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Koralewska N, Corradi E, Milewski MC, Masante L, Szczepanska A, Kierzek R, Figlerowicz M, Baudet ML, Kurzynska-Kokorniak A. Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo. Nucleic Acids Res 2024; 52:5804-5824. [PMID: 38676942 PMCID: PMC11162791 DOI: 10.1093/nar/gkae284] [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: 08/04/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors' sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We here develop a novel strategy based on short 2'-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA families in vitro and in vivo. Leveraging the highly conserved Xenopus miR-181a family as proof-of-concept, we demonstrate that 2'-OMe/LNA-ASOs targeting the apical region of pre-miRNAs achieve precursor-selective inhibition of mature miRNA-5p production. Furthermore, we extend the applicability of our approach to the human miR-16 family, illustrating its universality in targeting precursors generating identical miRNAs. Overall, our strategy enables efficient manipulation of miRNA expression, offering a powerful tool to dissect the functions of identical or highly similar miRNAs derived from different precursors within miRNA families.
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Affiliation(s)
- Natalia Koralewska
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Eloina Corradi
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Linda Masante
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Agnieszka Szczepanska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
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2
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Rumpel N, Riechert G, Schumann J. miRNA-Mediated Fine Regulation of TLR-Induced M1 Polarization. Cells 2024; 13:701. [PMID: 38667316 PMCID: PMC11049089 DOI: 10.3390/cells13080701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Macrophage polarization to the M1 spectrum is induced by bacterial cell wall components through stimulation of Toll-like family (TLR) receptors. By orchestrating the expression of relevant mediators of the TLR cascade, as well as associated pathways and feedback loops, macrophage polarization is coordinated to ensure an appropriate immune response. This is central to the successful control of pathogens and the maintenance of health. Macrophage polarization is known to be modulated at both the transcriptional and post-transcriptional levels. In recent years, the miRNA-based post-transcriptional regulation of M1 polarization has received increasing attention from the scientific community. Comparative studies have shown that TLR stimulation alters the miRNA profile of macrophages and that macrophages from the M1 or the M2 spectrum differ in terms of miRNAs expressed. Simultaneously, miRNAs are considered critical post-transcriptional regulators of macrophage polarization. In particular, miRNAs are thought to play a regulatory role in the switch between the early proinflammatory response and the resolution phase. In this review, we will discuss the current state of knowledge on the complex interaction of transcriptional and post-transcriptional regulatory mechanisms that ultimately determine the functionality of macrophages.
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Affiliation(s)
| | | | - Julia Schumann
- University Clinic and Outpatient Clinic for Anesthesiology and Operative Intensive Care, University Medicine Halle (Saale), Franzosenweg 1a, 06112 Halle (Saale), Germany
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3
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Bakhsh T, Alhazmi S, Farsi A, Yusuf AS, Alharthi A, Qahl SH, Alghamdi MA, Alzahrani FA, Elgaddar OH, Ibrahim MA, Bahieldin A. Molecular detection of exosomal miRNAs of blood serum for prognosis of colorectal cancer. Sci Rep 2024; 14:8902. [PMID: 38632250 PMCID: PMC11024162 DOI: 10.1038/s41598-024-58536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer affecting people. The discovery of new, non-invasive, specific, and sensitive molecular biomarkers for CRC may assist in the diagnosis and support therapeutic decision making. Exosomal miRNAs have been demonstrated in carcinogenesis and CRC development, which makes these miRNAs strong biomarkers for CRC. Deep sequencing allows a robust high-throughput informatics investigation of the types and abundance of exosomal miRNAs. Thus, exosomal miRNAs can be efficiently examined as diagnostic biomarkers for disease screening. In the present study, a number of 660 mature miRNAs were detected in patients diagnosed with CRC at different stages. Of which, 29 miRNAs were differentially expressed in CRC patients compared with healthy controls. Twenty-nine miRNAs with high abundance levels were further selected for subsequent analysis. These miRNAs were either highly up-regulated (e.g., let-7a-5p, let-7c-5p, let-7f-5p, let-7d-3p, miR-423-5p, miR-3184-5p, and miR-584) or down-regulated (e.g., miR-30a-5p, miR-99-5p, miR-150-5p, miR-26-5p and miR-204-5p). These miRNAs influence critical genes in CRC, leading to either tumor growth or suppression. Most of the reported diagnostic exosomal miRNAs were shown to be circulating in blood serum. The latter is a novel miRNA that was found in exosomal profile of blood serum. Some of the predicted target genes of highly expressed miRNAs participate in several cancer pathways, including CRC pathway. These target genes include tumor suppressor genes, oncogenes and DNA repair genes. Main focus was given to multiple critical signaling cross-talking pathways including transforming growth factor β (TGFβ) signaling pathways that are directly linked to CRC. In conclusion, we recommend further analysis in order to experimentally confirm exact relationships between selected differentially expressed miRNAs and their predicted target genes and downstream functional consequences.
