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Usha Satheesan S, Chowdhury S, Kolthur-Seetharam U. Metabolic and circadian inputs encode anticipatory biogenesis of hepatic fed microRNAs. Life Sci Alliance 2024; 7:e202302180. [PMID: 38408795 PMCID: PMC10897495 DOI: 10.26508/lsa.202302180] [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: 05/24/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Starvation and refeeding are mostly unanticipated in the wild in terms of duration, frequency, and nutritional value of the refed state. Notwithstanding this, organisms mount efficient and reproducible responses to restore metabolic homeostasis. Hence, it is intuitive to invoke expectant molecular mechanisms that build anticipatory responses to enable physiological toggling during fed-fast cycles. In this regard, we report anticipatory biogenesis of oscillatory hepatic microRNAs that peak during a fed state and inhibit starvation-responsive genes. Our results clearly demonstrate that the levels of primary and precursor microRNA transcripts increase during a fasting state, in anticipation of a fed response. We delineate the importance of both metabolic and circadian cues in orchestrating hepatic fed microRNA homeostasis in a physiological setting. Besides illustrating metabo-endocrine control, our findings provide a mechanistic basis for the overarching influence of starvation on anticipatory biogenesis. Importantly, by using pharmacological agents that are widely used in clinics, we point out the high potential of interventions to restore homeostasis of hepatic microRNAs, whose deregulated expression is otherwise well established to cause metabolic diseases.
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Affiliation(s)
- Sandra Usha Satheesan
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shreyam Chowdhury
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ullas Kolthur-Seetharam
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- https://ror.org/03ht1xw27 Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, India
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2
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Abdul Manap AS, Wisham AA, Wong FW, Ahmad Najmi HR, Ng ZF, Diba RS. Mapping the function of MicroRNAs as a critical regulator of tumor-immune cell communication in breast cancer and potential treatment strategies. Front Cell Dev Biol 2024; 12:1390704. [PMID: 38726321 PMCID: PMC11079208 DOI: 10.3389/fcell.2024.1390704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
Among women, breast cancer ranks as the most prevalent form of cancer, and the presence of metastases significantly reduces prognosis and diminishes overall survival rates. Gaining insights into the biological mechanisms governing the conversion of cancer cells, their subsequent spread to other areas of the body, and the immune system's monitoring of tumor growth will contribute to the advancement of more efficient and targeted therapies. MicroRNAs (miRNAs) play a critical role in the interaction between tumor cells and immune cells, facilitating tumor cells' evasion of the immune system and promoting cancer progression. Additionally, miRNAs also influence metastasis formation, including the establishment of metastatic sites and the transformation of tumor cells into migratory phenotypes. Specifically, dysregulated expression of these genes has been associated with abnormal expression of oncogenes and tumor suppressor genes, thereby facilitating tumor development. This study aims to provide a concise overview of the significance and function of miRNAs in breast cancer, focusing on their involvement as tumor suppressors in the antitumor immune response and as oncogenes in metastasis formation. Furthermore, miRNAs hold tremendous potential as targets for gene therapy due to their ability to modulate specific pathways that can either promote or suppress carcinogenesis. This perspective highlights the latest strategies developed for miRNA-based therapies.
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Affiliation(s)
- Aimi Syamima Abdul Manap
- Department of Biomedical Science, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | | | - Fei Wen Wong
- Faculty of Biosciences, MAHSA University, Kuala Langat, Selangor, Malaysia
| | | | - Zhi Fei Ng
- Faculty of Biosciences, MAHSA University, Kuala Langat, Selangor, Malaysia
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3
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Chen Y, Mateski J, Gerace L, Wheeler J, Burl J, Prakash B, Svedin C, Amrick R, Adams BD. Non-coding RNAs and neuroinflammation: implications for neurological disorders. Exp Biol Med (Maywood) 2024; 249:10120. [PMID: 38463392 PMCID: PMC10911137 DOI: 10.3389/ebm.2024.10120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Neuroinflammation is considered a balanced inflammatory response important in the intrinsic repair process after injury or infection. Under chronic states of disease, injury, or infection, persistent neuroinflammation results in a heightened presence of cytokines, chemokines, and reactive oxygen species that result in tissue damage. In the CNS, the surrounding microglia normally contain macrophages and other innate immune cells that perform active immune surveillance. The resulting cytokines produced by these macrophages affect the growth, development, and responsiveness of the microglia present in both white and gray matter regions of the CNS. Controlling the levels of these cytokines ultimately improves neurocognitive function and results in the repair of lesions associated with neurologic disease. MicroRNAs (miRNAs) are master regulators of the genome and subsequently control the activity of inflammatory responses crucial in sustaining a robust and acute immunological response towards an acute infection while dampening pathways that result in heightened levels of cytokines and chemokines associated with chronic neuroinflammation. Numerous reports have directly implicated miRNAs in controlling the abundance and activity of interleukins, TGF-B, NF-kB, and toll-like receptor-signaling intrinsically linked with the development of neurological disorders such as Parkinson's, ALS, epilepsy, Alzheimer's, and neuromuscular degeneration. This review is focused on discussing the role miRNAs play in regulating or initiating these chronic neurological states, many of which maintain the level and/or activity of neuron-specific secondary messengers. Dysregulated miRNAs present in the microglia, astrocytes, oligodendrocytes, and epididymal cells, contribute to an overall glial-specific inflammatory niche that impacts the activity of neuronal conductivity, signaling action potentials, neurotransmitter robustness, neuron-neuron specific communication, and neuron-muscular connections. Understanding which miRNAs regulate microglial activation is a crucial step forward in developing non-coding RNA-based therapeutics to treat and potentially correct the behavioral and cognitive deficits typically found in patients suffering from chronic neuroinflammation.
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Affiliation(s)
- Yvonne Chen
- Department of Biology, Brandeis University, Waltham, MA, United States
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
| | - Julia Mateski
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biological Sciences, Gustavus Adolphus College, St. Peter, MN, United States
| | - Linda Gerace
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Missouri State University, Springfield, MO, United States
| | - Jonathan Wheeler
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Electrical and Computer Engineering Tech, New York Institute of Tech, Old Westbury, NY, United States
| | - Jan Burl
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Southern New Hampshire University, Manchester, NH, United States
| | - Bhavna Prakash
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Medicine, Tufts Medical Center, Medford, MA, United States
| | - Cherie Svedin
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biology, Utah Tech University, St. George, UT, United States
| | - Rebecca Amrick
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Villanova University, Villanova, PA, United States
| | - Brian D Adams
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
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4
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Kimura M, Kothari S, Gohir W, Camargo JF, Husain S. MicroRNAs in infectious diseases: potential diagnostic biomarkers and therapeutic targets. Clin Microbiol Rev 2023; 36:e0001523. [PMID: 37909789 PMCID: PMC10732047 DOI: 10.1128/cmr.00015-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
MicroRNAs (miRNAs) are conserved, short, non-coding RNAs that play a crucial role in the post-transcriptional regulation of gene expression. They have been implicated in the pathogenesis of cancer and neurological, cardiovascular, and autoimmune diseases. Several recent studies have suggested that miRNAs are key players in regulating the differentiation, maturation, and activation of immune cells, thereby influencing the host immune response to infection. The resultant upregulation or downregulation of miRNAs from infection influences the protein expression of genes responsible for the immune response and can determine the risk of disease progression. Recently, miRNAs have been explored as diagnostic biomarkers and therapeutic targets in various infectious diseases. This review summarizes our current understanding of the role of miRNAs during viral, fungal, bacterial, and parasitic infections from a clinical perspective, including critical functional mechanisms and implications for their potential use as biomarkers and therapeutic targets.
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Affiliation(s)
- Muneyoshi Kimura
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Sagar Kothari
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Wajiha Gohir
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Jose F. Camargo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shahid Husain
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
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5
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Srivastava A, Srivastava A, Singh RK. Insight into the Epigenetics of Kaposi's Sarcoma-Associated Herpesvirus. Int J Mol Sci 2023; 24:14955. [PMID: 37834404 PMCID: PMC10573522 DOI: 10.3390/ijms241914955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetic reprogramming represents a series of essential events during many cellular processes including oncogenesis. The genome of Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic herpesvirus, is predetermined for a well-orchestrated epigenetic reprogramming once it enters into the host cell. The initial epigenetic reprogramming of the KSHV genome allows restricted expression of encoded genes and helps to hide from host immune recognition. Infection with KSHV is associated with Kaposi's sarcoma, multicentric Castleman's disease, KSHV inflammatory cytokine syndrome, and primary effusion lymphoma. The major epigenetic modifications associated with KSHV can be labeled under three broad categories: DNA methylation, histone modifications, and the role of noncoding RNAs. These epigenetic modifications significantly contribute toward the latent-lytic switch of the KSHV lifecycle. This review gives a brief account of the major epigenetic modifications affiliated with the KSHV genome in infected cells and their impact on pathogenesis.
