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Satheeshan G, Si AK, Rutta J, Venkatesh T. Exosome theranostics: Comparative analysis of P body and exosome proteins and their mutations for clinical applications. Funct Integr Genomics 2024; 24:124. [PMID: 38995459 DOI: 10.1007/s10142-024-01404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Exosomes are lipid-bilayered vesicles, originating from early endosomes that capture cellular proteins and genetic materials to form multi-vesicular bodies. These exosomes are secreted into extracellular fluids such as cerebrospinal fluid, blood, urine, and cell culture supernatants. They play a key role in intercellular communication by carrying active molecules like lipids, cytokines, growth factors, metabolites, proteins, and RNAs. Recently, the potential of exosomal delivery for therapeutic purposes has been explored due to their low immunogenicity, nano-scale size, and ability to cross cellular barriers. This review comprehensively examines the biogenesis of exosomes, their isolation techniques, and their diverse applications in theranostics. We delve into the mechanisms and methods for loading exosomes with mRNA, miRNA, proteins, and drugs, highlighting their transformative role in delivering therapeutic payloads. Additionally, the utility of exosomes in stem cell therapy is discussed, showcasing their potential in regenerative medicine. Insights into exosome cargo using pre- or post-loading techniques are critical for exosome theranostics. We review exosome databases such as ExoCarta, Expedia, and ExoBCD, which document exosome cargo. From these databases, we identified 25 proteins common to both exosomes and P-bodies, known for mutations in the COSMIC database. Exosome databases do not integrate with mutation analysis programs; hence, we performed mutation analysis using additional databases. Accounting for the mutation status of parental cells and exosomal cargo is crucial in exosome theranostics. This review provides a comprehensive report on exosome databases, proteins common to exosomes and P-bodies, and their mutation analysis, along with the latest studies on exosome-engineered theranostics.
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Affiliation(s)
- Greeshma Satheeshan
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Ayan Kumar Si
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Joel Rutta
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Thejaswini Venkatesh
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India.
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2
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Zhai P, Tong T, Wang X, Li C, Liu C, Qin X, Li S, Xie F, Mao J, Zhang J, Guo H. Nuclear miR-451a activates KDM7A and leads to cetuximab resistance in head and neck squamous cell carcinoma. Cell Mol Life Sci 2024; 81:282. [PMID: 38943031 DOI: 10.1007/s00018-024-05324-x] [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: 10/30/2023] [Revised: 05/29/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Cetuximab resistance has been a major challenge for head and neck squamous cell carcinoma (HNSCC) patients receiving targeted therapy. However, the mechanism that causes cetuximab resistance, especially microRNA (miRNA) regulation, remains unclear. Growing evidence suggests that miRNAs may act as "nuclear activating miRNAs" for targeting promoter regions or enhancers related to target genes. This study elucidates a novel mechanism underlying cetuximab resistance in HNSCC involving the nuclear activation of KDM7A transcription via miR-451a. Herein, small RNA sequencing, quantitative real-time polymerase chain reaction (qRT‒PCR) and fluorescence in situ hybridization (FISH) results provided compelling evidence of miR-451a nuclear enrichment in response to cetuximab treatment. Chromatin isolation via RNA purification, microarray analysis, and bioinformatic analysis revealed that miR-451a interacts with an enhancer region in KDM7A, activating its expression and further facilitating cetuximab resistance. It has also been demonstrated that the activation of KDM7A by nuclear miR-451a is induced by cetuximab treatment and is AGO2 dependent. Logistic regression analyses of 87 HNSCC samples indicated the significance of miR-451a and KDM7A in the development of cetuximab resistance. These discoveries support the potential of miR-451a and KDM7A as valuable biomarkers for cetuximab resistance and emphasize the function of nuclear-activating miRNAs.
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Affiliation(s)
- Peisong Zhai
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Tong Tong
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200001, People's Republic of China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200002, People's Republic of China
| | - Xiaoning Wang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Chuwen Li
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Chun Liu
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Xing Qin
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Shu Li
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Fei Xie
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China
| | - Jiayi Mao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Jianjun Zhang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, People's Republic of China.
| | - Haiyan Guo
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China.
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3
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Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [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: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
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Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
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Billi M, De Marinis E, Gentile M, Nervi C, Grignani F. Nuclear miRNAs: Gene Regulation Activities. Int J Mol Sci 2024; 25:6066. [PMID: 38892257 PMCID: PMC11172810 DOI: 10.3390/ijms25116066] [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: 04/22/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which contribute to the regulation of many physiological and pathological processes. Conventionally, miRNAs perform their activity in the cytoplasm where they regulate gene expression by interacting in a sequence-specific manner with mature messenger RNAs. Recent studies point to the presence of mature miRNAs in the nucleus. This review summarizes current findings regarding the molecular activities of nuclear miRNAs. These molecules can regulate gene expression at the transcriptional level by directly binding DNA on the promoter or the enhancer of regulated genes. miRNAs recruit different protein complexes to these regions, resulting in activation or repression of transcription, through a number of molecular mechanisms. Hematopoiesis is presented as a paradigmatic biological process whereby nuclear miRNAs possess a relevant regulatory role. Nuclear miRNAs can influence gene expression by affecting nuclear mRNA processing and by regulating pri-miRNA maturation, thus impacting the biogenesis of miRNAs themselves. Overall, nuclear miRNAs are biologically active molecules that can be critical for the fine tuning of gene expression and deserve further studies in a number of physiological and pathological conditions.
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Affiliation(s)
- Monia Billi
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
| | - Elisabetta De Marinis
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Martina Gentile
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Clara Nervi
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Francesco Grignani
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
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Cabrera GT, Meijboom KE, Abdallah A, Tran H, Foster Z, Weiss A, Wightman N, Stock R, Gendron T, Gruntman A, Giampetruzzi A, Petrucelli L, Brown RH, Mueller C. Artificial microRNA suppresses C9ORF72 variants and decreases toxic dipeptide repeat proteins in vivo. Gene Ther 2024; 31:105-118. [PMID: 37752346 DOI: 10.1038/s41434-023-00418-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 05/28/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons, causing progressive muscle weakness and respiratory failure. The presence of an expanded hexanucleotide repeat in chromosome 9 open reading frame 72 (C9ORF72) is the most frequent mutation causing familial ALS and frontotemporal dementia (FTD). To determine if suppressing expression of C9ORF72 gene products can reduce toxicity, we designed a set of artificial microRNAs (amiRNA) targeting the human C9ORF72 gene. Here we report that an AAV9-mediated amiRNA significantly suppresses expression of the C9ORF72 mRNA, protein, and toxic dipeptide repeat proteins generated by the expanded repeat in the brain and spinal cord of C9ORF72 transgenic mice.
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Affiliation(s)
- Gabriela Toro Cabrera
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Katharina E Meijboom
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Abbas Abdallah
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Helene Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Zachariah Foster
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Nicholas Wightman
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Rachel Stock
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Tania Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Alisha Gruntman
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Anthony Giampetruzzi
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
| | - Christian Mueller
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs. Nucleic Acids Res 2024; 52:1930-1952. [PMID: 38109320 PMCID: PMC10899759 DOI: 10.1093/nar/gkad1155] [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: 07/19/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023] Open
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yi Han
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Tao Wang
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235, USA
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
- Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
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7
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Gu J, Li Y, Tian Y, Zhang Y, Cheng Y, Tang Y. Noncanonical functions of microRNAs in the nucleus. Acta Biochim Biophys Sin (Shanghai) 2024; 56:151-161. [PMID: 38167929 PMCID: PMC10984876 DOI: 10.3724/abbs.2023268] [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: 09/02/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) that play their roles in the regulation of physiological and pathological processes. Originally, it was assumed that miRNAs only modulate gene expression posttranscriptionally in the cytoplasm by inducing target mRNA degradation. However, with further research, evidence shows that mature miRNAs also exist in the cell nucleus, where they can impact gene transcription and ncRNA maturation in several ways. This review provides an overview of novel models of nuclear miRNA functions. Some of the models remain to be verified by experimental evidence, and more details of the miRNA regulation network remain to be discovered in the future.
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Affiliation(s)
- Jiayi Gu
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yuanan Li
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Youtong Tian
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yehao Zhang
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yongjun Cheng
- Department of Rheumatologythe First People’s Hospital of WenlingWenling317500China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology/Department of RheumatologyRenji HospitalShanghai Jiao Tong University School of MedicineShanghai200001China
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalShanghai200031China
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Ishikawa T, Sugawara K, Zhang J, Funatsu T, Okabe K. Direct observation of cytoskeleton-dependent trafficking of miRNA visualized by the introduction of pre-miRNA. iScience 2024; 27:108811. [PMID: 38303695 PMCID: PMC10831896 DOI: 10.1016/j.isci.2024.108811] [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: 04/06/2023] [Revised: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNA (miRNA) plays physiologically and pathologically important roles in post-transcriptional regulation. Although miRNA has been suggested to dynamically interact with cellular organelles, the dynamicity of intracellular miRNA behavior has remained unclear. Here, by introducing fluorescently labeled pre-miRNA into living cells, we improved the miRNA visualization method using exogenous miRNA precursors. Through the combination of our miRNA visualization method and single-molecule sensitive fluorescence microscopy, we quantitatively analyzed the process of miRNA maturation. Furthermore, single-particle tracking of fluorescent miRNA in cells revealed the directed movements of miRNA on cytoskeletal components (i.e., microtubules and actin filaments). Our results also suggest that cytoskeleton-dependent miRNA trafficking is associated with the interaction of miRNAs with the nucleus and the endoplasmic reticulum/Golgi apparatus. Our method should facilitate the elucidation of the mechanism and physiological significance of the subcellular localization and organelle interaction of miRNA.
