1
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Zhang J, Zhu H, Li L, Gao Y, Yu B, Ma G, Jin X, Sun Y. New mechanism of LncRNA: In addition to act as a ceRNA. Noncoding RNA Res 2024; 9:1050-1060. [PMID: 39022688 PMCID: PMC11254507 DOI: 10.1016/j.ncrna.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/20/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.
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Affiliation(s)
- Jiahao Zhang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Huike Zhu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Linjing Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Sciences, Northwest Normal University, Gansu Province, Lanzhou, 730070, China
| | - Boyi Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guorong Ma
- The First Clinical Medical College of Gansu University of Chinese Medicine Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Xiaodong Jin
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
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2
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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024; 32:2905-2929. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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3
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Caporali A, Anwar M, Devaux Y, Katare R, Martelli F, Srivastava PK, Pedrazzini T, Emanueli C. Non-coding RNAs as therapeutic targets and biomarkers in ischaemic heart disease. Nat Rev Cardiol 2024; 21:556-573. [PMID: 38499868 DOI: 10.1038/s41569-024-01001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 03/20/2024]
Abstract
The adult heart is a complex, multicellular organ that is subjected to a series of regulatory stimuli and circuits and has poor reparative potential. Despite progress in our understanding of disease mechanisms and in the quality of health care, ischaemic heart disease remains the leading cause of death globally, owing to adverse cardiac remodelling, leading to ischaemic cardiomyopathy and heart failure. Therapeutic targets are urgently required for the protection and repair of the ischaemic heart. Moreover, personalized clinical biomarkers are necessary for clinical diagnosis, medical management and to inform the individual response to treatment. Non-coding RNAs (ncRNAs) deeply influence cardiovascular functions and contribute to communication between cells in the cardiac microenvironment and between the heart and other organs. As such, ncRNAs are candidates for translation into clinical practice. However, ncRNA biology has not yet been completely deciphered, given that classes and modes of action have emerged only in the past 5 years. In this Review, we discuss the latest discoveries from basic research on ncRNAs and highlight both the clinical value and the challenges underscoring the translation of these molecules as biomarkers and therapeutic regulators of the processes contributing to the initiation, progression and potentially the prevention or resolution of ischaemic heart disease and heart failure.
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Affiliation(s)
- Andrea Caporali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxemburg
| | - Rajesh Katare
- Department of Physiology, HeartOtago, University of Otago, Dunedin, New Zealand
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | | | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- School of Cardiovascular and Metabolic Medicine & Sciences, King's College London, London, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, UK
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, UK.
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4
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Ma RT, Wang Y, Ji F, Chen JN, Wang TJ, Liu Y, Hou MX, Guo ZG. YTHDF1's grip on CRC vasculature: insights into LINC01106 and miR-449b-5p-VEGFA axis. Cancer Cell Int 2024; 24:195. [PMID: 38835070 DOI: 10.1186/s12935-024-03360-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Investigating the unexplored territory of lncRNA m6A modification in colorectal cancer (CRC) vasculature, this study focuses on LINC01106 and YTHDF1. METHODS Clinical assessments reveal upregulated LINC01106 promoting vascular generation via the miR-449b-5p-VEGFA pathway. RESULTS YTHDF1, elevated in CRC tissues, emerges as an adverse prognostic factor. Functional experiments showcase YTHDF1's inhibitory effects on CRC cell dynamics. Mechanistically, Me-CLIP identifies m6A-modified LINC01106, validated as a YTHDF1 target through Me-RIP. CONCLUSIONS This study sheds light on the YTHDF1-mediated m6A modification of LINC01106, presenting it as a key player in suppressing CRC vascular generation.
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Affiliation(s)
- Rui-Ting Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China
| | - Yuanyuan Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Feng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Jian-Nan Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Tian-Jun Wang
- Nanjing Medical University, Nanjing, Jiangsu, 210097, China
| | - Yan Liu
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China
| | - Ming-Xing Hou
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China.
| | - Zhi-Gang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.
- The Academy of Life Sciences, Nanjing Normal University, Nanjing, 210097, China.
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5
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024:elae018. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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6
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Jimenez SA, Piera-Velazquez S. Cellular Transdifferentiation: A Crucial Mechanism of Fibrosis in Systemic Sclerosis. Curr Rheumatol Rev 2024; 20:388-404. [PMID: 37921216 DOI: 10.2174/0115733971261932231025045400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 11/04/2023]
Abstract
Systemic Sclerosis (SSc) is a systemic autoimmune disease of unknown etiology with a highly complex pathogenesis that despite extensive investigation is not completely understood. The clinical and pathologic manifestations of the disease result from three distinct processes: 1) Severe and frequently progressive tissue fibrosis causing exaggerated and deleterious accumulation of interstitial collagens and other extracellular matrix molecules in the skin and various internal organs; 2) extensive fibroproliferative vascular lesions affecting small arteries and arterioles causing tissue ischemic alterations; and 3) cellular and humoral immunity abnormalities with the production of numerous autoantibodies, some with very high specificity for SSc. The fibrotic process in SSc is one of the main causes of disability and high mortality of the disease. Owing to its essentially universal presence and the severity of its clinical effects, the mechanisms involved in the development and progression of tissue fibrosis have been extensively investigated, however, despite intensive investigation, the precise molecular mechanisms have not been fully elucidated. Several recent studies have suggested that cellular transdifferentiation resulting in the phenotypic conversion of various cell types into activated myofibroblasts may be one important mechanism. Here, we review the potential role that cellular transdifferentiation may play in the development of severe and often progressive tissue fibrosis in SSc.
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Affiliation(s)
- Sergio A Jimenez
- Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia 19107, USA
| | - Sonsoles Piera-Velazquez
- Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia 19107, USA
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8
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Ghosh A, Som A. Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells. Differentiation 2024; 135:100738. [PMID: 38008592 DOI: 10.1016/j.diff.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Growing evidence has shown that besides the protein coding genes, the non-coding elements of the genome are indispensable for maintaining the property of self-renewal in human embryonic stem cells and in cell fate determination. However, the regulatory mechanisms and the landscape of interactions between the coding and non-coding elements is poorly understood. In this work, we used weighted gene co-expression network analysis (WGCNA) on transcriptomic data retrieved from RNA-seq and small RNA-seq experiments and reconstructed the core human pluripotency network (called PluriMLMiNet) consisting of 375 mRNA, 57 lncRNA and 207 miRNAs. Furthermore, we derived networks specific to the naïve and primed states of human pluripotency (called NaiveMLMiNet and PrimedMLMiNet respectively) that revealed a set of molecular markers (RPS6KA1, ZYG11A, ZNF695, ZNF273, and NLRP2 for naive state, and RAB34, TMEM178B, PTPRZ1, USP44, KIF1A and LRRN1 for primed state) which can be used to distinguish the pluripotent state from the non-pluripotent state and also to identify the intra-pluripotency states (i.e., naïve and primed state). The lncRNA DANT1 was found to be a crucial as it formed a bridge between the naive and primed state-specific networks. Analysis of the genes neighbouring DANT1 suggested its possible role as a competing endogenous RNA (ceRNA) for the induction and maintenance of human pluripotency. This was computationally validated by predicting the missing DANT1-miRNA interactions to complete the ceRNA circuit. Here we first report that DANT1 might harbour binding sites for miRNAs hsa-miR-30c-2-3p, hsa-miR-210-3p and hsa-let-7b-5p which may influence pluripotency.