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Affiliation(s)
- Anusha Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ankit Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Rajnish Kumar Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Faculty of Medical Sciences, Charotar University of Science and Technology, Changa 388421, Gujarat, India
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6
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Lausten MA, Boman BM. A Review of IsomiRs in Colorectal Cancer. Noncoding RNA 2023; 9:34. [PMID: 37368334 DOI: 10.3390/ncrna9030034] [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: 04/29/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine.
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Affiliation(s)
- Molly A Lausten
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
| | - Bruce M Boman
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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7
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Azevedo ML, Silveira RG, Nedel F, Lund RG. MicroRNAs expressed during normal wound healing and their associated pathways: A systematic review and bioinformatics analysis. PLoS One 2023; 18:e0281913. [PMID: 37053170 PMCID: PMC10101427 DOI: 10.1371/journal.pone.0281913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/04/2023] [Indexed: 04/14/2023] Open
Abstract
MicroRNAs (miRNAs) are responsible for regulating gene expression post-transcriptionally. Are involved in several biological processes, such as wound healing. Understanding the miRNAs involved in this process is fundamental for the development of new therapies. So, due to the need to understand the role of these molecules, we aimed systematically review the literature in order to identify which miRNAs are involved in the wound healing and determine, through bioinformatics analysis, which signaling pathways are associated with these miRNAs. An electronic search was performed in the following databases: National Library of Medicine National Institutes of Health (PubMed), Science Direct, Scifinder, Scopus and Web of Science, using the descriptors: "(microRNA [MeSH])" and "(skin [MeSH])" and "(wound healing [MeSH])". After the search, two independent and previously calibrated reviewers selected the articles that analyzed the expression pattern of miRNAs in wound healing in in vivo studies, using the software Zotero bibliography manager. Following, bioinformatic analysis was performed using the software DIANA Tools, mirPath v.3 and the data was interpreted. The bioinformatics analysis revealed that on the day 1 there were 13 union pathways, eight of which were statistically significant. Still on the day 1, among the miRNAs that had a decrease in their expression, 12 of 17 union pathways found were statistically significant. On the day 5, among the miRNAs with an increase in expression, 16 union pathways were found, 12 of which were statistically significant. Finally, among the miRNAs with decreased expression, 11 of 15 union pathways found were statistically significant. Although it has been found substantial heterogeneity in the studies, with this systematic review, it was possible to study the panorama of miRNAs that may be altered in the wound healing. The present review summarizes existing evidence of miRNAs associated to wound healing, and these findings can contribute to new therapeutic approaches.
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Affiliation(s)
- Morgana Lüdtke Azevedo
- Graduated Program in Biochemistry and Bioprospecting, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Roberta Giorgi Silveira
- Graduated Program in Health and Behavior, Catholic University of Pelotas, Pelotas, RS, Brazil
| | - Fernanda Nedel
- Graduated Program in Health and Behavior, Catholic University of Pelotas, Pelotas, RS, Brazil
| | - Rafael Guerra Lund
- Graduated Program in Biochemistry and Bioprospecting, Federal University of Pelotas, Pelotas, RS, Brazil
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8
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Vilimova M, Pfeffer S. Post-transcriptional regulation of polycistronic microRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1749. [PMID: 35702737 DOI: 10.1002/wrna.1749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/02/2023]
Abstract
An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Monika Vilimova
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
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9
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Putting the "mi" in omics: discovering miRNA biomarkers for pediatric precision care. Pediatr Res 2023; 93:316-323. [PMID: 35906312 PMCID: PMC9884316 DOI: 10.1038/s41390-022-02206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
In the past decade, growing interest in micro-ribonucleic acids (miRNAs) has catapulted these small, non-coding nucleic acids to the forefront of biomarker research. Advances in scientific knowledge have made it clear that miRNAs play a vital role in regulating cellular physiology throughout the human body. Perturbations in miRNA signaling have also been described in a variety of pediatric conditions-from cancer, to renal failure, to traumatic brain injury. Likewise, the number of studies across pediatric disciplines that pair patient miRNA-omics with longitudinal clinical data are growing. Analyses of these voluminous, multivariate data sets require understanding of pediatric phenotypic data, data science, and genomics. Use of machine learning techniques to aid in biomarker detection have helped decipher background noise from biologically meaningful changes in the data. Further, emerging research suggests that miRNAs may have potential as therapeutic targets for pediatric precision care. Here, we review current miRNA biomarkers of pediatric diseases and studies that have combined machine learning techniques, miRNA-omics, and patient health data to identify novel biomarkers and potential therapeutics for pediatric diseases. IMPACT: In the following review article, we summarized how recent developments in microRNA research may be coupled with machine learning techniques to advance pediatric precision care.
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10
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Grodzka O, Procyk G, Gąsecka A. The Role of MicroRNAs in Myocarditis-What Can We Learn from Clinical Trials? Int J Mol Sci 2022; 23:ijms232416022. [PMID: 36555663 PMCID: PMC9783955 DOI: 10.3390/ijms232416022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Myocarditis is an inflammatory disease of the heart with a viral infection as the most common cause. It affects most commonly young adults. Although endomyocardial biopsy and cardiac magnetic resonance are used in the diagnosis, neither of them demonstrates all the required qualities. There is a clear need for a non-invasive, generally available diagnostic tool that will still remain highly specific and sensitive. These requirements could be possibly met by microribonucleic acids (miRNAs), which are small, non-coding RNA molecules that regulate many fundamental cell functions. They can be isolated from cells, tissues, or body fluids. Recently, several clinical studies have shown the deregulation of different miRNAs in myocarditis. The phase of the disease has also been evidenced to influence miRNA levels. These changes have been observed both in adult and pediatric patients. Some studies have revealed a correlation between the change in particular miRNA concentration and the degree of cardiac damage and inflammation. All of this indicates miRNAs as potential novel biomarkers in the diagnosis of myocarditis, as well as a prognostic tool for this condition. This review aims to summarize the current knowledge about the role of miRNAs in myocarditis based on the results of clinical studies.
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Affiliation(s)
- Olga Grodzka
- Department of Neurology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland
| | - Grzegorz Procyk
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
- Correspondence: ; Tel.: +48-723-488-305
| | - Aleksandra Gąsecka
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland
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11
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Mechanism of miR-760 Reversing Lung Cancer Immune Escape by Downregulating IDO1 and Eliminating Regulatory T Cells Based on Mathematical Biology. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2960773. [PMID: 35872931 PMCID: PMC9303114 DOI: 10.1155/2022/2960773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022]
Abstract
In cancer biology, mathematical models have become indispensable. They are useful for gaining a mechanistic grasp of cancer's dynamic processes. In cancer research, mathematical modelling approaches are becoming more common. The complexity of cancer is well suited to quantitative approaches as it provides challenges and opportunities for new developments (Altrock et al., 2015). Background. MicroRNA-760 (miR-760), as an early discovered tumor suppressor gene, is poorly expressed in lung cancer (LC). Indoleamine 2,3-dioxygenase 1 (IDO1), as an important regulator of T cell function, is active in immune tolerance. We discovered that miR-760 has a targeted relationship with IDO1, but the regulatory mechanism between miR-760 and IDO1 is still unclear. Method. The miR-760 and IDO1 levels in NSCLC were tested via real-time quantitative polymerase chain reaction (qRT-PCR) and western blotting (WB). Cell growth was tested by CCK8, and NSCLC cell migration and invasion were analyzed through Transwell analysis. The binding conditions and target gene of miR-451 in NSCLC cells were determined via double luciferase reporter gene. The CD8+ T and CD4+ T cell ratio in CD45+cells was assessed by flow cytometry. Results. qRT-PCR revealed that miR-760 was low-expressed and IDO2 was highly expressed in LC. miR-760 mimics suppressed cell growth, invasiveness, and migration. We also observed that miR-760 could downregulate the IDO1 protein level. Significantly, we revealed that miR-760 could inhibit CD8+ T cell apoptosis by controlling IDO1 enzyme function. Conclusion. Our findings show that miR-760 inhibits CD8+ T cell responses in LC through regulating IDO1, laying the groundwork for the development of novel vaccination therapies for the treatment of LC.
