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Fujiwara Y, Takahashi RU, Saito M, Umakoshi M, Shimada Y, Koyama K, Yatabe Y, Watanabe SI, Koyota S, Minamiya Y, Tahara H, Kono K, Shiraishi K, Kohno T, Goto A, Tsuchiya N. Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma. Proc Natl Acad Sci U S A 2024; 121:e2407016121. [PMID: 39196622 DOI: 10.1073/pnas.2407016121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
The nature of microRNA (miRNA) dysfunction in carcinogenesis remains controversial because of the complex connection between miRNA structural diversity and biological processes. Here, we found that oncofetal IGF2BP3 regulates the selective production of a subset of 3'-isoforms (3'-isomiRs), including miR-21-5p and Let-7 family, which induces significant changes in their cellular seed occupancy and structural components, establishing a cancer-specific gene expression profile. The D-score, reflecting dominant production of a representative miR-21-5p+C (a 3'-isomiR), discriminated between clinical early-stage lung adenocarcinoma (LUAD) cases with low and high recurrence risks, and was associated with molecular features of cell cycle progression, epithelial-mesenchymal transition pressure, and immune evasion. We found that IGF2BP3 controls the production of miR-21-5p+C by directing the nuclear Drosha complex to select the cleavage site. IGF2BP3 was also involved in the production of 3'-isomiRs of miR-425-5p and miR-454-3p. IGF2BP3-regulated these three miRNAs are suggested to be associated with the regulation of p53, TGF-β, and TNF pathways in LUAD. Knockdown of IGF2BP3 also induced a selective upregulation of Let-7 3'-isomiRs, leading to increased cellular Let-7 seed occupancy and broad repression of its target genes encoding cell cycle regulators. The D-score is an index that reflects this cellular situation. Our results suggest that the aberrant regulation of miRNA structural diversity is a critical component for controlling cellular networks, thus supporting the establishment of a malignant gene expression profile in early stage LUAD.
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Affiliation(s)
- Yuko Fujiwara
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Michinobu Umakoshi
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kei Koyama
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Souichi Koyota
- Molecular Medicine Laboratory, Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Akita University Hospital, Akita 010-8543, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Naoto Tsuchiya
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Downie Ruiz Velasco A, Parsons A, Heatley M, Martin AG, Smart A, Shah N, Jopling C. MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1. Nucleic Acids Res 2024; 52:9210-9229. [PMID: 38884273 PMCID: PMC11347158 DOI: 10.1093/nar/gkae505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/03/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024] Open
Abstract
In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by the Microprocessor complex. Cotranscriptional splicing has been shown to influence Microprocessor cleavage when miRNAs are hosted in introns of protein-coding pri-miRNAs, but the impact of splicing on production of miRNAs hosted in long non-coding (lnc)RNAs is largely unknown. Here, we investigated the role of splicing in the biogenesis of miR-122, an lncRNA-hosted, highly expressed, medically important, liver-specific miRNA. We found that splicing inhibition by the SF3B1 inhibitor pladienolide B (PlaB) led to strong and rapid reduction in transcription of endogenous, but not plasmid-encoded, pri-miR-122, resulting in reduced production of mature miR-122. To allow detection of rapid changes in miRNA biogenesis despite the high stability of mature miRNAs, we used SLAMseq to globally quantify the effects of short-term splicing inhibition on miRNA synthesis. We observed an overall decrease in biogenesis of mature miRNAs following PlaB treatment. Surprisingly, miRNAs hosted in exons and introns were similarly affected. Together, this study provides new insights into the emerging role of splicing in transcription, demonstrating novel biological importance in promotion of miR-122 biogenesis from an lncRNA, and shows that SF3B1 is important for global miRNA biogenesis.
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Affiliation(s)
| | - Aimee L Parsons
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Matthew C Heatley
- The Digital Research Service, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Athena R G Martin
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alfredo D Smart
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Niraj Shah
- The Digital Research Service, University of Nottingham, Nottingham, NG7 2RD, UK
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3
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Kordic M, Martinovic D, Puizina E, Bozic J, Zubcic Z, Dediol E. Impact of Human Papillomavirus on microRNA-21 Expression in Oral and Oropharyngeal Cancer-A Systematic Review. Int J Mol Sci 2024; 25:8038. [PMID: 39125608 PMCID: PMC11311551 DOI: 10.3390/ijms25158038] [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: 06/06/2024] [Revised: 07/13/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Recently, microRNAs (miR) were identified to have potential links with oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) oncogenesis, specifically miR-21. Since HPV is a major risk factor for the development of these diseases, we aimed to search the literature regarding miR-21 expression in both HPV-positive and HPV-negative OSCC/OPSCC. The search was performed in the PubMed (MEDLINE), Scopus, Web of Science, and Cochrane electronic databases. The research question was as follows: Is there a difference in the tissue expression of miR-21 between patients with HPV-positive and those with HPV-negative OSCC/OPSCC? After conducting a meticulous search strategy, four studies were included, and they had a pooled sample size of 621 subjects with OSCC and/or OPSCC. Three studies did not find any significant difference in miR-21 expression between HPV-positive and HPV-negative OSCC/OPSCC. The findings of this systematic review showed that there are no differences in miR-21 expression between HPV-positive and HPV-negative OSCC/OPSCC. Nevertheless, it is worth noting that there are still insufficient studies regarding this important subject, because understanding how HPV influences miR-21 expression and its downstream effects can provide insights into the molecular mechanisms underlying OSCC/OPSCC development and progression.
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Affiliation(s)
- Mario Kordic
- Department of ENT and Maxillofacial Surgery, University Hospital Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Dinko Martinovic
- Department of Maxillofacial Surgery, University Hospital of Split, 21000 Split, Croatia; (D.M.); (E.P.)
| | - Ema Puizina
- Department of Maxillofacial Surgery, University Hospital of Split, 21000 Split, Croatia; (D.M.); (E.P.)
| | - Josko Bozic
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia;
| | - Zeljko Zubcic
- Department of ENT, University Hospital of Osijek, 31000 Osijek, Croatia;
| | - Emil Dediol
- Department of Maxillofacial Surgery, University Hospital Dubrava, 10000 Zagreb, Croatia
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4
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Gonzalez-Candia A, Figueroa EG, Krause BJ. Pharmacological and molecular mechanisms of miRNA-based therapies for targeting cardiovascular dysfunction. Biochem Pharmacol 2024:116318. [PMID: 38801924 DOI: 10.1016/j.bcp.2024.116318] [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: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Advances in understanding gene expression regulation through epigenetic mechanisms have contributed to elucidating the regulatory mechanisms of noncoding RNAs as pharmacological targets in several diseases. MicroRNAs (miRs) are a class of evolutionarily conserved, short, noncoding RNAs regulating in a concerted manner gene expression at the post-transcriptional level by targeting specific sequences of the 3'-untranslated region of mRNA. Conversely, mechanisms of cardiovascular disease (CVD) remain largely elusive due to their life-course origins, multifactorial pathophysiology, and co-morbidities. In this regard, CVD treatment with conventional medications results in therapeutic failure due to progressive resistance to monotherapy, which overlooks the multiple factors involved, and reduced adherence to poly-pharmacology approaches. Consequently, considering its role in regulating complete gene pathways, miR-based drugs have appreciably progressed into preclinical and clinical testing. This review summarizes the current knowledge about the mechanisms of miRs in cardiovascular disease, focusing specifically on describing how clinical chemistry and physics have improved the stability of the miR molecule. In addition, a comprehensive review of the main miRs involved in cardiovascular disease and the clinical trials in which these molecules are used as active pharmacological molecules is provided.
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Affiliation(s)
- Alejandro Gonzalez-Candia
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Esteban G Figueroa
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Bernardo J Krause
- Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile.
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5
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Saadh MJ, Mahdi MS, Allela OQB, Alazzawi TS, Ubaid M, Rakhimov NM, Athab ZH, Ramaiah P, Chinnasamy L, Alsaikhan F, Farhood B. Critical role of miR-21/exosomal miR-21 in autophagy pathway. Pathol Res Pract 2024; 257:155275. [PMID: 38643552 DOI: 10.1016/j.prp.2024.155275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/23/2024]
Abstract
Activation of autophagy, a process of cellular stress response, leads to the breakdown of proteins, organelles, and other parts of the cell in lysosomes, and can be linked to several ailments, such as cancer, neurological diseases, and rare hereditary syndromes. Thus, its regulation is very carefully monitored. Transcriptional and post-translational mechanisms domestically or in whole organisms utilized to control the autophagic activity, have been heavily researched. In modern times, microRNAs (miRNAs) are being considered to have a part in post-translational orchestration of the autophagic activity, with miR-21 as one of the best studied miRNAs, it is often more than expressed in cancer cells. This regulatory RNA is thought to play a major role in a plethora of processes and illnesses including growth, cancer, cardiovascular disease, and inflammation. Different studies have suggested that a few autophagy-oriented genes, such as PTEN, Rab11a, Atg12, SIPA1L2, and ATG5, are all targeted by miR-21, indicating its essential role in the regulation.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman 11831, Jordan
| | | | | | - Tuqa S Alazzawi
- College of dentist, National University of Science and Technology, Dhi Qar, Iraq
| | | | - Nodir M Rakhimov
- Department of Oncology, Samarkand State Medical University, 18 Amir Temur Street, Samarkand, Uzbekistan; Department of Oncology, Tashkent State Dental Institute, Tashkent, Uzbekistan
| | - Zainab H Athab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | | | | | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia jSchool of Pharmacy, Ibn Sina National College for Medical Studies, Jeddah, Saudi Arabia.
| | - Bagher Farhood
- Department of Medical Physics and Radiology, Faculty of Paramedical Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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6
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Renna FJ, Gonzalez CD, Vaccaro MI. Decoding the Versatile Landscape of Autophagic Protein VMP1 in Cancer: A Comprehensive Review across Tissue Types and Regulatory Mechanisms. Int J Mol Sci 2024; 25:3758. [PMID: 38612567 PMCID: PMC11011780 DOI: 10.3390/ijms25073758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Autophagy, a catabolic process orchestrating the degradation of proteins and organelles within lysosomes, is pivotal for maintaining cellular homeostasis. However, its dual role in cancer involves preventing malignant transformation while fostering progression and therapy resistance. Vacuole Membrane Protein 1 (VMP1) is an essential autophagic protein whose expression, per se, triggers autophagy, being present in the whole autophagic flux. In pancreatic cancer, VMP1-whose expression is linked to the Kirsten Rat Sarcoma Virus (KRAS) oncogene-significantly contributes to disease promotion, progression, and chemotherapy resistance. This investigation extends to breast cancer, colon cancer, hepatocellular carcinoma, and more, highlighting VMP1's nuanced nature, contingent on specific tissue contexts. The examination of VMP1's interactions with micro-ribonucleic acids (miRNAs), including miR-21, miR-210, and miR-124, enhances our understanding of its regulatory network in cancer. Additionally, this article discusses VMP1 gene fusions, especially with ribosomal protein S6 kinase B1 (RPS6KB1), shedding light on potential implications for tumor malignancy. By deciphering the molecular mechanisms linking VMP1 to cancer progression, this exploration paves the way for innovative therapeutic strategies to disrupt these pathways and potentially improve treatment outcomes.
