1
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Poliseno L, Lanza M, Pandolfi PP. Coding, or non-coding, that is the question. Cell Res 2024:10.1038/s41422-024-00975-8. [PMID: 39054345 DOI: 10.1038/s41422-024-00975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/30/2024] [Indexed: 07/27/2024] Open
Abstract
The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of "gene". While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy.
- Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Martina Lanza
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
- University of Siena, Siena, Italy
| | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Torino, Italy.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA.
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2
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Choudhury AR, Nagesh AM, Gupta S, Chaturvedi PK, Kumar N, Sandeep K, Pandey D. MicroRNA signature of stromal-epithelial interactions in prostate and breast cancers. Exp Cell Res 2024; 441:114171. [PMID: 39029573 DOI: 10.1016/j.yexcr.2024.114171] [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: 05/15/2024] [Revised: 07/01/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
Stromal-epithelial communication is an absolute necessity when it comes to the morphogenesis and pathogenesis of solid tissues, including the prostate and breast. So far, signalling pathways of several growth factors have been investigated. Besides such chemical factors, non-coding RNAs such as miRNAs have recently gained much interest because of their variety and complexity of action. Prostate and breast tissues being highly responsive to steroid hormones such as androgen and estrogen, respectively, it is not surprising that a huge set of available literature critically investigated the interplay between such hormones and miRNAs, especially in carcinogenesis. This review showcases our effort to highlight hormonally-related miRNAs that also somehow perturb the regular stromal-epithelial interactions during carcinogenesis in the prostate and breast. In future, we look forward to exploring how hormonal changes in the tissue microenvironment bring about miRNA-mediated changes in stromal-epithelial interactome in carcinogenesis and cancer progression.
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Affiliation(s)
- Ankit Roy Choudhury
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India; Department of Biology, Philipps University, Marburg, Germany
| | - A Muni Nagesh
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Neeraj Kumar
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Kumar Sandeep
- Department of Preventive Oncology, Dr. Bhim Rao Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Deepak Pandey
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India.
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3
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Yang Z, Liu X, Xu H, Teschendorff AE, Xu L, Li J, Fu M, Liu J, Zhou H, Wang Y, Zhang L, He Y, Lv K, Yang H. Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma. Commun Biol 2024; 7:824. [PMID: 38971948 PMCID: PMC11227553 DOI: 10.1038/s42003-024-06488-9] [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: 03/12/2024] [Accepted: 06/21/2024] [Indexed: 07/08/2024] Open
Abstract
The expression dysregulation of microRNAs (miRNA) has been widely reported during cancer development, however, the underling mechanism remains largely unanswered. In the present work, we performed a systematic integrative study for genome-wide DNA methylation, copy number variation and miRNA expression data to identify mechanisms underlying miRNA dysregulation in lower grade glioma. We identify 719 miRNAs whose expression was associated with alterations of copy number variation or promoter methylation. Integrative multi-omics analysis revealed four subtypes with differing prognoses. These glioma subtypes exhibited distinct immune-related characteristics as well as clinical and genetic features. By construction of a miRNA regulatory network, we identified candidate miRNAs associated with immune evasion and response to immunotherapy. Finally, eight prognosis related miRNAs were validated to promote cell migration, invasion and proliferation through in vitro experiments. Our study reveals the crosstalk among DNA methylation, copy number variation and miRNA expression for immune regulation in glioma, and could have important implications for patient stratification and development of biomarkers for immunotherapy approaches.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, and Intelligent Medicine Institute, Shanghai Medical College, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
| | - Xiaocen Liu
- Department of Nuclear Medicine, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China
| | - Hao Xu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Lingjie Xu
- Emergency Department, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jingyi Li
- Department of Medical Cosmetology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Minjie Fu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Jun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Hanyu Zhou
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Yingying Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Licheng Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Yungang He
- Shanghai Fifth People's Hospital, and Intelligent Medicine Institute, Shanghai Medical College, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Kun Lv
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China.
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China.
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China.
| | - Hui Yang
- Anhui Province Key Laboratory of Non-Coding RNA Basic and Clinical Transformation, Wuhu, 241001, Anhui, China.
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, Anhui, China.
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China.
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4
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [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: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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5
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Géli V, Nabet N. Saliva, a molecular reflection of the human body? Implications for diagnosis and treatment. Cell Stress 2024; 8:59-68. [PMID: 38826491 PMCID: PMC11144459 DOI: 10.15698/cst2024.05.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024] Open
Abstract
For many diseases, and cancer in particular, early diagnosis allows a wider range of therapies and a better disease management. This has led to improvements in diagnostic procedures, most often based on tissue biopsies or blood samples. Other biological fluids have been used to diagnose disease, and among them saliva offers a number of advantages because it can be collected non-invasively from large populations at relatively low cost. To what extent might saliva content reveal the presence of a tumour located at a distance from the oral cavity and the molecular information obtained from saliva be used to establish a diagnosis are current questions. This review focuses primarily on the content of saliva and shows how it potentially offers a source of diagnosis, possibly at an early stage, for pathologies such as cancers or endometriosis.
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6
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Chauhan S, Mathur R, Jha AK. The Impact of microRNA SNPS on Breast Cancer: Potential Biomarkers for Disease Detection. Mol Biotechnol 2024:10.1007/s12033-024-01113-w. [PMID: 38512426 DOI: 10.1007/s12033-024-01113-w] [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: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Breast cancer is considered a significant health concern worldwide, with genetic predisposition playing a critical role in its etiology. Single nucleotide polymorphisms (SNPs), particularly those within the 3' untranslated regions (3'UTRs) of target genes, are emerging as key factors in breast cancer susceptibility. Specifically, miRNAs have been recognized as possible novel approach for biomarkers discovery for both prognosis and diagnosis due to their direct association with cancer progression. Regional disparities in breast cancer incidence underscore the need for precise interventions, considering socio-cultural and economic factors. This review explores into the differential effects of SNP-miRNA interactions on breast cancer risk, emphasizing both risk-enhancing and protective associations across diverse populations. Furthermore, it explores the clinical implications of these findings, highlighting the potential of personalized approaches in breast cancer management. Additionally, it reviews the evolving therapeutic prospect of microRNAs (miRNAs), extending beyond cancer therapeutics to encompass various diseases, indicative of their versatility as therapeutic agents.
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Affiliation(s)
- Sakshi Chauhan
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Runjhun Mathur
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
- Dr APJ Abdul Kalam Technical University, Lucknow, Uttar Pradesh, India
| | - Abhimanyu Kumar Jha
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India.
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7
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Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 2024; 14:6588. [PMID: 38504112 PMCID: PMC10951430 DOI: 10.1038/s41598-024-56705-y] [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: 07/31/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024] Open
Abstract
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org.
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Affiliation(s)
- Fabien Degalez
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Mathieu Charles
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Sylvain Foissac
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Dailu Guan
- University of California Davis, Davis, USA
| | | | - Christophe Klopp
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
| | - Coralie Allain
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | | | | | - Hervé Acloque
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Elisabetta Giuffra
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
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8
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Kiel K, Król SK, Bronisz A, Godlewski J. MiR-128-3p - a gray eminence of the human central nervous system. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102141. [PMID: 38419943 PMCID: PMC10899074 DOI: 10.1016/j.omtn.2024.102141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
MicroRNA-128-3p (miR-128-3p) is a versatile molecule with multiple functions in the physiopathology of the human central nervous system. Perturbations of miR-128-3p, which is enriched in the brain, contribute to a plethora of neurodegenerative disorders, brain injuries, and malignancies, as this miRNA is a crucial regulator of gene expression in the brain, playing an essential role in the maintenance and function of cells stemming from neuronal lineage. However, the differential expression of miR-128-3p in pathologies underscores the importance of the balance between its high and low levels. Significantly, numerous reports pointed to miR-128-3p as one of the most depleted in glioblastoma, implying it is a critical player in the disease's pathogenesis and thus may serve as a therapeutic agent for this most aggressive form of brain tumor. In this review, we summarize the current knowledge of the diverse roles of miR-128-3p. We focus on its involvement in the neurogenesis and pathophysiology of malignant and neurodegenerative diseases. We also highlight the promising potential of miR-128-3p as an antitumor agent for the future therapy of human cancers, including glioblastoma, and as the linchpin of brain development and function, potentially leading to the development of new therapies for neurological conditions.