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Affiliation(s)
- Toshinari Ishikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, PRESTO, 4-8-1 Honcho, Kawaguchi, Saitama 332-0012, Japan
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9
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Broberg M, Helaakoski V, Kiiskinen T, Paunio T, Jones SE, Mars N, Lane JM, Saxena R, Ollila HM. Genetics of sleep medication purchases suggests causality from sleep problems to psychiatric traits. Sleep 2024; 47:zsad279. [PMID: 37982563 PMCID: PMC10851853 DOI: 10.1093/sleep/zsad279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/12/2023] [Indexed: 11/21/2023] Open
Abstract
STUDY OBJECTIVES Over 10% of the population in Europe and in the United States use sleep medication to manage sleep problems. Our objective was to elucidate genetic risk factors and clinical correlates that contribute to sleep medication purchase and estimate the comorbid impact of sleep problems. METHODS We performed epidemiological analysis for psychiatric diagnoses, and genetic association studies of sleep medication purchase in 797 714 individuals from FinnGen Release 7 (N = 311 892) and from the UK Biobank (N = 485 822). Post-association analyses included genetic correlation, co-localization, Mendelian randomization (MR), and polygenic risk estimation. RESULTS In a GWAS we identified 27 genetic loci significantly associated with sleep medication, located in genes associated with sleep; AUTS2, CACNA1C, MEIS1, KIRREL3, PAX8, GABRA2, psychiatric traits; CACNA1C, HIST1H2BD, NUDT12. TOPAZ1 and TSNARE1. Co-localization and expression analysis emphasized effects on the KPNA2, GABRA2, and CACNA1C expression in the brain. Sleep medications use was epidemiologically related to psychiatric traits in FinnGen (OR [95% (CI)] = 3.86 [3.78 to 3.94], p < 2 × 10-16), and the association was accentuated by genetic correlation and MR; depression (rg = 0.55 (0.027), p = 2.86 × 10-89, p MR = 4.5 × 10-5), schizophrenia (rg = 0.25 (0.026), p = 2.52 × 10-21, p MR = 2 × 10-4), and anxiety (rg = 0.44 (0.047), p = 2.88 × 10-27, p MR = 8.6 × 10-12). CONCLUSIONS These results demonstrate the genetics behind sleep problems and the association between sleep problems and psychiatric traits. Our results highlight the scientific basis for sleep management in treating the impact of psychiatric diseases.
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Affiliation(s)
- Martin Broberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Viola Helaakoski
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tiina Paunio
- Genomics and Biomarkers Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Samuel E Jones
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jacqueline M Lane
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA and
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA and
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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10
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Yadav V, Jena MK, Parashar G, Parashar NC, Joshi H, Ramniwas S, Tuli HS. Emerging role of microRNAs as regulators of protein kinase C substrate MARCKS and MARCKSL1 in cancer. Exp Cell Res 2024; 434:113891. [PMID: 38104645 DOI: 10.1016/j.yexcr.2023.113891] [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: 09/24/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
MicroRNAs (miRNAs) have emerged as pivotal regulators of gene expression, playing essential roles in diverse cellular processes, including the development and progression of cancer. Among the numerous proteins influenced by miRNAs, the MARCKS/MARCKSL1 protein, a key regulator of cellular cytoskeletal dynamics and membrane-cytosol communication, has garnered significant attention due to its multifaceted involvement in various cancer-related processes, including cell migration, invasion, metastasis, and drug resistance. Motivated by the encouraging early clinical success of peptides targeting MARCKS in several pathological conditions, this review article delves into the intricate interplay between miRNAs and the MARCKS protein in cancer. Herein, we have highlighted the latest findings on specific miRNAs that modulate MARCKS/MARCKSL1 expression, providing a comprehensive overview of their roles in different cancer types. We have underscored the need for in-depth investigations into the therapeutic feasibility of targeting the miRNA-MARCKS axis in cancer, taking cues from the successes witnessed in related fields. Unlocking the full potential of miRNA-mediated MARCKS regulation could pave the way for innovative and effective therapeutic interventions against various cancer types.
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Affiliation(s)
- Vikas Yadav
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, 4000, Liège, Belgium; Department of Translational Medicine, Clinical Research Centre, Skåne University Hospital, Lund University, SE 20213, Malmö, Sweden.
| | - Manoj Kumar Jena
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Gaurav Parashar
- Division of Biomedical & Life Sciences, School of Science, Navrachana University, Vadodara, Gujarat, 391410, India
| | - Nidarshana Chaturvedi Parashar
- Department of Biosciences & Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Seema Ramniwas
- University Centre for Research & Development, University Institute of Pharmaceutical Sciences, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Hardeep Singh Tuli
- Department of Biosciences & Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
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11
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Wang YL, Feng LL, Shi J, Chen WY, Bie SY, Bai SM, Zeng GD, Wang RZ, Zheng J, Wan XB, Fan XJ. CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair. Nucleus 2023; 14:2293599. [PMID: 38105528 PMCID: PMC10730229 DOI: 10.1080/19491034.2023.2293599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 putative miR-7-binding sites, as an enhancer of miRISC condensation and DNA repair. Both in vivo and in vitro experiments confirmed the condensation of TNRC6B and AGO2, two core protein components of human miRISC. Moreover, overexpressing ciRS-7 largely increased the condensate number of TNRC6B and AGO2 in cells, while silencing ciRS-7 reduced it. Additionally, miR-7 overexpression also promoted miRISC condensation. Consistent with the previous report that AGO2 participated in RAD51-mediated DNA damage repair, the overexpression of ciRS-7 significantly promoted irradiation-induced DNA damage repair by enhancing RAD51 recruitment. Our results uncover a new role of circRNA in liquid-liquid phase separation and provide new insight into the regulatory mechanism of ciRS-7 on miRISC function and DNA repair.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Li-Li Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Wan-Ying Chen
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
| | - Shu-Ying Bie
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Rui-Zhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
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12
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Sala L, Kumar M, Prajapat M, Chandrasekhar S, Cosby RL, La Rocca G, Macfarlan TS, Awasthi P, Chari R, Kruhlak M, Vidigal JA. AGO2 silences mobile transposons in the nucleus of quiescent cells. Nat Struct Mol Biol 2023; 30:1985-1995. [PMID: 37985687 DOI: 10.1038/s41594-023-01151-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/27/2023] [Indexed: 11/22/2023]
Abstract
Argonaute 2 (AGO2) is a cytoplasmic component of the miRNA pathway, with essential roles in development and disease. Yet little is known about its regulation in vivo. Here we show that in quiescent mouse splenocytes, AGO2 localizes almost exclusively to the nucleus. AGO2 subcellular localization is modulated by the Pi3K-AKT-mTOR pathway, a well-established regulator of quiescence. Signaling through this pathway in proliferating cells promotes AGO2 cytoplasmic accumulation, at least in part by stimulating the expression of TNRC6, an essential AGO2 binding partner in the miRNA pathway. In quiescent cells in which mTOR signaling is low, AGO2 accumulates in the nucleus, where it binds to young mobile transposons co-transcriptionally to repress their expression via its catalytic domain. Our data point to an essential but previously unrecognized nuclear role for AGO2 during quiescence as part of a genome-defense system against young mobile elements and provide evidence of RNA interference in the soma of mammals.
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Affiliation(s)
- Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Manish Kumar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Mahendra Prajapat
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Srividya Chandrasekhar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Rachel L Cosby
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA
- The National Institute for General Medical Sciences, The National Institutes of Health, Bethesda, MD, USA
| | - Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, The National Institutes of Health, Frederick, MD, USA
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, The National Institutes of Health, Frederick, MD, USA
| | - Michael Kruhlak
- CCR Confocal Microscopy Core Facility, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA.
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13
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Kozłowska-Masłoń J, Guglas K, Kolenda T, Lamperska K, Makałowska I. miRNA in head and neck squamous cell carcinomas: promising but still distant future of personalized oncology. Rep Pract Oncol Radiother 2023; 28:681-697. [PMID: 38179293 PMCID: PMC10764040 DOI: 10.5603/rpor.96666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/24/2023] [Indexed: 01/06/2024] Open
Abstract
Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Lack of appropriate preventive screening tests, late detection, and high heterogeneity of these tumors are the main reasons for the unsatisfactory effects of therapy and, consequently, unfavorable outcomes for patients. An opportunity to improve the quality of diagnostics and treatment of this group of cancers are microRNAs (miRNAs) - molecules with a great potential both as biomarkers and therapeutic targets. This review aims to present the characteristics of these short non-coding RNAs (ncRNAs) and summarize the current reports on their use in oncology focused on medical strategies tailored to patients' needs.