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Affiliation(s)
- Tahani Bakhsh
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
| | - Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, 80200, Jedaah, Saudi Arabia
- Neuroscience and Geroscience Research Unit, King Fahad Medical Research Centre, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
- Central lab of biological Sciences, Faculty of Sciences, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
| | - Ali Farsi
- Department of Surgery, Faculty of Medicine, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulaziz S Yusuf
- Department of Biochemistry, Faculty of science, Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Medical Laboratory Sciences Department, Fakeeh College for Medical Sciences, 21461, Jeddah, Saudi Arabia
| | - Amani Alharthi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, 11952, Majmaah, Saudi Arabia
| | - Safa H Qahl
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Maha Ali Alghamdi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Faisal A Alzahrani
- Department of Biochemistry, Faculty of science, Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Ola H Elgaddar
- Department of Chemical Pathology, Alexandria University, Alexandria, Egypt
| | - Mohanad A Ibrahim
- Data Science Program, King Abdullah International Medical Research Center, 11481, Riyadh, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.
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4
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Harris SE, Alexis MS, Giri G, Cavazos FF, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577729. [PMID: 38352439 PMCID: PMC10862761 DOI: 10.1101/2024.01.29.577729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
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Affiliation(s)
- Sarah E. Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | - Maria S. Alexis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Remix Therapeutics, Cambridge, MA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
| | | | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA
- Center for RNA Biology and Medicine, Riverside, CA
| | - Maria M. Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | | | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
- RNA Discovery Center, University of North Carolina, Chapel Hill, NC
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5
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Parsamanesh N, Poudineh M, Siami H, Butler AE, Almahmeed W, Sahebkar A. RNA interference-based therapies for atherosclerosis: Recent advances and future prospects. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 204:1-43. [PMID: 38458734 DOI: 10.1016/bs.pmbts.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Atherosclerosis represents a pathological state that affects the arterial system of the organism. This chronic, progressive condition is typified by the accumulation of atheroma within arterial walls. Modulation of RNA molecules through RNA-based therapies has expanded the range of therapeutic options available for neurodegenerative diseases, infectious diseases, cancer, and, more recently, cardiovascular disease (CVD). Presently, microRNAs and small interfering RNAs (siRNAs) are the most widely employed therapeutic strategies for targeting RNA molecules, and for regulating gene expression and protein production. Nevertheless, for these agents to be developed into effective medications, various obstacles must be overcome, including inadequate binding affinity, instability, challenges of delivering to the tissues, immunogenicity, and off-target toxicity. In this comprehensive review, we discuss in detail the current state of RNA interference (RNAi)-based therapies.