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Affiliation(s)
- Klaudia Kiel
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Sylwia Katarzyna Król
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Agnieszka Bronisz
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Jakub Godlewski
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
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9
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Li J, Hong X, Jiang M, Kho AT, Tiwari A, Wang AL, Chase RP, Celedón JC, Weiss ST, McGeachie MJ, Tantisira KG. A novel piwi-interacting RNA associates with type 2-high asthma phenotypes. J Allergy Clin Immunol 2024; 153:695-704. [PMID: 38056635 DOI: 10.1016/j.jaci.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs), comprising the largest noncoding RNA group, regulate transcriptional processes. Whether piRNAs are associated with type 2 (T2)-high asthma is unknown. OBJECTIVE We sought to investigate the association between piRNAs and T2-high asthma in childhood asthma. METHODS We sequenced plasma samples from 462 subjects in the Childhood Asthma Management Program (CAMP) as the discovery cohort and 1165 subjects in the Genetics of Asthma in Costa Rica Study (GACRS) as a replication cohort. Sequencing reads were filtered first, and piRNA reads were annotated and normalized. Linear regression was used for the association analysis of piRNAs and peripheral blood eosinophil count, total serum IgE level, and long-term asthma exacerbation in children with asthma. Mediation analysis was performed to investigate the effect direction. We then ascertained if the circulating piRNAs were present in asthmatic airway epithelial cells in a Gene Expression Omnibus (GEO; www.ncbi.nlm.nih.gov/geo) public data set. RESULTS Fifteen piRNAs were significantly associated with eosinophil count in CAMP (P ≤ .05), and 3 were successfully replicated in GACRS. Eleven piRNAs were associated with total IgE in CAMP, and one of these was replicated in GACRS. All 22 significant piRNAs were identified in epithelial cells in vitro, and 6 of these were differentially expressed between subjects with asthma and healthy controls. Fourteen piRNAs were associated with long-term asthma exacerbation, and effect of piRNAs on long-term asthma exacerbation are mediated through eosinophil count and serum IgE level. CONCLUSION piRNAs are associated with peripheral blood eosinophils and total serum IgE in childhood asthma and may play important roles in T2-high asthma.
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Affiliation(s)
- Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Computational Health Informatics Program, Boston Children's Hospital, Boston, Mass
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pa
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Partners Personalized Medicine, Partners Healthcare, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, Calif.
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10
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Shaikh FS, Siegel RJ, Srivastava A, Fox DA, Ahmed S. Challenges and promise of targeting miRNA in rheumatic diseases: a computational approach to identify miRNA association with cell types, cytokines, and disease mechanisms. Front Immunol 2024; 14:1322806. [PMID: 38264662 PMCID: PMC10803576 DOI: 10.3389/fimmu.2023.1322806] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that alter the expression of target genes at the post-transcriptional level, influencing diverse outcomes in metabolism, cell differentiation, proliferation, cell survival, and cell death. Dysregulated miRNA expression is implicated in various rheumatic conditions, including ankylosing spondylitis (AS), gout, juvenile idiopathic arthritis (JIA), osteoarthritis (OA), psoriatic arthritis, rheumatoid arthritis (RA), Sjogren's syndrome, systemic lupus erythematosus (SLE) and systemic sclerosis. For this review, we used an open-source programming language- PowerShell, to scan the massive number of existing primary research publications on PubMed on miRNAs in these nine diseases to identify and count unique co-occurrences of individual miRNAs and the disease name. These counts were used to rank the top seven most relevant immuno-miRs based on their research volume in each rheumatic disease. Individual miRNAs were also screened for publication with the names of immune cells, cytokines, and pathological processes involved in rheumatic diseases. These occurrences were tabulated into matrices to identify hotspots for research relevance. Based on this information, we summarize the basic and clinical findings for the top three miRNAs - miR-146, miR-155, and miR-21 - whose relevance spans across multiple rheumatic diseases. Furthermore, we highlight some unique miRNAs for each disease and why some rheumatic conditions lack research in this emerging epigenetics field. With the overwhelming number of publications on miRNAs in rheumatic diseases, this review serves as a 'relevance finder' to guide researchers in selecting miRNAs based on the compiled existing knowledge of their involvement in disease pathogenesis. This approach applies to other disease contexts with the end goal of developing miRNA-based therapeutics.
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Affiliation(s)
- Farheen S. Shaikh
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Ruby J. Siegel
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Aayush Srivastava
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - David A. Fox
- Department of Medicine, Division of Rheumatology and Clinical Autoimmunity Center of Excellence, University of Michigan Medical System, Ann Arbor, MI, United States
| | - Salahuddin Ahmed
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
- Division of Rheumatology, University of Washington School of Medicine, Seattle, WA, United States
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11
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Gholami M. Genetic variants and haplotype structures of miRNA host genes in cancer and obesity. J Biomol Struct Dyn 2024:1-7. [PMID: 38174558 DOI: 10.1080/07391102.2023.2300056] [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: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E-8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E-8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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12
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Zhu Y, Huang C, Zhang C, Zhou Y, Zhao E, Zhang Y, Pan X, Huang H, Liao W, Wang X. LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation. Nat Commun 2023; 14:8141. [PMID: 38065939 PMCID: PMC10709323 DOI: 10.1038/s41467-023-43974-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
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Grants
- 2020N368 Shenzhen Science and Technology Innovation Commission
- C4024-22GF Research Grants Council, University Grants Committee (RGC, UGC)
- 14104223 Research Grants Council, University Grants Committee (RGC, UGC)
- 11103619 Research Grants Council, University Grants Committee (RGC, UGC)
- 14111522 Research Grants Council, University Grants Committee (RGC, UGC)
- R4017-18 Research Grants Council, University Grants Committee (RGC, UGC)
- 82173289 National Natural Science Foundation of China (National Science Foundation of China)
- 81872401 National Natural Science Foundation of China (National Science Foundation of China)
- Guangdong Basic and Applied Basic Research Foundation (Project No.2019B030302012), a startup grant (Project No. 4937084), direct grant (2021.077), Faculty Postdoctoral Fellowship Scheme 2021/22 (Project No. FPFS/2122/32), Shenzhen Bay Scholars Program.
- Guangdong Basic and Applied Basic Research Foundation (2021A1515010425)
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Affiliation(s)
- Yixiao Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chengmei Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yi Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Enen Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yaxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xingyan Pan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Wenting Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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13
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Mönttinen HAM, Frilander MJ, Löytynoja A. Generation of de novo miRNAs from template switching during DNA replication. Proc Natl Acad Sci U S A 2023; 120:e2310752120. [PMID: 38019864 PMCID: PMC10710096 DOI: 10.1073/pnas.2310752120] [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: 06/26/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The mechanisms generating novel genes and genetic information are poorly known, even for microRNA (miRNA) genes with an extremely constrained design. All miRNA primary transcripts need to fold into a stem-loop structure to yield short gene products ([Formula: see text]22 nt) that bind and repress their mRNA targets. While a substantial number of miRNA genes are ancient and highly conserved, short secondary structures coding for entirely novel miRNA genes have been shown to emerge in a lineage-specific manner. Template switching is a DNA-replication-related mutation mechanism that can introduce complex changes and generate perfect base pairing for entire hairpin structures in a single event. Here, we show that the template-switching mutations (TSMs) have participated in the emergence of over 6,000 suitable hairpin structures in the primate lineage to yield at least 18 new human miRNA genes, that is 26% of the miRNAs inferred to have arisen since the origin of primates. While the mechanism appears random, the TSM-generated miRNAs are enriched in introns where they can be expressed with their host genes. The high frequency of TSM events provides raw material for evolution. Being orders of magnitude faster than other mechanisms proposed for de novo creation of genes, TSM-generated miRNAs enable near-instant rewiring of genetic information and rapid adaptation to changing environments.
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Affiliation(s)
- Heli A. M. Mönttinen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
| | - Mikko J. Frilander
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
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14
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Shang T, Pang S, Dong Y. Knockdown of long non-coding RNA LINC01123 plays a molecular sponge on miR-625-5p to inhibit the process of colorectal cancer cells via LASP1. J Mol Histol 2023; 54:521-537. [PMID: 37676533 DOI: 10.1007/s10735-023-10141-w] [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: 03/15/2023] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Colorectal cancer (CRC) at an advanced stage of cancer has a lower 5-year survival rate. Research on the molecular biological mechanisms of CRC is helpful for disease prevention and treatment. Long non-coding RNAs (lncRNAs) were shown to be suitable as therapeutic targets for CRC. Previously, our research team found that LINC01123 promoted proliferation and metastasis in CRC by regulating miR-625-5p and the LIM and SH3 protein 1 (LASP1). Therefore, this study speculated that the molecular sponge effect of LINC01123 on miR-625-5p affected the process of CRC via regulating LASP1. The LINC01123-silenced CRC cell models (using the LOVO and SW480 cells) and xenograft tumor models were established to verify the above conjecture. As a result, it was found that silencing LINC01123 inhibited viability, proliferation, metastasis, and invasion but promoted apoptosis in LOVO and SW480 cells. Additionally, the knockdown of LINC01123 inhibited the LASP1, N-cadherin, PCNA, and Bcl-2 protein levels and raised the E-cadherin, Bax, and Caspase-3 protein levels in vitro. Furthermore, it showed that LINC01123, as a molecular sponge, targeted the miR-625-5p/LASP1 axis. The results of the xenograft tumor assay further verified the above effects of LINCO1123-silenced on tumor growth in vivo. And the miR-625-5p mimics treatment promoted the aforementioned effects of silencing LINC01123 on CRC cells while overexpressing LASP1 has an antagonistic effect to silencing LINC01123. In conclusion, this study suggests that silencing LINC01123 inhibits the process of CRC via sponging to the miR-625-5p/LASP1 axis. This finding hopes to provide research fundamentals on the biological mechanism study of CRC.