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Affiliation(s)
- Arindam Ghosh
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India; Institute of Biomedicine, University of Eastern Finland, FI-70210, Kuopio, Finland.
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India.
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9
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Wang J, Wang W, Ma F, Qian H. A hidden translatome in tumors-the coding lncRNAs. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2755-2772. [PMID: 37154857 DOI: 10.1007/s11427-022-2289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 05/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers. Through the application and development of ribosome analysis and sequencing technologies, advanced studies have discovered the translation of lncRNAs. Although lncRNAs were originally defined as noncoding RNAs, many lncRNAs actually contain small open reading frames that are translated into peptides. This opens a broad area for the functional investigation of lncRNAs. Here, we introduce prospective methods and databases for screening lncRNAs with functional polypeptides. We also summarize the specific lncRNA-encoded proteins and their molecular mechanisms that promote or inhibit cancerous. Importantly, the role of lncRNA-encoded peptides/proteins holds promise in cancer research, but some potential challenges remain unresolved. This review includes reports on lncRNA-encoded peptides or proteins in cancer, aiming to provide theoretical basis and related references to facilitate the discovery of more functional peptides encoded by lncRNA, and to further develop new anti-cancer therapeutic targets as well as clinical biomarkers of diagnosis and prognosis.
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Affiliation(s)
- Jinsong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenna Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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10
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Hor YZ, Salvamani S, Gunasekaran B, Yian KR. CRNDE: A Pivotal Oncogenic Long Non-Coding RNA in Cancers. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:511-526. [PMID: 38161583 PMCID: PMC10751873 DOI: 10.59249/vhye2306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Colorectal Neoplasia Differentially Expressed (CRNDE), a long non-coding RNA that was initially identified as aberrantly expressed in colorectal cancer (CRC) has also been observed to exhibit elevated expression in various other human malignancies. Recent research has accumulated substantial evidence implicating CRNDE as an oncogenic player, exerting influence over critical cellular processes linked to cancer progression. Particularly, its regulatory interactions with microRNAs and proteins have been shown to modulate pathways that contribute to carcinogenesis and tumorigenesis. This review will comprehensively outline the roles of CRNDE in colorectal, liver, glioma, lung, cervical, gastric and prostate cancer, elucidating the mechanisms involved in modulating proliferation, apoptosis, migration, invasion, angiogenesis, and radio/chemoresistance. Furthermore, the review highlights CRNDE's potential as a multifaceted biomarker, owing to its presence in diverse biological samples and stable properties, thereby underscoring its diagnostic, therapeutic, and prognostic applications. This review aims to provide comprehensive insights of CRNDE-mediated oncogenesis and identify CRNDE as a promising target for future clinical interventions.
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Affiliation(s)
- Yi Zhen Hor
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Shamala Salvamani
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied
Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Koh Rhun Yian
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
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11
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Yang K, Xiao Y, Zhong L, Zhang W, Wang P, Ren Y, Shi L. p53-regulated lncRNAs in cancers: from proliferation and metastasis to therapy. Cancer Gene Ther 2023; 30:1456-1470. [PMID: 37679529 DOI: 10.1038/s41417-023-00662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been identified as master gene regulators through various mechanisms such as transcription, translation, protein modification and RNA-protein complexes. LncRNA dysregulation is frequently associated with a variety of biological functions and human diseases including cancer. The p53 network is a key tumor-suppressive mechanism that transcriptionally activates target genes to suppress cellular proliferation in human malignancies. Recent research indicates that lncRNAs play an important role in the p53 signaling pathway. In this review, we summarize the current knowledge of lncRNAs in p53-relevant functions and provide an overview of how these altered lncRNAs contribute to tumor initiation and progression. We also discuss the association between lncRNA and up- or downstream genes of p53. These findings imply that lncRNAs can help identify cellular vulnerabilities that may prove to be promising potential biomarkers and therapeutic targets for cancer treatment.
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Affiliation(s)
- Kaixin Yang
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yinan Xiao
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Linghui Zhong
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Wenyang Zhang
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Peng Wang
- College of Animal Science and Technology, Hebei North University, Zhangjiakou, 075131, People's Republic of China
| | - Yaru Ren
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Lei Shi
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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12
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Zhang L, Tang M, Diao H, Xiong L, Yang X, Xing S. LncRNA-encoded peptides: unveiling their significance in cardiovascular physiology and pathology-current research insights. Cardiovasc Res 2023; 119:2165-2178. [PMID: 37517040 DOI: 10.1093/cvr/cvad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/17/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), which are RNA transcripts exceeding 200 nucleotides were believed to lack any protein-coding capacity. But advancements in -omics technology have revealed that some lncRNAs have small open reading frames (sORFs) that can be translated by ribosomes to encode peptides, some of which have important biological functions. These encoded peptides subserve important biological functions by interacting with their targets to modulate transcriptional or signalling axes, thereby enhancing or suppressing cardiovascular disease (CVD) occurrence and progression. In this review, we summarize what is known about the research strategy of lncRNA-encoded peptides, mainly comprising predictive websites/tools and experimental methods that have been widely used for prediction, identification, and validation. More importantly, we have compiled a list of lncRNA- encoded peptides, with a focus on those that play significant roles in cardiovascular physiology and pathology, including ENSRNOT (RNO)-sORF6/RNO-sORF7/RNO-sORF8, dwarf open reading frame (DOWRF), myoregulin (NLN), etc. Additionally, we have outlined the functions and mechanisms of these peptides in cardiovascular physiology and pathology, such as cardiomyocyte hypertrophy, myocardial contraction, myocardial infarction, and vascular remodelling. Finally, an overview of the existing challenges and potential future developments in the realm of lncRNA-encoded peptides was provided, with consideration given to prospective avenues for further research. Given that many lncRNA-encoded peptides have not been functionally annotated yet, their application in CVD diagnosis and treatment still requires further research.
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Affiliation(s)
- Li Zhang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Mi Tang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Haoyang Diao
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Liling Xiong
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Xiao Yang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Shasha Xing
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
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Abstract
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.