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Affiliation(s)
- Felipe J. Renna
- Instituto de Bioquimica y Medicina Molecular Prof Alberto Boveris (IBIMOL), CONICET, Universidad de Buenos Aires, Buenos Aires C1113AAC, Argentina;
| | - Claudio D. Gonzalez
- Instituto de Investigaciones, IUC, Medicina Traslacional, Hospital Universitario CEMIC, Buenos Aires C1431FWN, Argentina;
| | - Maria I. Vaccaro
- Instituto de Bioquimica y Medicina Molecular Prof Alberto Boveris (IBIMOL), CONICET, Universidad de Buenos Aires, Buenos Aires C1113AAC, Argentina;
- Instituto de Investigaciones, IUC, Medicina Traslacional, Hospital Universitario CEMIC, Buenos Aires C1431FWN, Argentina;
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Rafiyian M, Gouyandeh F, Saati M, Davoodvandi A, Rasooli Manesh SM, Asemi R, Sharifi M, Asemi Z. Melatonin affects the expression of microRNA-21: A mini-review of current evidence. Pathol Res Pract 2024; 254:155160. [PMID: 38277748 DOI: 10.1016/j.prp.2024.155160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
Melatonin (MLT) is an endogenous hormone produced by pineal gland which possess promising anti-tumor effects. Anti-inflammatory and anti-oxidant properties of MLT, along with its immunomodulatory, proapoptotic, and anti-angiogenic properties, are often referred to the main mechanisms of its anti-tumor effects. Recent evidence has suggested that epigenetic alterations are also involved in the anti-tumor properties of MLT. Among these MLT-induced epigenetic alterations is modulation of the expression of several oncogenic and tumor suppressor microRNAs(miRNAs). MiRNAs are among the most promising and potential therapeutic and diagnostic tools in different diseases and enhanced the development of better therapeutic drugs. Suppression of oncomicroRNAs such as microRNA-21, - 20a, and - 27a as well as, up-regulation of microRNA-34 a/c are among the most important effects of MLT on microRNAs homeostasis. Recently, miR-21 has attracted the attention of scientists due to the its wide range of effects on different cancers and diseases. Regulation of this RNA may be a key to the development of better therapeutic targets. The present review will summarize the findings of in vitro and experimental studies of MLT-induced impacts on the expression of microRNAs which are involved in different models and numerous stages of tumor initiation, growth, metastasis, and chemo-resistance.
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Affiliation(s)
- Mahdi Rafiyian
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Farzaneh Gouyandeh
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Maryam Saati
- Department of Nursing, Semnan Branch, Islamic Azad University, Semnan, Islamic Republic of Iran
| | - Amirhossein Davoodvandi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | | | - Reza Asemi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehran Sharifi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Khalaji A, Mehrtabar S, Jabraeilipour A, Doustar N, Rahmani Youshanlouei H, Tahavvori A, Fattahi P, Alavi SMA, Taha SR, Fazlollahpour-Naghibi A, Shariat Zadeh M. Inhibitory effect of microRNA-21 on pathways and mechanisms involved in cardiac fibrosis development. Ther Adv Cardiovasc Dis 2024; 18:17539447241253134. [PMID: 38819836 PMCID: PMC11143841 DOI: 10.1177/17539447241253134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/18/2024] [Indexed: 06/01/2024] Open
Abstract
Cardiac fibrosis is a pivotal cardiovascular disease (CVD) process and represents a notable health concern worldwide. While the complex mechanisms underlying CVD have been widely investigated, recent research has highlighted microRNA-21's (miR-21) role in cardiac fibrosis pathogenesis. In this narrative review, we explore the molecular interactions, focusing on the role of miR-21 in contributing to cardiac fibrosis. Various signaling pathways, such as the RAAS, TGF-β, IL-6, IL-1, ERK, PI3K-Akt, and PTEN pathways, besides dysregulation in fibroblast activity, matrix metalloproteinases (MMPs), and tissue inhibitors of MMPs cause cardiac fibrosis. Besides, miR-21 in growth factor secretion, apoptosis, and endothelial-to-mesenchymal transition play crucial roles. miR-21 capacity regulatory function presents promising insights for cardiac fibrosis. Moreover, this review discusses numerous approaches to control miR-21 expression, including antisense oligonucleotides, anti-miR-21 compounds, and Notch signaling modulation, all novel methods of cardiac fibrosis inhibition. In summary, this narrative review aims to assess the molecular mechanisms of cardiac fibrosis and its essential miR-21 function.
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Affiliation(s)
- Amirreza Khalaji
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Mehrtabar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Nadia Doustar
- Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | | | - Amir Tahavvori
- Department of Internal Medicine, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Payam Fattahi
- Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Seyed Reza Taha
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Andarz Fazlollahpour-Naghibi
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
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Kim TJ, Kim YG, Jung W, Jang S, Ko HG, Park CH, Byun JS, Kim DY. Non-Coding RNAs as Potential Targets for Diagnosis and Treatment of Oral Lichen Planus: A Narrative Review. Biomolecules 2023; 13:1646. [PMID: 38002328 PMCID: PMC10669845 DOI: 10.3390/biom13111646] [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: 09/25/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Oral lichen planus (OLP) is a chronic inflammatory disease that is characterized by the infiltration of T cells into the oral mucosa, causing the apoptosis of basal keratinocytes. OLP is a multifactorial disease of unknown etiology and is not solely caused by the malfunction of a single key gene but rather by various intracellular and extracellular factors. Non-coding RNAs play a critical role in immunological homeostasis and inflammatory response and are found in all cell types and bodily fluids, and their expression is closely regulated to preserve normal physiologies. The dysregulation of non-coding RNAs may be highly implicated in the onset and progression of diverse inflammatory disorders, including OLP. This narrative review summarizes the role of non-coding RNAs in molecular and cellular changes in the oral epithelium during OLP pathogenesis.
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Affiliation(s)
- Tae-Jun Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Yu Gyung Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Won Jung
- Department of Oral Medicine, Institute of Oral Bioscience, School of Dentistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Sungil Jang
- Department of Oral Biochemistry, Institute of Oral Bioscience, School of Dentistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hyoung-Gon Ko
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Chan Ho Park
- Department of Dental Biomaterials, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Jin-Seok Byun
- Department of Oral Medicine, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
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Skourti E, Volpe A, Lang C, Johnson P, Panagaki F, Fruhwirth GO. Spatiotemporal quantitative microRNA-155 imaging reports immune-mediated changes in a triple-negative breast cancer model. Front Immunol 2023; 14:1180233. [PMID: 37359535 PMCID: PMC10285160 DOI: 10.3389/fimmu.2023.1180233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction MicroRNAs are small non-coding RNAs and represent key players in physiology and disease. Aberrant microRNA expression is central to the development and progression of cancer, with various microRNAs proposed as potential cancer biomarkers and drug targets. There is a need to better understand dynamic microRNA expression changes as cancers progress and their tumor microenvironments evolve. Therefore, spatiotemporal and non-invasive in vivo microRNA quantification in tumor models would be highly beneficial. Methods We developed an in vivo microRNA detector platform in which the obtained signals are positively correlated to microRNA presence, and which permitted stable expression in cancer cells as needed for long-term experimentation in tumor biology. It exploits a radionuclide-fluorescence dual-reporter for quantitative in vivo imaging of a microRNA of choice by radionuclide tomography and fluorescence-based downstream ex vivo tissue analyses. We generated and characterized breast cancer cells stably expressing various microRNA detectors and validated them in vitro. Results We found the microRNA detector platform to report on microRNA presence in cells specifically and accurately, which was independently confirmed by real-time PCR and through microRNA modulation. Moreover, we established various breast tumor models in animals with different levels of residual immune systems and observed microRNA detector read-outs by imaging. Applying the detector platform to the progression of a triple-negative breast cancer model, we found that miR-155 upregulation in corresponding tumors was dependent on macrophage presence in tumors, revealing immune-mediated phenotypic changes in these tumors as they progressed. Conclusion While applied to immunooncology in this work, this multimodal in vivo microRNA detector platform will be useful whenever non-invasive quantification of spatiotemporal microRNA changes in living animals is of interest.
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Affiliation(s)
- Elena Skourti
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Alessia Volpe
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Cameron Lang
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Preeth Johnson
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Fani Panagaki
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Department of Physics, King’s College London, London, United Kingdom
| | - Gilbert O. Fruhwirth
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
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11
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Pan SC, Lai CH, Vu VT, Vu CA, Huang CJ, Cheng CM, Chen WY. Paper-Based Exosomal MicroRNA-21 Detection for Wound Monitoring: A Proof of Concept and Clinical Validation Trial Study. Int J Mol Sci 2023; 24:9822. [PMID: 37372974 DOI: 10.3390/ijms24129822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Emerging evidence has shown that microRNAs play pivotal roles in wound healing. MicroRNA-21 (miR-21) was previously found to upregulate in order to fulfill an anti-inflammation role for wounds. Exosomal miRNAs have been identified and explored as essential markers for diagnostic medicine. However, the role of exosomal miR-21 in wounds has yet to be well studied. In order to facilitate the early management of poorly healing wounds, we developed an easy-to-use, rapid, paper-based microfluidic-exosomal miR-21 extraction device to determine wound prognosis in a timely manner. We isolated and then quantitatively examined exosomal miR-21 in wound fluids from normal tissues and acute and chronic wounds. Eight improving wounds displayed lower levels of exosomal miR-21 expression after wound debridement. However, four instances of increased exosomal miR-21 expression levels were notably associated with patients with poor healing wounds despite aggressive wound debridement, indicating a predictive role of tissue exosomal miR-21 for wound outcome. Paper-based nucleic acid extraction device provides a rapid and user-friendly approach for evaluating exosomal miR-21 in wound fluids as a means of monitoring wounds. Our data suggest that tissue exosomal miR-21 is a reliable marker for determining current wound status.
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Affiliation(s)
- Shin-Chen Pan
- Department of Surgery, Section of Plastic and Reconstructive Surgery, National Cheng Kung University Hospital, College of Medicine, International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan 704, Taiwan
| | - Chi-Hung Lai
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Van-Truc Vu
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Cao-An Vu
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
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12
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Circular Sponge against miR-21 Enhances the Antitumor Activity of Doxorubicin against Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms232314803. [PMID: 36499129 PMCID: PMC9736351 DOI: 10.3390/ijms232314803] [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: 09/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
Breast cancer is the most common type of cancer in women, with chemotherapy being the main strategy. However, its effectiveness is reduced by drug resistance mechanisms. miR-21 is upregulated in breast cancer that has been linked to drug resistance and carcinogenic processes. Our aim was to capture miR-21 with a circular sponge (Circ-21) and thus inhibit the carcinogenic processes and drug resistance mechanisms in which it participates. Proliferation, migration, colony formation, cell cycle, and poly [ADP-ribose] polymerase 1 (PARP-1) and vascular endothelial growth factor (VEGF) detection assays were performed with MCF7 breast cancer cells and MCF10A non-tumor cells. In addition, doxorubicin resistance tests and detection of drug resistance gene expression were performed in MCF7 cells. Reduction in proliferation, as well as migration and colony formation, increased PARP-1 expression, inhibition of VEGF expression and cell cycle arrest in G2/M phase were displayed in the Circ-21 MCF7, which were not observed in the MCF10A cells. Furthermore, in the MCF7 cells, the Circ-21 enhanced the antitumor activity of doxorubicin and decreased the expression of resistance genes: ABCA1, ABCC4, and ABCC5. Based on these results, the use of Circ-21 can be considered a first step for the establishment of an effective gene therapy in the treatment of breast cancer.