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Affiliation(s)
- Tao Shang
- Anus-intestines Department, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, China
| | - Shikai Pang
- Department of General Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, China
| | - Yunfei Dong
- Anus-intestines Department, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310000, China.
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15
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Abegunde SO, Grieve S, Reiman T. TAZ upregulates MIR-224 to inhibit oxidative stress response in multiple myeloma. Cancer Rep (Hoboken) 2023; 6:e1879. [PMID: 37539777 PMCID: PMC10598259 DOI: 10.1002/cnr2.1879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/11/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Oxidative stress within the bone marrow niche of multiple myeloma contributes to disease progression and drug resistance. Recent studies have associated the Hippo pathway with miRNA biogenesis and oxidative stress in solid tumors. Oxidative stress and miRNA pathway inter-relates in several cancers. Our group recently showed that TAZ functions as a tumor suppressor in MM. However, the role of TAZ in oxidative stress in MM is unknown. AIMS We sought to examine the role of TAZ in myeloma cells' response to BM oxidative stress. We postulated that TAZ might be associated with an oxidative stress phenotype and distinct miRNA signature in MM. METHODS AND RESULTS Using human myeloma cell lines and clinical samples, we demonstrate that TAZ promotes myeloma cells' sensitivity to oxidative stress and anticancer-induced cytotoxicity by inducing miR-224 to repress the NRF2 antioxidant program in MM. We show that low expression of TAZ protein confers an oxidative stress-resistant phenotype in MM. Furthermore, we provide evidence that overexpression of miR-224 in myeloma cells expressing low amounts of TAZ protein inhibits cell growth and enhances sensitivity to anti-myeloma therapeutics. CONCLUSION Our findings uncover a potential role for TAZ in oxidative stress response in MM via the miR-224-NRF2 molecular pathway. This provides the scientific ground to explore miR-224 as a potential molecular target to modify TAZ expression and enhance myeloma sensitivity to treatment.
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Affiliation(s)
- Samuel O. Abegunde
- Department of BiologyUniversity of New BrunswickSaint JohnNew BrunswickCanada
- Dalhousie Medicine NBSaint JohnNew BrunswickCanada
| | | | - Tony Reiman
- Department of BiologyUniversity of New BrunswickSaint JohnNew BrunswickCanada
- Dalhousie Medicine NBSaint JohnNew BrunswickCanada
- Saint John Regional HospitalSaint JohnNew BrunswickCanada
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16
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Ahmadi SM, Amirkhanloo S, Yazdian-Robati R, Ebrahimi H, Pirhayati FH, Almalki WH, Ebrahimnejad P, Kesharwani P. Recent advances in novel miRNA mediated approaches for targeting breast cancer. J Drug Target 2023; 31:777-793. [PMID: 37480323 DOI: 10.1080/1061186x.2023.2240979] [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: 01/26/2023] [Revised: 04/18/2023] [Accepted: 05/05/2023] [Indexed: 07/24/2023]
Abstract
Breast cancer (BC) is considered one of the most frequent cancers among woman worldwide. While conventional therapy has been successful in treating many cases of breast cancer, drug resistance, heterogenicity, tumour features and recurrence, invasion, metastasis and the presence of breast cancer stem cells can hinder the effect of treatments, and can reduce the quality of life of patients. MicroRNAs (miRNAs) are short non-coding RNA molecules that play a crucial role in the development and progression of breast cancer. Several studies have reported that aberrant expression of specific miRNAs is associated with the pathogenesis of breast cancer. However, miRNAs are emerging as potential biomarkers and therapeutic targets for breast cancer. Understanding their role in breast cancer biology could help develop more effective treatments for this disease. The present study discusses the biogenesis and function of miRNAs, as well as miRNA therapy approaches for targeting and treating breast cancer cells.
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Affiliation(s)
- Seyedeh Melika Ahmadi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shervin Amirkhanloo
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rezvan Yazdian-Robati
- Pharmaceutical Sciences Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Ebrahimi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Waleed H Almalki
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Pedram Ebrahimnejad
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
- Pharmaceutical Sciences Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
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17
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Ornos ED, Cando LF, Catral CD, Quebral EP, Tantengco OA, Arevalo MVP, Dee EC. Molecular basis of sex differences in cancer: Perspective from Asia. iScience 2023; 26:107101. [PMID: 37404373 PMCID: PMC10316661 DOI: 10.1016/j.isci.2023.107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
Cancer is a leading cause of mortality and morbidity globally. Sex differences in cancer are evident in death rates and treatment responses in several cancers. Asian patients have unique cancer epidemiology influenced by their genetic ancestry and sociocultural factors in the region. In this review, we show molecular associations that potentially mediate sex disparities observed in cancer in Asian populations. Differences in sex characteristics are evident at the cytogenetic, genetic, and epigenetic levels mediating processes that include cell cycle, oncogenesis, and metastasis. Larger clinical and in vitro studies that explore mechanisms can confirm the associations of these molecular markers. In-depth studies of these markers can reveal their importance as diagnostics, prognostics, and therapeutic efficacy markers. Sex differences should be considered in designing novel cancer therapeutics in this era of precision medicine.
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Affiliation(s)
- Eric David Ornos
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | - Leslie Faye Cando
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | | | - Elgin Paul Quebral
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Virology Laboratory, Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ourlad Alzeus Tantengco
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Department of Physiology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines
- Department of Biology, College of Science, De La Salle University, Manila 0922, Philippines
| | | | - Edward Christopher Dee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10028, USA
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18
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Zhu L, Jiao H, Gao W, Huang L, Shi C, Zhang F, Wu J, Luo J. Fatty Acid Desaturation Is Suppressed in Mir-26a/b Knockout Goat Mammary Epithelial Cells by Upregulating INSIG1. Int J Mol Sci 2023; 24:10028. [PMID: 37373175 DOI: 10.3390/ijms241210028] [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: 05/17/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNA-26 (miR-26a and miR-26b) plays a critical role in lipid metabolism, but its endogenous regulatory mechanism in fatty acid metabolism is not clear in goat mammary epithelial cells (GMECs). GMECs with the simultaneous knockout of miR-26a and miR-26b were obtained using the CRISPR/Cas9 system with four sgRNAs. In knockout GMECs, the contents of triglyceride, cholesterol, lipid droplets, and unsaturated fatty acid (UFA) were significantly reduced, and the expression of genes related to fatty acid metabolism was decreased, but the expression level of miR-26 target insulin-induced gene 1 (INSIG1) was significantly increased. Interestingly, the content of UFA in miR-26a and miR-26b simultaneous knockout GMECs was significantly lower than that in wild-type GMECs and miR-26a- and miR-26b-alone knockout cells. After decreasing INSIG1 expression in knockout cells, the contents of triglycerides, cholesterol, lipid droplets, and UFAs were restored, respectively. Our studies demonstrate that the knockout of miR-26a/b suppressed fatty acid desaturation by upregulating the target INSIG1. This provides reference methods and data for studying the functions of miRNA families and using miRNAs to regulate mammary fatty acid synthesis.
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Affiliation(s)
- Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Hongyun Jiao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Wenchang Gao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lian Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jiao Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
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19
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526143. [PMID: 36778497 PMCID: PMC9915486 DOI: 10.1101/2023.01.29.526143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., whole transcriptomes, nascent transcriptomes, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens targeting a variety of biological processes, we were able to decipher the complexity of RNA regulations at multiple levels (e.g., synthesis, processing, degradation), and revealed key regulators involved in miRNA and mitochondrial RNA processing pathways. Our technique opens the possibility of systematically decoding the genome-wide regulatory network underlying RNA temporal dynamics at scale and cost-effectively.
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20
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Han X, Li B, Zhang S. MIR503HG: A potential diagnostic and therapeutic target in human diseases. Biomed Pharmacother 2023; 160:114314. [PMID: 36736276 DOI: 10.1016/j.biopha.2023.114314] [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: 12/07/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
LncRNAs are involved in many physiological and pathological processes, including chromatin remodeling, transcription, posttranscriptional gene expression, mRNA stability, translation, and posttranslational modification, and their functions depend on subcellular localization. MIR503HG is a lncRNA as well as a host gene for the miRNAs miR-503 and miR-424. MIR503HG functions independently or synergistically with miR-503. MIR503HG affects cell proliferation, invasion, metastasis, apoptosis, angiogenesis, and other biological behaviors. The mechanism of MIR503HG in disease includes interaction with protein, sponging miRNA to regulate downstream target gene, and participation in NF-κB, TGF-β, ERK/MAPK, and PI3K/AKT signaling pathways. In this review, we summarize the molecular mechanisms of MIR503HG in disease and its potential applications in diagnosis, prognosis, and treatment. We also raise some unanswered questions in this area, providing insights for future research.