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Affiliation(s)
- Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Catalonia
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia
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14
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Meng K, Lu S, Li Y, Hu L, Zhang J, Cao Y, Wang Y, Zhang CZ, He Q. LINC00493-encoded microprotein SMIM26 exerts anti-metastatic activity in renal cell carcinoma. EMBO Rep 2023; 24:e56282. [PMID: 37009826 PMCID: PMC10240204 DOI: 10.15252/embr.202256282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Human microproteins encoded by long non-coding RNAs (lncRNA) have been increasingly discovered, however, complete functional characterization of these emerging proteins is scattered. Here, we show that LINC00493-encoded SMIM26, an understudied microprotein localized in mitochondria, is tendentiously downregulated in clear cell renal cell carcinoma (ccRCC) and correlated with poor overall survival. LINC00493 is recognized by RNA-binding protein PABPC4 and transferred to ribosomes for translation of a 95-amino-acid protein SMIM26. SMIM26, but not LINC00493, suppresses ccRCC growth and metastatic lung colonization by interacting with acylglycerol kinase (AGK) and glutathione transport regulator SLC25A11 via its N-terminus. This interaction increases the mitochondrial localization of AGK and subsequently inhibits AGK-mediated AKT phosphorylation. Moreover, the formation of the SMIM26-AGK-SCL25A11 complex maintains mitochondrial glutathione import and respiratory efficiency, which is abrogated by AGK overexpression or SLC25A11 knockdown. This study functionally characterizes the LINC00493-encoded microprotein SMIM26 and establishes its anti-metastatic role in ccRCC, and therefore illuminates the importance of hidden proteins in human cancers.
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Affiliation(s)
- Kun Meng
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
| | - Shaohua Lu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- Sino‐French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory DiseaseGuangzhou Medical UniversityGuangzhouChina
| | - Yu‐Ying Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Li‐Ling Hu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Jing Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
| | - Yun Cao
- Department of Pathology, State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yang Wang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Chris Zhiyi Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Qing‐Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
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15
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Shliapina VL, Dontsova OA, Rubtsova MP. Deletion of 184-188 Nucleotides of Human Telomerase RNA Does Not Affect the Telomerase Functioning. DOKL BIOCHEM BIOPHYS 2023; 510:104-109. [PMID: 37582872 DOI: 10.1134/s1607672923700205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 08/17/2023]
Abstract
Telomerase is a ribonucleoprotein complex, the main components of which are telomerase RNA and reverse transcriptase. Previously, it was shown in our laboratory that human telomerase RNA contains an open reading frame starting at adenine in position 176. The open reading frame encodes the hTERP protein, and the deletion of nucleotides 184-188 of human telomerase RNA disrupts the open reading frame and leads to the absence of hTERP. Human telomerase RNA has a conserved structure, changes in which affect telomerase activity. In this work, we have shown that the deletion of nucleotides 184-188 of telomerase RNA does not affect the functioning of telomerase.
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Affiliation(s)
- V L Shliapina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Department of Chemistry, Moscow State University, Moscow, Russia.
| | - O A Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - M P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Moscow State University, Moscow, Russia
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16
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Yang J, Liu M, Fang X, Zhang H, Ren Q, Zheng Y, Wang Y, Zhou Y. Advances in peptides encoded by non-coding RNAs: A cargo in exosome. Front Oncol 2022; 12:1081997. [PMID: 36620552 PMCID: PMC9822543 DOI: 10.3389/fonc.2022.1081997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qian Ren
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
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17
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Cheng C, Liu D, Liu Z, Li M, Wang Y, Sun B, Kong R, Chen H, Wang G, Li L, Hu J, Li Y, Chen H, Zhao Z, Zhang T, Zhu S, Pan S. Positive feedback regulation of lncRNA TPT1-AS1 and ITGB3 promotes cell growth and metastasis in pancreatic cancer. Cancer Sci 2022; 113:2986-3001. [PMID: 35534983 PMCID: PMC9459417 DOI: 10.1111/cas.15388] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/08/2022] [Accepted: 04/18/2022] [Indexed: 11/29/2022] Open
Abstract
Emerging evidence has indicated that long noncoding RNAs (lncRNAs) are potential biomarkers and play crucial roles in cancer development. However, the functions and underlying mechanisms of lncRNA TPT1-AS1 in pancreatic ductal adenocarcinoma (PDAC) remain elusive. RNAseq data of PDAC tissues and normal tissues were analyzed, and lncRNAs which were associated with PDAC prognosis were identified. The clinical relevance of TPT1-AS1 for PDAC patients was explored, and the effects of TPT1-AS1 in PDAC progression were investigated in vitro and in vivo. LncRNA TPT1-AS1 was highly expressed in PDAC, and high TPT1-AS1 levels predicted a poor prognosis. Moreover, functional experiments revealed that TPT1-AS1 promoted pancreatic cancer cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition (EMT) process in vitro and in vivo. Mechanistically, TPT1-AS1 functioned as an endogenous sponge for miR-30a-5p, which increased integrin β3 (ITGB3) level in pancreatic cancer cells. Conversely, our data revealed that ITGB3 could activate the transcription factor signal transducer and activator of transcription 3 (STAT3), which in turn bound directly to the TPT1-AS1 promoter and affected the expression of TPT1-AS1, thus forming a positive feedback loop with TPT1-AS1. Taken together, our results uncovered a reciprocal loop of TPT1-AS1 and ITGB3 which contributed to pancreatic cancer growth and development, and indicated that TPT1-AS1 might serve as a novel potential diagnostic biomarker and therapeutic target for PDAC patients.
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Affiliation(s)
- Chundong Cheng
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Danxi Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Zonglin Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Mengyang Li
- Department of Medical OncologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Yongwei Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Bei Sun
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Rui Kong
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Hua Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Gang Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Le Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Jisheng Hu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Yilong Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Hongze Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Zhongjie Zhao
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Tao Zhang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Siqiang Zhu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
| | - Shangha Pan
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Hepatosplenic SurgeryMinistry of EducationHarbinChina
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18
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Pan J, Wang R, Shang F, Ma R, Rong Y, Zhang Y. Functional Micropeptides Encoded by Long Non-Coding RNAs: A Comprehensive Review. Front Mol Biosci 2022; 9:817517. [PMID: 35769907 PMCID: PMC9234465 DOI: 10.3389/fmolb.2022.817517] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/24/2022] [Indexed: 12/03/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) were originally defined as non-coding RNAs (ncRNAs) which lack protein-coding ability. However, with the emergence of technologies such as ribosome profiling sequencing and ribosome-nascent chain complex sequencing, it has been demonstrated that most lncRNAs have short open reading frames hence the potential to encode functional micropeptides. Such micropeptides have been described to be widely involved in life-sustaining activities in several organisms, such as homeostasis regulation, disease, and tumor occurrence, and development, and morphological development of animals, and plants. In this review, we focus on the latest developments in the field of lncRNA-encoded micropeptides, and describe the relevant computational tools and techniques for micropeptide prediction and identification. This review aims to serve as a reference for future research studies on lncRNA-encoded micropeptides.