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13
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Larrue R, Fellah S, Van der Hauwaert C, Hennino MF, Perrais M, Lionet A, Glowacki F, Pottier N, Cauffiez C. The Versatile Role of miR-21 in Renal Homeostasis and Diseases. Cells 2022; 11:cells11213525. [PMID: 36359921 PMCID: PMC9657972 DOI: 10.3390/cells11213525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA species that control gene expression and confer robustness to biological processes. Over the last two decades, their important roles during kidney development, homeostasis and the treatment of diseases have been established, in particular during the onset and progression of various forms of acute and chronic renal disorders. In recent years, miR-21, one of the best-characterized miRNAs to date, has received much attention in renal physiology in particular given its high degree of conservation and expression in kidneys, as well as its potent pathogenic role in various debilitating renal diseases. This review summarizes the current knowledge on miR-21’s involvement in both renal homeostasis and diseases, in particular its double-edged-sword role in acute versus chronic kidney injuries. Finally, we also discuss the potential of miR-21 as a biomarker and therapeutic target in renal diseases.
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Affiliation(s)
- Romain Larrue
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Sandy Fellah
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Cynthia Van der Hauwaert
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
- CHU Lille, Département de la Recherche en Santé, F-59000 Lille, France
| | | | - Michaël Perrais
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Arnaud Lionet
- CHU Lille, Service de Néphrologie, F-59000 Lille, France
| | - François Glowacki
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
- CHU Lille, Service de Néphrologie, F-59000 Lille, France
| | - Nicolas Pottier
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Christelle Cauffiez
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
- Correspondence:
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14
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Li J, Wen W, Zhang S, Zhou C, Feng Y, Li X. The Expression and Function of lincRNA-154324 and the Adjoining Protein-Coding Gene vmp1 in the Caudal Fin Regeneration of Zebrafish. Int J Mol Sci 2022; 23:ijms23168944. [PMID: 36012210 PMCID: PMC9409064 DOI: 10.3390/ijms23168944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Caudal fin regeneration is regulated by a variety of mechanisms, but the role of long non-coding RNA (lncRNA) has rarely been studied. The present study aimed to describe the landscape of lncRNAs during caudal fin regeneration using whole transcriptome sequencing, and then to conduct a functional study on the target lncRNAs using real-time fluorescent quantitative PCR (RT-qPCR), in situ hybridization, and the CRISPR/Cas9 method for lncRNA gene knockout. The results of the transcriptome sequencing showed that a total of 381 lncRNAs were differentially expressed, among which ENSDART00000154324 (lincRNA-154324) was found to be highly related to caudal fin regeneration, and thus it was chosen as the target lncRNA for the subsequent functional study. The results regarding the temporal and spatial expression of lincRNA-154324 and the gene knockout results from CRISPR/Cas9 indicated that lincRNA-154324 is involved in the caudal fin regeneration of zebrafish. Importantly, we serendipitously discovered that the cis correlation coefficient between lincRNA-154324 and its neighboring gene vacuole membrane protein 1 (vmp1) is extremely high, and they are essential for the process of caudal fin regeneration. Moreover, studies have found that vmp1 plays an important role in protein secretion, organelle formation, multicellular development, and autophagy. Collectively, our result may provide a framework for the identification and analysis of lncRNAs involved in the regeneration of the zebrafish caudal fin.
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Affiliation(s)
- Jing Li
- The School of Medical Humanities, Xinxiang Medical University, Xinxiang 453003, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Wenjun Wen
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Shuqiang Zhang
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Chune Zhou
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Yiyi Feng
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Xiaoyu Li
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: or
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15
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Nieland L, van Solinge TS, Cheah PS, Morsett LM, El Khoury J, Rissman JI, Kleinstiver BP, Broekman ML, Breakefield XO, Abels ER. CRISPR-Cas knockout of miR21 reduces glioma growth. Mol Ther Oncolytics 2022; 25:121-136. [PMID: 35572197 PMCID: PMC9052041 DOI: 10.1016/j.omto.2022.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/04/2022] [Indexed: 12/21/2022] Open
Abstract
Non-coding RNAs, including microRNAs (miRNAs), support the progression of glioma. miR-21 is a small, non-coding transcript involved in regulating gene expression in multiple cellular pathways, including the regulation of proliferation. High expression of miR-21 has been shown to be a major driver of glioma growth. Manipulating the expression of miRNAs is a novel strategy in the development of therapeutics in cancer. In this study we aimed to target miR-21. Using CRISPR genome-editing technology, we disrupted the miR-21 coding sequences in glioma cells. Depletion of this miRNA resulted in the upregulation of many downstream miR-21 target mRNAs involved in proliferation. Phenotypically, CRISPR-edited glioma cells showed reduced migration, invasion, and proliferation in vitro. In immunocompetent mouse models, miR-21 knockout tumors showed reduced growth resulting in an increased overall survival. In summary, we show that by knocking out a key miRNA in glioma, these cells have decreased proliferation capacity both in vitro and in vivo. Overall, we identified miR-21 as a potential target for CRISPR-based therapeutics in glioma.
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Affiliation(s)
- Lisa Nieland
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
- Department of Neurosurgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Thomas S. van Solinge
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
| | - Pike See Cheah
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang 43400, Malaysia
| | - Liza M. Morsett
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Joseph El Khoury
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Joseph I. Rissman
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Marike L.D. Broekman
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
- Department of Neurosurgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
- Department of Neurosurgery, Haaglanden Medical Center, 2512 VA The Hague, the Netherlands
| | - Xandra O. Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
| | - Erik R. Abels
- Departments of Neurology and Radiology, Massachusetts General Hospital, Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
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16
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Dioguardi M, Spirito F, Sovereto D, Alovisi M, Troiano G, Aiuto R, Garcovich D, Crincoli V, Laino L, Cazzolla AP, Caloro GA, Di Cosola M, Lo Muzio L. MicroRNA-21 Expression as a Prognostic Biomarker in Oral Cancer: Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19063396. [PMID: 35329083 PMCID: PMC8948874 DOI: 10.3390/ijerph19063396] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 01/27/2023]
Abstract
Oral carcinoma represents one of the main carcinomas of the head and neck region, with a 5-year survival rate of less than 50%. Smoking and tobacco use are recognized risk factors. Prognostic survival biomarkers can be a valid tool for assessing a patient’s life expectancy and directing therapy towards specific targets. Among the biomarkers, the alteration of miR-21 expression in tumor tissues is increasingly reported as a valid prognostic biomarker of survival for oral cancer. The purpose of this meta-analysis was, therefore, to investigate and summarize the results in the literature concerning the potential prognostic expression of tissue miR-21 in patients with OSCC. Methods: The systematic review was conducted following the PRISMA guidelines using electronic databases, such as PubMed, Scopus, and the Cochrane Central Register of Controlled Trials, with the use of combinations of keywords, such as miR-21 AND oral cancer, microRNA AND oral cancer, and miR-21. The meta-analysis was performed using the RevMan 5.41 software. Results: At the end of the article-selection process, 10 studies were included in the meta-analysis, and the result for the main outcome was a pooled HR per overall survival (OS) of 1.29 (1.16–1.44) between high and low expression of miR-21. Conclusions: The data in the literature and the results emerging from the systematic review indicate that miR-21 can provide a prognostic indication in oral cancer.
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Affiliation(s)
- Mario Dioguardi
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
- Correspondence:
| | - Francesca Spirito
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
| | - Diego Sovereto
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
| | - Mario Alovisi
- Department of Surgical Sciences, Dental School, University of Turin, 10127 Turin, Italy;
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
| | - Riccardo Aiuto
- Department of Biomedical, Surgical and Dental Science, University of Milan, 20122 Milan, Italy;
| | - Daniele Garcovich
- Department of Dentistry, Universidad Europea de Valencia, Paseo de la Alameda 7, 46010 Valencia, Spain;
| | - Vito Crincoli
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Division of Complex Operating Unit of Dentistry, “Aldo Moro” University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Luigi Laino
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania “Luigi Vanvitelli”, 80121 Naples, Italy;
| | - Angela Pia Cazzolla
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
| | - Giorgia Apollonia Caloro
- Unità Operativa Nefrologia e Dialisi, Presidio Ospedaliero Scorrano, ASL (Azienda Sanitaria Locale) Lecce, Via Giuseppina Delli Ponti, 73020 Scorrano, Italy;
| | - Michele Di Cosola
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (G.T.); (A.P.C.); (M.D.C.); (L.L.M.)
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17
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Bai X, Bian Z. MicroRNA-21 Is a Versatile Regulator and Potential Treatment Target in Central Nervous System Disorders. Front Mol Neurosci 2022; 15:842288. [PMID: 35173580 PMCID: PMC8841607 DOI: 10.3389/fnmol.2022.842288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous, non-coding, single-stranded RNAs with a length of approximately 22 nucleotides that are found in eukaryotes. miRNAs are involved in the regulation of cell differentiation, proliferation, invasion, apoptosis, and metabolism by regulating the expression of their target genes. Emerging studies have suggested that various miRNAs play key roles in the pathogenesis of central nervous system (CNS) disorders and may be viable therapeutic targets. In particular, miR-21 has prominently emerged as a focus of increasing research on the mechanisms of its involvement in CNS disorders. Herein, we reviewed recent studies on the critical roles of miR-21, including its dysregulated expression and target genes, in the regulation of pathophysiological processes of CNS disorders, with a special focus on apoptosis and inflammation. Collectively, miR-21 is a versatile regulator in the progression of CNS disorders and could be a promising biomarker and therapeutic target for these diseases. An in-depth understanding of the mechanisms by which miR-21 affects the pathogenesis of CNS disorders could pave the way for miR-21 to serve as a therapeutic target for these conditions.
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Affiliation(s)
- Xue Bai
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhigang Bian
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Zhigang Bian,
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18
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Erdem M, Ozgul İ, Dioken DN, Gurcuoglu I, Guntekin Ergun S, Cetin-Atalay R, Can T, Erson-Bensan AE. Identification of an mRNA isoform switch for HNRNPA1 in breast cancers. Sci Rep 2021; 11:24444. [PMID: 34961772 PMCID: PMC8712528 DOI: 10.1038/s41598-021-04007-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life. In breast cancers, this isoform is downregulated in favor of a stable isoform. The stable isoform is expressed more in breast cancers, and more HNRNPA1 protein is synthesized from this isoform. High HNRNPA1 protein levels correlate with poor survival in patients. In support of this, silencing of HNRNPA1 causes a reversal in neoplastic phenotypes, including proliferation, clonogenic potential, migration, and invasion. In addition, silencing of HNRNPA1 results in the downregulation of microRNAs that map to intragenic regions. Among these miRNAs, miR-21 is known for its transcriptional upregulation in breast and numerous other cancers. Altogether, the cancer-specific isoform switch we describe here for HNRNPA1 emphasizes the need to study gene expression at the isoform level in cancers to identify novel cases of oncogene activation.
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Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - İbrahim Ozgul
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Didem Naz Dioken
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Irmak Gurcuoglu
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Sezen Guntekin Ergun
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Medical Biology, Hacettepe University, Ankara, Turkey
| | - Rengul Cetin-Atalay
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Tolga Can
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Computer Engineering, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah, Ankara, 06800, Turkey
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey.