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Affiliation(s)
- Xue Han
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Shenyang, Liaoning Province, China.
| | - Bo Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Shenyang, Liaoning Province, China. libo--
| | - Shitai Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Shenyang, Liaoning Province, China.
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21
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Chen YF, Xu AP. Circular RNA circDLG1 (has_circ_0068706) functions as an oncogene in nonsmall cell lung cancer through regulating AKT/mTOR signaling and direct binding to miR-144. Kaohsiung J Med Sci 2023; 39:446-457. [PMID: 36876724 DOI: 10.1002/kjm2.12662] [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: 09/02/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 03/07/2023] Open
Abstract
Nonsmall cell lung cancer (NSCLC) is a major subtype of lung cancer, causing substantial cancer-related deaths worldwide. However, the molecular basis of NSCLC development and progression remains understudied. Recently, a circular RNA, circDLG1, has been implicated in carcinogenesis and cancer metastasis. Yet, how circDLG1 affects NSCLC progression has not been reported. Here this study aims to elucidate the role of circDLG1 in NSCLC. First, we found that circDLG1 was significantly upregulated in both the GEO dataset and NSCLC tissues. Next, we silenced the expression of circDLG1 in NSCLC cell lines. Knockdown of circDLG1 upregulated miR-144 and downregulated Protein kinase B (AKT)/mechanistic target of rapamycin (mTOR), resulting in suppression of the proliferation activity and metastasis ability of NSCLC. In addition, circDLG1 knockdown significantly decreased the expression of the mesenchymal markers, proliferating cell nuclear antigen (PCNA), and N-cadherin, while increasing the expression level of E-cadherin. In conclusion, we demonstrate that circDLG1 promotes the pathogenesis and progression of NSCLC by regulating the miR-144/AKT/mTOR signaling axis, providing potential diagnostic and therapeutic targets for designing innovative treatment strategies.
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Affiliation(s)
- Yong-Feng Chen
- Department of Respiratory and Critical Care, Tongxiang First People's Hospital, Tongxiang, People's Republic of China
| | - Ai-Ping Xu
- Department of Respiratory and Critical Care, Tongxiang First People's Hospital, Tongxiang, People's Republic of China
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22
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Lafferty MJ, Aygün N, Patel NK, Krupa O, Liang D, Wolter JM, Geschwind DH, de la Torre-Ubieta L, Stein JL. MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size. eLife 2023; 12:e79488. [PMID: 36629315 PMCID: PMC9859047 DOI: 10.7554/elife.79488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
Expression quantitative trait loci (eQTL) data have proven important for linking non-coding loci to protein-coding genes. But eQTL studies rarely measure microRNAs (miRNAs), small non-coding RNAs known to play a role in human brain development and neurogenesis. Here, we performed small-RNA sequencing across 212 mid-gestation human neocortical tissue samples, measured 907 expressed miRNAs, discovering 111 of which were novel, and identified 85 local-miRNA-eQTLs. Colocalization of miRNA-eQTLs with GWAS summary statistics yielded one robust colocalization of miR-4707-3p expression with educational attainment and brain size phenotypes, where the miRNA expression increasing allele was associated with decreased brain size. Exogenous expression of miR-4707-3p in primary human neural progenitor cells decreased expression of predicted targets and increased cell proliferation, indicating miR-4707-3p modulates progenitor gene regulation and cell fate decisions. Integrating miRNA-eQTLs with existing GWAS yielded evidence of a miRNA that may influence human brain size and function via modulation of neocortical brain development.
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Affiliation(s)
- Michael J Lafferty
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Niyanta K Patel
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Justin M Wolter
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- UNC Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel HillChapel HillUnited States
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Traber GM, Yu AM. RNAi-Based Therapeutics and Novel RNA Bioengineering Technologies. J Pharmacol Exp Ther 2023; 384:133-154. [PMID: 35680378 PMCID: PMC9827509 DOI: 10.1124/jpet.122.001234] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/26/2023] Open
Abstract
RNA interference (RNAi) provides researchers with a versatile means to modulate target gene expression. The major forms of RNAi molecules, genome-derived microRNAs (miRNAs) and exogenous small interfering RNAs (siRNAs), converge into RNA-induced silencing complexes to achieve posttranscriptional gene regulation. RNAi has proven to be an adaptable and powerful therapeutic strategy where advancements in chemistry and pharmaceutics continue to bring RNAi-based drugs into the clinic. With four siRNA medications already approved by the US Food and Drug Administration (FDA), several RNAi-based therapeutics continue to advance to clinical trials with functions that closely resemble their endogenous counterparts. Although intended to enhance stability and improve efficacy, chemical modifications may increase risk of off-target effects by altering RNA structure, folding, and biologic activity away from their natural equivalents. Novel technologies in development today seek to use intact cells to yield true biologic RNAi agents that better represent the structures, stabilities, activities, and safety profiles of natural RNA molecules. In this review, we provide an examination of the mechanisms of action of endogenous miRNAs and exogenous siRNAs, the physiologic and pharmacokinetic barriers to therapeutic RNA delivery, and a summary of the chemical modifications and delivery platforms in use. We overview the pharmacology of the four FDA-approved siRNA medications (patisiran, givosiran, lumasiran, and inclisiran) as well as five siRNAs and several miRNA-based therapeutics currently in clinical trials. Furthermore, we discuss the direct expression and stable carrier-based, in vivo production of novel biologic RNAi agents for research and development. SIGNIFICANCE STATEMENT: In our review, we summarize the major concepts of RNA interference (RNAi), molecular mechanisms, and current state and challenges of RNAi drug development. We focus our discussion on the pharmacology of US Food and Drug Administration-approved RNAi medications and those siRNAs and miRNA-based therapeutics that entered the clinical investigations. Novel approaches to producing new true biological RNAi molecules for research and development are highlighted.
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Affiliation(s)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, University of California (UC) Davis School of Medicine, Sacramento, California
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24
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Kołosowska KA, Schratt G, Winterer J. microRNA-dependent regulation of gene expression in GABAergic interneurons. Front Cell Neurosci 2023; 17:1188574. [PMID: 37213213 PMCID: PMC10196030 DOI: 10.3389/fncel.2023.1188574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/20/2023] [Indexed: 05/23/2023] Open
Abstract
Information processing within neuronal circuits relies on their proper development and a balanced interplay between principal and local inhibitory interneurons within those circuits. Gamma-aminobutyric acid (GABA)ergic inhibitory interneurons are a remarkably heterogeneous population, comprising subclasses based on their morphological, electrophysiological, and molecular features, with differential connectivity and activity patterns. microRNA (miRNA)-dependent post-transcriptional control of gene expression represents an important regulatory mechanism for neuronal development and plasticity. miRNAs are a large group of small non-coding RNAs (21-24 nucleotides) acting as negative regulators of mRNA translation and stability. However, while miRNA-dependent gene regulation in principal neurons has been described heretofore in several studies, an understanding of the role of miRNAs in inhibitory interneurons is only beginning to emerge. Recent research demonstrated that miRNAs are differentially expressed in interneuron subclasses, are vitally important for migration, maturation, and survival of interneurons during embryonic development and are crucial for cognitive function and memory formation. In this review, we discuss recent progress in understanding miRNA-dependent regulation of gene expression in interneuron development and function. We aim to shed light onto mechanisms by which miRNAs in GABAergic interneurons contribute to sculpting neuronal circuits, and how their dysregulation may underlie the emergence of numerous neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Jochen Winterer
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
- *Correspondence: Jochen Winterer,
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25
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Centomo ML, Vitiello M, Poliseno L, Pandolfi PP. An Immunocompetent Environment Unravels the Proto-Oncogenic Role of miR-22. Cancers (Basel) 2022; 14:cancers14246255. [PMID: 36551740 PMCID: PMC9776418 DOI: 10.3390/cancers14246255] [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: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
MiR-22 was first identified as a proto-oncogenic microRNA (miRNA) due to its ability to post-transcriptionally suppress the expression of the potent PTEN (Phosphatase And Tensin Homolog) tumor suppressor gene. miR-22 tumorigenic role in cancer was subsequently supported by its ability to positively trigger lipogenesis, anabolic metabolism, and epithelial-mesenchymal transition (EMT) towards the metastatic spread. However, during the following years, the picture was complicated by the identification of targets that support a tumor-suppressive role in certain tissues or cell types. Indeed, many papers have been published where in vitro cellular assays and in vivo immunodeficient or immunosuppressed xenograft models are used. However, here we show that all the studies performed in vivo, in immunocompetent transgenic and knock-out animal models, unanimously support a proto-oncogenic role for miR-22. Since miR-22 is actively secreted from and readily exchanged between normal and tumoral cells, a functional immune dimension at play could well represent the divider that allows reconciling these contradictory findings. In addition to a critical review of this vast literature, here we provide further proof of the oncogenic role of miR-22 through the analysis of its genomic locus vis a vis the genetic landscape of human cancer.