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Affiliation(s)
- Jianfeng Pan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rong Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- *Correspondence: Yanjun Zhang,
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19
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Hu JX, Zheng ZQ, Kang T, Qian W, Huang SH, Li BG. LncRNA LINC00961 regulates endothelial‑mesenchymal transition via the PTEN‑PI3K‑AKT pathway. Mol Med Rep 2022; 26:246. [PMID: 35656895 PMCID: PMC9185682 DOI: 10.3892/mmr.2022.12762] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
The long noncoding RNA LINC00961 plays a crucial role in cancer and cardiovascular diseases. In the present study, the role and underlying mechanism of LINC00961 in endothelial-mesenchymal transition (EndMT) induced by transforming growth factor beta (TGF-β), was investigated. Human cardiac microvascular endothelial cells were transfected with LV-LINC00961 or short hairpin LINC00961 plasmids to overexpress or knock down LINC00961 in the cells, respectively. The cells were then exposed to TGF-β in serum-free medium for 48 h to induce EndMT. Flow cytometric analysis, Cell Counting Kit-8 assay and immunofluorescence staining were performed to examine the cell apoptosis rate, assess cell viability, and identify CD31+/α-SMA+ double-positive cells, respectively. Western blotting and reverse transcription- quantitative polymerase chain reaction were used to evaluate protein and mRNA expression, respectively. Injury to endothelial cells and EndMT was induced by TGF-β in a time-dependent manner. LINC00961 overexpression promoted injury and EndMT, whereas LINC00961 knockdown had the opposite effects. Knockdown of LINC00961 attenuated EndMT and injury to endothelial cells induced by TGF-β via the PTEN-PI3K-AKT pathway. Inhibition of LINC00961 expression may prevent the occurrence of EndMT-related cardiovascular diseases, such as myocardial fibrosis and heart failure. Therefore, LINC00961 shows potential as a therapeutic target for cardiovascular diseases.
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Affiliation(s)
- Jin-Xing Hu
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
| | - Ze-Qi Zheng
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
| | - Ting Kang
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
| | - Wei Qian
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
| | - Shan-Hua Huang
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
| | - Bin-Gong Li
- Department of Cardiology, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330033, P.R. China
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20
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Costallat M, Batsché E, Rachez C, Muchardt C. The 'Alu-ome' shapes the epigenetic environment of regulatory elements controlling cellular defense. Nucleic Acids Res 2022; 50:5095-5110. [PMID: 35544277 PMCID: PMC9122584 DOI: 10.1093/nar/gkac346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/13/2022] Open
Abstract
Promoters and enhancers are sites of transcription initiation (TSSs) and carry specific histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval ranging from TSS to first upstream Alu, accommodates all H3K4me3 and most H3K27ac marks, while excluding DNA methylation. Remarkably, the average length of these intervals greatly varies in-between tissues, being longer in stem- and shorter in immune-cells. The very shortest TSS-to-first-Alu intervals were observed at promoters active in T-cells, particularly at immune genes, where first-Alus were traversed by RNA polymerase II transcription, while accumulating H3K4me1 signal. Finally, DNA methylation at first-Alus was found to evolve with age, regressing from young to middle-aged, then recovering later in life. Thus, the first-Alus upstream of TSSs appear as dynamic boundaries marking the transition from DNA methylation to active histone modifications at regulatory elements, while also participating in the recording of immune gene transcriptional events by positioning H3K4me1-modified nucleosomes.
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Affiliation(s)
- Mickael Costallat
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Eric Batsché
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Christophe Rachez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Christian Muchardt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
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21
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Cancer-related micropeptides encoded by ncRNAs: Promising drug targets and prognostic biomarkers. Cancer Lett 2022; 547:215723. [DOI: 10.1016/j.canlet.2022.215723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023]
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22
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Mathew S, Sivasubbu S. Long Non Coding RNA Based Regulation of Cerebrovascular Endothelium. Front Genet 2022; 13:834367. [PMID: 35495157 PMCID: PMC9043600 DOI: 10.3389/fgene.2022.834367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and high throughput discovery of long non coding RNAs (lncRNAs) has far outstripped the functional annotation of these novel transcripts in their respective cellular contexts. The cells of the blood brain barrier (BBB), especially the cerebrovascular endothelial cells (CVECs), are strictly regulated to maintain a controlled state of homeostasis for undisrupted brain function. Several key pathways are understood in CVEC function that lead to the development and maintenance of their barrier properties, the dysregulation of which leads to BBB breakdown and neuronal injury. Endothelial lncRNAs have been discovered and functionally validated in the past decade, spanning a wide variety of regulatory mechanisms in health and disease. We summarize here the lncRNA-mediated regulation of established pathways that maintain or disrupt the barrier property of CVECs, including in conditions such as ischemic stroke and glioma. These lncRNAs namely regulate the tight junction assembly/disassembly, angiogenesis, autophagy, apoptosis, and so on. The identification of these lncRNAs suggests a less understood mechanistic layer, calling for further studies in appropriate models of the blood brain barrier to shed light on the lncRNA-mediated regulation of CVEC function. Finally, we gather various approaches for validating lncRNAs in BBB function in human organoids and animal models and discuss the therapeutic potential of CVEC lncRNAs along with the current limitations.
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Affiliation(s)
- Samatha Mathew
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Sridhar Sivasubbu,
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23
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Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
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24
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Hennessy EJ. LncRNAs and Cardiovascular Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:71-95. [PMID: 35220566 DOI: 10.1007/978-3-030-92034-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A novel class of RNA molecule emerged from human transcriptome sequencing studies termed long non-coding RNAs. These RNA molecules differ from other classes of non-coding RNAs such as microRNAs in their sizes, sequence motifs and structures. Studies have demonstrated that long non-coding RNAs play a prominent role in the development and progression of cardiovascular disease. They provide the cell with tiered levels of gene regulation interacting with DNA, other RNA molecules or proteins acting in various capacities to control a variety of cellular mechanisms. Cell specificity is a hallmark of lncRNA studies and they have been identified in macrophages, smooth muscle cells, endothelial cells and hepatocytes. Recent lncRNA studies have uncovered functional micropeptides encoded within lncRNA genes that can have a different function to the lncRNA. Disease associated mutations in the genome tend to occur in non-coding regions signifying the importance of non-coding genes in disease associations. There is a great deal of work to be done in the non-coding RNA field and tremendous therapeutic potential due to their cell type specificity. A better understanding of the functions and interactions of lncRNAs will inevitably have clinical implications.