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
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19
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Amirfallah A, Knutsdottir H, Arason A, Hilmarsdottir B, Johannsson OT, Agnarsson BA, Barkardottir RB, Reynisdottir I. Hsa-miR-21-3p associates with breast cancer patient survival and targets genes in tumor suppressive pathways. PLoS One 2021; 16:e0260327. [PMID: 34797887 PMCID: PMC8604322 DOI: 10.1371/journal.pone.0260327] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/06/2021] [Indexed: 12/22/2022] Open
Abstract
Breast cancer is the cancer most often diagnosed in women. MicroRNAs (MIRs) are short RNA molecules that bind mRNA resulting in their downregulation. MIR21 has been shown to be an oncomiR in most cancer types, including breast cancer. Most of the effects of miR-21 have been attributed to hsa-miR-21-5p that is transcribed from the leading strand of MIR21, but hsa-miR-21-3p (miR-21-3p), transcribed from the lagging strand, is much less studied. The aim of the study is to analyze whether expression of miR-21-3p is prognostic for breast cancer. MiR-21-3p association with survival, clinical and pathological characteristics was analyzed in a large breast cancer cohort and validated in three separate cohorts, including TCGA and METABRIC. Analytical tools were also used to infer miR-21-3p function and to identify potential target genes and functional pathways. The results showed that in the exploration cohort, high miR-21-3p levels associated with shorter survival and lymph node positivity. In the three validation cohorts, high miR-21-3p levels associated with pathological characteristics that predict worse prognosis. Specifically, in the largest validation cohort, METABRIC (n = 1174), high miR-21-3p levels associated with large tumors, a high grade, lymph node and HER2 positivity, and shorter breast-cancer-specific survival (HR = 1.38, CI 1.13–1.68). This association remained significant after adjusting for confounding factors. The genes with expression levels that correlated with miR-21-3p were enriched in particular pathways, including the epithelial-to-mesenchymal transition and proliferation. Among the most significantly downregulated targets were MAT2A and the tumor suppressive genes STARD13 and ZNF132. The results from this study emphasize that both 3p- and 5p-arms from a MIR warrant independent study. The data show that miR-21-3p overexpression in breast tumors is a marker of worse breast cancer progression and it affects genes in pathways that drive breast cancer by down-regulating tumor suppressor genes. The results suggest miR-21-3p as a potential biomarker.
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Affiliation(s)
- Arsalan Amirfallah
- Cell Biology Unit, Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Adalgeir Arason
- Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit, Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bylgja Hilmarsdottir
- Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit, Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Oskar T. Johannsson
- Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjarni A. Agnarsson
- Department of Oncology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa B. Barkardottir
- Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit, Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Inga Reynisdottir
- Cell Biology Unit, Department of Pathology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- * E-mail:
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Celik Cogal G, Das PK, Yurdabak Karaca G, Bhethanabotla VR, Uygun Oksuz A. Fluorescence Detection of miRNA-21 Using Au/Pt Bimetallic Tubular Micromotors Driven by Chemical and Surface Acoustic Wave Forces. ACS APPLIED BIO MATERIALS 2021; 4:7932-7941. [PMID: 35006774 DOI: 10.1021/acsabm.1c00854] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this study, surface acoustic wave (SAW) systems are described for the removal of molecules that are unbound to micromotors, thereby lowering the detection limit of the cancer-related biomarker miRNA-21. For this purpose, in the first step, mass production of the Au/Pt bimetallic tubular micromotor was performed with a simple membrane template electrodeposition. The motions of catalytic Au/Pt micromotors in peroxide fuel media were analyzed under the SAW field effect. The changes in the micromotor speed were investigated depending on the type and concentration of surfactants in the presence and absence of SAW streaming. Our detection strategy was based on immobilization of probe dye-labeled single-stranded probe DNA (6-carboxyfluorescein dye-labeled-single-stranded DNA) to Au/Pt micromotors that recognize target miRNA-21. Before/after hybridization of miRNA-21 (for both w/o SAW and SAW streaming conditions), the changes in the speed of micromotors and their fluorescence intensities were studied. The response of fluorescence intensities was observed to be linearly varied with the increase of the miRNA-21 concentration from 0.5 to 5 nM under both w/o SAW and with SAW. The resulting fluorescence sensor showed a limit of detection of 0.19 nM, more than 2 folds lower compared to w/o SAW conditions. Thus, the sensor and behaviors of Au/Pt tubular micromotors were improved by acoustic removal systems.
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Affiliation(s)
- Gamze Celik Cogal
- Department of Chemistry, Suleyman Demirel University, Isparta 32260, Turkey
| | - Pradipta K Das
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620-5250, United States
| | - Gozde Yurdabak Karaca
- Department of Chemistry, Suleyman Demirel University, Isparta 32260, Turkey.,Department of Bioengineering, Faculty of Engineering, Suleyman Demirel University, Isparta 32260, Turkey
| | - Venkat R Bhethanabotla
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620-5250, United States
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21
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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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22
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Liu B, Shyr Y, Liu Q. Pan-Cancer Analysis Reveals Common and Specific Relationships between Intragenic miRNAs and Their Host Genes. Biomedicines 2021; 9:1263. [PMID: 34572448 PMCID: PMC8471046 DOI: 10.3390/biomedicines9091263] [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] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous non-coding RNAs that play important roles in regulating gene expression. Most miRNAs are located within or close to genes (host). miRNAs and their host genes have either coordinated or independent transcription. We performed a comprehensive investigation on co-transcriptional patterns of miRNAs and host genes based on 4707 patients across 21 cancer types. We found that only 11.6% of miRNA-host pairs were co-transcribed consistently and strongly across cancer types. Most miRNA-host pairs showed a strong coexpression only in some specific cancer types, demonstrating a high heterogenous pattern. For two particular types of intergenic miRNAs, readthrough and divergent miRNAs, readthrough miRNAs showed higher coexpression with their host genes than divergent ones. miRNAs located within non-coding genes had tighter co-transcription with their hosts than those located within protein-coding genes, especially exonic and junction miRNAs. A few precursor miRNAs changed their dominate form between 5' and 3' strands in different cancer types, including miR-486, miR-99b, let-7e, miR-125a, let-7g, miR-339, miR-26a, miR-16, and miR-218, whereas only two miRNAs with multiple host genes switched their co-transcriptional partner in different cancer types (miR-219a-1 with SLC39A7/HSD17B8 and miR-3615 with RAB37/SLC9A3R1). miRNAs generated from distinct precursors (such as miR-125b from miR-125b-1 or miR-125b-2) were more likely to have cancer-dependent main contributors. miRNAs and hosts were less co-expressed in KIRC than other cancer types, possibly due to its frequent VHL mutations. Our findings shed new light on miRNA biogenesis and cancer diagnosis and treatments.
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Affiliation(s)
- Baohong Liu
- Key Laboratory of Veterinary Parasitology of Gansu Province, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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23
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Olivieri F, Prattichizzo F, Giuliani A, Matacchione G, Rippo MR, Sabbatinelli J, Bonafè M. miR-21 and miR-146a: The microRNAs of inflammaging and age-related diseases. Ageing Res Rev 2021; 70:101374. [PMID: 34082077 DOI: 10.1016/j.arr.2021.101374] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
The first paper on "inflammaging" published in 2001 paved the way for a unifying theory on how and why aging turns out to be the main risk factor for the development of the most common age-related diseases (ARDs). The most exciting challenge on this topic was explaining how systemic inflammation steeps up with age and why it shows different rates among individuals of the same chronological age. The "epigenetic revolution" in the past twenty years conveyed that the assessment of the individual genetic make-up is not enough to depict the trajectories of age-related inflammation. Accordingly, others and we have been focusing on the role of non-coding RNA, i.e. microRNAs (miRNAs), in inflammaging. The results obtained in the latest 10 years underpinned the key role of a miRNA subset that we have called inflammamiRs, owing to their ability to master (NF-κB)-driven inflammatory pathways. In this review, we will focus on two inflammamiRs, i.e. miR-21-5p and miR-146a-5p, which target a variety of molecules belonging to the NF-κB/NLRP3 pathways. The interplay between miR-146a-5p and IL-6 in the context of aging and ARDs will also be highlighted. We will also provide the most relevant evidence suggesting that circulating inflammamiRs, along with IL-6, can measure the degree of inflammaging.
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24
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The Role of miRNA in the Pathophysiology of Neuroendocrine Tumors. Int J Mol Sci 2021; 22:ijms22168569. [PMID: 34445276 PMCID: PMC8395312 DOI: 10.3390/ijms22168569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Neuroendocrine tumors (NETs) represent a tumor group that is both rare and heterogeneous. Prognosis is largely determined by the tumor grading and the site of the primary tumor and metastases. Despite intensive research efforts, only modest advances in diagnostic and therapeutic approaches have been achieved in recent years. For patients with non-respectable tumor stages, prognosis is poor. In this context, the development of novel diagnostic tools for early detection of NETs and prediction of tumor response to therapy as well as estimation of the overall prognosis would greatly improve the clinical management of NETs. However, identification of novel diagnostic molecules is hampered by an inadequate understanding of the pathophysiology of neuroendocrine malignancies. It has recently been demonstrated that microRNA (miRNA), a family of small RNA molecules with an established role in the pathophysiology of quite different cancer entities, may also play a role as a biomarker. Here, we summarize the available knowledge on the role of miRNAs in the development of NET and highlight their potential use as serum-based biomarkers in the context of this disease. We discuss important challenges currently preventing their use in clinical routine and give an outlook on future directions of miRNA research in NET.
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Corà D, Bussolino F, Doronzo G. TFEB Signalling-Related MicroRNAs and Autophagy. Biomolecules 2021; 11:985. [PMID: 34356609 PMCID: PMC8301958 DOI: 10.3390/biom11070985] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022] Open
Abstract
The oncogenic Transcription Factor EB (TFEB), a member of MITF-TFE family, is known to be the most important regulator of the transcription of genes responsible for the control of lysosomal biogenesis and functions, autophagy, and vesicles flux. TFEB activation occurs in response to stress factors such as nutrient and growth factor deficiency, hypoxia, lysosomal stress, and mitochondrial damage. To reach the final functional status, TFEB is regulated in multimodal ways, including transcriptional rate, post-transcriptional regulation, and post-translational modifications. Post-transcriptional regulation is in part mediated by miRNAs. miRNAs have been linked to many cellular processes involved both in physiology and pathology, such as cell migration, proliferation, differentiation, and apoptosis. miRNAs also play a significant role in autophagy, which exerts a crucial role in cell behaviour during stress or survival responses. In particular, several miRNAs directly recognise TFEB transcript or indirectly regulate its function by targeting accessory molecules or enzymes involved in its post-translational modifications. Moreover, the transcriptional programs triggered by TFEB may be influenced by the miRNA-mediated regulation of TFEB targets. Finally, recent important studies indicate that the transcription of many miRNAs is regulated by TFEB itself. In this review, we describe the interplay between miRNAs with TFEB and focus on how these types of crosstalk affect TFEB activation and cellular functions.
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Affiliation(s)
- Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, 28100 Novara, Italy;
- Center for Translational Research on Autoimmune and Allergic Diseases—CAAD, 28100 Novara, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, Laboratory of Vascular Oncology, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, Laboratory of Vascular Oncology, 10060 Candiolo, Italy
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26
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Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nat Immunol 2021; 22:914-927. [PMID: 34099919 PMCID: PMC8480231 DOI: 10.1038/s41590-021-00944-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising <75 miRNAs; however, each cell type had a unique miRNA signature. Integration of miRNA expression with chromatin accessibility revealed putative regulatory elements for differentially expressed miRNAs, including miR-21a, miR-146a and miR-223. The integrated maps suggest that many miRNAs utilize multiple promoters to reach high abundance and identified dominant and divergent miRNA regulatory elements between lineages and during development that may be used by clustered miRNAs, such as miR-99a/let-7c/miR-125b, to achieve distinct expression. These studies, with web-accessible data, help delineate the cis-regulatory elements controlling miRNA signatures of the immune system.