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Affiliation(s)
- Maria Laura Centomo
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
- William N. Pennington Cancer Institute, Renown Health, Nevada System of Higher Education, Reno, NV 89502, USA
- Center for Genomic Medicine, Desert Research Institute, Reno, NV 89512, USA
| | - Marianna Vitiello
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124 Pisa, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124 Pisa, Italy
- Correspondence: (L.P.); (P.P.P.); Tel.: +39-050-315-2780 (L.P.); +1-775-982-6210 (P.P.P.); Fax: +39-050-315-3327 (L.P.); +1-775-982-4288 (P.P.P.)
| | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
- William N. Pennington Cancer Institute, Renown Health, Nevada System of Higher Education, Reno, NV 89502, USA
- Center for Genomic Medicine, Desert Research Institute, Reno, NV 89512, USA
- Correspondence: (L.P.); (P.P.P.); Tel.: +39-050-315-2780 (L.P.); +1-775-982-6210 (P.P.P.); Fax: +39-050-315-3327 (L.P.); +1-775-982-4288 (P.P.P.)
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26
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Masalha M, Meningher T, Mizrahi A, Barzilai A, Tabibian-Keissar H, Gur-Wahnon D, Ben-Dov IZ, Kapenhas J, Jacob-Hirsch J, Leibowitz R, Sidi Y, Avni D. MiR-199a-3p Induces Mesenchymal to Epithelial Transition of Keratinocytes by Targeting RAP2B. Int J Mol Sci 2022; 23:ijms232315401. [PMID: 36499729 PMCID: PMC9741271 DOI: 10.3390/ijms232315401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Cutaneous squamous cell carcinoma (CSCC) is an epidermal skin cancer that evolves from normal epidermis along several pre-malignant stages. Previously we found specific miRNAs alterations in each step along these stages. miR-199a-3p expression decreases at the transition to later stages. A crucial step for epithelial carcinoma cells to acquire invasive capacity is the disruption of cell-cell contacts and the gain of mesenchymal motile phenotype, a process known as epithelial-to-mesenchymal transition (EMT). This study aims to study the role of decreased expression of miR-199a-3p in keratinocytes' EMT towards carcinogenesis. First, we measured miR-199a-3p in different stages of epidermal carcinogenesis. Then, we applied Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) assay to search for possible biochemical targets of miR-199a-3p and verified that Ras-associated protein B2 (RAP2B) is a bona-fide target of miR-199a-3p. Next, we analyzed RAP2B expression, in CSCC biopsies. Last, we evaluated possible mechanisms leading to decreased miR-199a-3p expression. miR-199a-3p induces a mesenchymal to epithelial transition (MET) in CSSC cells. Many of the under-expressed genes in CSCC overexpressing miR-199a-3p, are possible targets of miR-199a-3p and play roles in EMT. RAP2B is a biochemical target of miR-199a-3p. Overexpression of miR-199a-3p in CSCC results in decreased phosphorylated focal adhesion kinase (FAK). In addition, inhibiting FAK phosphorylation inhibits EMT marker genes' expression. In addition, we proved that DNA methylation is part of the mechanism by which miR-199a-3p expression is inhibited. However, it is not by the methylation of miR-199a putative promoter. These findings suggest that miR-199a-3p inhibits the EMT process by targeting RAP2B. Inhibitors of RAP2B or FAK may be effective therapeutic agents for CSCC.
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Affiliation(s)
- Moamen Masalha
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Meningher
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Adi Mizrahi
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Aviv Barzilai
- Department of Dermatology, Institute of Pathology Sheba Medical Center, Tel Hashomer 52621, Israel
| | | | - Devorah Gur-Wahnon
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Iddo Z. Ben-Dov
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Joshua Kapenhas
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | | | - Raya Leibowitz
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Oncology institute, Shamir Medical Center, Zerifin 70300, Israel
| | - Yechezkel Sidi
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research, Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: ; Tel.: +972-3-5307479
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27
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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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28
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Outeiro-Pinho G, Barros-Silva D, Moreira-Silva F, Lobo J, Carneiro I, Morais A, Martins EP, Gonçalves CS, Costa BM, Correia MP, Henrique R, Jerónimo C. Epigenetically-regulated miR-30a/c-5p directly target TWF1 and hamper ccRCC cell aggressiveness. Transl Res 2022; 249:110-127. [PMID: 35697274 DOI: 10.1016/j.trsl.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 10/31/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is highly prone to metastasize and displays an extremely low 5-year survival rate. Not only miRNAs (miRs) are key gene expression regulators but can also be epigenetically modified. Abnormal miR expression has been linked with epithelial-mesenchymal transition (EMT)-driven ccRCC progression. MiR-30a/c-5p were found downregulated in ccRCC and associated with aggressiveness. Herein, we sought to unravel miR-30a/c-5p mechanistic role in ccRCC. RNA sequencing and genome-wide methylome data of ccRCC and normal tissue samples from The Cancer Genome Atlas database were integrated to identify candidate miRs cytosine-phosphate-guanine (CpG) loci deregulated in ccRCC. TargetScan was searched to identify miR putative targets. MiR-30a/c-5p expression and promoter methylation was evaluated in vitro, by PCR. Western blot, functional and luciferase assays were performed after cell transfection with either pre-miR, antimiR, or siRNA against twinfilin-1 (TWF1). Immunohistochemistry (IHC) was performed in ccRCC tissues. We found miR-30c-5p downregulation and aberrant promoter methylation in ccRCC tissues. In vitro studies revealed concomitant miR-30a/c-5p downregulation and increased promoter methylation, as well as a significant re-expression following decitabine treatment. Functional assays demonstrated that both miRs significantly decreased cell aggressiveness and the protein levels of EMT-promoting players, while upregulating epithelial markers, namely Claudin-1 and ZO-1. Importantly, we confirmed TWF1 as a direct target of both miRs, and its potential involvement in epithelial-mesenchymal transition/mesenchymal-epithelial transition regulation. IHC analysis revealed higher TWF1 expression in primary tissues from patients that developed metastases, after surgical treatment. Our results implicate miR-30a/c-5p in ccRCC cells' aggressiveness attenuation by directly targeting TWF1 and hampering EMT.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Master in Molecular Medicine and Oncology, Faculty of Medicine-University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Isa Carneiro
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - António Morais
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, Porto, Portugal
| | - Eduarda P Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Margareta P Correia
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal.
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29
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Evolving understandings for the roles of non-coding RNAs in autoimmunity and autoimmune disease. J Autoimmun 2022:102948. [DOI: 10.1016/j.jaut.2022.102948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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30
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Consequences of genetic variants in miRNA genes. Comput Struct Biotechnol J 2022; 20:6443-6457. [DOI: 10.1016/j.csbj.2022.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022] Open
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Khan N, Umar MS, Haq M, Rauf T, Zubair S, Owais M. Exosome-encapsulated ncRNAs: Emerging yin and yang of tumor hallmarks. Front Genet 2022; 13:1022734. [PMID: 36338993 PMCID: PMC9632295 DOI: 10.3389/fgene.2022.1022734] [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: 08/18/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
Tumorigenesis is a multifaceted process, where multiple physiological traits serving as cancer’s distinctive characteristics are acquired. “Hallmarks of cancer” is a set of cognitive abilities acquired by human cells that are pivotal to their tumor-forming potential. With limited or no protein-coding ability, non-coding RNAs (ncRNAs) interact with their target molecules and yield significant regulatory effects on several cell cycle processes. They play a “yin” and “yang” role, thereby functioning both as oncogenic and tumor suppressor and considered important in the management of various types of cancer entities. ncRNAs serve as important post-transcriptional and translational regulators of not only unrestricted expansion and metastasis of tumor cells but also of various biological processes, such as genomic mutation, DNA damage, immune escape, and metabolic disorder. Dynamical attributes such as increased proliferative signaling, migration, invasion, and epithelial–mesenchymal transition are considered to be significant determinants of tumor malignancy, metastatic dissemination, and therapeutic resistance. Furthermore, these biological attributes engage tumor cells with immune cells within the tumor microenvironment to promote tumor formation. We elaborate the interaction of ncRNAs with various factors in order to regulate cancer intra/intercellular signaling in a specific tumor microenvironment, which facilitates the cancer cells in acquiring malignant hallmarks. Exosomes represent a means of intercellular communication and participate in the maintenance of the tumor hallmarks, adding depth to the intricate, multifactorial character of malignant neoplasia. To summarize, ncRNAs have a profound impact on tumors, affecting their microcirculation, invasiveness, altered metabolism, microenvironment, and the capacity to modify the host immunological environment. Though the significance of ncRNAs in crosstalk between the tumor and its microenvironment is being extensively explored, we intend to review the hallmarks in the light of exosome-derived non-coding RNAs and their impact on the tumor microenvironment.