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Affiliation(s)
- Elizabeth J Hennessy
- University of Pennsylvania, Perelman School of Medicine, Institute for Translational Medicine and Therapeutics (ITMAT), Philadelphia, PA, USA.
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25
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The dark proteome: translation from noncanonical open reading frames. Trends Cell Biol 2022; 32:243-258. [PMID: 34844857 PMCID: PMC8934435 DOI: 10.1016/j.tcb.2021.10.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Omics-based technologies have revolutionized our understanding of the coding potential of the genome. In particular, these studies revealed widespread unannotated open reading frames (ORFs) throughout genomes and that these regions have the potential to encode novel functional (micro-)proteins and/or hold regulatory roles. However, despite their genomic prevalence, relatively few of these noncanonical ORFs have been functionally characterized, likely in part due to their under-recognition by the broader scientific community. The few that have been investigated in detail have demonstrated their essentiality in critical and divergent biological processes. As such, here we aim to discuss recent advances in understanding the diversity of noncanonical ORFs and their roles, as well as detail biologically important examples within the context of the mammalian genome.
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26
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Mabeta P, Hull R, Dlamini Z. LncRNAs and the Angiogenic Switch in Cancer: Clinical Significance and Therapeutic Opportunities. Genes (Basel) 2022; 13:152. [PMID: 35052495 PMCID: PMC8774855 DOI: 10.3390/genes13010152] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/05/2023] Open
Abstract
Angiogenesis is one of the hallmarks of cancer, and the establishment of new blood vessels is vital to allow for a tumour to grow beyond 1-2 mm in size. The angiogenic switch is the term given to the point where the number or activity of the pro-angiogenic factors exceeds that of the anti-angiogenic factors, resulting in the angiogenic process proceeding, giving rise to new blood vessels accompanied by increased tumour growth, metastasis, and potential drug resistance. Long noncoding ribonucleic acids (lncRNAs) have been found to play a role in the angiogenic switch by regulating gene expression, transcription, translation, and post translation modification. In this regard they play both anti-angiogenic and pro-angiogenic roles. The expression levels of the pro-angiogenic lncRNAs have been found to correlate with patient survival. These lncRNAs are also potential drug targets for the development of therapies that will inhibit or modify tumour angiogenesis. Here we review the roles of lncRNAs in regulating the angiogenic switch. We cover specific examples of both pro and anti-angiogenic lncRNAs and discuss their potential use as both prognostic biomarkers and targets for the development of future therapies.
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Affiliation(s)
- Peace Mabeta
- Angiogenesis Laboratory, Department of Physiology, Faculty of Health Sciences, University of Pretoria, Hatfield 0028, South Africa
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa;
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa;
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa;
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Lee J, Wacholder A, Carvunis AR. Evolutionary Characterization of the Short Protein SPAAR. Genes (Basel) 2021; 12:genes12121864. [PMID: 34946813 PMCID: PMC8702040 DOI: 10.3390/genes12121864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs exclusively among placental mammals. This lack of distant homology could be caused by challenges in homology detection of short sequences, or it could indicate a recent de novo emergence from a noncoding sequence. By integrating syntenic alignments and homology searches, we identify SPAAR orthologs in marsupials and monotremes, establishing that SPAAR has existed at least since the emergence of mammals. SPAAR shows substantial primary sequence divergence but retains a conserved protein structure. In primates, we infer two independent evolutionary events leading to the de novo origination of 5' elongated isoforms of SPAAR from a noncoding sequence and find evidence of adaptive evolution in this extended region. Thus, SPAAR may be of ancient origin, but it appears to be experiencing continual evolutionary innovation in mammals.
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Affiliation(s)
- Jiwon Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence: ; Tel.: +1-412-648-3335
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28
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Bonilauri B, Holetz FB, Dallagiovanna B. Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins. Biomolecules 2021; 11:1673. [PMID: 34827671 PMCID: PMC8615451 DOI: 10.3390/biom11111673] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.
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Affiliation(s)
- Bernardo Bonilauri
- Laboratory of Basic Biology of Stem Cells (LABCET), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
| | - Fabiola Barbieri Holetz
- Laboratory of Gene Expression Regulation (LABREG), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
| | - Bruno Dallagiovanna
- Laboratory of Basic Biology of Stem Cells (LABCET), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
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29
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Sergiev PV, Rubtsova MP. Little but Loud. The Diversity of Functions of Small Proteins and Peptides - Translational Products of Short Reading Frames. BIOCHEMISTRY (MOSCOW) 2021; 86:1139-1150. [PMID: 34565317 DOI: 10.1134/s0006297921090091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cell functioning is tightly regulated process. For many years, research in the fields of proteomics and functional genomics has been focused on the role of proteins in cell functioning. The advances in science have led to the uncovering that short open reading frames, previously considered non-functional, serve a variety of functions. Short reading frames in polycistronic mRNAs often regulate their stability and translational efficiency of the main reading frame. The improvement of proteomic analysis methods has made it possible to identify the products of translation of short open reading frames in quantities that suggest the existence of functional role of those peptides and short proteins. Studies demonstrating their role unravel a new level of the regulation of cell functioning and its adaptation to changing conditions. This review is devoted to the analysis of functions of recently discovered peptides and short proteins.
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Affiliation(s)
- Petr V Sergiev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Skoltech Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria P Rubtsova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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30
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Wu R, Hu W, Chen H, Wang Y, Li Q, Xiao C, Fan L, Zhong Z, Chen X, Lv K, Zhong S, Shi Y, Chen J, Zhu W, Zhang J, Hu X, Wang J. A Novel Human Long Noncoding RNA SCDAL Promotes Angiogenesis through SNF5-Mediated GDF6 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004629. [PMID: 34319658 PMCID: PMC8456203 DOI: 10.1002/advs.202004629] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Indexed: 06/08/2023]
Abstract
Angiogenesis is essential for vascular development. The roles of regulatory long noncoding RNAs (lncRNAs) in mediating angiogenesis remain under-explored. Human embryonic stem cell-derived mesenchymal stem cells (hES-MSCs) are shown to exert more potent cardioprotective effects against cardiac ischemia than human bone marrow-derived MSCs (hBM-MSCs), associated with enhanced neovascularization. The purpose of this study is to search for angiogenic lncRNAs enriched in hES-MSCs, and investigate their roles and mechanisms. AC103746.1 is one of the most highly expressed intergenic lncRNAs detected in hES-MSCs versus hBM-MSCs, and named as SCDAL (stem cell-derived angiogenic lncRNA). SCDAL knockdown significantly reduce the angiogenic potential and reparative effects of hES-MSCs in the infarcted hearts, while overexpression of SCDAL in either hES-MSCs or hBM-MSCs exhibits augmented angiogenesis and cardiac function recovery. Mechanistically, SCDAL induces growth differentiation factor 6 (GDF6) expression via direct interaction with SNF5 at GDF6 promoter. Secreted GDF6 promotes endothelial angiogenesis via non-canonical vascular endothelial growth factor receptor 2 activation. Furthermore, SCDAL-GDF6 is expressed in human endothelial cells, and directly enhances endothelial angiogenesis in vitro and in vivo. Thus, these findings uncover a previously unknown lncRNA-dependent regulatory circuit for angiogenesis. Targeted intervention of the SCDAL-GDF6 pathway has potential as a therapy for ischemic heart diseases.