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12
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Li S, Zhang X, Yao Y, Zhu Y, Zheng X, Liu F, Feng W. Inducible miR-150 Inhibits Porcine Reproductive and Respiratory Syndrome Virus Replication by Targeting Viral Genome and Suppressor of Cytokine Signaling 1. Viruses 2022; 14:v14071485. [PMID: 35891465 PMCID: PMC9318191 DOI: 10.3390/v14071485] [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: 06/18/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/11/2022] Open
Abstract
Hosts exploit various approaches to defend against porcine reproductive and respiratory syndrome virus (PRRSV) infection. microRNAs (miRNAs) have emerged as key negative post-transcriptional regulators of gene expression and have been reported to play important roles in regulating virus infection. Here, we identified that miR-150 was differentially expressed in virus permissive and non-permissive cells. Subsequently, we demonstrated that PRRSV induced the expression of miR-150 via activating the protein kinase C (PKC)/c-Jun amino-terminal kinases (JNK)/c-Jun pathway, and overexpression of miR-150 suppressed PRRSV replication. Further analysis revealed that miR-150 not only directly targeted the PRRSV genome, but also facilitated type I IFN signaling. RNA immunoprecipitation assay demonstrated that miR-150 targeted the suppressor of cytokine signaling 1 (SOCS1), which is a negative regulator of Janus activated kinase (JAK)/signal transducer and activator of the transcription (STAT) signaling pathway. The inverse correlation between miR-150 and SOCS1 expression implies that miR-150 plays a role in regulating ISG expression. In conclusion, miR-150 expression is upregulated upon PRRSV infection. miR-150 feedback positively targets the PRRSV genome and promotes type I IFN signaling, which can be seen as a host defensive strategy.
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Affiliation(s)
- Sihan Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xuan Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yao Yao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yingqi Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaojie Zheng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fang Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenhai Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (S.L.); (X.Z.); (Y.Y.); (Y.Z.); (X.Z.); (F.L.)
- Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-10-62733335; Fax: +86-10-62732012
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Hecker M, Fitzner B, Putscher E, Schwartz M, Winkelmann A, Meister S, Dudesek A, Koczan D, Lorenz P, Boxberger N, Zettl UK. Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis. EBioMedicine 2022; 80:104052. [PMID: 35561450 PMCID: PMC9111935 DOI: 10.1016/j.ebiom.2022.104052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Background Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with a well-established genetic contribution to susceptibility. Over 200 genetic regions have been linked to the inherited risk of developing MS, but the disease-causing variants and their functional effects at the molecular level are still largely unresolved. We hypothesised that MS-associated single-nucleotide polymorphisms (SNPs) affect the recognition and enzymatic cleavage of primary microRNAs (pri-miRNAs). Methods Our study focused on 11 pri-miRNAs (9 primate-specific) that are encoded in genetic risk loci for MS. The levels of mature miRNAs and potential isoforms (isomiRs) produced from those pri-miRNAs were measured in B cells obtained from the peripheral blood of 63 MS patients and 28 healthy controls. We tested for associations between SNP genotypes and miRNA expression in cis using quantitative trait locus (cis-miR-eQTL) analyses. Genetic effects on miRNA stem-loop processing efficiency were verified using luciferase reporter assays. Potential direct miRNA target genes were identified by transcriptome profiling and computational binding site assessment. Findings Mature miRNAs and isomiRs from hsa-mir-26a-2, hsa-mir-199a-1, hsa-mir-4304, hsa-mir-4423, hsa-mir-4464 and hsa-mir-4492 could be detected in all B-cell samples. When MS patient subgroups were compared with healthy controls, a significant differential expression was observed for miRNAs from the 5’ and 3’ strands of hsa-mir-26a-2 and hsa-mir-199a-1. The cis-miR-eQTL analyses and reporter assays pointed to a slightly more efficient Drosha-mediated processing of hsa-mir-199a-1 when the MS risk allele T of SNP rs1005039 is present. On the other hand, the MS risk allele A of SNP rs817478, which substitutes the first C in a CNNC sequence motif, was found to cause a markedly lower efficiency in the processing of hsa-mir-4423. Overexpression of hsa-mir-199a-1 inhibited the expression of 60 protein-coding genes, including IRAK2, MIF, TNFRSF12A and TRAF1. The only target gene identified for hsa-mir-4423 was TMEM47. Interpretation We found that MS-associated SNPs in sequence determinants of pri-miRNA processing can affect the expression of mature miRNAs. Our findings complement the existing literature on the dysregulation of miRNAs in MS. Further studies on the maturation and function of miRNAs in different cell types and tissues may help to gain a more detailed functional understanding of the genetic basis of MS. Funding This study was funded by the Rostock University Medical Center (FORUN program, grant: 889002), Sanofi Genzyme (grant: GZ-2016-11560) and Merck Serono GmbH (Darmstadt, Germany, an affiliate of Merck KGaA, CrossRef Funder ID: 10.13039/100009945, grant: 4501860307). NB was supported by the Stiftung der Deutschen Wirtschaft (sdw) and the FAZIT foundation. EP was supported by the Landesgraduiertenförderung Mecklenburg-Vorpommern.
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Dozier C, Montigny A, Viladrich M, Culerrier R, Combier JP, Besson A, Plaza S. Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila. Int J Mol Sci 2022; 23:5764. [PMID: 35628573 PMCID: PMC9144653 DOI: 10.3390/ijms23105764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regulatory elements involved in lncRNA decay. Here, we investigated the possible involvement of smORFs in the regulation of lnc pri-miRNAs in Human and Drosophila, focusing on pri-miRNAs previously shown to contain translatable smORFs. We show that smORFs regulate the expression levels of human pri-miR-155 and pri-miR-497, and Drosophila pri-miR-8 and pri-miR-14, and also affect the expression and activity of their associated miRNAs. This smORF-dependent regulation is independent of the nucleotidic and amino acidic sequences of the smORFs and is sensitive to the ribosome-stalling drug cycloheximide, suggesting the involvement of translational events. This study identifies smORFs as new cis-acting elements involved in the regulation of pri-miRNAs and miRNAs expression, in both Human and Drosophila melanogaster.
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Affiliation(s)
- Christine Dozier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Mireia Viladrich
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Raphael Culerrier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
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15
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as Biomarkers for Birth Defects. Microrna 2022; 11:2-11. [PMID: 35168515 DOI: 10.2174/2211536611666220215123423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 11/22/2022]
Abstract
It is estimated that 2-4% of live births will have a birth defect (BD). The availability of biomarkers for the prenatal detection of BDs will facilitate early risk assessment, prompt medical intervention and ameliorating disease severity. miRNA expression levels are often found to be altered in many diseases. There is, thus, a growing interest in determining whether miRNAs, particularly extracellular miRNAs, can predict, diagnose, or monitor BDs. These miRNAs, typically encapsulated in exosomes, are released by cells (including those of the fetus and placenta) into the extracellular milieu, such as blood, urine, saliva and cerebrospinal fluid, thereby enabling interaction with target cells. Exosomal miRNAs are stable, protected from degradation, and retain functionality. The observation that placental and fetal miRNAs can be detected in maternal serum, provides a strong rationale for adopting miRNAs as noninvasive prenatal biomarkers for BDs. In this mini-review, we examine the current state of research involving the use of miRNAs as prognostic and diagnostic biomarkers for BD.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
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16
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TGF-β Induction of miR-143/145 Is Associated to Exercise Response by Influencing Differentiation and Insulin Signaling Molecules in Human Skeletal Muscle. Cells 2021; 10:cells10123443. [PMID: 34943951 PMCID: PMC8700369 DOI: 10.3390/cells10123443] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022] Open
Abstract
Physical training improves insulin sensitivity and can prevent type 2 diabetes (T2D). However, approximately 20% of individuals lack a beneficial outcome in glycemic control. TGF-β, identified as a possible upstream regulator involved in this low response, is also a potent regulator of microRNAs (miRNAs). The aim of this study was to elucidate the potential impact of TGF-β-driven miRNAs on individual exercise response. Non-targeted long and sncRNA sequencing analyses of TGF-β1-treated human skeletal muscle cells corroborated the effects of TGF-β1 on muscle cell differentiation, the induction of extracellular matrix components, and identified several TGF-β1-regulated miRNAs. qPCR validated a potent upregulation of miR-143-3p/145-5p and miR-181a2-5p by TGF-β1 in both human myoblasts and differentiated myotubes. Healthy subjects who were overweight or obese participated in a supervised 8-week endurance training intervention (n = 40) and were categorized as responder or low responder in glycemic control based on fold change ISIMats (≥+1.1 or <+1.1, respectively). In skeletal muscle biopsies of low responders, TGF-β signaling and miR-143/145 cluster levels were induced by training at much higher rates than among responders. Target-mining revealed HDACs, MYHs, and insulin signaling components INSR and IRS1 as potential miR-143/145 cluster targets. All these targets were down-regulated in TGF-β1-treated myotubes. Transfection of miR-143-3p/145-5p mimics in differentiated myotubes validated MYH1, MYH4, and IRS1 as miR-143/145 cluster targets. Elevated TGF-β signaling and miR-143/145 cluster induction in skeletal muscle of low responders might obstruct improvements in insulin sensitivity by training in two ways: by a negative impact of miR-143-3p on muscle cell fusion and myofiber functionality and by directly impairing insulin signaling via a reduction in INSR by TGF-β and finetuned IRS1 suppression by miR-143-3p.