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Affiliation(s)
- Nazoora Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohd Saad Umar
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohamed Haq
- University of Houston, Houston, TX, United States
| | - Talha Rauf
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Swaleha Zubair
- Department of Computer Science, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
- *Correspondence: Mohammad Owais,
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Babu P, Palaniappan A. miR2Trait: an integrated resource for investigating miRNA-disease associations. PeerJ 2022; 10:e14146. [PMID: 36217386 PMCID: PMC9547587 DOI: 10.7717/peerj.14146] [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: 06/07/2022] [Accepted: 09/07/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function causes cascading effects leading to pathophenotypes. A better understanding of the role of miRNAs in diseases is essential for human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogs, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. miR2Trait provides resources to compute the disease enrichment of a user-given set of miRNAs and analyze the miRNA profile of a specified diseasome. Reproducible examples demonstrating use-cases for each of these resource components are illustrated. Furthermore we used these tools to construct pairwise miRNA-miRNA and disease-disease enrichment networks, and identified 23 central miRNAs that could underlie major regulatory functions in the human genome. miR2Trait is available as an open-source command-line interface in Python3 (URL: https://github.com/miR2Trait) with a companion wiki documenting the scripts and data resources developed, under MIT license for commercial and non-commercial use. A minimal web-based implementation has been made available at https://sas.sastra.edu/pymir18. Supplementary information is available at: https://doi.org/10.6084/m9.figshare.8288825.v3.
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Affiliation(s)
- Poornima Babu
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
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Kim WR, Park EG, Lee YJ, Bae WH, Lee DH, Kim HS. Integration of TE Induces Cancer Specific Alternative Splicing Events. Int J Mol Sci 2022; 23:ijms231810918. [PMID: 36142830 PMCID: PMC9502224 DOI: 10.3390/ijms231810918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing of messenger RNA (mRNA) precursors contributes to genetic diversity by generating structurally and functionally distinct transcripts. In a disease state, alternative splicing promotes incidence and development of several cancer types through regulation of cancer-related biological processes. Transposable elements (TEs), having the genetic ability to jump to other regions of the genome, can bring about alternative splicing events in cancer. TEs can integrate into the genome, mostly in the intronic regions, and induce cancer-specific alternative splicing by adjusting various mechanisms, such as exonization, providing splicing donor/acceptor sites, alternative regulatory sequences or stop codons, and driving exon disruption or epigenetic regulation. Moreover, TEs can produce microRNAs (miRNAs) that control the proportion of transcripts by repressing translation or stimulating the degradation of transcripts at the post-transcriptional level. Notably, TE insertion creates a cancer-friendly environment by controlling the overall process of gene expression before and after transcription in cancer cells. This review emphasizes the correlative interaction between alternative splicing by TE integration and cancer-associated biological processes, suggesting a macroscopic mechanism controlling alternative splicing by TE insertion in cancer.
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Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
- Correspondence:
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S-Adenosylmethionine Inhibits Colorectal Cancer Cell Migration through Mirna-Mediated Targeting of Notch Signaling Pathway. Int J Mol Sci 2022; 23:ijms23147673. [PMID: 35887021 PMCID: PMC9320859 DOI: 10.3390/ijms23147673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/10/2022] Open
Abstract
Metastasis is a leading cause of mortality and poor prognosis in colorectal cancer (CRC). Thus, the identification of new compounds targeting cell migration represents a major clinical challenge. Recent findings evidenced a central role for dysregulated Notch in CRC and a correlation between Notch overexpression and tumor metastasis. MicroRNAs (miRNAs) have been reported to cross-talk with Notch for its regulation. Therefore, restoring underexpressed miRNAs targeting Notch could represent an encouraging therapeutic approach against CRC. In this context, S-adenosyl-L-methionine (AdoMet), the universal biological methyl donor, being able to modulate the expression of oncogenic miRNAs could act as a potential antimetastatic agent. Here, we showed that AdoMet upregulated the onco-suppressor miRNAs-34a/-34c/-449a and inhibited HCT-116 and Caco-2 CRC cell migration. This effect was associated with reduced expression of migration-/EMT-related protein markers. We also found that, in colorectal and triple-negative breast cancer cells, AdoMet inhibited the expression of Notch gene, which, by luciferase assay, resulted the direct target of miRNAs-34a/-34c/-449a. Gain- and loss-of-function experiments with miRNAs mimics and inhibitors demonstrated that AdoMet exerted its inhibitory effects by upregulating miRNAs-34a/-34c/-449a. Overall, these data highlighted AdoMet as a novel Notch inhibitor and suggested that the antimetastatic effects of AdoMet involve the miRNA-mediated targeting of Notch signaling pathway.
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Deciphering the Molecular Mechanism of Incurable Muscle Disease by a Novel Method for the Interpretation of miRNA Dysregulation. Noncoding RNA 2022; 8:ncrna8040048. [PMID: 35893231 PMCID: PMC9326546 DOI: 10.3390/ncrna8040048] [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: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
It is now well-established that microRNA dysregulation is a hallmark of human diseases, and that aberrant expression of miRNA is not randomly associated with human pathologies but plays a causal role in the pathological process. Investigations of the molecular mechanism that links miRNA dysregulation to pathophysiology can therefore further the understanding of human diseases. The biological effect of miRNA is thought to be mediated principally by miRNA target genes. Consequently, the target genes of dysregulated miRNA serve as a proxy for the biological interpretation of miRNA dysregulation, which is performed by target gene pathway enrichment analysis. However, this method unfortunately often fails to provide testable hypotheses concerning disease mechanisms. In this paper, we describe a method for the interpretation of miRNA dysregulation, which is based on miRNA host genes rather than target genes. Using this approach, we have recently identified the perturbations of lipid metabolism, and cholesterol in particular, in Duchenne muscular dystrophy (DMD). The host gene-based interpretation of miRNA dysregulation therefore represents an attractive alternative method for the biological interpretation of miRNA dysregulation.
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Urinary microRNAs and Their Significance in Prostate Cancer Diagnosis: A 5-Year Update. Cancers (Basel) 2022; 14:cancers14133157. [PMID: 35804929 PMCID: PMC9265126 DOI: 10.3390/cancers14133157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Current diagnostics of prostate cancer often show unsatisfactory results, leading to delayed detection or overtreatment. Urinary microRNAs are a class of promising non-invasive biomarkers. Although many studies have been conducted on this topic in the last five years, there is little agreement on the data obtained. This review aims to discuss new knowledge but also focuses on technical aspects affecting urinary miRNA analysis. Abstract Current routine screening methods for the diagnosis of prostate cancer (PCa) have significantly increased early detection of the disease but often show unsatisfactory analytical parameters. A class of promising markers represents urinary microRNAs (miRNAs). In the last five years, there has been an extensive increase in the number of studies on this topic. Thus, this review aims to update knowledge and point out technical aspects affecting urinary miRNA analysis. The review of relevant literature was carried out by searching the PubMed database for the keywords: microRNA, miRNA, urine, urinary, prostate cancer, and diagnosis. Papers discussed in this review were retrieved using PubMed, and the search strategy was as follows: (urine OR urinary) WITH (microRNA OR miRNA) AND prostate cancer. The search was limited to the last 5 years, January 2017 to December 2021. Based on the defined search strategy, 31 original publications corresponding to the research topic were identified, read and reviewed to present the latest findings and to assess possible translation of urinary miRNAs into clinical practice. Reviews or older publications were read and cited if they valuably extended the context and contributed to a better understanding. Urinary miRNAs are potentially valuable markers for the diagnosis of prostate cancer. Despite promising results, there is still a need for independent validation of exploratory data, which follows a strict widely accepted methodology taking into account the shortcomings and factors influencing the analysis.