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Affiliation(s)
- Rongrong Wu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Wangxing Hu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Huan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Yingchao Wang
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Qingju Li
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Changchen Xiao
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Lin Fan
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Zhiwei Zhong
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Xiaoying Chen
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Kaiqi Lv
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Shuhan Zhong
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Yanna Shi
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jinghai Chen
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Wei Zhu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jianyi Zhang
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamSchool of Medicine and School of EngineeringBirminghamAL35294USA
| | - Xinyang Hu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jian'an Wang
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
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Douka K, Birds I, Wang D, Kosteletos A, Clayton S, Byford A, Vasconcelos EJR, O'Connell MJ, Deuchars J, Whitehouse A, Aspden JL. Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation. RNA (NEW YORK, N.Y.) 2021; 27:1082-1101. [PMID: 34193551 PMCID: PMC8370745 DOI: 10.1261/rna.078782.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/22/2021] [Indexed: 06/10/2023]
Abstract
The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%-70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. Fifteen of 45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea, suggesting they are under strong selective constraint in this clade. The profiling of publicly available data sets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development, and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localizes to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells, indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a noncanonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.
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Affiliation(s)
- Katerina Douka
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Isabel Birds
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andreas Kosteletos
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sophie Clayton
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Abigail Byford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Mary J O'Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jim Deuchars
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
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Konina D, Sparber P, Viakhireva I, Filatova A, Skoblov M. Investigation of LINC00493/SMIM26 Gene Suggests Its Dual Functioning at mRNA and Protein Level. Int J Mol Sci 2021; 22:ijms22168477. [PMID: 34445188 PMCID: PMC8395196 DOI: 10.3390/ijms22168477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The amount of human long noncoding RNA (lncRNA) genes is comparable to protein-coding; however, only a small number of lncRNAs are functionally annotated. Previously, it was shown that lncRNAs can participate in many key cellular processes, including regulation of gene expression at transcriptional and post-transcriptional levels. The lncRNA genes can contain small open reading frames (sORFs), and recent studies demonstrated that some of the resulting short proteins could play an important biological role. In the present study, we investigate the widely expressed lncRNA LINC00493. We determine the structure of the LINC00493 transcript, its cell localization and influence on cell physiology. Our data demonstrate that LINC00493 has an influence on cell viability in a cell-type-specific manner. Furthermore, it was recently shown that LINC00493 has a sORF that is translated into small protein SMIM26. The results of our knockdown and overexpression experiments suggest that both LINC00493/SMIM26 transcript and protein affect cell viability, but in the opposite manner.
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Affiliation(s)
- Daria Konina
- Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, 141701 Dolgoprudny, Russia
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Peter Sparber
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Iuliia Viakhireva
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Alexandra Filatova
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Mikhail Skoblov
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
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Li Y, Zhang J, Sun H, Chen Y, Li W, Yu X, Zhao X, Zhang L, Yang J, Xin W, Jiang Y, Wang G, Shi W, Zhu D. lnc-Rps4l-encoded peptide RPS4XL regulates RPS6 phosphorylation and inhibits the proliferation of PASMCs caused by hypoxia. Mol Ther 2021; 29:1411-1424. [PMID: 33429084 PMCID: PMC8058491 DOI: 10.1016/j.ymthe.2021.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/29/2020] [Accepted: 01/02/2021] [Indexed: 02/06/2023] Open
Abstract
Pulmonary artery smooth muscle cells (PASMCs) proliferation caused by hypoxia is an important pathological process of pulmonary hypertension (PH). Prevention of PASMCs proliferation can effectively reduce PH mortality. Long non-coding RNAs (lncRNAs) are involved in the proliferation process. Recent evidence has demonstrated that functional peptides encoded by lncRNAs play important roles in cell pathophysiological process. Our previous study has demonstrated that lnc-Rps4l with high coding ability mediates the PASMCs proliferation under hypoxic conditions. We hypothesize in this study that a lnc-Rps4l-encoded peptide is involved in hypoxic-induced PASMCs proliferation. The presence of peptide 40S ribosomal protein S4 X isoform-like (RPS4XL) encoded by lnc-Rps4l in PASMCs under hypoxic conditions was confirmed by bioinformatics, immunofluorescence, and immunohistochemistry. Inhibition of proliferation by the peptide RPS4XL was demonstrated in hypoxic PASMCs by MTT, bromodeoxyuridine (BrdU) incorporation, and immunofluorescence assays. By using the bioinformatics, coimmunoprecipitation (coIP), and mass spectrometry, RPS6 was identified to interact with RPS4XL. Furthermore, lnc-Rps4l-encoded peptide RPS4XL inhibited the RPS6 process via binding to RPS6 and inhibiting RPS6 phosphorylation at p-RPS6 (Ser240+Ser244) phosphorylation site. These results systematically elucidate the role and regulatory network of Rps4l-encoded peptide RPS4XL in PASMCs proliferation. These discoveries provide potential targets for early diagnosis and a leading compound for treatment of hypoxic PH.
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Affiliation(s)
- Yiying Li
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Junting Zhang
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Hanliang Sun
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Yujie Chen
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Wendi Li
- College of Pharmacy, Harbin University of Commerce, Harbin, Heilongjiang Province 150081, P.R. China
| | - Xiufeng Yu
- Central Laboratory of Harbin Medical University (Daqing), Daqing 163319, P.R. China
| | - Xijuan Zhao
- Central Laboratory of Harbin Medical University (Daqing), Daqing 163319, P.R. China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing 163319, P.R. China
| | - Jianfeng Yang
- College of Pharmacy, Harbin Medical University, Daqing 163319, P.R. China
| | - Wei Xin
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Yuan Jiang
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China
| | - Guilin Wang
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, Heilongjiang Province 163319, P.R. China
| | - Wenbin Shi
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, Heilongjiang Province 163319, P.R. China
| | - Daling Zhu
- Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, P.R. China; Central Laboratory of Harbin Medical University (Daqing), Daqing 163319, P.R. China.