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Affiliation(s)
- Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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14
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Li M, Zhai P, Mu X, Song J, Zhang H, Su J. Hypoxic BMSC-derived exosomal miR-652-3p promotes proliferation and metastasis of hepatocarcinoma cancer cells via targeting TNRC6A. Aging (Albany NY) 2023; 15:12780-12793. [PMID: 37976119 DOI: 10.18632/aging.205025] [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: 09/21/2022] [Accepted: 08/20/2023] [Indexed: 11/19/2023]
Abstract
Cancer microenvironment plays an important role in the proliferation and metastasis of hepatocarcinoma cancer cells (HCC). Exosomes from bone marrow-derived mesenchymal stem cells (BMSCs) are a component of the cancer microenvironment. In this study, we reveal that miRNA-652-3P from BMSC-derived exosomes promotes proliferation and metastasis in HCC. The ability of cancer proliferation, migration and invasion can be evaluated after co-culture by CCK-8, wound healing and transwell assay. Isolated exosomes were identified by transmission electron microscopy (TEM) and the biomarkers of the purified exosomes were showed in West-blotting (WB). MiR-652-3p was detected in the HepG2 and 7721 after co-culturing with exosome derived from BMSCs under different conditions. Target authentication was performed by a luciferase reporter assay to confirm the presumptive target of miR-652-3p. After overexpressing miR-652-3p, the mRNA and protein expression level of TNRC6A in HCC was examined by q-PCR and WB. Further, we observed greater miR-652-3p upregulation in hypoxic BMSCs-exosomes than in normal- exosomes. In addition, a miR-652-3p inhibitor attenuates the proliferation and metastasis of HCC cells after co-culturing with BMSCs. Our data demonstrate that hypoxic BMSCs-derived exosomal miR-652-3p promotes proliferation in HCC cells by inhibiting TNRC6A. The BMSCs-derived exosomal miR-652-3p may help find patient-targeted therapies in hepatocarcinoma cancer.
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Affiliation(s)
- Mei Li
- Department of Minimally Invasive, Shaanxi Cancer Hospital, Xi’an 710061, Shaanxi, China
| | - Pengtao Zhai
- Department of Minimally Invasive, Shaanxi Cancer Hospital, Xi’an 710061, Shaanxi, China
| | - Xudong Mu
- Department of Minimally Invasive, Shaanxi Cancer Hospital, Xi’an 710061, Shaanxi, China
| | - Juanrong Song
- Department of Minimally Invasive, Shaanxi Cancer Hospital, Xi’an 710061, Shaanxi, China
| | - Huilin Zhang
- Digestive Endoscopy Treatment Center, Xi’an International Medical Center Hospital, Gaoxin, Xi’an 710100, Shaanxi, China
| | - Juan Su
- Department of Gastroenterology, Xi’an International Medical Center Hospital, Gaoxin, Xi’an 710100, Shaanxi, China
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15
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Ismaeel A, Thomas NT, McCashland M, Vechetti IJ, Edman S, Lanner JT, Figueiredo VC, Fry CS, McCarthy JJ, Wen Y, Murach KA, von Walden F. Coordinated Regulation of Myonuclear DNA Methylation, mRNA, and miRNA Levels Associates With the Metabolic Response to Rapid Synergist Ablation-Induced Skeletal Muscle Hypertrophy in Female Mice. FUNCTION 2023; 5:zqad062. [PMID: 38020067 PMCID: PMC10666992 DOI: 10.1093/function/zqad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/16/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The central dogma of molecular biology dictates the general flow of molecular information from DNA that leads to a functional cellular outcome. In skeletal muscle fibers, the extent to which global myonuclear transcriptional alterations, accounting for epigenetic and post-transcriptional influences, contribute to an adaptive stress response is not clearly defined. In this investigation, we leveraged an integrated analysis of the myonucleus-specific DNA methylome and transcriptome, as well as myonuclear small RNA profiling to molecularly define the early phase of skeletal muscle fiber hypertrophy. The analysis of myonucleus-specific mature microRNA and other small RNA species provides new directions for exploring muscle adaptation and complemented the methylation and transcriptional information. Our integrated multi-omics interrogation revealed a coordinated myonuclear molecular landscape during muscle loading that coincides with an acute and rapid reduction of oxidative metabolism. This response may favor a biosynthesis-oriented metabolic program that supports rapid hypertrophic growth.
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Affiliation(s)
- Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40508, USA
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Nicholas T Thomas
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Athletic Training and Clinical Nutrition, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mariah McCashland
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln, Lincoln, NE 68583, USA
| | - Ivan J Vechetti
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln, Lincoln, NE 68583, USA
| | - Sebastian Edman
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17177, Sweden
| | - Johanna T Lanner
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna 17177, Sweden
| | - Vandré C Figueiredo
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Christopher S Fry
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Department of Athletic Training and Clinical Nutrition, College of Health Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40508, USA
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40508, USA
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40536, USA
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Kevin A Murach
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ferdinand von Walden
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17177, Sweden
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16
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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17
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Wang L, Wang J, Li Y, Dang S, Fan H, Xia S, Gan M, Tang T, Shao J, Jia X, Lai S. High expression of miR-30c-5p in satellite cells of high-fat diet-induced obese rabbits inhibited satellite cell proliferation and promoted differentiation. Gene 2023; 883:147656. [PMID: 37479097 DOI: 10.1016/j.gene.2023.147656] [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: 04/27/2023] [Revised: 06/28/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
It was revealed in our previous study that the expression of miR-30c-5p in the skeletal muscle of rabbits fed high-fat diet was highly expressed. In the present study, we further investigated the function of miR-30c-5p in proliferation and differentiation of skeletal muscle satellite cell (SMSC). The results obtained in the present study showed that the skeletal muscle fibers of the rabbits fed the standard normal diet (SND) were orderly, regular, and uniform after HE staining, however, the muscle fibers of the rabbits fed the high-fat diet (HFD) were generally atrophied, some were arranged disorderly, the intercellular space was enlarged, the nucleus was increased, and the morphology and position were abnormal. Compared with the SND group, it was observed that the weekly weight gain and fat percentage were relatively higher, and also the levels of the serum biochemical indexes such as glucose, cholesterol, and triglyceride increased significantly in the rabbits fed with HFD. In addition, the results after the transfection of miR-30c-5p mimic, mimic NC (negative control), miR-30c-5p inhibitor, and inhibitor NC into the SMSCs showed that the cell counting kit-8 (CCK-8) proliferation experiment suggested that the number of cells in the over expression group was significantly lower than that in the mimic NC group at 48, 72, 96 h of cell proliferation. At 48, 72, 120 h, the number of cells in the inhibitor group was significantly higher than that in the mimic NC group. The number of EdU positive cells decreased significantly in the over expression group compared with the mimic NC group, however, it increased significantly in the inhibitor group compared with the inhibitor NC group. Moreover, compared with the mimic NC group, the myotube area increased significantly in the miR-30c-5p mimic group, whereas it decreased significantly in the miR-30c-5p inhibitor group as compared with the inhibitor NC group. In addition, we found that trinucleotide repeat containing adaptor 6A (TNRC6A) was successfully validated as a target gene for miR-30c-5p. The expression of TNRC6A in the miR-30c-5p mimic group was significantly lower than that in the mimic NC group. It was further observed that the expression of TNRC6A increased significantly in the miR-30c-5p inhibitor group as compared to that in the inhibitor NC group. Taken together, the results obtained in this study showed that miR-30c-5p promotes the differentiation as well as inhibits the proliferation of rabbit skeletal muscle satellite cells, and TNRC6A is a target gene of miR-30c-5p.
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Affiliation(s)
- Li Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
| | - Yanhong Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Shuzhang Dang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Huimei Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Siqi Xia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mingchuan Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Tao Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jiahao Shao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
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18
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Sallis S, Bérubé-Simard FA, Grondin B, Leduc E, Azouz F, Bélanger C, Pilon N. The CHARGE syndrome-associated protein FAM172A controls AGO2 nuclear import. Life Sci Alliance 2023; 6:e202302133. [PMID: 37221016 PMCID: PMC10205598 DOI: 10.26508/lsa.202302133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
CHARGE syndrome is a neural crest-related disorder mainly caused by mutation of the chromatin remodeler-coding gene CHD7 Alternative causes include mutation of other chromatin and/or splicing factors. One of these additional players is the poorly characterized FAM172A, which we previously found in a complex with CHD7 and the small RNA-binding protein AGO2 at the chromatin-spliceosome interface. Focusing on the FAM172A-AGO2 interplay, we now report that FAM172A is a direct binding partner of AGO2 and, as such, one of the long sought-after regulators of AGO2 nuclear import. We show that this FAM172A function mainly relies on its classical bipartite nuclear localization signal and associated canonical importin-α/β pathway, being enhanced by CK2-induced phosphorylation and abrogated by a CHARGE syndrome-associated missense mutation. Overall, this study thus strengthens the notion that noncanonical nuclear functions of AGO2 and associated regulatory mechanisms might be clinically relevant.