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17
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Tanase DM, Gosav EM, Ouatu A, Badescu MC, Dima N, Ganceanu-Rusu AR, Popescu D, Floria M, Rezus E, Rezus C. Current Knowledge of MicroRNAs (miRNAs) in Acute Coronary Syndrome (ACS): ST-Elevation Myocardial Infarction (STEMI). Life (Basel) 2021; 11:life11101057. [PMID: 34685428 PMCID: PMC8541211 DOI: 10.3390/life11101057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
Regardless of the newly diagnostic and therapeutic advances, coronary artery disease (CAD) and more explicitly, ST-elevation myocardial infarction (STEMI), remains one of the leading causes of morbidity and mortality worldwide. Thus, early and prompt diagnosis of cardiac dysfunction is pivotal in STEMI patients for a better prognosis and outcome. In recent years, microRNAs (miRNAs) gained attention as potential biomarkers in myocardial infarction (MI) and acute coronary syndromes (ACS), as they have key roles in heart development, various cardiac processes, and act as indicators of cardiac damage. In this review, we describe the current available knowledge about cardiac miRNAs and their functions, and focus mainly on their potential use as novel circulating diagnostic and prognostic biomarkers in STEMI.
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Affiliation(s)
- Daniela Maria Tanase
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Evelina Maria Gosav
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
- Correspondence: (E.M.G.); (M.F.); (E.R.)
| | - Anca Ouatu
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Minerva Codruta Badescu
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Nicoleta Dima
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Ana Roxana Ganceanu-Rusu
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Diana Popescu
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Mariana Floria
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, Emergency Military Clinical Hospital Iasi, 700483 Iasi, Romania
- Correspondence: (E.M.G.); (M.F.); (E.R.)
| | - Elena Rezus
- Department of Rheumatology and Physiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- I Rheumatology Clinic, Clinical Rehabilitation Hospital, 700661 Iasi, Romania
- Correspondence: (E.M.G.); (M.F.); (E.R.)
| | - Ciprian Rezus
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.M.T.); (A.O.); (M.C.B.); (N.D.); (A.R.G.-R.); (D.P.); (C.R.)
- Internal Medicine Clinic, “Sf. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
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Vilimova M, Contrant M, Randrianjafy R, Dumas P, Elbasani E, Ojala PM, Pfeffer S, Fender A. Cis regulation within a cluster of viral microRNAs. Nucleic Acids Res 2021; 49:10018-10033. [PMID: 34417603 PMCID: PMC8464075 DOI: 10.1093/nar/gkab731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi's sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.
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Affiliation(s)
- Monika Vilimova
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Maud Contrant
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Ramy Randrianjafy
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated structural Biology, 1 rue Laurent Fries, BP10142, 67404 Illkirch-Graffenstaden, France
| | - Endrit Elbasani
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Aurélie Fender
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
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Hu Y, Qian X. Hsa_circ_0074491 regulates the malignance of cholesteatoma keratinocytes by modulating the PI3K/Akt pathway by binding to miR-22-3p and miR-125a-5p: An observational study. Medicine (Baltimore) 2021; 100:e27122. [PMID: 34664835 PMCID: PMC8447995 DOI: 10.1097/md.0000000000027122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Cholesteatoma is a benign cystic lesion that can continue to grow like a tumor. Circular ribonucleic acid (RNA) hsa_circ_0074491 (circ_0074491) has been reported to be down-regulated in cholesteatoma tissues. However, the role and regulatory mechanism of circ_0074491 in the growth of cholesteatoma are unclear.The expression of circ_0074491, microRNA (miR)-22-3p, and miR-125a-5p in cholesteatoma tissues was detected by quantitative real-time polymerase chain reaction. The proliferation, cell cycle, apoptosis, migration, and invasion of cholesteatoma keratinocytes were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, plate clone, flow cytometry, or transwell assays. Several protein levels were examined by western blotting. The targeting relationship between miR-22-3p or miR-125a-5p and circ_0074491 was verified via dual-luciferase reporter and RNA pull-down assays.We observed the downregulation of circ_0074491 in cholesteatoma tissues. Furthermore, circ_0074491 knockdown facilitated cell proliferation, migration, invasion, and repressed cell apoptosis in cholesteatoma keratinocytes. Circ_0074491 was verified as a decoy for miR-22-3p and miR-125a-5p in cholesteatoma keratinocytes. Both miR-22-3p and miR-125a-5p silencing reversed the impacts of circ_0074491 silencing on proliferation, apoptosis, migration, and invasion of cholesteatoma keratinocytes. Also, circ_0074491 knockdown activated the PI3K/Akt pathway in cholesteatoma keratinocytes via miR-22-3p and miR-125a-5p.Circ_0074491 played a suppressive role in cholesteatoma through inactivating the PI3K/Akt pathway via binding to miR-22-3p and miR-125a-5p, which provided a novel evidence for the involvement of circRNA in the development of cholesteatoma.
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Rodríguez ML, Millán I, Ortega ÁL. Cellular targets in diabetic retinopathy therapy. World J Diabetes 2021; 12:1442-1462. [PMID: 34630899 PMCID: PMC8472497 DOI: 10.4239/wjd.v12.i9.1442] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/08/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Despite the existence of treatment for diabetes, inadequate metabolic control triggers the appearance of chronic complications such as diabetic retinopathy. Diabetic retinopathy is considered a multifactorial disease of complex etiology in which oxidative stress and low chronic inflammation play essential roles. Chronic exposure to hyperglycemia triggers a loss of redox balance that is critical for the appearance of neuronal and vascular damage during the development and progression of the disease. Current therapies for the treatment of diabetic retinopathy are used in advanced stages of the disease and are unable to reverse the retinal damage induced by hyperglycemia. The lack of effective therapies without side effects means there is an urgent need to identify an early action capable of preventing the development of the disease and its pathophysiological consequences in order to avoid loss of vision associated with diabetic retinopathy. Therefore, in this review we propose different therapeutic targets related to the modulation of the redox and inflammatory status that, potentially, can prevent the development and progression of the disease.
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Affiliation(s)
- María Lucía Rodríguez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot 46100, Valencia, Spain
| | - Iván Millán
- Neonatal Research Group, Health Research Institute La Fe, Valencia 46026, Valencia, Spain
| | - Ángel Luis Ortega
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot 46100, Valencia, Spain
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21
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Moreau PR, Tomas Bosch V, Bouvy-Liivrand M, Õunap K, Örd T, Pulkkinen HH, Pölönen P, Heinäniemi M, Ylä-Herttuala S, Laakkonen JP, Linna-Kuosmanen S, Kaikkonen MU. Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types. Arterioscler Thromb Vasc Biol 2021; 41:2149-2167. [PMID: 33980036 PMCID: PMC8216629 DOI: 10.1161/atvbaha.121.315579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Pierre R. Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Vanesa Tomas Bosch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Maria Bouvy-Liivrand
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio (M.B.-L., P.P., M.H.)
- Now with Genevia Technologies Oy, Tampere, Finland (M.B.-L.)
| | - Kadri Õunap
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Heidi H. Pulkkinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Petri Pölönen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio (M.B.-L., P.P., M.H.)
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN (P.P.)
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio (M.B.-L., P.P., M.H.)
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Johanna P. Laakkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
| | - Suvi Linna-Kuosmanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
- Now with MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, and Broad Institute of MIT and Harvard, Cambridge, MA (S.L.-K.)
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (P.R.M., V.T.B., K.O., T.O., H.H.P., S.Y.-H., J.P.L., S.L.-K., M.U.K.)
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22
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Zhu S, Choudhury NR, Rooney S, Pham NT, Koszela J, Kelly D, Spanos C, Rappsilber J, Auer M, Michlewski G. RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels. Nucleic Acids Res 2021; 49:6456-6473. [PMID: 34107032 PMCID: PMC8216281 DOI: 10.1093/nar/gkab484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
RNA-protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as 'incurable'. Here, we developed a fluorescent on-bead screening platform, RNA Pull-Down COnfocal NAnoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7's primary target is an mRNA of α-synuclein, which contributes to the aetiology of Parkinson's disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-synuclein. This opens up new therapeutic avenues towards treatment of Parkinson's disease as well as provides a novel methodology to search for modulators of RNA-protein interaction.
