPT2. Am J Transl Res 2020; 12:2257-2266. [PMID: 32509217 PMCID: PMC7269989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Non-coding RNA has been reported to be crucial regulator for cancer progression. This work was aimed to investigate the roles and associated mechanisms of non-coding RNA activated by DNA damage (NORAD) in hepatocellular carcinoma (HCC) progression. In this work, we explored the expression of NORAD, microRNA-144-3p (miR-144-3p), and septin 2 (SEPT2) in HCC tissues and cells. Effects of knockdown of ectopic of NORAD on HCC cell proliferation, colony formation, and apoptosis were explored. Rescue experiments were conducted to explore whether NORAD regulates HCC cell behaviors via the miR-144-3p/SEPT2 axis. Moreover, the effect of NORAD on HCC tumor progression in vivo was analyzed. We showed NORAD expression was elevated in both HCC tissues and cells. NORAD knockdown inhibits HCC cell growth but promotes apoptosis, while the overexpression of NORAD has opposite effects. Besides that, we found knockdown of NPRAD inhibits tumor growth. Moreover, we showed miR-144-3p expression was inversely correlated with NORAD and SEPT2, while NORAD and SEPT2 was positively correlated in HCC tissues. Functional assays showed NORAD functions as ceRNA through binding with miR-144-3p to regulate SEPT2 expression in HCC. Collectively, we showed NORAD serves as an oncogenic lncRNA to promote HCC progression via the miR-144-3p/SEPT2 axis.
Collapse
Affiliation(s)
- Qing Tian
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
| | - Xiaodong Yan
- First Central Clinic College, Tianjin Medical UniversityTianjin 300052, P. R. China
| | - Long Yang
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
| | - Zirong Liu
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
| | - Zheyue Yuan
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
- First Central Clinic College, Tianjin Medical UniversityTianjin 300052, P. R. China
| | - Zhongyang Shen
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
| | - Yamin Zhang
- Department of Hepatobiliary Surgery, Tianjin First Central HospitalTianjin 300192, P. R. China
- Tianjin Key Laboratory for Transplantation, Tianjin First Central HospitalTianjin 300192, P. R. China
| |
Collapse
|
197
|
Du WW, Yang W, Li X, Fang L, Wu N, Li F, Chen Y, He Q, Liu E, Yang Z, Awan FM, Liu M, Yang BB. The Circular RNA circSKA3 Binds Integrin β1 to Induce Invadopodium Formation Enhancing Breast Cancer Invasion. Mol Ther 2020; 28:1287-1298. [PMID: 32229309 PMCID: PMC7210749 DOI: 10.1016/j.ymthe.2020.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/14/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
Metastatic cancer cells invade surrounding tissues by forming dynamic actin-based invadopodia, which degrade the surrounding extracellular matrix and allow cancer cell invasion. Regulatory RNAs, including circular RNA, have been implicated in this process. By microarray, we found that the circular RNA circSKA3 was highly expressed in breast cancer cells and human breast cancer tissues. We further found that the invasive capacity of breast cancer cells was positively correlated with circSKA3 expression, through the formation of invadopodia. Mechanistically, we identified Tks5 and integrin β1 as circSKA3 binding partners in these tumor-derived invadopodia. Ectopic circSKA3 expression conferred increased tumor invasiveness in vitro and in vivo. We further identified the RNA-protein binding sites between circSKA3, Tks5 and integrin β1. In tumor formation assays, we found that circSKA3 expression promoted tumor progression and invadopodium formation. Mutation of the circSKA3 binding sites or transfection with blocking oligos abrogated the observed effects. Thus, we provide evidence that the circular RNA circSKA3 promotes tumor progression by complexing with Tks5 and integrin β1, inducing invadopodium formation.
Collapse
Affiliation(s)
- William W Du
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Weining Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Xiangmin Li
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ling Fang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; China-Japan Union Hospital of Jilin University, Jilin, China
| | - Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Yu Chen
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Qihan He
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Elizabeth Liu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Zhenguo Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Faryal Mehwish Awan
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Mingyao Liu
- Institutes of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Institutes of Medical Science, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
198
|
Meng N, Chen M, Chen D, Chen X, Wang J, Zhu S, He Y, Zhang X, Lu R, Yan G. Small Protein Hidden in lncRNA LOC90024 Promotes "Cancerous" RNA Splicing and Tumorigenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903233. [PMID: 32440474 PMCID: PMC7237858 DOI: 10.1002/advs.201903233] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 05/10/2023]
Abstract
Conventional therapies for late-stage colorectal cancer (CRC) have limited effects because of chemoresistance, recurrence, and metastasis. The "hidden" proteins/peptides encoded by long noncoding RNAs (lncRNAs) may be a novel resource bank for therapeutic options for patients with cancer. Here, lncRNA LOC90024 is discovered to encode a small 130-amino acid protein that interacts with several splicing regulators, such as serine- and arginine-rich splicing factor 3 (SRSF3), to regulate mRNA splicing, and the protein thus is named "Splicing Regulatory Small Protein" (SRSP). SRSP, but not LOC90024 lncRNA itself, promotes CRC tumorigenesis and progression, while silencing of SRSP suppresses CRC tumorigenesis. Mechanistically, SRSP increases the binding of SRSF3 to exon 3 of transcription factor Sp4, resulting in the inclusion of Sp4 exon 3 to induce the formation of the "cancerous" long Sp4 isoform (L-Sp4 protein) and inhibit the formation of the "noncancerous" short Sp4 isoform (S-Sp4 peptide), which lacks the transactivation domain. The upregulated SRSP level is positively associated with malignant phenotypes and poor prognosis in patients with CRC. Collectively, the findings uncover that a lncRNA-encoded small protein SRSP induces "cancerous" Sp4 splicing variant formation and may be a potential prognostic biomarker and therapeutic target for patients with CRC.