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Affiliation(s)
- Sephora Sallis
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Félix-Antoine Bérubé-Simard
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
| | - Benoit Grondin
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Elizabeth Leduc
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Fatiha Azouz
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Catherine Bélanger
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Canada
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19
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Arafat M, Sperling R. Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer. Noncoding RNA 2023; 9:42. [PMID: 37624034 PMCID: PMC10459839 DOI: 10.3390/ncrna9040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Non-coding RNAs (ncRNAs) play diverse roles in regulating cellular processes and have been implicated in pathological conditions, including cancer, where interactions between ncRNAs play a role. Relevant here are (i) microRNAs (miRNAs), mainly known as negative regulators of gene expression in the cytoplasm. However, identification of miRNAs in the nucleus suggested novel nuclear functions, and (ii) long non-coding RNA (lncRNA) regulates gene expression at multiple levels. The recent findings of miRNA in supraspliceosomes of human breast and cervical cancer cells revealed new candidates of lncRNA targets. Here, we highlight potential cases of crosstalk between lncRNA and supraspliceosomal miRNA expressed from the same genomic region, having complementary sequences. Through RNA:RNA base pairing, changes in the level of one partner (either miRNA or lncRNA), as occur in cancer, could affect the level of the other, which might be involved in breast and cervical cancer. An example is spliceosomal mir-7704 as a negative regulator of the oncogenic lncRNA HAGLR. Because the expression of spliceosomal miRNA is cell-type-specific, the list of cis-interacting lncRNA:spliceosomal miRNA presented here is likely just the tip of the iceberg, and such interactions are likely relevant to additional cancers. We thus highlight the potential of lncRNA:spliceosomal miRNA interactions as novel targets for cancer diagnosis and therapies.
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Affiliation(s)
- Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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20
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Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548119. [PMID: 37461596 PMCID: PMC10350042 DOI: 10.1101/2023.07.07.548119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Audrius Kilikevicius
- current address, Eli Lilly, Lilly Cambridge Innovation Center, Cambridge, MA 02142
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yi Han
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Tao Wang
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
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21
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Miśkiewicz J, Mielczarek-Palacz A, Gola JM. MicroRNAs as Potential Biomarkers in Gynecological Cancers. Biomedicines 2023; 11:1704. [PMID: 37371799 DOI: 10.3390/biomedicines11061704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/25/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNAs are non-coding transcripts that, thanks to the ability to regulate the mRNA of target genes, can affect the expression of genes encoding tumor suppressors and oncogenes. They can control many important cellular processes, including apoptosis, differentiation, growth, division, and metabolism. Therefore, miRNAs play an important role in the development of many cancers, including gynecological cancers. Ovarian cancer, endometrial cancer, cervical cancer, and vulvar cancer are the most common cancers in women and are a frequent cause of death. The heterogeneity of the pathogenesis of these gynecological diseases makes the diagnostic process a significant obstacle for modern medicine. To date, many studies have been carried out, in which particular attention has been paid to the molecular pathomechanism of these diseases, with particular emphasis on miRNAs. To date, the changed profile of many miRNAs, which influenced the promotion of proliferation, migration, invasion processes and the simultaneous inhibition of programmed cell death, has been proven many times. Detailed understanding of the molecular effects of miRNAs in the above-mentioned gynecological cancers will enable the development of potential predictive and prognostic biomarkers, as well as the optimization of the diagnostic process.
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Affiliation(s)
- Joanna Miśkiewicz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Aleksandra Mielczarek-Palacz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
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22
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Farina FM, Weber C, Santovito D. The emerging landscape of non-conventional RNA functions in atherosclerosis. Atherosclerosis 2023; 374:74-86. [PMID: 36725418 DOI: 10.1016/j.atherosclerosis.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Most of the human genome is transcribed into non-coding RNAs (ncRNAs), which encompass a heterogeneous family of transcripts including microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and others. Although the detailed modes of action of some classes are not fully elucidated, the common notion is that ncRNAs contribute to sculpting gene expression of eukaryotic cells at multiple levels. These range from the regulation of chromatin remodeling and transcriptional activity to post-transcriptional regulation of messenger RNA splicing, stability, and decay. Many of these functions ultimately govern the expression of coding and non-coding genes to affect diverse physiological and pathological mechanisms in vascular biology and beyond. As such, different classes of ncRNAs emerged as crucial regulators of vascular integrity as well as active players in the pathophysiology of atherosclerosis from the early stages of endothelial dysfunction to the clinically relevant complications. However, research in recent years revealed unexpected findings such as small ncRNAs being able to biophysically regulate protein function, the glycosylation of ncRNAs to be exposed on the cell surface, the release of ncRNAs in the extracellular space to act as ligands of receptors, and even the ability of non-coding portion of messenger RNAs to mediate structural functions. This evidence expanded the functional repertoire of ncRNAs far beyond gene regulation and highlighted an additional layer of biological control of cell function. In this Review, we will discuss these emerging aspects of ncRNA biology, highlight the implications for the mechanisms of vascular biology and atherosclerosis, and discuss possible translational implications.
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Affiliation(s)
- Floriana Maria Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
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23
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Liu H, Li H, Jiang Z, Jin S, Song R, Yang Y, Li J, Huang J, Zhang X, Dong X, Mori M, Fritzler MJ, He L, Cardoso WV, Lu J. A local translation program regulates centriole amplification in the airway epithelium. Sci Rep 2023; 13:7090. [PMID: 37127654 PMCID: PMC10151349 DOI: 10.1038/s41598-023-34365-8] [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: 01/10/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023] Open
Abstract
Biogenesis of organelles requires targeting of a subset of proteins to specific subcellular domains by signal peptides or mechanisms controlling mRNA localization and local translation. How local distribution and translation of specific mRNAs for organelle biogenesis is achieved remains elusive and likely to be dependent on the cellular context. Here we identify Trinucleotide repeat containing-6a (Tnrc6a), a component of the miRNA pathway, distinctively localized to apical granules of differentiating airway multiciliated cells (MCCs) adjacent to centrioles. In spite of being enriched in TNRC6A and the miRNA-binding protein AGO2, they lack enzymes for mRNA degradation. Instead, we found these apical granules enriched in components of the mRNA translation machinery and newly synthesized proteins suggesting that they are specific hubs for target mRNA localization and local translation in MCCs. Consistent with this, Tnrc6a loss of function prevented formation of these granules and led to a broad reduction, rather than stabilization of miRNA targets. These included downregulation of key genes involved in ciliogenesis and was associated with defective multicilia formation both in vivo and in primary airway epithelial cultures. Similar analysis of Tnrc6a disruption in yolk sac showed stabilization of miRNA targets, highlighting the potential diversity of these mechanisms across organs.
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Affiliation(s)
- Helu Liu
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Huijun Li
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Zhihua Jiang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Shibo Jin
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Rui Song
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Ying Yang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Jun Li
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Jingshu Huang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xiaoqing Zhang
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xuesong Dong
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Munemasa Mori
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Marvin J Fritzler
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Wellington V Cardoso
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
| | - Jining Lu
- The Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University Medical Center, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, 6705 Rockledge Drive, Room 407-J, MSC 7952, Bethesda, MD, 20892-7952, USA.
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24
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Kaneko Y, Naito Y, Koide R, Parrish NF, Takahashi T. The regulation of persistent Borna disease virus infection by RNA silencing factors in human cells. Biochem Biophys Res Commun 2023; 658:122-127. [PMID: 37030066 DOI: 10.1016/j.bbrc.2023.03.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 02/20/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Viral infection induces diverse cellular immune responses. Some viruses induce the production of antiviral cytokines, alterations of endogenous gene expression, and apoptosis; however, other viruses replicate without inducing such responses, enabling them to persistently infect cells. Infection by Borna disease virus type 1 (BoDV-1) can result in fatal immune-mediated encephalitis, including in humans, yet infection of cells in vitro is generally persistent. The regulatory mechanisms underlying this persistent infection remain unclear. Here, we show that an enhancer of RNA-silencing, TRBP, positively regulates BoDV RNA level in human cells. Knockdown of TRBP decreased BoDV RNA levels in persistently-infected cells, whereas overexpression of TRBP increased BoDV RNA levels. To investigate the mechanism underlying this phenomenon, we performed immunoprecipitation assays and found that TRBP interacts with BoDV RNA. Furthermore, we performed cell fractionation, which revealed that persistent infection with BoDV does not alter the localization of TRBP and other RNA silencing factors in cells. Our results showed the regulation of persistent BoDV infection by RNA-silencing factors in human cells.