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Affiliation(s)
- Negin Parsamanesh
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohadeseh Poudineh
- Student Research Committee, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Haleh Siami
- School of Medicine, Islamic Azad University of Medical Science, Tehran, Iran
| | - Alexandra E Butler
- Research Department, Royal College of Surgeons in Ireland, Bahrain, Adliya, Bahrain
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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6
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Rezaee D, Saadatpour F, Akbari N, Zoghi A, Najafi S, Beyranvand P, Zamani-Rarani F, Rashidi MA, Bagheri-Mohammadi S, Bakhtiari M. The role of microRNAs in the pathophysiology of human central nervous system: A focus on neurodegenerative diseases. Ageing Res Rev 2023; 92:102090. [PMID: 37832609 DOI: 10.1016/j.arr.2023.102090] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
microRNAs (miRNAs) are suggested to play substantial roles in regulating the development and various physiologic functions of the central nervous system (CNS). These include neurogenesis, cell fate and differentiation, morphogenesis, formation of dendrites, and targeting non-neural mRNAs. Notably, deregulation of an increasing number of miRNAs is associated with several neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and CNS tumors. They are particularly known to affect the amyloid β (Aβ) cleavage and accumulation, tau protein homeostasis, and expression of alpha-synuclein (α-syn), Parkin, PINK1, and brain-derived neurotrophic factor (BDNF) that play pivotal roles in the pathogenesis of neurodegenerative diseases. These include miR-16, miR-17-5p, miR-20a, miR-106a, miR-106b, miR-15a, miR-15b, miR-103, miR-107, miR-298, miR-328, miR-195, miR-485, and miR-29. In CNS tumors, several miRNAs, including miR-31, miR-16, and miR-21 have been identified to modulate tumorigenesis through impacting tumor invasion and apoptosis. In this review article, we have a look at the recent advances on our knowledge about the role of miRNAs in human brain development and functions, neurodegenerative diseases, and their clinical potentials.
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Affiliation(s)
- Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nayyereh Akbari
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anahita Zoghi
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Parisa Beyranvand
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fahimeh Zamani-Rarani
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Rashidi
- Student Research Committee, Department of Occupational Health and Safety, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Bakhtiari
- Department of Anatomical Sciences, Behbahan Faculty of Medical Sciences, Behbahan, Iran
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7
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Zhang L, Wang J, Cai G, Ma L, Zhao Z, Ma Q, Deng X. Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality. BMC Genomics 2023; 24:632. [PMID: 37872623 PMCID: PMC10594899 DOI: 10.1186/s12864-023-09741-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Tan and Hu sheep are well-known local breeds in China, producing lamb fur with unique ornamental and practical values highly appreciated by consumers worldwide. Fur quality is optimal at one month of age and gradually declines with time. Despite active research on its genetic mechanism using transcriptomic and whole genome bisulfite sequencing analysis, the main effective gene locus has not been found, and its regulatory mechanism is still unclear, which limits the breeding and improvement of fur traits. RESULTS Scapular skin samples from newborn (1-month old) and adult (24-month old) Tan sheep were utilized for small ribonucleic acid (RNA) sequencing Principal Component Analysis (PCA) showed that the newborn and adult groups were completely separated. Differential expression analysis of micro-RNAs (miRNAs) identified 32 up-regulated miRNAs and 48 down-regulated miRNAs in the newborn groups. All up-regulated miRNAs were located in the imprinted. Dlk1-Gtl2 locus on chromosome 18, whereas all down-regulated miRNAs were distributed across the sheep chromosomes, without a clear pattern of positional consistency. Further, by systematically analyzing the target genes and signaling pathways of all 32 up-regulated miRNAs, we found that the PI3K-AKT signaling pathway has the potential to be targeted and regulated by most of the miRNAs in the Dlk1-Gtl2 region. In addition, we also re-analyzed miRNA sequencing data from public databases on Hu lambs (full sibling Hu lambs with high- and low-quality fur characteristics). Again, it was found that most of the up-regulated miRNAs in lambs with high-quality fur were also located in the Dlk1-Gtl2 region, whereas this patter was not present for down-regulated miRNAs. CONCLUSION Sequencing of miRNAs in conjunction with public databases was employed to identify miRNAs within the imprinted Dlk1-Gtl2 region on chromosome 18, suggesting their potential roles as epigenetic regulators of fur traits. Small RNAs located at the Dlk1-Gtl2 locus were identified as having the potential to systematically regulate the PI3K-AKT signaling pathway, thereby indicating the relevance of the Dlk1-Gtl2/PI3K-AKT axis in the context of fur traits. Selection of parental specific expressed imprinted genes in the process of conserving and exploiting lamb fur traits should be emphasized.