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Affiliation(s)
- Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maxime Dhainaut
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Anela Bektesevic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Ben-Zvi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Rhoads
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Edy Y Kim
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bingfei Yu
- Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Yonit Lavin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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27
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An autoregulatory feedback loop of miR-21/VMP1 is responsible for the abnormal expression of miR-21 in colorectal cancer cells. Cell Death Dis 2020; 11:1067. [PMID: 33318473 PMCID: PMC7736343 DOI: 10.1038/s41419-020-03265-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 02/05/2023]
Abstract
MircoRNA-21 (miR-21) was found to be highly expressed in various solid tumors, and its oncogenic properties have been extensively studied in recent years. However, the reason why miR-21 is highly expressed in various tumors remains elusive. Here, we found that the expression of miR-21 was negatively correlated with the expression of vacuole membrane protein-1 (VMP1) in colorectal cancer. Transcription of VMP1 activated either by small activating RNA (saRNA) or transcriptional activator GLI3 inhibited miR-21 expression through reducing its transcripts of VMP1-miR-21 and pri-miR-21, while no significant change in miR-21 expression after exogenous overexpression VMP1 in colorectal cancer cell HCT116. Considering the overlapping location of VMP1 and miR-21 gene in genome, the result suggested that the transcription of miR-21 was inhibited by the endogenous transcriptional activation of VMP1. Furthermore, we identified that miR-21 inhibited the activation and nuclear translocation of transcription factor EB (TFEB) through reducing the inhibitory of PTEN on AKT phosphorylation, which can directly activate the transcription of VMP1. Loss of miR-21 significantly increased VMP1 expression, which could be blocked by PTEN inhibitor (VO-Ohpic) or TFEB siRNA. These results showed that miR-21 negatively regulated VMP1 transcription through the PTEN/AKT/TFEB pathway, and TFEB-induced transcriptional activation of VMP1 could inhibit miR-21 expression, thus forming a feedback regulatory loop of miR-21/VMP1. We further found that disrupting the miR-21/VMP1 feedback loop will decrease the expression of miR-21, reduce the malignancy, and increase their sensitivity to 5-fluorouracil in colorectal cancer cells. Taken together, our results revealed a novel regulatory mechanism of miR-21 expression, and targeting the miR-21/VMP1 feedback loop may provide a new approach to inhibit miR-21 expression in colorectal cancer cells.
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28
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Feng Y, Shu J, Yao L, Lan Y, Ye L, Mei W, Ding Y. Recognizing and stabilizing miR-21 by chiral ruthenium(II) complexes. BMC Chem 2020; 14:26. [PMID: 32266333 PMCID: PMC7119291 DOI: 10.1186/s13065-020-00672-8] [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: 04/11/2019] [Accepted: 03/09/2020] [Indexed: 12/19/2022] Open
Abstract
MiR-21, a non-coding miRNA with 22 nucleotides, plays an important part in the proliferation, invasion, and metastasis of tumor cells. The present study demonstrates that isomers of chiral ruthenium(II) complexes with alkynes (Λ-1 and Δ-1) were synthesized by Songogashira coupling reaction by using microwave-assisted synthetic technology. The isomers can recognize and stabilize miR-21, with the Λ-isomer showing a stronger binding capacity than the Δ-isomer. Further studies showed that both isomers can be uptaken by MDA-MB-231 cells and enriched in the nucleus. Treatment with the Λ-/Δ-isomer downregulated the expression of miR-21. In a word, the development of chiral ruthenium(II) complexes act as potential inhibitors against tumor cells by recognizing, stabilizing, and regulating the expression of miR-21.
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Affiliation(s)
- Yin Feng
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510062 China
| | - Jing Shu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006 China
- Guangdong Province Engineering Center for Molecular Probe & Biomedical Imaging, Guangzhou, 510006 China
| | - Liangzhong Yao
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510062 China
| | - Yutao Lan
- Guangdong Province Engineering Center for Molecular Probe & Biomedical Imaging, Guangzhou, 510006 China
- School of Nursing, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006 China
| | - Lianbao Ye
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006 China
- Guangdong Province Engineering Center for Molecular Probe & Biomedical Imaging, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Construction and Application of New Drug Screening Model System, Guangdong Pharmaceutical University, Guangzhou, 510006 China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006 China
- Guangdong Province Engineering Center for Molecular Probe & Biomedical Imaging, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Construction and Application of New Drug Screening Model System, Guangdong Pharmaceutical University, Guangzhou, 510006 China
| | - Ying Ding
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510062 China
- Guangdong Province Engineering Center for Molecular Probe & Biomedical Imaging, Guangzhou, 510006 China
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29
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Peñaloza E, Soto-Carrasco G, Krause BJ. MiR-21-5p directly contributes to regulating eNOS expression in human artery endothelial cells under normoxia and hypoxia. Biochem Pharmacol 2020; 182:114288. [PMID: 33075314 DOI: 10.1016/j.bcp.2020.114288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Clinical conditions associated with hypoxia and oxidative stress, such as fetal growth restriction (FGR), results in endothelial dysfunction. Previous reports show that changes in eNOS expression under these conditions are tightly controlled by DNA methylation and histone posttranslational modifications. However, the contribution of an orchestrating epigenetic mechanism, such as miRNAs, on the NO-related genes expression has not been addressed. We aimed to determine the levels of miRNAs highly expressed in normal endothelial cells (EC), miR-21 and miR-126, in FGR human umbilical artery EC (HUAEC), and their effects on hypoxia-dependent regulation of both, NO-related and oxidative stress-related genes. Results were validated by transcriptome analysis of HUAEC cultured under chronic low oxygen conditions. Cultured FGR-HUAEC showed decreased hsa-miR-21, DDAH1, SOD1, and NRF2, but increased miR-126, NOX4, and eNOS levels, compared with controls. MiR-21-5p levels in FGR were associated with increased hg-miR-21 gene promoter methylation, with no changes in hg-miR-126 gene promoter methylation. HUAEC exposed to hypoxia showed a transient increase in eNOS and DDAH11, paralleled by decrease miR-21-5p levels, but no changes in miR-126-3p and the other genes under study. Transcriptome profiling showed an inverse relationship among miR-21 and several transcripts targeted by miR-21 in HUAEC exposed to hypoxia, meanwhile miR-21-5p-mimic decreased eNOS and DDAH1 transcripts stability, blocking their induction by hypoxia. Consequently, FGR programs a hypoxia-related miRNA that contributes to the regulation of the NO pathway, involving a direct effect of miR-21-5p on eNOS transcript stability, not previously reported. Moreover, hypoxia downregulates miR-21-5p, contributing to increasing the expression of NO-related genes in arterial endothelial cells.
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Affiliation(s)
- Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | | | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile.
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Wang D, Cao X, Han Y, Yu D. LncRNA SNHG9 is Downregulated in Non-Small Cell Lung Cancer and Suppressed miR-21 Through Methylation to Promote Cell Proliferation. Cancer Manag Res 2020; 12:7941-7948. [PMID: 32943928 PMCID: PMC7473986 DOI: 10.2147/cmar.s253052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023] Open
Abstract
Background LncRNA SNHG9 has been shown to be an oncogenic lncRNA in glioblastoma, while its role in other cancers is unknown. The aim of this study was to investigate the role of SNHG9 in non-small cell lung cancer (NSCLC). Methods The differential expression of SNHG9 in NSCLC was first explored by analyzing the TCGA dataset, followed by measuring the expression levels of SNHG9 in paired NSCLC and non-tumor tissues by RT-qPCR. Expression of miR-21 was also determined by RT-qPCR. Correlations were analyzed by linear regression. The interaction between miR-21 and SNHG9 was detected using RNA pull-down. The expression relationship between SNHG9 and miR-21 was analyzed by SNHG9 or miR-21 overexpression experiments. The effects of overexpression of SNHG9 on the methylation of miR-21 were analyzed by methylation-specific PCR (MSP). Cell proliferation was evaluated by CCK-8 assay. Results By analyzing the TCGA dataset, we observed downregulation of SNHG9 in NSCLC, which was confirmed by measuring the expression levels of SNHG9 in paired NSCLC tumor tissues and non-tumor tissues from NSCLC patients involved in this study. MiR-21 was upregulated in NSCLC tumor tissues and inversely correlated with SNHG9 in cancer tissues but not in non-tumor tissues. The interaction between SNHG9 and miR-21 was predicted by bioinformatic analyses, which was further verified by RNA pull-down. In NSCLC cells, overexpression of SNHG9 led to downregulated miR-21 and increased methylation of miR-21 gene. In contrast, miR-21 did not affect the expression of SNHG9. In addition, overexpression of SNHG9 attenuated the enhancing effects of miR-21 on NSCLC proliferation. Conclusion SNHG9 might downregulate miR-21 through methylation to suppress cancer cell proliferation.
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Affiliation(s)
- Dingxue Wang
- Department of Oncology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, People's Republic of China
| | - Xiaoqing Cao
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Yi Han
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Daping Yu
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
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Bautista-Sánchez D, Arriaga-Canon C, Pedroza-Torres A, De La Rosa-Velázquez IA, González-Barrios R, Contreras-Espinosa L, Montiel-Manríquez R, Castro-Hernández C, Fragoso-Ontiveros V, Álvarez-Gómez RM, Herrera LA. The Promising Role of miR-21 as a Cancer Biomarker and Its Importance in RNA-Based Therapeutics. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:409-420. [PMID: 32244168 PMCID: PMC7118281 DOI: 10.1016/j.omtn.2020.03.003] [Citation(s) in RCA: 235] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs are small noncoding transcripts that posttranscriptionally regulate gene expression via base-pairing complementarity. Their role in cancer can be related to tumor suppression or oncogenic function. Moreover, they have been linked to processes recognized as hallmarks of cancer, such as apoptosis, invasion, metastasis, and proliferation. Particularly, one of the first oncomiRs found upregulated in a variety of cancers, such as gliomas, breast cancer, and colorectal cancer, was microRNA-21 (miR-21). Some of its target genes associated with cancer are PTEN (phosphatase and tensin homolog), PDCD4 (programmed cell death protein 4), RECK (reversion-inducing cysteine-rich protein with Kazal motifs), and STAT3 (signal transducer activator of transcription 3). As a result, miR-21 has been proposed as a plausible diagnostic and prognostic biomarker, as well as a therapeutic target for several types of cancer. Currently, research and clinical trials to inhibit miR-21 through anti-miR-21 oligonucleotides and ADM-21 are being conducted. As all of the evidence suggests, miR-21 is involved in carcinogenic processes; therefore, inhibiting it could have effects on more than one type of cancer. However, whether miR-21 can be used as a tissue-specific biomarker should be analyzed with caution. Consequently, the purpose of this review is to outline the available information and recent advances regarding miR-21 as a potential biomarker in the clinical setting and as a therapeutic target in cancer to highlight its importance in the era of precision medicine.