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Affiliation(s)
- Siran Zhu
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Nila Roy Choudhury
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Saul Rooney
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Nhan T Pham
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Joanna Koszela
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - David Kelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Manfred Auer
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Gracjan Michlewski
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, P.R. China
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23
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Overview of Evidence-Based Chemotherapy for Oral Cancer: Focus on Drug Resistance Related to the Epithelial-Mesenchymal Transition. Biomolecules 2021; 11:biom11060893. [PMID: 34208465 PMCID: PMC8234904 DOI: 10.3390/biom11060893] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing incidence of resistance to chemotherapeutic agents has become a major issue in the treatment of oral cancer (OC). Epithelial-mesenchymal transition (EMT) has attracted a great deal of attention in recent years with regard to its relation to the mechanism of chemotherapy drug resistance. EMT-activating transcription factors (EMT-ATFs), such as Snail, TWIST, and ZEB, can activate several different molecular pathways, e.g., PI3K/AKT, NF-κB, and TGF-β. In contrast, the activated oncological signal pathways provide reciprocal feedback that affects the expression of EMT-ATFs, resulting in a peritumoral extracellular environment conducive to cancer cell survival and evasion of the immune system, leading to resistance to multiple chemotherapeutic agents. We present an overview of evidence-based chemotherapy for OC treatment based on the National Comprehensive Cancer Network (NCCN) Chemotherapy Order Templates. We focus on the molecular pathways involved in drug resistance related to the EMT and highlight the signal pathways and transcription factors that may be important for EMT-regulated drug resistance. Rapid progress in antitumor regimens, together with the application of powerful techniques such as high-throughput screening and microRNA technology, will facilitate the development of therapeutic strategies to augment chemotherapy.
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24
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Garcia J, Delany AM. MicroRNAs regulating TGFβ and BMP signaling in the osteoblast lineage. Bone 2021; 143:115791. [PMID: 33285257 PMCID: PMC7787082 DOI: 10.1016/j.bone.2020.115791] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/21/2022]
Abstract
This review showcases miRNAs contributing to the regulation of bone forming osteoblasts through their effects on the TGFβ and BMP pathways, with a focus on ligands, receptors and SMAD-mediated signaling. The goal of this work is to provide a basis for broadly understanding the contribution of miRNAs to the modulation of TGFβ and BMP signaling in the osteoblast lineage, which may provide a rationale for potential therapeutic strategies. Therefore, the search strategy for this review was restricted to validated miRNA-target interactions within the canonical TGFβ and BMP signaling pathways; miRNA-target interactions based only bioinformatics are not presented. Specifically, this review discusses miRNAs targeting each of the TGFβ isoforms, as well as BMP2 and BMP7. Further, miRNAs targeting the signaling receptors TGFβR1 and TGFβR2, and those targeting the type 1 BMP receptors and BMPR2 are described. Lastly, miRNAs targeting the receptor SMADs, the common SMAD4 and the inhibitory SMAD7 are considered. Of these miRNAs, the miR-140 family plays a prominent role in inhibiting TGFβ signaling, targeting both ligand and receptor. Similarly, the miR-106 isoforms target both BMP2 and SMAD5 to inhibit osteoblastic differentiation. Many of the miRNAs targeting TGFβ and BMP signaling components are induced during fracture, mechanical unloading or estrogen deprivation. Localized delivery of miRNA-based therapeutics that modulate the BMP signaling pathway could promote bone formation.
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Affiliation(s)
- John Garcia
- Center for Molecular Oncology, UConn Health, Farmington, CT, 06030, USA
| | - Anne M Delany
- Center for Molecular Oncology, UConn Health, Farmington, CT, 06030, USA.
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25
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Liu T, Zhou H, Lu H, Luo C, Wang Q, Peng Y, Yang W, Xin Y. MiR-4729 regulates TIE1 mRNA m6A modification and angiogenesis in hemorrhoids by targeting METTL14. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:232. [PMID: 33708859 PMCID: PMC7940907 DOI: 10.21037/atm-20-3399] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Hemorrhoids are a frequently-occurring disease of the anorectal system that is often accompanied by vascular hyperplasia and edema. A METTL14-mediated RNA N-6 methyladenosine (m6A) modification can improve mRNA stability and increase its transcriptional and translational activities, closely related to the occurrence of many diseases. Methods Western blot, qPCR, and immunofluorescence staining were used to detect the levels of gene and protein expression. Haematoxylin and eosin staining was used for histopathological examination. RNA immunoprecipitation-PCR and RNA dot blotting were used to detect mRNA m6A modification. Results Obvious signs of angiogenesis (CD31+/vWF+) were identified in the hemorrhoids. High levels of METTL14 expression on vascular endothelial cells (CD31+) suggested that angiogenesis was accompanied by differential modification of m6A RNA. It was subsequently found that the level of miR-4729 expression was significantly decreased in hemorrhoid tissues. The luciferase reporter enzyme assay results suggested that miR-4729 silenced its expression by targeting the 3'UTR of METTL14 mRNA. MiR-4729 overexpression in human umbilical vein endothelial cells (HUVECs) inhibited the proliferation and migration of HUVECs in vitro and vascular structure formation in the outer matrix. MiR-4729 overexpression significantly inhibited endogenous METTL14 expression in HUVECs and reduced the entire m6A RNA modification, especially the level of m6A methylation at the specific site of the 3' UTR of TIE1 mRNA. Moreover, miR-4729 overexpression significantly inhibited the molecular loop of the TIE1/VEGFA signaling pathway in HUVECs. Conclusions Our findings confirmed that the down-regulation of miR-4729 in hemorrhoid vascular endothelial cells was one of the main reasons for vascular proliferation. The overexpression of miR-4729 in vascular endothelial cells decreased the global mRNA methylation and TIE1 mRNA 3'UTR-specific site methylation by silencing METTL14 expression, reducing TIE1 mRNA stability, down-regulating the TIE1/VEGFA signal molecular loop expression, and weakening angiogenesis ability.
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Affiliation(s)
- Te Liu
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Haikun Zhou
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong Lu
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chunsheng Luo
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qingming Wang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yunhua Peng
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Yang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yaojie Xin
- Department of Otolaryngology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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26
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Hong Y, Wang J, Zhang L, Sun W, Xu X, Zhang K. Plasma miR-193a-3p can be a potential biomarker for the diagnosis of diabetic nephropathy. Ann Clin Biochem 2021; 58:141-148. [PMID: 33302703 DOI: 10.1177/0004563220983851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Diabetic nephropathy is one of the most common microvascular complications in patients with diabetes. MicroRNA (miRNA, miR) is closely related to the formation, development and pathophysiology of diabetic nephropathy. We aimed to investigate whether miR-193a-3p could be used as a potential biomarker for the diagnosis of diabetic nephropathy. METHODS Plasma samples were collected from all the participants. TaqMan Low Density Array analysis was employed to obtain the miRNA profiles of plasma samples, and qRT-PCR was used to confirm the result. Receiver operating characteristic curves were employed to evaluate the specificity and sensitivity of miR-193a-3p for predicting diabetic nephropathy. RESULTS The expression of miR-193a-3p and miR-320c was elevated and miR-27a-3p was decreased in diabetic nephropathy patients compared to patients with type 2 diabetes and healthy controls. We found that, in diabetic nephropathy patients, the elevated miR-193a-3p expression had a negative correlation with the level of evaluate glomerular filtration rate, while a positive correlation with the level of proteinuria. We further demonstrated that miR-193a-3p could be employed to distinguish patients with diabetic nephropathy. The Kaplan-Meier analysis showed that the high expression of miR-193a-3p significantly shortened the dialysis-free survival of diabetic nephropathy patients. CONCLUSION In conclusion, miR-193a-3p is involved in diabetic nephropathy pathogenesis and may serve as a potentially novel diagnostic biomarker for diabetic nephropathy.
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Affiliation(s)
- Yan Hong
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Jidong Wang
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Lai Zhang
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Wenjuan Sun
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Xuefang Xu
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Kaiyue Zhang
- Department of Nephrology, the Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
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27
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Abstract
Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no connections between the function of the host genes and the function of their payloads have been reported. Here we investigate whether there is evidence for an association of host gene function or mechanisms with the type of payload. To assess this hypothesis we test whether the miRNA host genes (MIRHGs), snoRNA host genes (SNHGs), and other lncRNA host genes can be distinguished based on sequence and/or structure features unrelated to their payload. A positive answer would imply a functional and mechanistic correlation between host genes and their payload, provided the classification does not depend on the presence and type of the payload. A negative answer would indicate that to the extent that secondary functions are acquired, they are not strongly constrained by the prior, primary function of the payload. We find that the three classes can be distinguished reliably when the classifier is allowed to extract features from the payloads. They become virtually indistinguishable, however, as soon as only sequence and structure of parts of the host gene distal from the snoRNAs or miRNA payload is used for classification. This indicates that the functions of MIRHGs and SNHGs are largely independent of the functions of their payloads. Furthermore, there is no evidence that the MIRHGs and SNHGs form coherent classes of long non-coding RNAs distinguished by features other than their payloads.