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Affiliation(s)
- Letian Zhang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jiankui Wang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Ganxian Cai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China
| | - Zhengwei Zhao
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China
| | - Xuemei Deng
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
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Deka B, Rehman A, Singh KK. miR-6893-3p is a bonafide negative regulator of splicing activator, RNPS1. 3 Biotech 2023; 13:340. [PMID: 37705863 PMCID: PMC10495290 DOI: 10.1007/s13205-023-03761-2] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
RNA-binding protein with serine-rich domain 1, RNPS1, is a global guardian of splicing fidelity and has implications in cervical cancer cell progression. We previously observed elevated RNPS1 expression in cervical cancer cells compared to normal cells. To understand the mechanisms that lead to the dysregulation of RNPS1 expression in cervical cancer cells, we focused on microRNAs. Using an in silico approach, we predicted potential miRNA candidates targeting RNPS1. Among the candidate miRNAs, we found miR-6893-3p as a potential regulator of RNPS1 expression. Interestingly, the expression of miR-6893-3p is downregulated in cervical cancer cells compared to normal cells and its level is negatively correlated with the expression of RNPS1. Further, qPCR, Western blot analysis, and luciferase reporter assay confirmed that miR-6893-3p negatively regulates RNPS1 in HeLa cells. In this regard, overexpression of miR-6893-3p suppresses the endogenous mRNA and protein levels of RNPS1 in HeLa cells. Further investigation revealed that miR-6893-3p mediated regulation of RNPS1 is dependent on the binding of miR-6893-3p to a microRNA response element in the 3'UTR of RNPS1 mRNA. Furthermore, mechanistic analysis showed that targeted negative regulation of RNPS1 by miR-6893-3p occurs via enhanced mRNA degradation. Collectively, our findings establish miR-6893-3p as an important player in the post-transcriptional regulation of RNPS1 in HeLa cells. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03761-2.
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Affiliation(s)
- Bhagyashree Deka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Ayushi Rehman
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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Orbán TI. One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs. Biol Futur 2023:10.1007/s42977-023-00154-7. [PMID: 36847925 DOI: 10.1007/s42977-023-00154-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
With the development of modern molecular genetics, the original "one gene-one enzyme" hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited "RNA world", how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases.
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Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
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10
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Pulik Ł, Mierzejewski B, Sibilska A, Grabowska I, Ciemerych MA, Łęgosz P, Brzóska E. The role of miRNA and lncRNA in heterotopic ossification pathogenesis. Stem Cell Res Ther 2022; 13:523. [PMID: 36522666 PMCID: PMC9753082 DOI: 10.1186/s13287-022-03213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Heterotopic ossification (HO) is the formation of bone in non-osseous tissues, such as skeletal muscles. The HO could have a genetic or a non-genetic (acquired) background, that is, it could be caused by musculoskeletal trauma, such as burns, fractures, joint arthroplasty (traumatic HO), or cerebral or spinal insult (neurogenetic HO). HO formation is caused by the differentiation of stem or progenitor cells induced by local or systemic imbalances. The main factors described so far in HO induction are TGFβ1, BMPs, activin A, oncostatin M, substance P, neurotrophin-3, and WNT. In addition, dysregulation of noncoding RNAs, such as microRNA or long noncoding RNA, homeostasis may play an important role in the development of HO. For example, decreased expression of miRNA-630, which is responsible for the endothelial-mesenchymal transition, was observed in HO patients. The reduced level of miRNA-421 in patients with humeral fracture was shown to be associated with overexpression of BMP2 and a higher rate of HO occurrence. Down-regulation of miRNA-203 increased the expression of runt-related transcription factor 2 (RUNX2), a crucial regulator of osteoblast differentiation. Thus, understanding the various functions of noncoding RNAs can reveal potential targets for the prevention or treatment of HO.