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Affiliation(s)
- Diana Bautista-Sánchez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Abraham Pedroza-Torres
- CONACYT-Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | | | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Verónica Fragoso-Ontiveros
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Tlalpan, CP 14610, Mexico City, Mexico.
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Zhang HH, Huang ZX, Zhong SQ, Fei KL, Cao YH. miR‑21 inhibits autophagy and promotes malignant development in the bladder cancer T24 cell line. Int J Oncol 2020; 56:986-998. [PMID: 32319564 DOI: 10.3892/ijo.2020.4984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/08/2020] [Indexed: 11/06/2022] Open
Abstract
MicroRNA‑21 (miR‑21) is reported to exhibit cancer‑promoting activity in various types of cancer. It has been previously demonstrated that miR‑21 is overexpressed in bladder tumor tissue compared with normal mucosa. However, the functional mechanism of miR‑21 in bladder cancer remains largely unknown. Thus, the current study aimed to determine the roles of miR‑21 in autophagy and the malignant development of bladder cancer in T24 cells. Upregulation or downregulation of miR‑21 was achieved following the transfection of miR‑21 mimic or miR‑21 inhibitor. An MTT assay was additionally performed to measure cell growth. Wound healing and transwell invasion assays were used to detect cell migration and invasion. The apoptotic potential and cell cycle were examined via flow cytometry and reverse transcription‑quantitative PCR was performed to evaluate the expression of phosphatase and tensin homolog (PTEN), beclin 1, microtubule‑associated protein l light chain 3B (LC3‑II), cyclin D1, caspase‑3, E‑cadherin, matrix metallopeptidase‑9 (MMP‑9) and vimentin. The results revealed that the proliferation, migration and invasion of T24 cells was greatly increased in the miR‑21 mimic group, while apoptosis was greatly inhibited. Additionally, T24 cells treated with miR‑21 mimic exhibited G1‑phase arrest. In the miR‑21 mimic group, the expression of PTEN, beclin 1, LC3‑II, caspase‑3 and E‑cadherin were decreased, while the expression of cyclin D1, MMP‑9 and vimentin were increased. Opposite effects were observed in the miR‑21 inhibitor group. The data of the current study may indicate that miR‑21 overexpression inhibited autophagy and promoted the proliferation, migration, invasion and epithelial to mesenchymal transition of bladder cancer T24 cells. The results may further elucidate the molecular mechanism of miR‑21 in the development of bladder cancer.
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Affiliation(s)
- Hui-Hui Zhang
- Department of Urology, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, P.R. China
| | - Zhong-Xin Huang
- Department of Urology, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, P.R. China
| | - Su-Quan Zhong
- Department of Urology, Yue Bei People's Hospital, Shaoguan, Guangdong 512025, P.R. China
| | - Kui-Lin Fei
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - You-Han Cao
- Department of Urology, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, P.R. China
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Autin P, Blanquart C, Fradin D. Epigenetic Drugs for Cancer and microRNAs: A Focus on Histone Deacetylase Inhibitors. Cancers (Basel) 2019; 11:E1530. [PMID: 31658720 PMCID: PMC6827107 DOI: 10.3390/cancers11101530] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/09/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Over recent decades, it has become clear that epigenetic abnormalities are involved in the hallmarks of cancer. Histone modifications, such as acetylation, play a crucial role in cancer development and progression, by regulating gene expression, such as for oncogenes or tumor suppressor genes. Therefore, histone deacetylase inhibitors (HDACi) have recently shown efficacy against both hematological and solid cancers. Designed to target histone deacetylases (HDAC), these drugs can modify the expression pattern of numerous genes including those coding for micro-RNAs (miRNA). miRNAs are small non-coding RNAs that regulate gene expression by targeting messenger RNA. Current research has found that miRNAs from a tumor can be investigated in the tumor itself, as well as in patient body fluids. In this review, we summarized current knowledge about HDAC and HDACi in several cancers, and described their impact on miRNA expression. We discuss briefly how circulating miRNAs may be used as biomarkers of HDACi response and used to investigate response to treatment.
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Affiliation(s)
- Pierre Autin
- CRCINA, INSERM, Université d'Angers, Université de Nantes, 44007 Nantes, France.
| | - Christophe Blanquart
- CRCINA, INSERM, Université d'Angers, Université de Nantes, 44007 Nantes, France.
| | - Delphine Fradin
- CRCINA, INSERM, Université d'Angers, Université de Nantes, 44007 Nantes, France.
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Amirfallah A, Arason A, Einarsson H, Gudmundsdottir ET, Freysteinsdottir ES, Olafsdottir KA, Johannsson OT, Agnarsson BA, Barkardottir RB, Reynisdottir I. High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer. PLoS One 2019; 14:e0221413. [PMID: 31442252 PMCID: PMC6707546 DOI: 10.1371/journal.pone.0221413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Background Fusion genes result from genomic structural changes, which can lead to alterations in gene expression that supports tumor development. The aim of the study was to use fusion genes as a tool to identify new breast cancer (BC) genes with a role in BC progression. Methods Fusion genes from breast tumors and BC cell lines were collected from publications. RNA-Seq data from tumors and cell lines were retrieved from databanks and analyzed for fusions with SOAPfuse or the analysis was purchased. Fusion genes identified in both tumors (n = 1724) and cell lines (n = 45) were confirmed by qRT-PCR and sequencing. Their individual genes were ranked by selection criteria that included correlation of their mRNA level with copy number. The expression of the top ranked gene was measured by qRT-PCR in normal tissue and in breast tumors from an exploratory cohort (n = 141) and a validation cohort (n = 277). Expression levels were correlated with clinical and pathological factors as well as the patients’ survival. The results were followed up in BC cohorts from TCGA (n = 818) and METABRIC (n = 2509). Results Vacuole membrane protein 1 (VMP1) was the most promising candidate based on specific selection criteria. Its expression was higher in breast tumor tissue than normal tissue (p = 1x10-4), and its expression was significantly higher in HER2 positive than HER2 negative breast tumors in all four cohorts analyzed. High expression of VMP1 associated with breast cancer specific survival (BCSS) in cohort 1 (hazard ratio (HR) = 2.31, CI 1.27–4.18) and METABRIC (HR = 1.26, CI 1.02–1.57), and also after adjusting for HER2 expression in cohort 1 (HR = 2.03, CI 1.10–3.72). BCSS was not significant in cohort 2 or TCGA cohort, which may be due to differences in treatment regimens. Conclusions The results suggest that high VMP1 expression is a potential marker of poor prognosis in HER2 positive BC. Further studies are needed to elucidate how VMP1 could affect pathways supportive of tumorigenesis.
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Affiliation(s)
- Arsalan Amirfallah
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Adalgeir Arason
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Hjorleifur Einarsson
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Eydis Thorunn Gudmundsdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Edda Sigridur Freysteinsdottir
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Oskar Thor Johannsson
- Department of Oncology, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjarni Agnar Agnarsson
- Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa Bjork Barkardottir
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- Molecular Pathology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Inga Reynisdottir
- Cell Biology Unit at the Pathology Department, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- The Biomedical Center, University of Iceland, Reykjavik, Iceland
- * E-mail:
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Hua X, Tang R, Xu X, Wang Z, Xu Q, Chen L, Wingender E, Li J, Zhang C, Wang J. mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines. Nucleic Acids Res 2019; 46:D168-D174. [PMID: 29077896 PMCID: PMC5753250 DOI: 10.1093/nar/gkx996] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/16/2017] [Indexed: 01/03/2023] Open
Abstract
The cell-specific information of transcriptional regulation on microRNAs (miRNAs) is crucial to the precise understanding of gene regulations in various physiological and pathological processes existed in different tissues and cell types. The database, mirTrans, provides comprehensive information about cell-specific transcription of miRNAs including the transcriptional start sites (TSSs) of miRNAs, transcription factor (TF) to miRNA regulations and miRNA promoter sequences. mirTrans also maps the experimental H3K4me3 and DHS (DNase-I hypersensitive site) marks within miRNA promoters and expressed sequence tags (ESTs) within transcribed regions. The current version of database covers 35 259 TSSs and over 2.3 million TF-miRNA regulations for 1513 miRNAs in a total of 54 human cell lines. These cell lines span most of the biological systems, including circulatory system, digestive system and nervous system. Information for both the intragenic miRNAs and intergenic miRNAs is offered. Particularly, the quality of miRNA TSSs and TF-miRNA regulations is evaluated by literature curation. 23 447 TSS records and 2148 TF-miRNA regulations are supported by special experiments as a result of literature curation. EST coverage is also used to evaluate the accuracy of miRNA TSSs. Interface of mirTrans is friendly designed and convenient to make downloads (http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/ or http://120.27.239.192/mirtrans/).
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Affiliation(s)
- Xu Hua
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Rongjun Tang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Xiuxiu Xu
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Zhi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Qi Xu
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Luxiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Edgar Wingender
- Institute of Bioinformatics, University Medical Center Goettingen, Goldschmidtstrasse 1, D-37077 Goettingen, Germany
| | - Jie Li
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China.,Nanjing Shengnongding Biotech. Co. Ltd., Nanjing 211100, China
| | - Chenyu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
| | - Jin Wang
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210023, China
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Diagnostic significance of circulating miRNAs in systemic lupus erythematosus. PLoS One 2019; 14:e0217523. [PMID: 31163082 PMCID: PMC6548426 DOI: 10.1371/journal.pone.0217523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background In recent years, many studies focused on the association between the microRNAs (miRNAs) and the risk of systemic lupus erythematosus (SLE), especially miRNA-21 (miR-21). We aimed to investigate the role of circulating miRNAs, especially the miR-21, as a biomarker in detecting SLE. Methods We searched PubMed, EMBASE, the Cochrane Central Register of Controlled Trials, and China National Knowledge Infrastructure through Mar 3th, 2019. We performed this meta-analysis in a fixed/random-effect model using Meta-disc 1.4 and STATA 15.1. Results A total of 17 relevant studies were eligible to analyze pooled accuracy. The overall performance of total mixed miRNAs (TmiRs) detection was: pooled sensitivity, 0.71 (95% confidence interval [CI], 0.69 to 0.72); pooled specificity, 0.81 (95%CI, 0.79 to 0.83); and area under the summary receiver operating characteristic curves value (SROC), 0.8797. The miR-21 detection was: pooled sensitivity, 0.68 (95%CI, 0.62 to 0.74); pooled specificity, 0.77 (95%CI, 0.69 to 0.84); and SROC, 0.8281. The meta-regression analysis showed that the type of samples was the sources of heterogeneity. The subgroup analysis suggested that detection in plasma group had the largest AUC of SROC in all the subgroups: pooled sensitivity, 0.8 (95%CI, 0.78 to 0.82); pooled specificity, 0.83 (95%CI, 0.8 to 0.86); and SROC, 0.9068. Conclusions Our meta-analysis demonstrated that circulating miRNAs might be potential novel biomarkers for detecting SLE, especially miR-21. Moreover, plasma is recommended as the clinical specimen for diagnostic detection.