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28
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Wang MQ, Zhou CH, Cong S, Han DX, Wang CJ, Tian Y, Zhang JB, Jiang H, Yuan B. Lipopolysaccharide inhibits triglyceride synthesis in dairy cow mammary epithelial cells by upregulating miR-27a-3p, which targets the PPARG gene. J Dairy Sci 2020; 104:989-1001. [PMID: 33162072 DOI: 10.3168/jds.2020-18270] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
The fat content of milk determines the quality of milk, and triglycerides are the major components of milk fat. Milk fat synthesis is regulated by many factors. Lipopolysaccharide (LPS) has been shown to inhibit milk fat synthesis in bovine mammary epithelial cells, but research on the underlying mechanisms has been limited. MicroRNA (miRNA) are involved in many physiological processes, but there have been few studies on their regulation in milk fat synthesis. In this study, we aimed to investigate whether LPS upregulates miR-27a-3p, which targets PPARG, thereby inhibiting the synthesis of triglycerides in a dairy cow mammary epithelial cell line (MAC-T). After LPS stimulation of MAC-T cells, PPARG gene expression and milk fat synthesis were inhibited. TargetScan software was used to predict miRNA targeting PPARG, and miR-27a-3p was selected as a candidate. A dual luciferase reporter assay further confirmed the targeting connection between miR-27a-3p and the PPARG gene. To investigate the functions of miR-27a-3p, miR-27a-3p mimic and inhibitors were transfected into MAC-T cells. The mRNA and protein levels of PPAR-γ were negatively correlated with the expression of miR-27a-3p. Lipid droplet accumulation and triglyceride synthesis were also negatively correlated with miR-27a-3p expression. Inhibition of miR-27a-3p partially reversed the LPS-induced decreases in PPARG expression and milk fat synthesis. In summary, our results reveal that LPS can inhibit MAC-T cell milk fat synthesis by upregulating miR-27a-3p, which targets the PPARG gene.
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Affiliation(s)
- Ming-Qi Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Chang-Hai Zhou
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Shuai Cong
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Dong-Xu Han
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Chang-Jiang Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Yu Tian
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Jia-Bao Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China
| | - Hao Jiang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China.
| | - Bao Yuan
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun 130062, Jilin, P.R. China.
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29
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McLaurin DM, Logan MK, Lett KE, Hebert MD. Molecular determinants that govern scaRNA processing by Drosha/DGCR8. Biol Open 2020; 9:bio054619. [PMID: 33037012 PMCID: PMC7648615 DOI: 10.1242/bio.054619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
The Cajal body (CB) is a subnuclear domain that participates in the biogenesis of many different types of ribonucleoproteins (RNPs), including small nuclear RNPs (snRNPs), small Cajal body-specific RNPs (scaRNPs) and telomerase. Most scaRNAs, the RNA component of scaRNPs, accumulate in CBs. However, there are three scaRNAs (scaRNA 2, 9, and 17) that are known to be processed into small, nucleolar-enriched fragments. Evidence suggests that these fragments are packaged into a new class of RNPs, called regulatory RNPs (regRNPs), and may modify small nucleolar RNP (snoRNP) activity, thus playing a role in rRNA modification. However, the mechanism by which these fragments are produced is unknown. Previous work has reported the involvement of Drosha and DGCR8 in the cleavage of primary-scaRNA9. Here, we expand on that knowledge by identifying sequence elements necessary for the efficient production of these RNA fragments and demonstrate that primary scaRNA 2 and 17 are also processed by the Drosha-DGCR8 complex. Collectively, our work establishes new factors in the scaRNP biogenesis pathway and adds to the ever-expanding list of noncanonical functions for the microprocessor complex.
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Affiliation(s)
- Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Katheryn E Lett
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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30
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Medley JC, Panzade G, Zinovyeva AY. microRNA strand selection: Unwinding the rules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1627. [PMID: 32954644 PMCID: PMC8047885 DOI: 10.1002/wrna.1627] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
microRNAs (miRNAs) play a central role in the regulation of gene expression by targeting specific mRNAs for degradation or translational repression. Each miRNA is post‐transcriptionally processed into a duplex comprising two strands. One of the two miRNA strands is selectively loaded into an Argonaute protein to form the miRNA‐Induced Silencing Complex (miRISC) in a process referred to as miRNA strand selection. The other strand is ejected from the complex and is subject to degradation. The target gene specificity of miRISC is determined by sequence complementarity between the Argonaute‐loaded miRNA strand and target mRNA. Each strand of the miRNA duplex has the capacity to be loaded into miRISC and possesses a unique seed sequence. Therefore, miRNA strand selection plays a defining role in dictating the specificity of miRISC toward its targets and provides a mechanism to alter gene expression in a switch‐like fashion. Aberrant strand selection can lead to altered gene regulation by miRISC and is observed in several human diseases including cancer. Previous and emerging data shape the rules governing miRNA strand selection and shed light on how these rules can be circumvented in various physiological and pathological contexts. This article is categorized under:RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
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Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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31
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Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application. Int J Mol Sci 2020; 21:ijms21186827. [PMID: 32957662 PMCID: PMC7555669 DOI: 10.3390/ijms21186827] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy recently became a very promising diagnostic method that has several advantages over conventional invasive methods. Liquid biopsy may serve as a source of several important biomarkers including cell-free nucleic acids (cf-NAs). Cf-DNA is widely used in prenatal testing in order to characterize fetal genetic disorders. Analysis of cf-DNA may provide information about the mutation profile of tumor cells, while cell-free non-coding RNAs are promising biomarker candidates in the diagnosis and prognosis of cancer. Many of these markers have the potential to help clinicians in therapy selection and in the follow-up of patients. Thus, cf-NA-based diagnostics represent a new path in personalized medicine. Although several reviews are available in the field, most of them focus on a limited number of cf-NA types. In this review, we give an overview about all known cf-NAs including cf-DNA, cf-mtDNA and cell-free non-coding RNA (miRNA, lncRNA, circRNA, piRNA, YRNA, and vtRNA) by discussing their biogenesis, biological function and potential as biomarker candidates in liquid biopsy. We also outline possible future directions in the field.
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32
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Song C, Zhou H, Lu H, Luo C, Wang C, Wang Q, Peng Y, Xin Y, Liu T, Yang W. Aberrant expression for microRNA is potential crucial factors of haemorrhoid. Hereditas 2020; 157:25. [PMID: 32620169 PMCID: PMC7334851 DOI: 10.1186/s41065-020-00139-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Haemorrhoids occur commonly and frequently in the human digestive system. There are diverse causes of haemorrhoids and their in-depth pathogenesis is still currently unclear. METHODS In this study, we explored haemorrhoids from an epigenetics perspective by employing RNA-Seq for comprehensive and in-depth analysis of the differences in microRNA (miRNA) transcripts between haemorrhoidal tissue and normal tissue in 48 patients with Grade II and above haemorrhoids. RESULTS The results showed that 9 miRNAs were significantly upregulated (ratio > 3.5 and P-value < 0.01) and 16 miRNAs were significantly downregulated (ratio > 0.6 and P-value < 0.01) in haemorrhoid tissue. Subsequently, target gene prediction results showed that there were 184 potential target genes of significantly upregulated miRNAs (common to both TargetScan7.1 and MirdbV5 databases) and there were 372 potential target genes of significantly downregulated miRNAs. Gene ontology analysis results showed that the target genes of differentially expressed miRNAs in haemorrhoids are involved in regulating "cell composition" and "protein binding". Lastly, KEGG search found that the differentially expressed miRNAs that are associated with the occurrence of haemorrhoids mainly regulate the activity of endocytosis and the synaptic vesicle cycle. CONCLUSIONS In summary, the results of high-throughput RNA-Seq screening suggested that the occurrence of haemorrhoids may be intimately associated with aberrant miRNA transcription, resulting in aberrant target gene expression and an imbalance in certain signal transduction pathways.
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Affiliation(s)
- Chengkun Song
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Haikun Zhou
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Hong Lu
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Chunsheng Luo
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Chen Wang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Qingming Wang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Yunhua Peng
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China
| | - Yaojie Xin
- Department of Otolaryngology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, P.R. China. .,Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Wei Yang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, P.R. China.
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33
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Boxberger N, Hecker M, Zettl UK. Dysregulation of Inflammasome Priming and Activation by MicroRNAs in Human Immune-Mediated Diseases. THE JOURNAL OF IMMUNOLOGY 2019; 202:2177-2187. [PMID: 30962309 DOI: 10.4049/jimmunol.1801416] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022]
Abstract
Inflammasomes are protein complexes that respond to a wide range of pathogens and cellular damage signals. Their activation prompts the caspase-1-mediated cleavage of the proinflammatory cytokines IL-1β and IL-18. Inflammasome dysregulation has been demonstrated to play a role in a range of diseases involving the adaptive immune system like multiple sclerosis, rheumatic diseases, and type 1 diabetes. Priming and activation of inflammasomes can be modulated by microRNAs (miRNAs), small noncoding RNAs that regulate gene expression posttranscriptionally. miRNAs, such as miR-223-3p, have been demonstrated to directly target the inflammasome components NLRP3, caspase-1, and caspase-8. Other miRNAs like miR-155-5p modulate TLR-, IL-1R-, TNFR-, and IFNAR-mediated signaling pathways upstream of the inflammasomes. In this study, we discuss how a more detailed elucidation of miRNA-driven inflammasome regulation helps in understanding the molecular processes underlying immune-mediated human diseases, holds potential for the identification of biomarkers and may offer novel targets for the development of future therapeutics.