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Affiliation(s)
- Łukasz Pulik
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland.
| | - Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Aleksandra Sibilska
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Paweł Łęgosz
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland
| | - Edyta Brzóska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
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11
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Chaudhry T, Coxon CR, Ross K. Trading places: Peptide and small molecule alternatives to oligonucleotide-based modulation of microRNA expression. Drug Discov Today 2022; 27:103337. [PMID: 35995360 DOI: 10.1016/j.drudis.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
It is well established that microRNA (miRNA) dysregulation is involved in the development and progression of various diseases, especially cancer. Emerging evidence suggests that small molecule and peptide agents can interfere with miRNA disease pathways. Despite this, very little is known about structural features that drive drug-miRNA interactions and subsequent inhibition. In this review, we highlight the advances made in the development of small molecule and peptide inhibitors of miRNA processing. Specifically, we attempt to draw attention to peptide features that may be critical for interaction with the miRNA secondary structure to regulate miRNA expression. We hope that this review will help to establish peptides as exciting miRNA expression modulators and will contribute towards the development of the first miRNA-targeting peptide therapy.
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Affiliation(s)
- Talhat Chaudhry
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK
| | - Christopher R Coxon
- EaStChem School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH14 4AS, UK
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK.
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12
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Erfanparast L, Taghizadieh M, Shekarchi AA. Non-Coding RNAs and Oral Cancer: Small Molecules With Big Functions. Front Oncol 2022; 12:914593. [PMID: 35898889 PMCID: PMC9309727 DOI: 10.3389/fonc.2022.914593] [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: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022] Open
Abstract
Oral cancer remains a major public concern with considerable socioeconomic impact in the world. Despite substantial advancements have been made in treating oral cancer, the five-year survival rate for oral cancer remained undesirable, and the molecular mechanisms underlying OSCC carcinogenesis have not been fully understood. Noncoding RNAs (ncRNAs) include transfer RNAs (tRNAs), as well as small RNAs such as microRNAs, and the long ncRNAs such as HOTAIR are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including cancer cell development. Cell death, such as apoptosis, necrosis, and autophagy, plays a vital role in the progression of cancer. A better understanding of the regulatory relationships between ncRNAs and these various types of cancer cell death is therefore urgently required. The occurrence and development of oral cancer can be controlled by increasing or decreasing the expression of ncRNAs, a method which confers broad prospects for oral cancer treatment. Therefore, it is urgent for us to understand the influence of ncRNAs on the development of different modes of oral tumor death, and to evaluate whether ncRNAs have the potential to be used as biological targets for inducing cell death and recurrence of chemotherapy. The purpose of this review is to describe the impact of ncRNAs on cell apoptosis and autophagy in oral cancer in order to explore potential targets for oral cancer therapy.
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Affiliation(s)
- Leila Erfanparast
- Department of Pediatric Dentistry, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Mohammad Taghizadieh,
| | - Ali Akbar Shekarchi
- Department of Pathology, Tabriz University of Medical Sciences, Tabriz, Iran
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13
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Park EG, Kim WR, Lee YJ, Bae WH, Lee DH, Lee Y, Kim DH, Kim JN, Choi YH, Cha HJ, Kim S, Kim HS. Downregulated pol-miR-140-3p induces the expression of the kinesin family member 5A against Streptococcus parauberis infection in olive flounder. FISH & SHELLFISH IMMUNOLOGY 2022; 126:178-186. [PMID: 35643352 DOI: 10.1016/j.fsi.2022.05.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 04/08/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that participate in various biological and cellular processes by regulating target gene expression. miRNAs are also known to play vital roles in the pathogenesis of various diseases, including infections, as well as the disease progression and defense responses. In this study, we examined the expression levels of pol-miR-140-3p and its target gene, kinesin family member 5A (KIF5A), in association with the Streptococcus parauberis (S. parauberis) infection, a major bacterial pathogen that causes streptococcosis in olive flounder (Paralichthys olivaceus). KIF5A is a heavy chain isoform of kinesin-1, which is known to be brain-specific, and this study is the first examination of KIF5A expression related to the regulation of miRNA in olive flounder (named PoKIF5A). There were significant differences in expression levels between infected and healthy olive flounder as the expression of pol-miR-140-3p in the infected fish was lower than that in the control, while the expression of PoKIF5A was higher in the infected fish than in the healthy controls. These contradictory results suggest that downregulated pol-miR-140-3p induces the expression of PoKIF5A against S. parauberis infection in olive flounder.