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25
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Chen W, Ru J, Wu T, Man D, Wu J, Wu L, Sun Y, Yu H, Li M, Zhang G, Zhu X, Tong R, Xiao H, Li Y, Yang B. MiR-652-3p promotes malignancy and metastasis of cancer cells via inhibiting TNRC6A in hepatocellular carcinoma. Biochem Biophys Res Commun 2023; 640:1-11. [PMID: 36495604 DOI: 10.1016/j.bbrc.2022.11.100] [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: 09/29/2022] [Revised: 11/21/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) was one of the most prevalent life-threatening cancers. Metastasis is the leading cause of cancer-related death in HCC. MiRNAs play essential roles in cancer metastasis. METHODS Expression of miR-652-3p in HCC was assessed. Function experiments of miR-652-3p and trinucleotide repeat-containing gene 6A protein (TNRC6A) were performed both in vitro and in vivo. mRNA sequencing, PCR, and western blot were performed to verify the target genes and pathway of miR-652-3p. The lung metastasis and xenograft cancer model in nude mice was established to investigate the effects of the miR-652-3p and TRNC6A on tumor metastasis in vivo. The relationship between the expression of the miR-652-3p, TNRC6A and the prognosis of HCC patients was analyzed. RESULTS Upregulated miR-652-3p was found in the tumor tissues of HCC, especially in metastatic HCC patients. Overexpression of miR-652-3p promoted and knockdown of miR-652-3p suppressed HCC metastasis both in vitro and in vivo. MiR-652-3p promoted HCC metastasis via regulating the EMT pathway. TNRC6A was identified as a direct target of miR-652-3p, and the knockdown of TNRC6A restored repressed EMT and HCC metastasis caused by the inhibition of miR-652-3p. Clinical results revealed that high expression of miR-652-3p and low expression of TNRC6A were positively correlated to shortened overall survival and disease-free survival in HCC patients. CONCLUSIONS MiR-652-3p promotes EMT and HCC metastasis by inhibiting TNRC6A expression in HCC. MiR-652-3p and TNRC6A may serve as potential biomarkers to predict prognosis in HCC patients with metastasis.
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Affiliation(s)
- Wei Chen
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Junnan Ru
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Tong Wu
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Da Man
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Jingbang Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Lijuan Wu
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Yujing Sun
- General Practice Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Hanxi Yu
- Health Management Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Min Li
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Gangwei Zhang
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Xingxin Zhu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Rongliang Tong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Heng Xiao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yanhua Li
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Beng Yang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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26
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Depienne C, van den Maagdenberg AMJM, Kühnel T, Ishiura H, Corbett MA, Tsuji S. Insights into familial adult myoclonus epilepsy pathogenesis: How the same repeat expansion in six unrelated genes may lead to cortical excitability. Epilepsia 2023. [PMID: 36622139 DOI: 10.1111/epi.17504] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023]
Abstract
Familial adult myoclonus epilepsy (FAME) results from the same pathogenic TTTTA/TTTCA pentanucleotide repeat expansion in six distinct genes encoding proteins with different subcellular localizations and very different functions, which poses the issue of what causes the neurobiological disturbances that lead to the clinical phenotype. Postmortem and electrophysiological studies have pointed to cortical hyperexcitability as well as dysfunction and neurodegeneration of both the cortex and cerebellum of FAME subjects. FAME expansions, contrary to the same expansion in DAB1 causing spinocerebellar ataxia type 37, seem to have no or limited impact on their recipient gene expression, which suggests a pathophysiological mechanism independent of the gene and its function. Current hypotheses include toxicity of the RNA molecules carrying UUUCA repeats, or toxicity of polypeptides encoded by the repeats, a mechanism known as repeat-associated non-AUG translation. The analysis of postmortem brains of FAME1 expansion (in SAMD12) carriers has revealed the presence of RNA foci that could be formed by the aggregation of RNA molecules with abnormal UUUCA repeats, but evidence is still lacking for other FAME subtypes. Even when the expansion is located in a gene ubiquitously expressed, expression of repeats remains undetectable in peripheral tissues (blood, skin). Therefore, the development of appropriate cellular models (induced pluripotent stem cell-derived neurons) or the study of affected tissues in patients is required to elucidate how FAME repeat expansions located in unrelated genes lead to disease.
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Affiliation(s)
- Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hiroyuki Ishiura
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mark A Corbett
- Robinson Research Institute, University of Adelaide, Adelaide Medical School, Adelaide, South Australia, Australia
| | - Shoji Tsuji
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
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27
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Mauro M, Berretta M, Palermo G, Cavalieri V, La Rocca G. The Multiplicity of Argonaute Complexes in Mammalian Cells. J Pharmacol Exp Ther 2023; 384:1-9. [PMID: 35667689 PMCID: PMC9827513 DOI: 10.1124/jpet.122.001158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
Argonautes (AGOs) are a highly conserved family of proteins found in most eukaryotes and involved in mechanisms of gene regulation, both at the transcriptional and post-transcriptional level. Among other functions, AGO proteins associate with microRNAs (miRNAs) to mediate the post-transcriptional repression of protein-coding genes. In this process, AGOs associate with members of the trinucleotide repeat containing 6 protein (TNRC6) family to form the core of the RNA-induced silencing complex (RISC), the effector machinery that mediates miRNA function. However, the description of the exact composition of the RISC has been a challenging task due to the fact the AGO's interactome is dynamically regulated in a cell type- and condition-specific manner. Here, we summarize some of the most significant studies that have identified AGO complexes in mammalian cells, as well as the approaches used to characterize them. Finally, we discuss possible opportunities to exploit what we have learned on the properties of the RISC to develop novel anti-cancer therapies. SIGNIFICANCE STATEMENT: The RNA-induced silencing complex (RISC) is the molecular machinery that mediates miRNA function in mammals. Studies over the past two decades have shed light on important biochemical and functional properties of this complex. However, many aspects of this complex await further elucidation, mostly due to technical limitations that have hindered full characterization. Here, we summarize some of the most significant studies on the mammalian RISC and discuss possible sources of biases in the approaches used to characterize it.
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Affiliation(s)
- Maurizio Mauro
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Massimiliano Berretta
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Giuseppe Palermo
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Vincenzo Cavalieri
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Gaspare La Rocca
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
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Nalavade R, Singh M. Intracellular Compartmentalization: A Key Determinant of MicroRNA Functions. Microrna 2023; 12:114-130. [PMID: 37638608 DOI: 10.2174/2211536612666230330184006] [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: 11/24/2022] [Revised: 12/26/2022] [Accepted: 01/19/2023] [Indexed: 08/29/2023]
Abstract
Being an integral part of the eukaryotic transcriptome, miRNAs are regarded as vital regulators of diverse developmental and physiological processes. Clearly, miRNA activity is kept in check by various regulatory mechanisms that control their biogenesis and decay pathways. With the increasing technical depth of RNA profiling technologies, novel insights have unravelled the spatial diversity exhibited by miRNAs inside a cell. Compartmentalization of miRNAs adds complexity to the regulatory circuits of miRNA expression, thereby providing superior control over the miRNA function. This review provides a bird's eye view of miRNAs expressed in different subcellular locations, thus affecting the gene regulatory pathways therein. Occurrence of miRNAs in diverse intracellular locales also reveals various unconventional roles played by miRNAs in different cellular organelles and expands the scope of miRNA functions beyond their traditionally known repressive activities.
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Affiliation(s)
- Rohit Nalavade
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Mohini Singh
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, India
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29
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de Rooij LA, Mastebroek DJ, ten Voorde N, van der Wall E, van Diest PJ, Moelans CB. The microRNA Lifecycle in Health and Cancer. Cancers (Basel) 2022; 14:cancers14235748. [PMID: 36497229 PMCID: PMC9736740 DOI: 10.3390/cancers14235748] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ~22 nucleotides that regulate gene expression at the post-transcriptional level. They can bind to around 60% of all protein-coding genes with an average of 200 targets per miRNA, indicating their important function within physiological and pathological cellular processes. miRNAs can be quickly produced in high amounts through canonical and non-canonical pathways that involve a multitude of steps and proteins. In cancer, miRNA biogenesis, availability and regulation of target expression can be altered to promote tumour progression. This can be due to genetic causes, such as single nucleotide polymorphisms, epigenetic changes, differences in host gene expression, or chromosomal remodelling. Alternatively, post-transcriptional changes in miRNA stability, and defective or absent components and mediators of the miRNA-induced silencing complex can lead to altered miRNA function. This review provides an overview of the current knowledge on the lifecycle of miRNAs in health and cancer. Understanding miRNA function and regulation is fundamental prior to potential future application of miRNAs as cancer biomarkers.
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Affiliation(s)
- Laura Adriana de Rooij
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-887-556-557
| | - Dirk Jan Mastebroek
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nicky ten Voorde
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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Matulić M, Gršković P, Petrović A, Begić V, Harabajsa S, Korać P. miRNA in Molecular Diagnostics. Bioengineering (Basel) 2022; 9:bioengineering9090459. [PMID: 36135005 PMCID: PMC9495386 DOI: 10.3390/bioengineering9090459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/05/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized.
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Affiliation(s)
- Maja Matulić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Paula Gršković
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Andreja Petrović
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Institute of Clinical Pathology and Cytology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Valerija Begić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Primary School “Sesvetski Kraljevec”, 10361 Sesvetski Kraljevec, Croatia
| | - Suzana Harabajsa
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Department of Pathology and Cytology, Division of Pulmonary Cytology Jordanovac, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4606-278
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31
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Goenka A, Tiek DM, Song X, Iglesia RP, Lu M, Hu B, Cheng SY. The Role of Non-Coding RNAs in Glioma. Biomedicines 2022; 10:2031. [PMID: 36009578 PMCID: PMC9405925 DOI: 10.3390/biomedicines10082031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022] Open
Abstract
For decades, research in cancer biology has been focused on the protein-coding fraction of the human genome. However, with the discovery of non-coding RNAs (ncRNAs), it has become known that these entities not only function in numerous fundamental life processes such as growth, differentiation, and development, but also play critical roles in a wide spectrum of human diseases, including cancer. Dysregulated ncRNA expression is found to affect cancer initiation, progression, and therapy resistance, through transcriptional, post-transcriptional, or epigenetic processes in the cell. In this review, we focus on the recent development and advances in ncRNA biology that are pertinent to their role in glioma tumorigenesis and therapy response. Gliomas are common, and are the most aggressive type of primary tumors, which account for ~30% of central nervous system (CNS) tumors. Of these, glioblastoma (GBM), which are grade IV tumors, are the most lethal brain tumors. Only 5% of GBM patients survive beyond five years upon diagnosis. Hence, a deeper understanding of the cellular non-coding transcriptome might help identify biomarkers and therapeutic agents for a better treatment of glioma. Here, we delve into the functional roles of microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) in glioma tumorigenesis, discuss the function of their extracellular counterparts, and highlight their potential as biomarkers and therapeutic agents in glioma.