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Affiliation(s)
- Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and
| | - Michael Hecker
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and.,Steinbeis Transfer Center for Proteome Analysis, 18057 Rostock, Germany
| | - Uwe K Zettl
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and
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Loo TH, Ye X, Chai RJ, Ito M, Bonne G, Ferguson-Smith AC, Stewart CL. The mammalian LINC complex component SUN1 regulates muscle regeneration by modulating drosha activity. eLife 2019; 8:49485. [PMID: 31686651 PMCID: PMC6853637 DOI: 10.7554/elife.49485] [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: 06/19/2019] [Accepted: 10/27/2019] [Indexed: 01/13/2023] Open
Abstract
Here we show that a major muscle specific isoform of the murine LINC complex protein SUN1 is required for efficient muscle regeneration. The nucleoplasmic domain of the isoform specifically binds to and inhibits Drosha, a key component of the microprocessor complex required for miRNA synthesis. Comparison of the miRNA profiles between wildtype and SUN1 null myotubes identified a cluster of miRNAs encoded by a non-translated retrotransposon-like one antisense (Rtl1as) transcript that are decreased in the WT myoblasts due to SUN1 inhibition of Drosha. One of these miRNAs miR-127 inhibits the translation of the Rtl1 sense transcript, that encodes the retrotransposon-like one protein (RTL1), which is also required for muscle regeneration and is expressed in regenerating/dystrophic muscle. The LINC complex may therefore regulate gene expression during muscle regeneration by controlling miRNA processing. This provides new insights into the molecular pathology underlying muscular dystrophies and how the LINC complex may regulate mechanosignaling.
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Affiliation(s)
- Tsui Han Loo
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Xiaoqian Ye
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Ruth Jinfen Chai
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Mitsuteru Ito
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gisèle Bonne
- Center of Research in Myology, Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS 974, CNRS FRE 3617, Paris, France
| | | | - Colin L Stewart
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
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35
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Abstract
‘Dormancy’, in the context of carcinogenesis, is a biological phenomenon of decreased cancer cell proliferation and metabolism. In view of their ability to remain quiescent, cancer cells are able to avoid cell death induced by chemotherapeutic agents, and thereby give rise to tumor relapse at a later stage. Being a dynamic event, the dormant state is controlled by several epigenetic mechanisms, including the action of microRNAs. The present review highlights microRNAs that have been shown to be dysregulated in dormant cancer cells among different tumor types. MicroRNAs accomplish their control of cancer cell quiescence by targeting cell cycle regulators and signaling pathways involved in cell growth maintenance, including the AKT/phosphoinositide 3-kinase (PI3K) pathway. MicroRNAs, as components of intercellular vesicles, enable interactions to occur between cancer cells and cells of the microenvironment, resulting in the cancer cells either acquiring the quiescent state or, oppositely, stimulating them to proliferate. Taken together, the evidence obtained to date has collectively confirmed the involvement of microRNAsin cancer cell dormancy. Modulation of the various processes may enable optimization of the treatment of metastatic tumors.
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Affiliation(s)
- Tatiana G Ruksha
- Department of Pathological Physiology, Krasnoyarsk State Medical University, P. Zeleznyaka str., 1, Krasnoyarsk, 660022 Russia
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36
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Simmonds RE. Transient up-regulation of miR-155-3p by lipopolysaccharide in primary human monocyte-derived macrophages results in RISC incorporation but does not alter TNF expression. Wellcome Open Res 2019; 4:43. [PMID: 31641696 PMCID: PMC6790912 DOI: 10.12688/wellcomeopenres.15065.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The innate immune response is a tightly regulated process that reacts rapidly in response to pathogen-associated molecular patterns (PAMPs) such as lipopolysaccharide (LPS). Evidence is accumulating that microRNAs contribute to this, although few studies have examined the early events that constitute the “primary” response. Methods: LPS-dependent changes to miRNA expression were studied in primary human monocyte-derived macrophages (1°MDMs). An unbiased screen by microarray was validated by qPCR and a method for the absolute quantitation of miRNAs was also developed, utilising 5’ phosphorylated RNA oligonucleotide templates. RNA immunoprecipitation was performed to explore incorporation of miRNAs into the RNA-induced silencing complex (RISC). The effect of miRNA functional inhibition on TNF expression (mRNA and secretion) was investigated. Results: Of the 197 miRNAs expressed in 1°MDMs, only five were induced >1.5-fold. The most strongly induced was miR-155-3p, the partner strand to miR-155-5p, which are both derived from the MIR155HG/BIC gene (pri-miR-155). The abundance of miR-155-3p was induced transiently ~250-fold at 2-4hrs and then returned towards baseline, mirroring pri-miR-155. Other PAMPs, IL-1β, and TNF caused similar responses. IL-10, NF-κB, and JNK inhibition reduced these responses, unlike cytokine-suppressing mycolactone. Absolute quantitation revealed that miRNA abundance varies widely from donor-to-donor, and showed that miR-155-3p abundance is substantially less than miR-155-5p in unstimulated cells. However, at its peak there were 446-1,113 copies/cell, and miR-155-3p was incorporated into the RISC with an efficiency similar to miR-16-5p and miR-155-5p. Inhibition of neither miRNA affected TNF secretion after 2hrs in 1°MDMs, but technical challenges here are noted. Conclusions: Dynamic regulation of miRNAs during the primary response is rare, with the exception of miR-155-3p. Further work is required to establish whether its low abundance, even at the transient peak, is sufficient for biological activity and to determine whether there are specific mechanisms determining its biogenesis from miR-155 precursors
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Affiliation(s)
- Rachel E Simmonds
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.,Cytokine and Signal Transduction Laboratory, Kennedy Institute of Rheumatology, London, W6 8LH, UK
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37
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Argonaute-2 is associated to brown adipose tissue activation. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2393-2402. [DOI: 10.1016/j.bbadis.2019.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
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Pacheco A, Berger R, Freedman R, Law AJ. A VNTR Regulates miR-137 Expression Through Novel Alternative Splicing and Contributes to Risk for Schizophrenia. Sci Rep 2019; 9:11793. [PMID: 31409837 PMCID: PMC6692358 DOI: 10.1038/s41598-019-48141-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022] Open
Abstract
The MIR137HG gene encoding microRNA-137 (miR-137) is genome-wide associated with schizophrenia (SZ), however, the underlying molecular mechanisms remain unknown. Through cloning and sequencing of individual transcripts from fetal and adult human brain tissues we describe novel pri-miR-137 splice variants which exclude the mature miR-137 sequence termed ‘del-miR-137’ that would function to down-regulate miR-137 expression. Sequencing results demonstrate a significant positive association between del-miR-137 transcripts and the length of a proximal variable number tandem repeat (VNTR) element. Additionally, a significantly higher proportion of sequenced transcripts from fetal brain were del-miR-137 transcripts indicating neurodevelopmental splicing regulation. In-silico results predict an independent regulatory function for del-miR-137 transcripts through competitive endogenous RNA function. A case-control haplotype analysis (n = 998) in SZ implicates short VNTR length in risk, with longer lengths imparting a protective effect. Rare high risk haplotypes were also observed indicating multiple risk variants within the region. A second haplotype analysis was performed to evaluate recombination effects excluding the VNTR and results indicate that recombination of the region was found to independently contribute to risk. Evaluation of the evolutionary conservation of the VNTR reveals a human lineage specific expansion. These findings shed further light on the risk architecture of the miR-137 region and provide a novel regulatory mechanism through VNTR length and alternative MIR137HG transcripts which contribute to risk for SZ.
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Affiliation(s)
- Ashley Pacheco
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Ralph Berger
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Robert Freedman
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Amanda J Law
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA. .,University of Colorado, School of Medicine, Department of Medicine, Aurora, CO, 80045, USA. .,University of Colorado, School of Medicine, Department of Cell and Developmental Biology, Aurora, CO, 80045, USA.