Collapse
Affiliation(s)
- Nan Meng
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Min Chen
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - De Chen
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Xin‐Hui Chen
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Ji‐Zhong Wang
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Song Zhu
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Yu‐Tian He
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Xiao‐Lan Zhang
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and DegradationState Key Laboratory of Respiratory DiseaseGuangzhou Medical UniversityGuangzhou511436China
| | - Rui‐Xun Lu
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Guang‐Rong Yan
- Biomedicine Research CenterThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and DegradationState Key Laboratory of Respiratory DiseaseGuangzhou Medical UniversityGuangzhou511436China
| |
Collapse
|
199
|
An oncopeptide regulates m 6A recognition by the m 6A reader IGF2BP1 and tumorigenesis. Nat Commun 2020; 11:1685. [PMID: 32245947 PMCID: PMC7125119 DOI: 10.1038/s41467-020-15403-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic RNAs. The biological importance of m6A relies on m6A readers, which control mRNA fate and function. However, it remains unexplored whether additional regulatory subunits of m6A readers are involved in the m6A recognition on RNAs. Here we discover that the long noncoding RNA (lncRNA) LINC00266-1 encodes a 71-amino acid peptide. The peptide mainly interacts with the RNA-binding proteins, including the m6A reader IGF2BP1, and is thus named "RNA-binding regulatory peptide" (RBRP). RBRP binds to IGF2BP1 and strengthens m6A recognition by IGF2BP1 on RNAs, such as c-Myc mRNA, to increase the mRNA stability and expression of c-Myc, thereby promoting tumorigenesis. Cancer patients with RBRPhigh have a poor prognosis. Thus, the oncopeptide RBRP encoded by LINC00266-1 is a regulatory subunit of m6A readers and strengthens m6A recognition on the target RNAs by the m6A reader to exert its oncogenic functions.
Collapse
|
200
|
Huang A, Zheng H, Wu Z, Chen M, Huang Y. Circular RNA-protein interactions: functions, mechanisms, and identification. Theranostics 2020; 10:3503-3517. [PMID: 32206104 PMCID: PMC7069073 DOI: 10.7150/thno.42174] [Citation(s) in RCA: 460] [Impact Index Per Article: 115.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/29/2020] [Indexed: 12/30/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed, endogenous RNAs with no 5' end caps or 3' poly(A) tails. These RNAs are expressed in tissue-specific, cell-specific, and developmental stage-specific patterns. The biogenesis of circRNAs is now known to be regulated by multiple specific factors; however, circRNAs were previously thought to be insignificant byproducts of splicing errors. Recent studies have demonstrated their activity as microRNA (miRNA) sponges as well as protein sponges, decoys, scaffolds, and recruiters, and some circRNAs even act as translation templates in multiple pathophysiological processes. CircRNAs bind and sequester specific proteins to appropriate subcellular positions, and they participate in modulating certain protein-protein and protein-RNA interactions. Conversely, several proteins play an indispensable role in the life cycle of circRNAs from biogenesis to degradation. However, the exact mechanisms of these interactions between proteins and circRNAs remain unknown. Here, we review the current knowledge regarding circRNA-protein interactions and the methods used to identify and characterize these interactions. We also summarize new insights into the potential mechanisms underlying these interactions.
Collapse
Affiliation(s)
- Anqing Huang
- Department of Cardiology, Shunde Hospital, Southern Medical University, Jiazhi Road, Lunjiao Town, Shunde District, Foshan, 528300, China
| | - Haoxiao Zheng
- Department of Cardiology, Shunde Hospital, Southern Medical University, Jiazhi Road, Lunjiao Town, Shunde District, Foshan, 528300, China
| | - Zhiye Wu
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Minsheng Chen
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuli Huang
- Department of Cardiology, Shunde Hospital, Southern Medical University, Jiazhi Road, Lunjiao Town, Shunde District, Foshan, 528300, China
- The George Institute for Global Health, NSW 2042 Australia
| |
Collapse
|