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STABILITY OF SELECTED MICRORNAs IN HUMAN BLOOD, SEMEN AND SALIVA SAMPLES EXPOSED TO DIFFERENT ENVIRONMENTAL CONDITIONS. Forensic Sci Int 2022; 336:111338. [DOI: 10.1016/j.forsciint.2022.111338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
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Zhang Z, Li W, Jiang D, Gu L, Li B, Sang C, Rao D, Tang Z, Liu C. Silencing of long non-coding RNA linc01106 suppresses non-small cell lung cancer proliferation, migration and invasion by regulating microRNA-765. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2059578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- ZuXiong Zhang
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - WeiZhi Li
- Department of Cardiothoracic Surgery, Tumor Hospital of Ganzhou, Ganzhou, People’s Republic of China
| | - DaMei Jiang
- Department of Cardiothoracic Surgery, Ganzhou Municipal Hospital, Ganzhou, People’s Republic of China
| | - Liang Gu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Bin Li
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - ChengPeng Sang
- Department of Cardiothoracic Surgery, Gannan Medical University, Ganzhou, People’s Republic of China
| | - DingYu Rao
- Department of Cardiothoracic Surgery, Gannan Medical University, Ganzhou, People’s Republic of China
| | - ZhiXian Tang
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Chi Liu
- Department of Cardiothoracic Surgery, Sichuan Provincial People's Hospital, Chengdu, People’s Republic of China
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Hu DG, Mackenzie PI, Hulin JA, McKinnon RA, Meech R. Regulation of human UDP-glycosyltransferase ( UGT) genes by miRNAs. Drug Metab Rev 2022; 54:120-140. [PMID: 35275773 DOI: 10.1080/03602532.2022.2048846] [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] [Indexed: 11/03/2022]
Abstract
The human UGT gene superfamily is divided into four subfamilies (UGT1, UGT2, UGT3 and UGT8) that encodes 22 functional enzymes. UGTs are critical for the metabolism and clearance of numerous endogenous and exogenous compounds, including steroid hormones, bile acids, bilirubin, fatty acids, carcinogens, and therapeutic drugs. Therefore, the expression and activities of UGTs are tightly regulated by multiple processes at the transcriptional, post-transcriptional and post-translational levels. During recent years, nearly twenty studies have investigated the post-transcriptional regulation of UGT genes by miRNAs using human cancer cell lines (predominantly liver cancer). Overall, 14 of the 22 UGT mRNAs (1A1, 1A3, 1A4, 1A6, 1A8, 1A9, 1A10, 2A1, 2B4, 2B7, 2B10, 2B15, 2B17, UGT8) have been shown to be regulated by various miRNAs through binding to their respective 3' untranslated regions (3'UTRs). Three 3'UTRs (UGT1A, UGT2B7 and UGT2B15) contain the largest number of functional miRNA target sites; in particular, the UGT1A 3'UTR contains binding sites for 12 miRNAs (548d-5p, 183-5p, 214-5p, 486-3p, 200a-3p, 491-3p, 141-3p, 298, 103b, 376b-3p, 21-3p, 1286). Although all nine UGT1A family members have the same 3'UTR, these miRNA target sites appear to be functional in an isoform-specific and cellular context-dependent manner. Collectively, these observations demonstrate that miRNAs represent important post-transcriptional regulators of the UGT gene superfamily. In this article, we present a comprehensive review of reported UGT/miRNA regulation studies, describe polymorphisms within functional miRNA target sites that may affect their functionalities, and discuss potential cooperative and competitive regulation of UGT mRNAs by miRNAs through adjacently located miRNA target sites.
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Affiliation(s)
- Dong Gui Hu
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Peter I Mackenzie
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Julie-Ann Hulin
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Ross A McKinnon
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Robyn Meech
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
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MiR-520h inhibits viability and facilitates apoptosis of KGN cells through modulating IL6R and the JAK/STAT pathway. Reprod Biol 2022; 22:100607. [DOI: 10.1016/j.repbio.2022.100607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/22/2022]
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Abstract
This overview of the molecular pathology of lung cancer includes a review of the most salient molecular alterations of the genome, transcriptome, and the epigenome. The insights provided by the growing use of next-generation sequencing (NGS) in lung cancer will be discussed, and interrelated concepts such as intertumor heterogeneity, intratumor heterogeneity, tumor mutational burden, and the advent of liquid biopsy will be explored. Moreover, this work describes how the evolving field of molecular pathology refines the understanding of different histologic phenotypes of non-small-cell lung cancer (NSCLC) and the underlying biology of small-cell lung cancer. This review will provide an appreciation for how ongoing scientific findings and technologic advances in molecular pathology are crucial for development of biomarkers, therapeutic agents, clinical trials, and ultimately improved patient care.
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Affiliation(s)
- James J Saller
- Departments of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Theresa A Boyle
- Departments of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
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Wang J, Zhou L, Chen B, Yu Z, Zhang J, Zhang Z, Hu C, Bai Y, Ruan X, Wang S, Ouyang J, Wu A, Zhao X. Circular RNA circCSPP1 promotes the occurrence and development of colon cancer by sponging miR-431 and regulating ROCK1 and ZEB1. J Transl Med 2022; 20:58. [PMID: 35101080 PMCID: PMC8805259 DOI: 10.1186/s12967-022-03240-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/08/2022] [Indexed: 12/17/2022] Open
Abstract
Background Colon cancer is a common malignant tumor of the digestive tract, and its incidence is ranked third among gastrointestinal tumors. The present study aims to investigate the role of a novel circular RNA (circCSPP1) in colon cancer and its underlying molecular mechanisms. Methods Bioinformatics analysis and reverse transcription-quantitative PCR were used to detect the expression levels of circCSPP1 in colon cancer tissues and cell lines. The effects of circCSPP1 on the behavior of colon cancer cells were investigated using CCK-8, transwell and clonogenic assays. Bioinformatics analysis along with luciferase, fluorescence in situ hybridization and RNA pull-down assays were used to reveal the interaction between circCSPP1, microRNA (miR)-431, Rho associated coiled-coil containing protein kinase 1 (ROCK1) and zinc finger E-box binding homeobox 1 (ZEB1). Results It was found that circCSPP1 expression was significantly upregulated in colon cancer tissues and cell lines. Overexpression of circCSPP1 significantly promoted the proliferation, migration and invasion of colon cancer cells, whereas silencing of circCSPP1 exerted opposite effects. Mechanistically, circCSPP1 was found to bind with miR-431. In addition, ROCK1 and ZEB1 were identified as the target genes of miR-431. Rescue experiments further confirmed the interaction between circCSPP1, miR-431, ROCK1 and ZEB1. Moreover, circCSPP1 promoted the expression level of ROCK1, cyclin D1, cyclin-dependent kinase 4, ZEB1 and Snail, and lowered the E-cadherin expression level. Conclusion Taken together, the findings of the present study indicated that circCSPP1 may function as a competing endogenous RNA in the progression of colon cancer by regulating the miR-431/ROCK1 and miR-431/ZEB1 signaling axes. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03240-x.
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Gharbi S, Mohammadi Z, Dezaki MS, Dokanehiifard S, Dabiri S, Korsching E. Characterization of the first microRNA in human CDH1 that affects cell cycle and apoptosis and indicates breast cancers progression. J Cell Biochem 2022; 123:657-672. [PMID: 34997630 DOI: 10.1002/jcb.30211] [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: 09/27/2021] [Revised: 11/26/2021] [Accepted: 12/21/2021] [Indexed: 11/12/2022]
Abstract
The E-cadherin protein (Cadherin 1, gene: CDH1), a master regulator of the human epithelial homeostasis, contributes to the epithelial-mesenchymal transition (EMT) which confers cell migratory features to the cells. The EMT is central to many pathophysiological changes in cancer. Therefore, a better understanding of this regulatory scenario is beneficial for therapeutic regiments. The CDH1 gene is approximately 100 kbp long and consists of 16 exons with a relatively large second intron. Since none microRNA (miRNA) has been identified in CDH1 up to now we screened the CDH1 gene for promising miRNA hairpin structures in silico. Out of the 27 hairpin structures we identified, one stable RNA fold with a promising sequence motive was selected for experimental verification. The exogenous validation of the hairpin sequence was performed by transfection of HEK293T cells and the mature miRNA sequences could be verified by quantitative polymerase chain reaction. The endogenous expression of the mature miRNA provisionally named CDH1-i2-miR-1 could be confirmed in two normal (HEK293T, HUVEK) and five cancer cell lines (MCF7, MDA-MB-231, SW480, HT-29, A549). The functional characterization by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed a suppression of HEK293T cell proliferation. A flow cytometry-based approach showed the ability of CDH1-i2-miR-1 to arrest transfected cells on a G2/M state while annexin staining exemplified an apoptotic effect. BAX and PTEN expression levels were affected following the overexpression with the new miRNA. The in vivo expression level was assessed in 35 breast tumor tissues and their paired nonmalignant marginal part. A fourfold downregulation in the tumor specimens compared to their marginal controls could be observed. It can be concluded that the sequence of the hub gene CDH1 harbors at least one miRNA but eventually even more relevant for the pathophysiology of breast cancer.