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Affiliation(s)
- Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Deanna Marie Tiek
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xiao Song
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rebeca Piatniczka Iglesia
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Parayath NN, Gandham SK, Amiji MM. Tumor-targeted miRNA nanomedicine for overcoming challenges in immunity and therapeutic resistance. Nanomedicine (Lond) 2022; 17:1355-1373. [PMID: 36255330 PMCID: PMC9706370 DOI: 10.2217/nnm-2022-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
miRNA are critical messengers in the tumor microenvironment (TME) that influence various processes leading to immune suppression, tumor progression, metastasis and resistance. Strategies to modulate miRNAs in the TME have important implications in overcoming these challenges. However, miR delivery to specific cells in the TME has been challenging. This review discusses nanomedicine strategies to achieve cell-specific delivery of miRNAs. The key goal of delivery is to activate the tumor immune landscape as well as to prevent chemotherapy resistance. Specifically, the use of hyaluronic acid-based nanoparticle miRNA delivery to the TME is discussed. The discussion is focused on miRNA-125b for reprogramming tumor-associated macrophages to overcome immunosuppression and miRNA-let-7b to overcome resistance to anticancer chemotherapeutics because both these miRNAs have been extensively evaluated for delivery with hyaluronic acid-based delivery systems.
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Affiliation(s)
- Neha N Parayath
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Srujan K Gandham
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA,Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA 02115, USA,Author for correspondence: Tel.: +1 617 373 3137;
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33
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Douvris A, Viñas J, Burns KD. miRNA-486-5p: signaling targets and role in non-malignant disease. Cell Mol Life Sci 2022; 79:376. [PMID: 35731367 PMCID: PMC9217846 DOI: 10.1007/s00018-022-04406-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs, highly conserved between species, that are powerful regulators of gene expression. Aberrant expression of miRNAs alters biological processes and pathways linked to human disease. miR-486-5p is a muscle-enriched miRNA localized to the cytoplasm and nucleus, and is highly abundant in human plasma and enriched in small extracellular vesicles. Studies of malignant and non-malignant diseases, including kidney diseases, have found correlations with circulating miR-486-5p levels, supporting its role as a potential biomarker. Pre-clinical studies of non-malignant diseases have identified miR-486-5p targets that regulate major signaling pathways involved in cellular proliferation, migration, angiogenesis, and apoptosis. Validated miR-486-5p targets include phosphatase and tensin homolog (PTEN) and FoXO1, whose suppression activates phosphatidyl inositol-3-kinase (PI3K)/Akt signaling. Targeting of Smad1/2/4 and IGF-1 by miR-486-5p inhibits transforming growth factor (TGF)-β and insulin-like growth factor-1 (IGF-1) signaling, respectively. Other miR-486-5p targets include matrix metalloproteinase-19 (MMP-19), Sp5, histone acetyltransferase 1 (HAT1), and nuclear factor of activated T cells-5 (NFAT5). In this review, we examine the biogenesis, regulation, validated gene targets and biological effects of miR-486-5p in non-malignant diseases.
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Affiliation(s)
- Adrianna Douvris
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jose Viñas
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada
| | - Kevin D Burns
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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Liu J, Yang T, Huang Z, Chen H, Bai Y. Transcriptional regulation of nuclear miRNAs in tumorigenesis (Review). Int J Mol Med 2022; 50:92. [PMID: 35593304 DOI: 10.3892/ijmm.2022.5148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/28/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) are a type of endogenous non‑coding small RNA that regulates gene expression. miRNAs regulate gene expression at the post‑transcriptional level by targeting the 3'‑untranslated region (3'UTR) of cytoplasmic messenger RNAs (mRNAs). Recent research has confirmed the presence of mature miRNAs in the nucleus, which bind nascent RNA transcripts, gene promoter or enhancer regions, and regulate gene expression via epigenetic pathways. Some miRNAs have been shown to function as oncogenes or tumor suppressor genes by modulating molecular pathways involved in human cancers. Notably, a novel molecular mechanism underlying the dysregulation of miRNA expression in cancer has recently been discovered, indicating that miRNAs may be involved in tumorigenesis via a nuclear function that influences gene transcription and epigenetic states, elucidating their potential therapeutic implications. The present review article discusses the import of nuclear miRNAs, nucleus‑cytoplasm transport mechanisms and the nuclear functions of miRNAs in cancer. In addition, some software tools for predicting miRNA binding sites are also discussed. Nuclear miRNAs supplement miRNA regulatory networks in cancer as a non‑canonical aspect of miRNA action. Further research into this aspect may be critical for understanding the role of nuclear miRNAs in the development of human cancers.
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Affiliation(s)
- Junjie Liu
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, P.R. China
| | - Tianhao Yang
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, P.R. China
| | - Zishen Huang
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, P.R. China
| | - Huifang Chen
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, P.R. China
| | - Yinshan Bai
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, P.R. China
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35
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Fischer MA, Mahajan A, Cabaj M, Kimball TH, Morselli M, Soehalim E, Chapski DJ, Montoya D, Farrell CP, Scovotti J, Bueno CT, Mimila NA, Shemin RJ, Elashoff D, Pellegrini M, Monte E, Vondriska TM. DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation. Front Cardiovasc Med 2022; 9:837725. [PMID: 35620521 PMCID: PMC9127230 DOI: 10.3389/fcvm.2022.837725] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/17/2022] [Indexed: 12/14/2022] Open
Abstract
BackgroundAtrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF.MethodsWe enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort.ResultsA total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort.ConclusionsWe have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.
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Affiliation(s)
- Matthew A. Fischer
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- *Correspondence: Matthew A. Fischer
| | - Aman Mahajan
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Maximilian Cabaj
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Todd H. Kimball
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Marco Morselli
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Elizabeth Soehalim
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Douglas J. Chapski
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Dennis Montoya
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Colin P. Farrell
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jennifer Scovotti
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Claudia T. Bueno
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Naomi A. Mimila
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Richard J. Shemin
- Division of Cardiac Surgery, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States
| | - David Elashoff
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Emma Monte
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Thomas M. Vondriska
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, United States
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36
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Nuclear microRNAs release paused Pol II via the DDX21-CDK9 complex. Cell Rep 2022; 39:110673. [PMID: 35417682 DOI: 10.1016/j.celrep.2022.110673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 11/22/2022] Open
Abstract
RNA activation (RNAa) is an uncharacterized mechanism of transcriptional activation mediated by small RNAs, such as microRNAs (miRNAs). A critical issue in RNAa research is that it is difficult to distinguish between changes in gene expression caused indirectly by post-transcriptional regulation and direct induction of gene expression by RNAa. Therefore, in this study, we seek to identify a key factor involved in RNAa, using the induction of ZMYND10 by miR-34a as a system to evaluate RNAa. We identify the positive transcription elongation factors CDK9 and DDX21, which form a complex with nuclear AGO and TNRC6A, as important transcriptional activators of RNAa. In addition, we find that inhibition of DDX21 suppresses RNAa by miR-34a and other miRNAs without inhibiting post-transcriptional regulation. Our findings reveal a strong connection between RNAa and release of paused Pol II, facilitating RNAa research by making it possible to separately analyze post-transcriptional regulation and RNAa.
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37
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Santovito D, Weber C. Non-canonical features of microRNAs: paradigms emerging from cardiovascular disease. Nat Rev Cardiol 2022; 19:620-638. [PMID: 35304600 DOI: 10.1038/s41569-022-00680-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
Research showing that microRNAs (miRNAs) are versatile regulators of gene expression has instigated tremendous interest in cardiovascular research. The overwhelming majority of studies are predicated on the dogmatic notion that miRNAs regulate the expression of specific target mRNAs by inhibiting mRNA translation or promoting mRNA decay in the RNA-induced silencing complex (RISC). These efforts mostly identified and dissected contributions of multiple regulatory networks of miRNA-target mRNAs to cardiovascular pathogenesis. However, evidence from studies in the past decade indicates that miRNAs also operate beyond this canonical paradigm, featuring non-conventional regulatory functions and cellular localizations that have a pathophysiological role in cardiovascular disease. In this Review, we highlight the functional relevance of atypical miRNA biogenesis and localization as well as RISC heterogeneity. Moreover, we delineate remarkable non-canonical examples of miRNA functionality, including direct interactions with proteins beyond the Argonaute family and their role in transcriptional regulation in the nucleus and in mitochondria. We scrutinize the relevance of non-conventional biogenesis and non-canonical functions of miRNAs in cardiovascular homeostasis and pathology, and contextualize how uncovering these non-conventional properties can expand the scope of translational research in the cardiovascular field and beyond.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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38
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Müller M, Fäh T, Schaefer M, Hermes V, Luitz J, Stalder P, Arora R, Ngondo RP, Ciaudo C. AGO1 regulates pericentromeric regions in mouse embryonic stem cells. Life Sci Alliance 2022; 5:5/6/e202101277. [PMID: 35236760 PMCID: PMC8897595 DOI: 10.26508/lsa.202101277] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 01/09/2023] Open
Abstract
Depletion of AGO1 in mESCs leads to a redistribution of H3K9me3 and HP1α away from pericentromeric regions and is accompanied by an up-regulation of major satellites transcripts. Argonaute proteins (AGOs), which play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse embryonic stem cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1α, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly up-regulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1α in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts.