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Bresesti C, Vezzoli V, Cangiano B, Bonomi M. Long Non-Coding RNAs: Role in Testicular Cancers. Front Oncol 2021; 11:605606. [PMID: 33767982 PMCID: PMC7986848 DOI: 10.3389/fonc.2021.605606] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
In the last few years lncRNAs have gained increasing attention among the scientific community, thanks to the discovery of their implication in many physio-pathological processes. In particular, their contribution to tumor initiation, progression, and response to treatment has attracted the interest of experts in the oncologic field for their potential clinical application. Testicular cancer is one of the tumors in which lncRNAs role is emerging. Said malignancies already have very effective treatments, which although lead to the development of quite serious treatment-related conditions, such as secondary tumors, infertility, and cardiovascular diseases. It is therefore important to study the impact of lncRNAs in the tumorigenesis of testicular cancer in order to learn how to exploit them in a clinical setting and to substitute more toxic treatments. Eventually, the use of lncRNAs as biomarkers, drug targets, or therapeutics for testicular cancer may represent a valid alternative to that of conventional tools, leading to a better management of this malignancy and its related conditions, and possibly even to the treatment of poor prognosis cases.
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Affiliation(s)
- Chiara Bresesti
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Valeria Vezzoli
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Biagio Cangiano
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Marco Bonomi
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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35
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Spiroski AM, Sanders R, Meloni M, McCracken IR, Thomson A, Brittan M, Gray GA, Baker AH. The Influence of the LINC00961/SPAAR Locus Loss on Murine Development, Myocardial Dynamics, and Cardiac Response to Myocardial Infarction. Int J Mol Sci 2021; 22:ijms22020969. [PMID: 33478078 PMCID: PMC7835744 DOI: 10.3390/ijms22020969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 01/14/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have structural and functional roles in development and disease. We have previously shown that the LINC00961/SPAAR (small regulatory polypeptide of amino acid response) locus regulates endothelial cell function, and that both the lncRNA and micropeptide counter-regulate angiogenesis. To assess human cardiac cell SPAAR expression, we mined a publicly available scRNSeq dataset and confirmed LINC00961 locus expression and hypoxic response in a murine endothelial cell line. We investigated post-natal growth and development, basal cardiac function, the cardiac functional response, and tissue-specific response to myocardial infarction. To investigate the influence of the LINC00961/SPAAR locus on longitudinal growth, cardiac function, and response to myocardial infarction, we used a novel CRISPR/Cas9 locus knockout mouse line. Data mining suggested that SPAAR is predominantly expressed in human cardiac endothelial cells and fibroblasts, while murine LINC00961 expression is hypoxia-responsive in mouse endothelial cells. LINC00961–/– mice displayed a sex-specific delay in longitudinal growth and development, smaller left ventricular systolic and diastolic areas and volumes, and greater risk area following myocardial infarction compared with wildtype littermates. These data suggest the LINC00961/SPAAR locus contributes to cardiac endothelial cell and fibroblast function and hypoxic response, growth and development, and basal cardiovascular function in adulthood.
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Affiliation(s)
- Ana-Mishel Spiroski
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Rachel Sanders
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Marco Meloni
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Ian R. McCracken
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Adrian Thomson
- Edinburgh Preclinical Imaging, Edinburgh Preclinical Imaging, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Gillian A. Gray
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
| | - Andrew H. Baker
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (A.-M.S.); (R.S.); (M.M.); (I.R.M.); (M.B.); (G.A.G.)
- Correspondence: ; Tel.: +44-0131-24-26728
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Xing J, Liu H, Jiang W, Wang L. LncRNA-Encoded Peptide: Functions and Predicting Methods. Front Oncol 2021; 10:622294. [PMID: 33520729 PMCID: PMC7842084 DOI: 10.3389/fonc.2020.622294] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) was originally defined as the representative of the non-coding RNAs and unable to encode. However, recent reports suggest that some lncRNAs actually contain open reading frames that encode peptides. These coding products play important roles in the pathogenesis of many diseases. Here, we summarize the regulatory pathways of mammalian lncRNA-encoded peptides in influencing muscle function, mRNA stability, gene expression, and so on. We also address the promoting and inhibiting functions of the peptides in different cancers and other diseases. Then we introduce the computational predicting methods and data resources to predict the coding ability of lncRNA. The intention of this review is to provide references for further coding research and contribute to reveal the potential prospects for targeted tumor therapy.
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Affiliation(s)
- Jiani Xing
- Department of Pathophysiology, Medical College of Southeast University, Nanjing, China
| | - Haizhou Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Wei Jiang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Lihong Wang
- Department of Pathophysiology, Medical College of Southeast University, Nanjing, China.,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Nanjing, China
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Johnson SJ, Cooper TA. Overlapping mechanisms of lncRNA and expanded microsatellite RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1634. [PMID: 33191580 PMCID: PMC7880542 DOI: 10.1002/wrna.1634] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022]
Abstract
RNA has major regulatory roles in a wide range of biological processes and a surge of RNA research has led to the classification of numerous functional RNA species. One example is long noncoding RNAs (lncRNAs) that are structurally complex transcripts >200 nucleotides (nt) in length and lacking a canonical open reading frame (ORF). Despite a general lack of sequence conservation and low expression levels, many lncRNAs have been shown to have functionality in diverse biological processes as well as in mechanisms of disease. In parallel with the growing understanding of lncRNA functions, there is a growing subset of microsatellite expansion disorders in which the primary mechanism of pathogenesis is an RNA gain of function arising from RNA transcripts from the mutant allele. Microsatellite expansion disorders are caused by an expansion of short (3-10 nt) repeats located within coding genes. Expanded repeat-containing RNA mediates toxicity through multiple mechanisms, the details of which remain only partially understood. The purpose of this review is to highlight the links between functional mechanisms of lncRNAs and the potential pathogenic mechanisms of expanded microsatellite RNA. These shared mechanisms include protein sequestration, peptide translation, micro-RNA (miRNA) processing, and miRNA sequestration. Recognizing the parallels between the normal functions of lncRNAs and the negative impact of expanded microsatellite RNA on biological processes can provide reciprocal understanding to the roles of both RNA species. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Sara J Johnson
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Thomas A Cooper
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
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Ono K, Horie T, Baba O, Kimura M, Tsuji S, Rodriguez RR, Miyagawa S, Kimura T. Functional non-coding RNAs in vascular diseases. FEBS J 2020; 288:6315-6330. [PMID: 33340430 PMCID: PMC9292203 DOI: 10.1111/febs.15678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/01/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022]
Abstract
Recently, advances in genomic technology such as RNA sequencing and genome‐wide profiling have enabled the identification of considerable numbers of non‐coding RNAs (ncRNAs). MicroRNAs have been studied for decades, leading to the identification of those with disease‐causing and/or protective effects in vascular disease. Although other ncRNAs such as long ncRNAs have not been fully described yet, recent studies have indicated their important functions in the development of vascular diseases. Here, we summarize the current understanding of the mechanisms and functions of ncRNAs, focusing on microRNAs, circular RNAs and long ncRNAs in vascular diseases.