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Affiliation(s)
- Sedigheh Gharbi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zahra Mohammadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Saedi Dezaki
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sadat Dokanehiifard
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shahriar Dabiri
- Department of Pathology, Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
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Ruiz-Manriquez LM, Estrada-Meza C, Benavides-Aguilar JA, Ledesma-Pacheco SJ, Torres-Copado A, Serrano-Cano FI, Bandyopadhyay A, Pathak S, Chakraborty S, Srivastava A, Sharma A, Paul S. Phytochemicals mediated modulation of microRNAs and long non-coding RNAs in cancer prevention and therapy. Phytother Res 2021; 36:705-729. [PMID: 34932245 DOI: 10.1002/ptr.7338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/07/2021] [Accepted: 11/04/2021] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two main categories of noncoding RNAs (ncRNAs) that can influence essential biological functions in various ways, as well as their expression and function are tightly regulated in physiological homeostasis. Additionally, the dysregulation of these ncRNAs seems to be crucial to the pathogenesis of human diseases. The latest findings indicate that ncRNAs execute vital roles in cancer initiation and progression, and the cancer phenotype can be reversed by modulating their expression. Available scientific discoveries suggest that phytochemicals such as polyphenols, alkaloids, terpenoids, and organosulfur compounds can significantly modulate multiple cancer-associated miRNAs and lncRNAs, thereby inhibiting cancer initiation and development. However, despite promising outcomes of experimental research, only a few clinical trials are currently being conducted to evaluate the therapeutic effectiveness of these compounds. Nevertheless, understanding phytochemical-mediated ncRNA regulation in cancer and the underlying molecular mechanisms on tumor pathophysiology can aid in the development of novel therapeutic strategies to combat this deadly disease.
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Affiliation(s)
- Luis M Ruiz-Manriquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | - Carolina Estrada-Meza
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | | | - S Janin Ledesma-Pacheco
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | - Andrea Torres-Copado
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | - Francisco I Serrano-Cano
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | - Anindya Bandyopadhyay
- C4 Rice Center, International Rice Research Institute, Manila, Philippines.,Synthetic Biology, Biofuel and Genome Editing R&D, Reliance Industries Ltd, Navi Mumbai, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Samik Chakraborty
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, San Pablo, Mexico
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Kaushik P, Kumar A. Emerging role and function of miR-198 in human health and diseases. Pathol Res Pract 2021; 229:153741. [PMID: 34952425 DOI: 10.1016/j.prp.2021.153741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 01/10/2023]
Abstract
Ever since their discovery, microRNAs (miRNAs/miRs) have astonished us by the plethora of processes they regulate, and thus adding another dimension to the gene regulation. They have been implicated in several diseases affecting cardiovascular, neurodegenerative, hepatic, autoimmune and inflammatory functions. A primate specific exonic miRNA, miR-198 has been vastly studied during the past decade, and shown to have a critical role in wound healing. The aberrant expression of miR-198 was first reported in schizophrenia, linking it to neural development. Later, its dysregulation and tumor suppressive role was reported in hepatocellular carcinoma. However, this was just a beginning, and after which there was an explosion of reports linking miR-198 deregulation to cancers and other ailments. The first target to be identified for miR-198 was Cyclin T1 in monocytes affecting HIV1 replication. Depending on the type of cancer, miR-198 has been shown to function either as a tumor suppressor or an oncomir. Interestingly, miR-198 is not only known to regulate multiple targets and pathways, but also is itself regulated by several circular RNAs and long-non-coding RNAs, highlighting a complex regulatory network. This review highlights the currently understood mechanism and regulation of miR-198 in different diseases, and its possible diagnostic and therapeutic potential.
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Affiliation(s)
- Pankhuri Kaushik
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India.
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TGF-β Induction of miR-143/145 Is Associated to Exercise Response by Influencing Differentiation and Insulin Signaling Molecules in Human Skeletal Muscle. Cells 2021; 10:cells10123443. [PMID: 34943951 PMCID: PMC8700369 DOI: 10.3390/cells10123443] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022] Open
Abstract
Physical training improves insulin sensitivity and can prevent type 2 diabetes (T2D). However, approximately 20% of individuals lack a beneficial outcome in glycemic control. TGF-β, identified as a possible upstream regulator involved in this low response, is also a potent regulator of microRNAs (miRNAs). The aim of this study was to elucidate the potential impact of TGF-β-driven miRNAs on individual exercise response. Non-targeted long and sncRNA sequencing analyses of TGF-β1-treated human skeletal muscle cells corroborated the effects of TGF-β1 on muscle cell differentiation, the induction of extracellular matrix components, and identified several TGF-β1-regulated miRNAs. qPCR validated a potent upregulation of miR-143-3p/145-5p and miR-181a2-5p by TGF-β1 in both human myoblasts and differentiated myotubes. Healthy subjects who were overweight or obese participated in a supervised 8-week endurance training intervention (n = 40) and were categorized as responder or low responder in glycemic control based on fold change ISIMats (≥+1.1 or <+1.1, respectively). In skeletal muscle biopsies of low responders, TGF-β signaling and miR-143/145 cluster levels were induced by training at much higher rates than among responders. Target-mining revealed HDACs, MYHs, and insulin signaling components INSR and IRS1 as potential miR-143/145 cluster targets. All these targets were down-regulated in TGF-β1-treated myotubes. Transfection of miR-143-3p/145-5p mimics in differentiated myotubes validated MYH1, MYH4, and IRS1 as miR-143/145 cluster targets. Elevated TGF-β signaling and miR-143/145 cluster induction in skeletal muscle of low responders might obstruct improvements in insulin sensitivity by training in two ways: by a negative impact of miR-143-3p on muscle cell fusion and myofiber functionality and by directly impairing insulin signaling via a reduction in INSR by TGF-β and finetuned IRS1 suppression by miR-143-3p.
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Yang S, Chen K, Cao K, Xu S, Ma C, Cai Y, Hu Y, Zhou Y. miR-182-5p Inhibits NKAPL Expression and Promotes the Proliferation of Osteosarcoma. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-021-0019-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Song F, Li F. MicroRNA-29a suppresses the growth of human cervical cancer cells by targeting cell division cycle 42 (CDC42). JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1991732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Fang Song
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Fengshuang Li
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, People’s Republic of China
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Chen S, Zhou L, Ran R, Huang J, Zheng Y, Xing M, Cai Y. Circ_0016760 accelerates non-small-cell lung cancer progression through miR-646/AKT3 signaling in vivo and in vitro. Thorac Cancer 2021; 12:3223-3235. [PMID: 34658165 PMCID: PMC8636202 DOI: 10.1111/1759-7714.14191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Currently, the prognosis of non-small-cell lung cancer (NSCLC) patients remains dismal due to recurrence and metastasis. The purpose of our study was to explore the role of circular RNA_0016760 (circ_0016760) in NSCLC progression and its associated mechanism. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was implemented to measure the expression of circ_0016760, microRNA-646 (miR-646) and AK strain thymoma serine/threonine kinase 3 (AKT3). The protein level of AKT3 was examined by Western blot assay. Cell Counting Kit 8 assay, transwell assays, and flow cytometry were conducted to analyze cell proliferation, metastasis, and apoptosis. Dual-luciferase reporter assay was used to confirm the interactions that were predicted by bioinformatics software (Circular RNA Interactome and TargetScan). A xenograft tumor model was built to investigate the role of circ_0016760 in vivo. RESULTS Circ_0016760 and AKT3 were highly expressed in NSCLC tissue specimens and cell lines. Circ_0016760 interference suppressed cell proliferation, migration, and invasion and promoted the apoptosis of NSCLC cells. Circ_0016760 interacted with miR-646 and negatively regulated its expression. MiR-646 silencing partly counteracted circ_0016760 knockdown-mediated influences in NSCLC cells. MiR-646 bound to the AKT3 3' untranslated region in NSCLC cells, and miR-646 overexpression-induced effects in NSCLC cells were partly overturned by the addition of AKT3 overexpression plasmid. Circ_0016760 silencing reduced the expression of AKT3 through enhancing miR-646 expression. Circ_0016760 knockdown suppressed NSCLC tumor growth in vivo. CONCLUSION Circ_0016760 played an oncogenic role to promote the proliferation, migration, and invasion and restrained the apoptosis of NSCLC cells via miR-646/AKT3 signaling.
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Affiliation(s)
- Shan Chen
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Long Zhou
- Department of Pulmonary and Critical Care Medicine, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Ruizhi Ran
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Jinqi Huang
- Department of Cardiothoracic Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Yong Zheng
- Department of Cardiothoracic Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Maohui Xing
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Yanli Cai
- Department of Cardiothoracic Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
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Splice and Dice: Intronic microRNAs, Splicing and Cancer. Biomedicines 2021; 9:biomedicines9091268. [PMID: 34572454 PMCID: PMC8465124 DOI: 10.3390/biomedicines9091268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/17/2022] Open
Abstract
Introns span only a quarter of the human genome, yet they host around 60% of all known microRNAs. Emerging evidence indicates the adaptive advantage of microRNAs residing within introns is attributed to their complex co-regulation with transcription and alternative splicing of their host genes. Intronic microRNAs are often co-expressed with their host genes, thereby providing functional synergism or antagonism that is exploited or decoupled in cancer. Additionally, intronic microRNA biogenesis and the alternative splicing of host transcript are co-regulated and intertwined. The importance of intronic microRNAs is under-recognized in relation to the pathogenesis of cancer.
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