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Affiliation(s)
- Madlen Müller
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Tara Fäh
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Moritz Schaefer
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Janina Luitz
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zürich, Zürich, Switzerland
| | - Rajika Arora
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences (IMHS), Chair of RNAi and Genome Integrity, Zurich, Switzerland
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La Rocca G, Cavalieri V. Roles of the Core Components of the Mammalian miRISC in Chromatin Biology. Genes (Basel) 2022; 13:genes13030414. [PMID: 35327968 PMCID: PMC8954937 DOI: 10.3390/genes13030414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/20/2022] [Accepted: 02/23/2022] [Indexed: 12/16/2022] Open
Abstract
The Argonaute (AGO) and the Trinucleotide Repeat Containing 6 (TNRC6) family proteins are the core components of the mammalian microRNA-induced silencing complex (miRISC), the machinery that mediates microRNA function in the cytoplasm. The cytoplasmic miRISC-mediated post-transcriptional gene repression has been established as the canonical mechanism through which AGO and TNRC6 proteins operate. However, growing evidence points towards an additional mechanism through which AGO and TNRC6 regulate gene expression in the nucleus. While several mechanisms through which miRISC components function in the nucleus have been described, in this review we aim to summarize the major findings that have shed light on the role of AGO and TNRC6 in mammalian chromatin biology and on the implications these novel mechanisms may have in our understanding of regulating gene expression.
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Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Correspondence: (G.L.R.); (V.C.)
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Correspondence: (G.L.R.); (V.C.)
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40
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Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
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41
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Peters L, Depienne C, Klebe S. Familial adult myoclonic epilepsy (FAME): clinical features, molecular characteristics, pathophysiological aspects and diagnostic work-up. MED GENET-BERLIN 2021; 33:311-318. [PMID: 38835431 PMCID: PMC11006339 DOI: 10.1515/medgen-2021-2100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/16/2021] [Indexed: 06/06/2024]
Abstract
Familial adult myoclonic epilepsy (FAME) is a rare autosomal dominant disorder characterized by myoclonus and seizures. The genetic variant underlying FAME is an intronic repeat expansion composed of two different pentamers: an expanded TTTTA, which is the motif originally present at the locus, and an insertion of TTTCA repeats, which is usually located at the 3' end and likely corresponds to the pathogenic part of the expansion. This repeat expansion has been identified so far in six genes located on different chromosomes, which remarkably encode proteins with distinct cellular localizations and functions. Although the exact pathophysiological mechanisms remain to be clarified, it is likely that FAME repeat expansions lead to disease independently of the gene where they occur. We herein review the clinical and molecular characteristics of this singular genetic disorder, which interestingly shares clinical features with other more common neurological disorders whose etiology remains mainly unsolved.
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Affiliation(s)
- Lorenz Peters
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
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42
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microRNAs in Human Adipose Tissue Physiology and Dysfunction. Cells 2021; 10:cells10123342. [PMID: 34943849 PMCID: PMC8699244 DOI: 10.3390/cells10123342] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a large amount of evidence on the role of microRNA (miRNA) in regulating adipose tissue physiology. Indeed, miRNAs control critical steps in adipocyte differentiation, proliferation and browning, as well as lipolysis, lipogenesis and adipokine secretion. Overnutrition leads to a significant change in the adipocyte miRNOME, resulting in adipose tissue dysfunction. Moreover, via secreted mediators, dysfunctional adipocytes may impair the function of other organs and tissues. However, given their potential to control cell and whole-body energy expenditure, miRNAs also represent critical therapeutic targets for treating obesity and related metabolic complications. This review attempts to integrate present concepts on the role miRNAs play in adipose tissue physiology and obesity-related dysfunction and data from pre-clinical and clinical studies on the diagnostic or therapeutic potential of miRNA in obesity and its related complications.
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43
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Johnson ST, Chu Y, Liu J, Corey DR. Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing. RNA (NEW YORK, N.Y.) 2021; 27:1004-1016. [PMID: 34108231 PMCID: PMC8370741 DOI: 10.1261/rna.078709.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/04/2021] [Indexed: 05/11/2023]
Abstract
TNRC6 is a scaffolding protein that bridges interactions between small RNAs, argonaute (AGO) protein, and effector proteins to control gene expression. There are three paralogs in mammalian cells, TNRC6A, TNRC6B, and TNRC6C These paralogs have ∼40% amino acid sequence identity and the extent of their unique or redundant functions is unclear. Here, we use knockout cell lines, enhanced crosslinking immunoprecipitation (eCLIP), and high-throughput RNA sequencing (RNA-seq) to explore the roles of TNRC6 paralogs in RNA-mediated control of gene expression. We find that the paralogs are largely functionally redundant and changes in levels of gene expression are well-correlated with those observed in AGO knockout cell lines. Splicing changes observed in AGO knockout cell lines are also observed in TNRC6 knockout cells. These data further define the roles of the TNRC6 isoforms as part of the RNA interference (RNAi) machinery.
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Affiliation(s)
- Samantha T Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Yongjun Chu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Jing Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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44
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Semina EV, Rysenkova KD, Troyanovskiy KE, Shmakova AA, Rubina KA. MicroRNAs in Cancer: From Gene Expression Regulation to the Metastatic Niche Reprogramming. BIOCHEMISTRY (MOSCOW) 2021; 86:785-799. [PMID: 34284705 DOI: 10.1134/s0006297921070014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By 2003, the Human Genome project had been completed; however, it turned out that 97% of genome sequences did not encode proteins. The explanation came later when it was found the untranslated DNA contain sequences for short microRNAs (miRNAs) and long noncoding RNAs that did not produce any mRNAs or tRNAs, but instead were involved in the regulation of gene expression. Initially identified in the cytoplasm, miRNAs have been found in all cell compartments, where their functions are not limited to the degradation of target mRNAs. miRNAs that are secreted into the extracellular space as components of exosomes or as complexes with proteins, participate in morphogenesis, regeneration, oncogenesis, metastasis, and chemoresistance of tumor cells. miRNAs play a dual role in oncogenesis: on one hand, they act as oncogene suppressors; on the other hand, they function as oncogenes themselves and inactivate oncosuppressors, stimulate tumor neoangiogenesis, and mediate immunosuppressive processes in the tumors, The review presents current concepts of the miRNA biogenesis and their functions in the cytoplasm and nucleus with special focus on the noncanonical mechanisms of gene regulation by miRNAs and involvement of miRNAs in oncogenesis, as well as the authors' opinion on the role of miRNAs in metastasis and formation of the premetastatic niche.