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Fu K, Tian S, Tan H, Wang C, Wang H, Wang M, Wang Y, Chen Z, Wang Y, Yue Q, Xu Q, Zhang S, Li H, Xie J, Lin M, Luo M, Chen F, Ye L, Zheng K. Biological and RNA regulatory function of MOV10 in mammalian germ cells. BMC Biol 2019; 17:39. [PMID: 31088452 PMCID: PMC6515687 DOI: 10.1186/s12915-019-0659-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background RNA regulation by RNA-binding proteins (RBPs) involve extremely complicated mechanisms. MOV10 and MOV10L1 are two homologous RNA helicases implicated in distinct intracellular pathways. MOV10L1 participates specifically in Piwi-interacting RNA (piRNA) biogenesis and protects mouse male fertility. In contrast, the functional complexity of MOV10 remains incompletely understood, and its role in the mammalian germline is unknown. Here, we report a study of the biological and molecular functions of the RNA helicase MOV10 in mammalian male germ cells. Results MOV10 is a nucleocytoplasmic protein mainly expressed in spermatogonia. Knockdown and transplantation experiments show that MOV10 deficiency has a negative effect on spermatogonial progenitor cells (SPCs), limiting proliferation and in vivo repopulation capacity. This effect is concurrent with a global disturbance of RNA homeostasis and downregulation of factors critical for SPC proliferation and/or self-renewal. Unexpectedly, microRNA (miRNA) biogenesis is impaired due partially to decrease of miRNA primary transcript levels and/or retention of miRNA via splicing control. Genome-wide analysis of RNA targetome reveals that MOV10 binds preferentially to mRNAs with long 3′-UTR and also interacts with various non-coding RNA species including those in the nucleus. Intriguingly, nuclear MOV10 associates with an array of splicing factors, particularly with SRSF1, and its intronic binding sites tend to reside in proximity to splice sites. Conclusions These data expand the landscape of MOV10 function and highlight a previously unidentified role initiated from the nucleus, suggesting that MOV10 is a versatile RBP involved in a broader RNA regulatory network. Electronic supplementary material The online version of this article (10.1186/s12915-019-0659-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaiqiang Fu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Suwen Tian
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.,Department of Preventive Medicine, Heze Medical College, Heze, 274000, China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Caifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hanben Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuanyuan Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Zhen Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qiushi Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Shuya Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Haixin Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Mingyan Lin
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Mengcheng Luo
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
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Xu S, Shi L. High expression of miR-155 and miR-21 in the recurrence or metastasis of non-small cell lung cancer. Oncol Lett 2019; 18:758-763. [PMID: 31289551 PMCID: PMC6539534 DOI: 10.3892/ol.2019.10337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022] Open
Abstract
High expression of miR-155 and miR-21 in the recurrence or metastasis of non-small cell lung cancer (NSCLC) was investigated. Retrospective analysis on the clinical information of 180 patients with NSCLC was carried out. The patients were admitted to Daqing Oil Field General Hospital from February 2012 to March 2015 and they were the research group. Moreover, the physical examination information of 88 normal medical examinees were selected at the same period of time as the control group. In the research group, 68 patients diagnosed with NSCLC were the newly diagnosed group and 112 cases of recurrence or metastasis of NSCLC were the recurrence group. The quantitative real-time polymerase chain reaction was used to detect the expression levels of serum miR-115 and miR-21. In addition, the expression levels between miR-155 and miR-21 and the relationship between the recurrence rate and metastasis of NSCLC were analyzed. The impact on the prognosis of patients were also analyzed. The expression levels of serum miR-155 and miR-21 were higher in the research group than those in the control group (P<0.05). The expression levels of serum miR-155 and miR-21 were higher in the recurrence group than those in the newly diagnosed group (P<0.05). We followed up the patients in the research group for 36 months, the median survival time and mortality rate in the recurrence group was higher than that of in the newly diagnosed group (χ2=9.705, P<0.01). In conclusion, miR-155 and miR-21 were highly expressed in the serum of patients, however, the recurrence and metastasis of NSCLC were even higher. The highly expressed levels of miR-155 and miR-21 were associated with the recurrence and metastasis in NSCLC patients, affecting the prognosis of patients.
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Affiliation(s)
- Shuang Xu
- Department of Cardiothoracic Surgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163000, P.R. China
| | - Lei Shi
- Department of Hematology and Oncology, Daqing Longnan Hospital, Daqing, Heilongjiang 163000, P.R. China
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Sekar D, Mani P, Biruntha M, Sivagurunathan P, Karthigeyan M. Dissecting the functional role of microRNA 21 in osteosarcoma. Cancer Gene Ther 2019; 26:179-182. [PMID: 30905966 DOI: 10.1038/s41417-019-0092-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
Abstract
Osteosarcoma (OS) is considered to be a malignant bone tumour that mainly affects the long bones, but it is also involved in other bones of the body. Currently, surgery and chemotherapy have achieved some response to patients with OS, but they are not increasing the survival rate as well as treatment options. Researchers made lot of drug options for OS, but yet, no treatment is existing in sight for the disease and needs a new insight into the molecular and signaling pathways for the disease. Now, it is necessary to develop a novel and alternative strategy for the prognosis, diagnosis and treatment options for OS. MicroRNAs (miRNAs) are a small non-coding RNA, and their size ranges from 18 to 22 nt in length. In the nucleus, miRNAs originate and transcribe into primary transcripts and later cleaved to produce stem loop-structured precursor nucleotides. microRNA 21 (miR-21) is considered to be a trivial marker for many diseases and has been upregulated in many cancers. Moreover, it plays a main role in proliferation, migration, invasion and apoptosis. miR-21 and its associated pathways are very important and play a critical role in the pathogenesis of OS and are considered to be a biomarker and a therapeutic target for OS. To our knowledge, there is no paper that demonstrates the responsibility and the role of miR-21 in OS and the number of studies related to miR-21 in OS is spare. Therefore, the main aim of this paper is to give an outline of the recent clinical investigation and importance of miR-21 in OS. It has been suggested that the up- and downregulation of miRNAs plays a crucial role in the pathogenesis and progression of OS. Normally, miR-21 was found to be upregulated in OS; however, we summarize the clinical relevance and the recent research findings associated with miR-21 in OS.
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Affiliation(s)
- Durairaj Sekar
- Dental Research Cell (DRC-BRULAC), Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Science (SIMATS), Saveetha University, Chennai, 600077, India.
| | - Panagal Mani
- Department of Biotechnology, Annai College of Arts and Science, Kumbakonam, Tamil Nadu, 612001, India
| | - M Biruntha
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - P Sivagurunathan
- Department of Microbiology, Faculty of Science, Annamalai University, Chidambaram, Tamil Nadu, 608002, India
| | - M Karthigeyan
- Department of Zoology, Arumugam Pillai Seethai Ammal College, Tiruppattur, Tamil Nadu, India
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Yue S, Song X, Song W, Bi S. An enzyme-free molecular catalytic device: dynamically self-assembled DNA dendrimers for in situ imaging of microRNAs in live cells. Chem Sci 2019; 10:1651-1658. [PMID: 30842828 PMCID: PMC6369435 DOI: 10.1039/c8sc04756a] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA has become a promising material to construct high-order structures and molecular devices owing to its sequence programmability. Herein, a DNA machine based on branched catalytic hairpin assembly (bCHA) is introduced for dynamic self-assembly of DNA dendrimers. For this system, a Y-shaped hairpin trimer tethered with three kinds of hairpins (H1, H2 and H3) is constructed. The introduction of an initiator (I) triggers a cascade of CHA reactions among hairpin trimers, leading to the formation of DNA dendrimers. Through labeling fluorophore/quencher pairs in the hairpin trimers, this catalytic DNA machine is applied as a versatile amplification platform to analyze nucleic acids using microRNA-155 (miR-155) as a model analyte. Benefiting from the "diffusion effect", the proposed bCHA achieves a greatly improved sensitivity in comparison with traditional CHA. This catalytic amplifier exhibits high sensitivity toward miR-155 detection with a dynamic range from 2.5 nM to 500 nM and demonstrates excellent selectivity to distinguish the single-base mismatched sequence from the perfectly complementary one, which is further applied to detect low-abundance miR-155 spiked in complex matrices with minimal interference. This method is further applied for in situ imaging of miR-155 in different live cells. The bCHA reaction can be specifically triggered by intracellular miR-155, achieving monitoring of the dynamic miRNA expression and distribution. Overall, our proposed enzyme-free dynamic DNA self-assembly strategy provides a versatile approach for the development of DNA nanotechnology in biosensing and bioimaging, and monitoring the cellular miRNA-related biological events.
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Affiliation(s)
- Shuzhen Yue
- College of Chemistry and Chemical Engineering , Qingdao University , Qingdao 266071 , P. R. China .
| | - Xinyue Song
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers , College of Chemistry and Chemical Engineering , Linyi University , Linyi 276000 , P. R. China
| | - Weiling Song
- Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science , MOE , Shandong Key Laboratory of Biochemical Analysis , Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong , College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Sai Bi
- College of Chemistry and Chemical Engineering , Qingdao University , Qingdao 266071 , P. R. China .
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Zennami K, Choi SM, Liao R, Li Y, Dinalankara W, Marchionni L, Rafiqi FH, Kurozumi A, Hatano K, Lupold SE. PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance. Mol Cancer Res 2019; 17:618-627. [PMID: 30518628 PMCID: PMC6359980 DOI: 10.1158/1541-7786.mcr-18-0837] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/09/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022]
Abstract
Androgen receptor (AR) transcriptional activity contributes to prostate cancer development and castration resistance. The growth and survival pathways driven by AR remain incompletely defined. Here, we found PDCD4 to be a new target of AR signaling and a potent regulator of prostate cancer cell growth, survival, and castration resistance. The 3' untranslated region of PDCD4 is directly targeted by the androgen-induced miRNA, miR-21. Androgen treatment suppressed PDCD4 expression in a dose responsive and miR-21-dependent manner. Correspondingly, AR inhibition dose-responsively induced PDCD4 expression. Using data from prostate cancer tissue samples in The Cancer Genome Atlas (TCGA), we found a significant and inverse correlation between miR-21 and PDCD4 mRNA and protein levels. Higher Gleason grade tumors exhibited significantly higher levels of miR-21 and significantly lower levels of PDCD4 mRNA and protein. PDCD4 knockdown enhanced androgen-dependent cell proliferation and cell-cycle progression, inhibited apoptosis, and was sufficient to drive androgen-independent growth. On the other hand, PDCD4 overexpression inhibited miR-21-mediated growth and androgen independence. The stable knockdown of PDCD4 in androgen-dependent prostate cancer cells enhanced subcutaneous tumor take rate in vivo, accelerated tumor growth, and was sufficient for castration-resistant tumor growth. IMPLICATIONS: This study provides the first evidence that PDCD4 is an androgen-suppressed protein capable of regulating prostate cancer cell proliferation, apoptosis, and castration resistance. These results uncover miR-21 and PDCD4-regulated pathways as potential new targets for castration-resistant prostate cancer.