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Affiliation(s)
- Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Takahiro Horie
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Osamu Baba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Masahiro Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Shuhei Tsuji
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | | | - Sawa Miyagawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Japan
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Bogard B, Francastel C, Hubé F. Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel? RNA Biol 2020; 17:1707-1720. [PMID: 32559119 PMCID: PMC7714488 DOI: 10.1080/15476286.2020.1783868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
The findings that an RNA is not necessarily either coding or non-coding, or that a precursor RNA can produce different types of mature RNAs, whether coding or non-coding, long or short, have challenged the dichotomous view of the RNA world almost 15 years ago. Since then, and despite an increasing number of studies, the diversity of information that can be conveyed by RNAs is rarely searched for, and when it is known, it remains largely overlooked in further functional studies. Here, we provide an update with prominent examples of multiple functions that are carried by the same RNA or are produced by the same precursor RNA, to emphasize their biological relevance in most living organisms. An important consequence is that the overall function of their locus of origin results from the balance between various RNA species with distinct functions and fates. The consideration of the molecular basis of this multiplicity of information is obviously crucial for downstream functional studies when the targeted functional molecule is often not the one that is believed.
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Affiliation(s)
- Baptiste Bogard
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | | | - Florent Hubé
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
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Zhou B, Yang H, Yang C, Bao YL, Yang SM, Liu J, Xiao YF. Translation of noncoding RNAs and cancer. Cancer Lett 2020; 497:89-99. [PMID: 33038492 DOI: 10.1016/j.canlet.2020.10.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
The human genome contains thousands of noncoding RNAs (ncRNAs), which are thought to lack open reading frames (ORFs) and cannot be translated. Some ncRNAs reportedly have important functions, including epigenetic regulation, chromatin remolding, protein modification, and RNA degradation, but the functions of most ncRNAs remain elusive. Through the application and development of ribosome profiling and sequencing technologies, an increasing number of studies have discovered the translation of ncRNAs. Although ncRNAs were initially defined as noncoding RNAs, a number of ncRNAs actually contain ORFs that are translated into peptides. Here, we summarize the available methods, tools, and databases for identifying and validating ncRNA-encoded peptides/proteins, and the recent findings regarding ncRNA-encoded small peptides/proteins in cancer are compiled and synthesized. Importantly, the role of ncRNA-encoding peptides/proteins has application prospects in cancer research, but some potential challenges remain unresolved. The aim of this review is to provide a theoretical basis that might promote the discovery of more peptides/proteins encoded by ncRNAs and aid the further development of novel diagnostic and prognostic cancer markers and therapeutic targets.
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Affiliation(s)
- Bo Zhou
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Chuan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Yu-Lu Bao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Jiao Liu
- Department of Endoscope, General Hospital of Northern Theater Command, Shenyang, 110016, Liaoning, China.
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China.
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Mehrpour Layeghi S, Arabpour M, Esmaeili R, Naghizadeh MM, Tavakkoly Bazzaz J, Shakoori A. Evaluation of the potential role of long non-coding RNA LINC00961 in luminal breast cancer: a case-control and systems biology study. Cancer Cell Int 2020; 20:478. [PMID: 33024416 PMCID: PMC7531117 DOI: 10.1186/s12935-020-01569-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/23/2020] [Indexed: 01/09/2023] Open
Abstract
Background Luminal subtype is the most common subgroup of breast cancer (BC), accounting for more than 70% of this cancer. Long non-coding RNAs (lncRNAs) are a group of RNAs which play critical roles in diverse cellular processes. It is proved that dysregulation of them can contribute to the development of various cancers, including BC. LINC00961 was reported to be downregulated in several cancers, however, its expression level in BC remains largely unknown. The purpose of the present study was to investigate the possible role of LINC00961 in luminal A and B subtypes of BC. Methods To obtain novel lncRNAs associated with different cancers and differentially expressed lncRNAs (DElncRNAs) between BC tumor and normal tissues, Lnc2Cancer and GDC databases were used, respectively. After performing literature review, the expression level of the selected lncRNA (LINC00961) was evaluated in 79 luminal A and B BC specimens and adjacent non-cancerous tissues by Quantitative Reverse Transcription PCR (qRT-PCR). LINC00961 expression was also evaluated in two luminal A BC cell lines, compared to a normal breast cell line. The comparison of the differences between tumor and adjacent non-tumor samples was performed by paired sample t-test. Moreover, correlation analysis between LINC00961 expression and clinicopathological features was performed using the chi-square, fisher exact, and independent t-test. In order to investigate the possible roles of LINC00961 in luminal A and B BC, different bioinformatics analyses such as functional annotation of the LINC00961 co-expressed genes and protein–protein interaction (PPI) networks construction were also performed. Results LINC00961 was selected as a significant DElncRNA which had not been studied in BC. According to q-RT PCR assay, LINC00961 was downregulated in luminal BC tissues and cell lines. Its expression was correlated with smoking status and the age of menarche in luminal BC patients. Also, the results of the bioinformatics analysis were consistent with the data obtained from q-RT PCR assay. The final results indicated that LINC00961 might be involved in multiple cancer-associated pathways such as chemokine, Ras and PI3K–Akt signaling pathways, GPCR ligand binding, and signal transduction in luminal subtypes of BC. CDH5, GNG11, GNG8, SELL, S1PR1, CCL19, FYN, ACAN, CD3E, ACVRL1, CAV1, and PPARGC1A were identified as the top hub genes of the PPI networks across luminal subgroup. Conclusion Our findings suggested that LINC00961 was significantly downregulated in luminal A and B subtypes of BC. Moreover, bioinformatics analysis provided a basis for better identification of the potential role of LINC00961 in luminal subtype of BC.
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Affiliation(s)
- Sepideh Mehrpour Layeghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maedeh Arabpour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | | | - Javad Tavakkoly Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori
- Medical Genetic Ward, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.,Breast Disease Research Center (BDRC), Tehran University of Medical Sciences, Tehran, Iran
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Brandes RP, Oo JA, Leisegang MS. Thymosin beta-4x LINCs SPAAR to its non-coding function. Cardiovasc Res 2020; 116:1927-1928. [PMID: 32282872 DOI: 10.1093/cvr/cvaa098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ralf P Brandes
- Institute für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - James A Oo
- Institute für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Matthias S Leisegang
- Institute für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern Kai 7, 60590 Frankfurt am Main, Germany
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