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Affiliation(s)
- Eun Gyung Park
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, 49104, Republic of Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, 49104, Republic of Korea
| | - Jeong Nam Kim
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Korean Medicine, Dong-eui University, Busan, 47227, Republic of Korea
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan, 49104, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea; Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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14
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Douvris A, Viñas J, Burns KD. miRNA-486-5p: signaling targets and role in non-malignant disease. Cell Mol Life Sci 2022; 79:376. [PMID: 35731367 PMCID: PMC9217846 DOI: 10.1007/s00018-022-04406-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs, highly conserved between species, that are powerful regulators of gene expression. Aberrant expression of miRNAs alters biological processes and pathways linked to human disease. miR-486-5p is a muscle-enriched miRNA localized to the cytoplasm and nucleus, and is highly abundant in human plasma and enriched in small extracellular vesicles. Studies of malignant and non-malignant diseases, including kidney diseases, have found correlations with circulating miR-486-5p levels, supporting its role as a potential biomarker. Pre-clinical studies of non-malignant diseases have identified miR-486-5p targets that regulate major signaling pathways involved in cellular proliferation, migration, angiogenesis, and apoptosis. Validated miR-486-5p targets include phosphatase and tensin homolog (PTEN) and FoXO1, whose suppression activates phosphatidyl inositol-3-kinase (PI3K)/Akt signaling. Targeting of Smad1/2/4 and IGF-1 by miR-486-5p inhibits transforming growth factor (TGF)-β and insulin-like growth factor-1 (IGF-1) signaling, respectively. Other miR-486-5p targets include matrix metalloproteinase-19 (MMP-19), Sp5, histone acetyltransferase 1 (HAT1), and nuclear factor of activated T cells-5 (NFAT5). In this review, we examine the biogenesis, regulation, validated gene targets and biological effects of miR-486-5p in non-malignant diseases.
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Affiliation(s)
- Adrianna Douvris
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jose Viñas
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada
| | - Kevin D Burns
- Division of Nephrology, Department of Medicine and Kidney Research Centre, The Ottawa Hospital Research Institute, University of Ottawa, 1967 Riverside Dr., Rm. 535, Ottawa, ON, K1H 7W9, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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15
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Raigorodskaya MP, Zhiyanov AP, Averinskaya DA, Tonevitsky EA. Changes in the Expression of miRNA Isoforms and Their Targets in HT-29 Cells after Hypoxic Exposure. Bull Exp Biol Med 2022; 173:123-127. [PMID: 35624351 DOI: 10.1007/s10517-022-05506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/28/2022]
Abstract
Tumor hypoxia is one of the main causes of progression and metastasis of colorectal cancer. Changes in the expression of miRNA responsible for post-translation regulation of gene expression is an important molecular mechanism of cell response to hypoxia. We performed sequencing of miRNA and mRNA of human colorectal adenocarcinoma HT-29 cells treated with two chemical agents mimicking hypoxia: cobalt (II) chloride and oxyquinoline. Bioinformatics analysis revealed differentially expressed miRNA isoforms (hsa-miR-210-3p|0, hsa-miR- 22-3p|0, hsa-let-7a-3p|0, hsa-miR-615-3p|0, and hsa-miR-4521|0) and their targets that changed their expression in both models of hypoxia. Thus, we identified new regulatory mechanisms of cell response to hypoxia.
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Affiliation(s)
- M P Raigorodskaya
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
| | - A P Zhiyanov
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia.
| | - D A Averinskaya
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
| | - E A Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
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16
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The Complex Interaction between P53 and miRNAs Joins New Awareness in Physiological Stress Responses. Cells 2022; 11:cells11101631. [PMID: 35626668 PMCID: PMC9139524 DOI: 10.3390/cells11101631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 12/14/2022] Open
Abstract
This review emphasizes the important role of cross-talk between P53 and microRNAs in physiological stress signaling. P53 responds to stress in a variety of ways ranging from activating survival-promotion pathways to triggering programmed cell death to eliminate damaged cells. In physiological stress generated by any external or internal condition that challenges cell homeostasis, P53 exerts its function as a transcription factor for target genes or by regulating the expression and maturation of a class of small non-coding RNA molecules (miRNAs). The miRNAs control the level of P53 through direct control of P53 or through indirect control of P53 by targeting its regulators (such as MDMs). In turn, P53 controls the expression level of miRNAs targeted by P53 through the regulation of their transcription or biogenesis. This elaborate regulatory scheme emphasizes the relevance of miRNAs in the P53 network and vice versa.