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Affiliation(s)
- Kenji Zennami
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Su Mi Choi
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Ross Liao
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Ying Li
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Wikum Dinalankara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Luigi Marchionni
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Fatema H Rafiqi
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Akira Kurozumi
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Koji Hatano
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Shawn E Lupold
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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42
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Xu YF, Li YQ, Liu N, He QM, Tang XR, Wen X, Yang XJ, Sun Y, Ma J, Tang LL. Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing. J Biomed Sci 2018; 25:74. [PMID: 30352587 PMCID: PMC6198351 DOI: 10.1186/s12929-018-0477-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Alternative polyadenylation (APA) is a widespread phenomenon in the posttranscriptional regulation of gene expression that generates mRNAs with alternative 3′-untranslated regions (3’UTRs). APA contributes to the pathogenesis of various diseases, including cancer. However, the potential role of APA in the development of nasopharyngeal carcinoma (NPC) remains largely unknown. Methods A strategy of sequencing APA sites (SAPAS) based on second-generation sequencing technology was carried out to explore the global patterns of APA sites and identify genes with tandem 3’UTRs in samples from 6 NPC and 6 normal nasopharyngeal epithelial tissue (NNET). Sequencing results were then validated using quantitative RT-PCR in a larger cohort of 16 NPC and 16 NNET samples. Results The sequencing data showed that the use of tandem APA sites was prevalent in NPC, and numerous genes with APA-switching events were discovered. In total, we identified 195 genes with significant differences in the tandem 3’UTR length between NPC and NNET; including 119 genes switching to distal poly (A) sites and 76 genes switching to proximal poly (A) sites. Several gene ontology (GO) terms were enriched in the list of genes with switched APA sites, including regulation of cell migration, macromolecule catabolic process, protein catabolic process, proteolysis, small conjugating protein ligase activity, and ubiquitin-protein ligase activity. Conclusions APA site-switching events are prevalent in NPC. APA-mediated regulation of gene expression may play an important role in the development of NPC, and more detailed studies targeting genes with APA-switching events may contribute to the development of novel future therapeutic strategies for NPC. Electronic supplementary material The online version of this article (10.1186/s12929-018-0477-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ya-Fei Xu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, 518060, People's Republic of China
| | - Ying-Qing Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Na Liu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Qing-Mei He
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Xin-Ran Tang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Xin Wen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Xiao-Jing Yang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Ying Sun
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China
| | - Jun Ma
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China.
| | - Ling-Long Tang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, People's Republic of China.
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Malhotra A, Sharma U, Puhan S, Chandra Bandari N, Kharb A, Arifa PP, Thakur L, Prakash H, Vasquez KM, Jain A. Stabilization of miRNAs in esophageal cancer contributes to radioresistance and limits efficacy of therapy. Biochimie 2018; 156:148-157. [PMID: 30326253 DOI: 10.1016/j.biochi.2018.10.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/11/2018] [Indexed: 12/15/2022]
Abstract
The five-year survival rate of esophageal cancer patients is less than 20%. This may be due to increased resistance (acquired or intrinsic) of tumor cells to chemo/radiotherapies, often caused by aberrant cell cycle, deregulated apoptosis, increases in growth factor signaling pathways, and/or changes in the proteome network. In addition, deregulation in non-coding RNA-mediated signaling pathways may contribute to resistance to therapies. At the molecular level, these resistance factors have now been linked to various microRNA (miRNAs), which have recently been shown to control cell development, differentiation and neoplasia. The increased stability and dysregulated expression of miRNAs have been associated with increased resistance to various therapies in several cancers, including esophageal cancer. Therefore, miRNAs represent the next generation of molecules with tremendous potential as biomarkers and therapeutic targets. However, detailed studies on miRNA-based therapeutic interventions are still in their infancy. Hence, in this review, we have summarized the current status of microRNAs in dictating the resistance/sensitivity of tumor cells to chemotherapy and radiotherapy. In addition, we have discussed various strategies to increase radiosensitivity, including targeted therapy, and the use of miRNAs as radiosensitive/radioresistance biomarkers for esophageal cancer in the clinical setting.
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Affiliation(s)
- Akshay Malhotra
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Uttam Sharma
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Shyamly Puhan
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Naga Chandra Bandari
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Anjali Kharb
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - P P Arifa
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Lovlesh Thakur
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Hridayesh Prakash
- Laboratory Oncology Unit, Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India; Institute of Virology and Immunology, Amity University, NOIDA, India.
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA
| | - Aklank Jain
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India.
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La Sala L, Micheloni S, De Nigris V, Prattichizzo F, Ceriello A. Novel insights into the regulation of miRNA transcriptional control: implications for T2D and related complications. Acta Diabetol 2018; 55:989-998. [PMID: 29732466 DOI: 10.1007/s00592-018-1149-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/21/2018] [Indexed: 12/19/2022]
Abstract
In recent years, epigenetics has emerged as an important form of biological regulation involving chromatin control of gene expression. The mechanisms of this fine-tuned regulation are susceptible to changes forced by environmental stimuli and nutritional factors and may be potentially reversible. Dysregulation of epigenetic processes has important consequences for the pathogenesis of complex and multifactorial diseases such as type 2 diabetes (T2D) and vascular complications. Along with DNA methylation (DNA-me), histone modifications and RNA-based mechanisms as the major epigenetic controllers, small non-coding RNAs known as microRNAs (miRNAs) have their own important implications for the pathogenesis of diabetes. There is increasing evidence supporting the role of miRNAs in modulating gene expression, cumulatively contributing to epigenetic gene silencing by acting either on the methylation status of the cells or in alternative roles. Although significant progress has been made in the characterization of miRNA functions, most miRNA promoters have not yet been characterized, and the transcriptional regulation of miRNAs remains elusive. The present work is centred on the new biological insights pertaining to the epigenetics-miRNA regulatory axis, focusing on the development of T2D and cardiovascular complications, and the ability of these mechanisms to interact in a network of DNA-me regulation. The genomic organization of inter- and intragenic miRNA genes is discussed, and the mutual connections between pre-mRNA splicing and miRNA biogenesis are summarized, along with the discovery of novel miRNA transcriptional regulation sites.
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Affiliation(s)
- Lucia La Sala
- Department of Cardiovascular and Dysmetabolic Diseases, IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, MI, Italy.
| | - Stefano Micheloni
- Department of Cardiovascular and Dysmetabolic Diseases, IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, MI, Italy
| | - Valeria De Nigris
- Institut d'Investigación Biomédiques August Pi i Sunyer (IDIBAPS) and Centro de Investigación Biomedica en Red de Diabetes y Enfermedades Metabolicas Asociadas (CIBERDEM), Hospital Clinic, Barcelona, Spain
| | - Francesco Prattichizzo
- Department of Cardiovascular and Dysmetabolic Diseases, IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, MI, Italy
| | - Antonio Ceriello
- Department of Cardiovascular and Dysmetabolic Diseases, IRCCS MultiMedica, Via Fantoli 16/15, 20138, Milan, MI, Italy
- Institut d'Investigación Biomédiques August Pi i Sunyer (IDIBAPS) and Centro de Investigación Biomedica en Red de Diabetes y Enfermedades Metabolicas Asociadas (CIBERDEM), Hospital Clinic, Barcelona, Spain
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Elghoroury EA, ElDine HG, Kamel SA, Abdelrahman AH, Mohammed A, Kamel MM, Ibrahim MH. Evaluation of miRNA-21 and miRNA Let-7 as Prognostic Markers in Patients With Breast Cancer. Clin Breast Cancer 2018; 18:e721-e726. [DOI: 10.1016/j.clbc.2017.11.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/14/2017] [Accepted: 11/30/2017] [Indexed: 01/04/2023]
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Liu B, Shyr Y, Cai J, Liu Q. Interplay between miRNAs and host genes and their role in cancer. Brief Funct Genomics 2018; 18:255-266. [PMID: 30785618 PMCID: PMC6609535 DOI: 10.1093/bfgp/elz002] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/21/2018] [Accepted: 01/23/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous non-coding functional RNAs that post-transcriptionally regulate gene expression. They play essential roles in nearly all biological processes including cell development and differentiation, DNA damage repair, cell death as well as intercellular communication. They are highly involved in cancer, acting as tumor suppressors and/or promoters to modulate cell proliferation, epithelial-mesenchymal transition and tumor invasion and metastasis. Recent studies have shown that more than half of miRNAs are located within protein-coding or non-coding genes. Intragenic miRNAs and their host genes either share the promoter or have independent transcription. Meanwhile, miRNAs work as partners or antagonists of their host genes by fine-tuning their target genes functionally associated with host genes. This review outlined the complicated relationship between intragenic miRNAs and host genes. Focusing on miRNAs known as oncogenes or tumor suppressors in specific cancer types, it studied co-expression relationships between these miRNAs and host genes in the cancer types using TCGA data sets, which validated previous findings and revealed common, tumor-specific and even subtype-specific patterns. These observations will help understand the function of intragenic miRNAs and further develop miRNA therapeutics in cancer.
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Affiliation(s)
- Baohong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
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47
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Evolutionary optimization of convolutional neural networks for cancer miRNA biomarkers classification. Appl Soft Comput 2018. [DOI: 10.1016/j.asoc.2017.12.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Zouari M, Campuzano S, Pingarrón J, Raouafi N. Ultrasensitive determination of microribonucleic acids in cancer cells with nanostructured-disposable electrodes using the viral protein p19 for recognition of ribonucleic acid/microribonucleic acid homoduplexes. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2017.12.190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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49
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Gangwar RS, Rajagopalan S, Natarajan R, Deiuliis JA. Noncoding RNAs in Cardiovascular Disease: Pathological Relevance and Emerging Role as Biomarkers and Therapeutics. Am J Hypertens 2018; 31:150-165. [PMID: 29186297 DOI: 10.1093/ajh/hpx197] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
Noncoding RNAs (ncRNA) include a diverse range of functional RNA species-microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) being most studied in pathophysiology. Cardiovascular morbidity is associated with differential expression of myriad miRNAs; miR-21, miR-155, miR-126, miR-146a/b, miR-143/145, miR-223, and miR-221 are the top 9 most reported miRNAs in hypertension and atherosclerotic disease. A single miRNA may have hundreds of messenger RNA targets, which makes a full appreciation of the physiologic ramifications of such broad-ranging effects a challenge. miR-21 is the most prominent ncRNA associated with hypertension and atherosclerotic disease due to its role as a "mechano-miR", responding to arterial shear stresses. "Immuno-miRs", such as miR-155 and miR-223, affect cardiovascular disease (CVD) via regulation of hematopoietic cell differentiation, chemotaxis, and activation in response to many pro-atherogenic stimuli. "Myo-miRs", such as miR-1 and miR-133, affect cardiac muscle plasticity and remodeling in response to mechanical overload. This in-depth review analyzes observational and experimental reports of ncRNAs in CVD, including future applications of ncRNA-based strategies in diagnosis, prediction (e.g., survival and response to small molecule therapy), and biologic therapy.
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Affiliation(s)
- Roopesh S Gangwar
- Cardiovascular Research Institute (CVRI), Case Western Reserve University, Cleveland, Ohio, USA
| | - Sanjay Rajagopalan
- Cardiovascular Research Institute (CVRI), Case Western Reserve University, Cleveland, Ohio, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Jeffrey A Deiuliis
- Cardiovascular Research Institute (CVRI), Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, USA
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50
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Frequent miRNA-convergent fusion gene events in breast cancer. Nat Commun 2017; 8:788. [PMID: 28983113 PMCID: PMC5629207 DOI: 10.1038/s41467-017-01176-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/24/2017] [Indexed: 12/18/2022] Open
Abstract
Studies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. Here, we show, using breast cancer as an example, that miRNA host genes are specifically enriched in fusion genes and that many different, low-frequency, 5ʹ partners may deregulate the same miRNA irrespective of the coding potential of the fusion transcript. These results indicate that the concept of recurrence, defined by the rate of functionally important aberrations, needs to be revised to encompass convergent fusions that affect a miRNA independently of transcript structure and protein-coding potential. Fusion gene research traditionally focuses on fusions that result in hybrid proteins or promoter switching events. Here, the authors demonstrate enrichment of fusions in miRNA host genes in breast cancer, highlighting that disparate fusions could have convergent impact on miRNA.
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