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Wang C, Lu H, Luo C, Song C, Wang Q, Peng Y, Xin Y, Liu T, Yang W. miR-412-5p targets Xpo1 to regulate angiogenesis in hemorrhoid tissue. Gene 2019; 705:167-176. [PMID: 31026569 DOI: 10.1016/j.gene.2019.04.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/28/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
Hemorrhoid is a common and recurrent proctological disease, which is often accompanied by angiogenesis and edema. MicroRNAs in the DLK1-DIO3 imprinted clusters are involved in the development and pathogenesis of mammalian hemorrhoids. Results of the present study indicated multiple, differential expression of DLK1-DIO3 imprinted cluster microRNA between hemorrhoid and normal tissues, where miR-412-5p expression in hemorrhoid tissue was significantly decreased. Fluorescein reporter assays showed that miR-412-5p silenced Xpo1 mRNA expression by targeting its 3'-UTR. Overexpression of miR-412-5p in human umbilical vein endothelial cells (HUVECs) indicated that proliferation, migration and formation of vascular structures in HUVECs were inhibited in vitro. In addition, overexpression of miR-412-5p significantly inhibited Xpo1 expression and promoted upregulation of the p53 protein and its retention in the nucleus. Simultaneously, expression of p66SHC and p16 proteins was activated. In summary, downregulation of endogenous miR-412-5p expression in hemorrhoid vascular endothelial cells leads to high expression of the target gene Xpo1 and translocation of the p53 protein out of the nucleus, rendering it unable to activate p66SHC and p16. This ultimately weakens regulation of the vascular endothelial cell cycle, thereby accelerating the division of hemorrhoid vascular endothelial cells, leading to angiogenesis.
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Affiliation(s)
- Chen Wang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hong Lu
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chunsheng Luo
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chengkun Song
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qingming Wang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yunhua Peng
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yaojie Xin
- Department of Otolaryngology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200031, China; Department of Pathology, Yale University School of Medicine, CT 06520, USA.
| | - Wei Yang
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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40
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Just W. Prague Special Issue. FEBS Lett 2019; 592:1907-1908. [PMID: 29939401 DOI: 10.1002/1873-3468.13110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Over-expression of Hsp83 in grossly depleted hsrω lncRNA background causes synthetic lethality and l(2)gl phenocopy in Drosophila. J Biosci 2019. [DOI: 10.1007/s12038-019-9852-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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Simmonds RE. Transient up-regulation of miR-155-3p by lipopolysaccharide in primary human monocyte-derived macrophages results in RISC incorporation but does not alter TNF expression. Wellcome Open Res 2019; 4:43. [DOI: 10.12688/wellcomeopenres.15065.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
Abstract
Background: The innate immune response is a tightly regulated process that reacts rapidly in response to pathogen-associated molecular patterns (PAMPs) such as lipopolysaccharide (LPS). Evidence is accumulating that microRNAs contribute to this, although few studies have examined the early events that constitute the “primary” response. Methods: LPS-dependent changes to miRNA expression were studied in primary human monocyte-derived macrophages (1°MDMs). An unbiased screen by microarray was validated by qPCR and a method for the absolute quantitation of miRNAs was also developed, utilising 5’ phosphorylated RNA oligonucleotide templates. RNA immunoprecipitation was performed to explore incorporation of miRNAs into the RNA-induced silencing complex (RISC). The effect of miRNA functional inhibition on TNF expression (mRNA and secretion) was investigated. Results: Of the 197 miRNAs expressed in 1°MDMs, only five were induced >1.5-fold. The most strongly induced was miR-155-3p, the partner strand to miR-155-5p, which are both derived from the BIC gene (B cell integration cluster, MIR155HG). The abundance of miR-155-3p was induced transiently ~250-fold at 2-4hrs and then returned towards baseline, mirroring the BIC mRNA. Other PAMPs, IL-1β, and TNF caused similar responses. IL-10, NF-κB, and JNK inhibition suppressed these responses, unlike cytokine-suppressing mycolactone. Absolute quantitation showed that miRNA abundance varies widely from donor-to-donor, and showed that miR-155-3p abundance is substantially less than miR-155-5p in unstimulated cells. However, at its peak there were 446-1,113 copies/cell, and miR-155-3p was incorporated into the RISC with an efficiency similar to miR-16-5p and miR-155-5p. Inhibition of neither miRNA affected TNF expression in 1°MDMs, but technical challenges here are noted. Conclusions: Dynamic regulation of miRNAs during the primary response is rare, with the exception of miR-155-3p, which transiently achieves levels that might have a biological effect. Further work on this candidate would need to overcome the technical challenges of the broad-ranging effects of liposomes on 1°MDMs.
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43
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Weidle UH, Birzele F, Nopora A. MicroRNAs as Potential Targets for Therapeutic Intervention With Metastasis of Non-small Cell Lung Cancer. Cancer Genomics Proteomics 2019; 16:99-119. [PMID: 30850362 PMCID: PMC6489690 DOI: 10.21873/cgp.20116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 02/08/2023] Open
Abstract
The death toll of non-small cell lung cancer (NSCLC) patients is primarily due to metastases, which are poorly amenable to therapeutic intervention. In this review we focus on miRs associated with metastasis of NSCLC as potential new targets for anti-metastatic therapy. We discuss miRs validated as therapeutic targets by in vitro data, identification of target(s) and pathway(s) and in vivo efficacy data in at least one clinically-relevant metastasis-related model. A few of the discussed miRs correlate with the clinical status of NSCLC patients. Using miRs as therapeutic agents has the advantage that targeting a single miR can potentially interfere with several metastatic pathways. Depending on their mode of action, the corresponding miRs can be up- or down-regulated compared to normal matching tissues. Here, we describe therapeutic approaches for reconstitution therapy and miR inhibition, general principles of anti-metastatic therapy as well as current technical pitfalls.
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Affiliation(s)
- Ulrich H Weidle
- Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Fabian Birzele
- Roche Innovation Center Basel, F. Hofman La Roche, Basel, Switzerland
| | - Adam Nopora
- Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
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44
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Shcherbata HR. miRNA functions in stem cells and their niches: lessons from the Drosophila ovary. CURRENT OPINION IN INSECT SCIENCE 2019; 31:29-36. [PMID: 31109670 DOI: 10.1016/j.cois.2018.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 06/09/2023]
Abstract
From the very beginning of the miRNA era, Drosophila has served as an excellent model for explanation of miRNA biogenesis. Now Drosophila continues to be used in numerous studies aiming to decipher biological roles of individual miRNAs in a living organism. MiRNAs have emerged as an important regulatory class that adjusts gene expression in response to stress; therefore, it is particularly important to elucidate miRNA-based regulatory networks that appear in response to fluctuations in intrinsic and extrinsic environments. This review explores the major advances in understanding condition-dependent roles of miRNAs in adult stem cell biology using the Drosophila ovarian germline stem cell niche community as a model system.
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Affiliation(s)
- Halyna R Shcherbata
- Max Planck Research Group of Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany; Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
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45
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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46
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Urbanek-Trzeciak MO, Jaworska E, Krzyzosiak WJ. miRNAmotif-A Tool for the Prediction of Pre-miRNA⁻Protein Interactions. Int J Mol Sci 2018; 19:ijms19124075. [PMID: 30562930 PMCID: PMC6321451 DOI: 10.3390/ijms19124075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding post-transcriptional gene regulators. In mammalian cells, mature miRNAs are produced from primary precursors (pri-miRNAs) using canonical protein machinery, which includes Drosha/DGCR8 and Dicer, or the non-canonical mirtron pathway. In plant cells, mature miRNAs are excised from pri-miRNAs by the DICER-LIKE1 (DCL1) protein complex. The involvement of multiple regulatory proteins that bind directly to distinct miRNA precursors in a sequence- or structure-dependent manner adds to the complexity of the miRNA maturation process. Here, we present a web server that enables searches for miRNA precursors that can be recognized by diverse RNA-binding proteins based on known sequence motifs to facilitate the identification of other proteins involved in miRNA biogenesis. The database used by the web server contains known human, murine, and Arabidopsis thaliana pre-miRNAs. The web server can also be used to predict new RNA-binding protein motifs based on a list of user-provided sequences. We show examples of miRNAmotif applications, presenting precursors that contain motifs recognized by Lin28, MCPIP1, and DGCR8 and predicting motifs within pre-miRNA precursors that are recognized by two DEAD-box helicases—DDX1 and DDX17. miRNAmotif is released as an open-source software under the MIT License. The code is available at GitHub (www.github.com/martynaut/mirnamotif). The webserver is freely available at http://mirnamotif.ibch.poznan.pl.
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Affiliation(s)
- Martyna O Urbanek-Trzeciak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Edyta Jaworska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Wlodzimierz J Krzyzosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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47
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Role of MicroRNAs in Renal Parenchymal Diseases-A New Dimension. Int J Mol Sci 2018; 19:ijms19061797. [PMID: 29914215 PMCID: PMC6032378 DOI: 10.3390/ijms19061797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 11/18/2022] Open
Abstract
Since their discovery in 1993, numerous microRNAs (miRNAs) have been identified in humans and other eukaryotic organisms, and their role as key regulators of gene expression is still being elucidated. It is now known that miRNAs not only play a central role in the processes that ensure normal development and physiology, but they are often dysregulated in various diseases. In this review, we present an overview of the role of miRNAs in normal renal development and physiology, in maladaptive renal repair after injury, and in the pathogenesis of renal parenchymal diseases. In addition, we describe methods used for their detection and their potential as therapeutic targets. Continued research on renal miRNAs will undoubtedly improve our understanding of diseases affecting the kidneys and may also lead to new therapeutic agents.
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