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17
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Abstract
MicroRNAs (miRNAs) are key players in gene regulation that target specific mRNAs for degradation or translational repression. Each miRNA is synthesized as a miRNA duplex comprising two strands (5p and 3p). However, only one of the two strands becomes active and is selectively incorporated into the RNA-induced silencing complex in a process known as miRNA strand selection. Recently, significant progress has been made in understanding the factors and processes involved in strand selection. Here, we explore the selection and functionality of the miRNA star strand (either 5p or 3p), which is generally present in the cell at low levels compared to its partner strand and, historically, has been thought to possess no biological activity. We also highlight the concepts of miRNA arm switching and miRNA isomerism. Finally, we offer insights into the impact of aberrant strand selection on immunity and cancer. Leading us through this journey is miR-155, a well-established regulator of immunity and cancer, and the increasing evidence that its 3p strand plays a role in these arenas. Interestingly, the miR-155-5p/-3p ratio appears to vary dependent on the timing of the immune response, and the 3p strand seems to play a regulatory role upon its partner 5p strand.
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Affiliation(s)
- Owen Dawson
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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18
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Ottaviani L, Juni RP, de Abreu RC, Sansonetti M, Sampaio-Pinto V, Halkein J, Hegenbarth JC, Ring N, Knoops K, Kocken JMM, Jesus C, Ernault AC, El Azzouzi H, Rühle F, Olieslagers S, Fernandes H, Ferreira L, Braga L, Stoll M, Nascimento DS, de Windt LJ, da Costa Martins PA. Intercellular transfer of miR-200c-3p impairs the angiogenic capacity of cardiac endothelial cells. Mol Ther 2022; 30:2257-2273. [PMID: 35278675 DOI: 10.1016/j.ymthe.2022.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022] Open
Abstract
As mediators of intercellular communication, extracellular vesicles containing molecular cargo such as microRNAs, are secreted by cells and taken up by recipient cells to influence their cellular phenotype and function. Here, we report that cardiac stress-induced differential microRNA content, with miR-200c-3p being one of the most enriched, in cardiomyocyte-derived extracellular vesicles mediates functional crosstalk with endothelial cells. Silencing of miR-200c-3p in mice subjected to chronic increased cardiac pressure overload resulted in attenuated hypertrophy, smaller fibrotic areas, higher capillary density and preserved cardiac ejection fraction. Interestingly, we were able to maximal rescue microvascular and cardiac function with very low doses of antagomir, which specifically silences miR-200c-3p expression in the non-myocyte cells. Our results reveal vesicle transfer of miR-200c-3p from cardiomyocytes to cardiac endothelial cells, underlining the importance of cardiac intercellular communication in the pathophysiology of heart failure.
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Affiliation(s)
- L Ottaviani
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - R P Juni
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - R C de Abreu
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands; CNC - Center for Neuroscience and Cell Biology,CIBB - Centre for Innovative Biomedicine and Biotechnology, University Coimbra, Portugal
| | - M Sansonetti
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - V Sampaio-Pinto
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands; i3S - Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; ICBAS - Instituto de Ciências Biomêdicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - J Halkein
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - J C Hegenbarth
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - N Ring
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - K Knoops
- Microscope CORE lab, The Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, The Netherlands
| | - J M M Kocken
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - C Jesus
- CNC - Center for Neuroscience and Cell Biology,CIBB - Centre for Innovative Biomedicine and Biotechnology, University Coimbra, Portugal; Faculty of Medicine University of Coimbra, Coimbra, Portugal
| | - A C Ernault
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - H El Azzouzi
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - F Rühle
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany
| | - S Olieslagers
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - H Fernandes
- CNC - Center for Neuroscience and Cell Biology,CIBB - Centre for Innovative Biomedicine and Biotechnology, University Coimbra, Portugal; Faculty of Medicine University of Coimbra, Coimbra, Portugal
| | - L Ferreira
- CNC - Center for Neuroscience and Cell Biology,CIBB - Centre for Innovative Biomedicine and Biotechnology, University Coimbra, Portugal; Faculty of Medicine University of Coimbra, Coimbra, Portugal
| | - L Braga
- Functional Cell Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - M Stoll
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy; Department of Biochemistry, Genetic Epidemiology and Statistical Genetics, CARIM School for Cardiovascular Diseases, Maastricht Center for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - D S Nascimento
- i3S - Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; ICBAS - Instituto de Ciências Biomêdicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - L J de Windt
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands
| | - P A da Costa Martins
- CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Molecular Genetics, Faculty of Sciences and Engineering, Maastricht University, Maastricht, The Netherlands; Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Porto, Portugal.