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Affiliation(s)
- Ekaterina V Semina
- National Cardiology Research Center, Ministry of Health of the Russian Federation, Moscow, 121552, Russia. .,Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | - Karina D Rysenkova
- National Cardiology Research Center, Ministry of Health of the Russian Federation, Moscow, 121552, Russia.,Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | | | - Anna A Shmakova
- National Cardiology Research Center, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
| | - Kseniya A Rubina
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
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45
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Santovito D, Egea V, Bidzhekov K, Natarelli L, Mourão A, Blanchet X, Wichapong K, Aslani M, Brunßen C, Horckmans M, Hristov M, Geerlof A, Lutgens E, Daemen MJAP, Hackeng T, Ries C, Chavakis T, Morawietz H, Naumann R, von Hundelshausen P, Steffens S, Duchêne J, Megens RTA, Sattler M, Weber C. Noncanonical inhibition of caspase-3 by a nuclear microRNA confers endothelial protection by autophagy in atherosclerosis. Sci Transl Med 2021; 12:12/546/eaaz2294. [PMID: 32493793 DOI: 10.1126/scitranslmed.aaz2294] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 04/02/2020] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are versatile regulators of gene expression with profound implications for human disease including atherosclerosis, but whether they can exert posttranslational functions to control cell adaptation and whether such noncanonical features harbor pathophysiological relevance is unknown. Here, we show that miR-126-5p sustains endothelial integrity in the context of high shear stress and autophagy. Bound to argonaute-2 (Ago2), miR-126-5p forms a complex with Mex3a, which occurs on the surface of autophagic vesicles and guides its transport into the nucleus. Mutational studies and biophysical measurements demonstrate that Mex3a binds to the central U- and G-rich regions of miR-126-5p with nanomolar affinity via its two K homology domains. In the nucleus, miR-126-5p dissociates from Ago2 and binds to caspase-3 in an aptamer-like fashion with its seed sequence, preventing dimerization of the caspase and inhibiting its activity to limit apoptosis. The antiapoptotic effect of miR-126-5p outside of the RNA-induced silencing complex is important for endothelial integrity under conditions of high shear stress promoting autophagy: ablation of Mex3a or ATG5 in vivo attenuates nuclear import of miR-126-5p, aggravates endothelial apoptosis, and exacerbates atherosclerosis. In human plaques, we found reduced nuclear miR-126-5p and active caspase-3 in areas of disturbed flow. The direct inhibition of caspase-3 by nuclear miR-126-5p reveals a noncanonical mechanism by which miRNAs can modulate protein function.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Virginia Egea
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kiril Bidzhekov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - André Mourão
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Xavier Blanchet
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Coy Brunßen
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Michael Horckmans
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles (ULB), B-1070 Brussels, Belgium
| | - Michael Hristov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Arie Geerlof
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Mat J A P Daemen
- Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Tilman Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Christian Ries
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Triantafyllos Chavakis
- Institute of Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Henning Morawietz
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Ronald Naumann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Philipp von Hundelshausen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Sabine Steffens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Michael Sattler
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands.,Munich Cluster for Systems Neurology (SyNergy), D-81377 Munich, Germany
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46
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Jia R, Song Z, Lin J, Li Z, Shan G, Huang C. Gawky modulates MTF-1-mediated transcription activation and metal discrimination. Nucleic Acids Res 2021; 49:6296-6314. [PMID: 34107019 PMCID: PMC8216474 DOI: 10.1093/nar/gkab474] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Metal-induced genes are usually transcribed at relatively low levels under normal conditions and are rapidly activated by heavy metal stress. Many of these genes respond preferentially to specific metal-stressed conditions. However, the mechanism by which the general transcription machinery discriminates metal stress from normal conditions and the regulation of MTF-1-meditated metal discrimination are poorly characterized. Using a focused RNAi screening in Drosophila Schneider 2 (S2) cells, we identified a novel activator, the Drosophila gawky, of metal-responsive genes. Depletion of gawky has almost no effect on the basal transcription of the metallothionein (MT) genes, but impairs the metal-induced transcription by inducing the dissociation of MTF-1 from the MT promoters and the deficient nuclear import of MTF-1 under metal-stressed conditions. This suggests that gawky serves as a 'checkpoint' for metal stress and metal-induced transcription. In fact, regular mRNAs are converted into gawky-controlled transcripts if expressed under the control of a metal-responsive promoter, suggesting that whether transcription undergoes gawky-mediated regulation is encrypted therein. Additionally, lack of gawky eliminates the DNA binding bias of MTF-1 and the transcription preference of metal-specific genes. This suggests a combinatorial control of metal discrimination by gawky, MTF-1, and MTF-1 binding sites.
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Affiliation(s)
- Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
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47
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Jiang C, Zhao Q, Wang C, Peng M, Hao G, Liu Z, Fu W, Zhao K. Downregulation of Long Noncoding RNA LINC00261 Attenuates Myocardial Infarction through the miR-522-3p/Trinucleotide Repeat-Containing Gene 6a (TNRC6A) Axis. Cardiovasc Ther 2021; 2021:6628194. [PMID: 34239606 PMCID: PMC8235986 DOI: 10.1155/2021/6628194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Myocardial infarction (MI) is cardiac tissue necrosis caused by acute and persistent ischemic hypoxia of the coronary arteries. This study is aimed at investigating the expression of long noncoding RNA (lncRNA) LINC00261 in MI and its effect on myocardial cells. METHODS qRT-PCR was performed to detect the expression levels of LINC00261, miR-522-3p, and TNRC6A in normal and MI cells. Western blotting analysis was performed to detect the expression of TNRC6A protein. Viability and apoptosis of myocardial cells after MI with the knockout of LINC00261 or TNRC6A were detected. The relationships among miR-522-3p, LINC00261, and TNRC6A in cardiomyocytes were evaluated using a double luciferase reporter gene assay. Hypoxic preconditioning in normal cells was used to construct a simulated MI environment to investigate the effect of LINC00261 on apoptosis of cardiac cells. RESULTS LINC00261 and TNRC6A were upregulated, while miR-522-3p was downregulated in coronary heart disease tissues with MI. Knockout of LINC00261 can increase the viability of cardiomyocytes and inhibit cell apoptosis. LINC00261 targets miR-522-3p in cardiomyocytes. In addition, miR-522-3p targets TNRC6A in cardiomyocytes. TNRC6A regulates cell viability and apoptosis of cardiomyocytes after MI, and TNRC6A-induced MI can be reversed by overexpression of miR-522-3p. CONCLUSIONS LINC00261 downregulated miR-522-3p in cardiomyocytes after MI by directly targeting miR-522-3p. TNRC6A is the direct target of miR-522-3p. Our results indicated that LINC00261 might serve as a therapeutic target for the treatment of MI.
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Affiliation(s)
- Chaoxin Jiang
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong 528200, China
| | - Qing Zhao
- Department of Clinical Laboratory, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510240, China
| | - Chenlong Wang
- Department of Laboratory Medicine, Nanhai Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Minyan Peng
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong 528200, China
| | - Guoqing Hao
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong 528200, China
| | - Zhifeng Liu
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, Guangdong 528200, China
| | - Wenjin Fu
- Department of Laboratory, Affiliated Houjie Hospital, Guangdong Medical College, Dongguan, Guangdong 523945, China
| | - Kewei Zhao
- Department of Clinical Laboratory, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510240, China
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48
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Mortazavi SS, Bahmanpour Z, Daneshmandpour Y, Roudbari F, Sheervalilou R, Kazeminasab S, Emamalizadeh B. An updated overview and classification of bioinformatics tools for MicroRNA analysis, which one to choose? Comput Biol Med 2021; 134:104544. [PMID: 34119921 DOI: 10.1016/j.compbiomed.2021.104544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 12/16/2022]
Abstract
The term 'MicroRNA' (miRNA) refers to a class of small endogenous non-coding RNAs (ncRNAs) regenerated from hairpin transcripts. Recent studies reveal miRNAs' regulatory involvement in essential biological processes through translational repression or mRNA degradation. Recently, there is a growing body of literature focusing on the importance of miRNAs and their functions. In this respect, several databases have been developed to manage the dispersed data produced. Therefore, it is necessary to know the parameters and characteristics of each database to benefit their data. Besides, selecting the correct database is of great importance to scientists who do not have enough experience in this field. A comprehensive classification along with an explanation of the information contained in each database leads to facilitating access to these resources. In this regard, we have classified relevant databases into several categories, including miRNA sequencing and annotation, validated/predicted miRNA targets, disease-related miRNA, SNP in miRNA sequence or target site, miRNA-related pathways, or gene ontology, and mRNA-miRNA interactions. Hence, this review introduces available miRNA databases and presents a convenient overview to inform researchers of different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant information rapidly.
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Affiliation(s)
| | - Zahra Bahmanpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Somayeh Kazeminasab
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Vice-Chancellor, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Emamalizadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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49
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Systematic Analysis of Targets of Pumilio-Mediated mRNA Decay Reveals that PUM1 Repression by DNA Damage Activates Translesion Synthesis. Cell Rep 2021; 31:107542. [PMID: 32375027 DOI: 10.1016/j.celrep.2020.107542] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/28/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts. However, the identification of degradation target mRNAs of RBPs remains difficult. By the combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to human Pumilio 1 (PUM1), we identify 48 mRNAs that both bind to PUM1 and exhibit PUM1-dependent degradation. Analysis of changes in the abundance of PUM1 and its degradation target mRNAs in RNA-seq data indicate that DNA-damaging agents negatively regulate PUM1-mediated mRNA decay. Cells exposed to cisplatin have reduced PUM1 abundance and increased PCNA and UBE2A mRNAs encoding proteins involved in DNA damage tolerance by translesion synthesis (TLS). Cells overexpressing PUM1 exhibit impaired DNA synthesis and TLS and increased sensitivity to the cytotoxic effect of cisplatin. Thus, our method identifies target mRNAs of PUM1-mediated decay and reveals that cells respond to DNA damage by inhibiting PUM1-mediated mRNA decay to activate TLS.
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50
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Subcellular Localization of miRNAs and Implications in Cellular Homeostasis. Genes (Basel) 2021; 12:genes12060856. [PMID: 34199614 PMCID: PMC8226975 DOI: 10.3390/genes12060856] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are thought to act as post-transcriptional regulators in the cytoplasm by either dampening translation or stimulating degradation of target mRNAs. With the increasing resolution and scope of RNA mapping, recent studies have revealed novel insights into the subcellular localization of miRNAs. Based on miRNA subcellular localization, unconventional functions and mechanisms at the transcriptional and post-transcriptional levels have been identified. This minireview provides an overview of the subcellular localization of miRNAs and the mechanisms by which they regulate transcription and cellular homeostasis in mammals, with a particular focus on the roles of phase-separated biomolecular condensates.
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