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19
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Meng Y, Ma X, Li J, Shao C. Creating and maintaining a high-confidence microRNA repository for crop research: A brief review and re-examination of the current crop microRNA registries. JOURNAL OF PLANT PHYSIOLOGY 2022; 270:153636. [PMID: 35124290 DOI: 10.1016/j.jplph.2022.153636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
miRBase was established as an authoritative microRNA (miRNA) database with a uniform nomenclature system and a searchable web interface. Recent popularization of the next-generation sequencing technology in small RNA cloning led to an explosive growth of the miRNA repository. Although a specific definition system has been proposed for the plant miRNAs, the quality of the plant miRNA registries deposited in miRBase is largely dependent on the submitters. With the growing concerns over the annotation quality, a set of criteria for identification of the high-confidence (HC) miRNAs was recently developed by miRBase. Since miRNAs could serve as a powerful tool for crop genetic improvement and breeding, we present a brief overview of the miRBase-registered crop miRNAs in this study. A total of 54 plants were identified from the 82 Viridiplantae species in the current version of miRBase, and were regarded as the crops. A total of 6316 precursors encoding 7422 mature miRNAs (miRBase release 22.1) were included in our survey. Based on the HC annotation criteria, we performed structure- and sequencing data-based analyses of the confidence of the crop miRNAs. According to the results, we propose suggestions for improvements of the HC annotation system and, moreover, discuss strategies for creating and maintaining an HC miRNA repository of crops. Finally, we hope that this study inspires more efforts devoted to HC miRNA discoveries for crop research.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jie Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou, 313000, China
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20
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MicroRNA let-7 and viral infections: focus on mechanisms of action. Cell Mol Biol Lett 2022; 27:14. [PMID: 35164678 PMCID: PMC8853298 DOI: 10.1186/s11658-022-00317-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
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21
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Gharbi S, Mohammadi Z, Dezaki MS, Dokanehiifard S, Dabiri S, Korsching E. Characterization of the first microRNA in human CDH1 that affects cell cycle and apoptosis and indicates breast cancers progression. J Cell Biochem 2022; 123:657-672. [PMID: 34997630 DOI: 10.1002/jcb.30211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/26/2021] [Accepted: 12/21/2021] [Indexed: 11/12/2022]
Abstract
The E-cadherin protein (Cadherin 1, gene: CDH1), a master regulator of the human epithelial homeostasis, contributes to the epithelial-mesenchymal transition (EMT) which confers cell migratory features to the cells. The EMT is central to many pathophysiological changes in cancer. Therefore, a better understanding of this regulatory scenario is beneficial for therapeutic regiments. The CDH1 gene is approximately 100 kbp long and consists of 16 exons with a relatively large second intron. Since none microRNA (miRNA) has been identified in CDH1 up to now we screened the CDH1 gene for promising miRNA hairpin structures in silico. Out of the 27 hairpin structures we identified, one stable RNA fold with a promising sequence motive was selected for experimental verification. The exogenous validation of the hairpin sequence was performed by transfection of HEK293T cells and the mature miRNA sequences could be verified by quantitative polymerase chain reaction. The endogenous expression of the mature miRNA provisionally named CDH1-i2-miR-1 could be confirmed in two normal (HEK293T, HUVEK) and five cancer cell lines (MCF7, MDA-MB-231, SW480, HT-29, A549). The functional characterization by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed a suppression of HEK293T cell proliferation. A flow cytometry-based approach showed the ability of CDH1-i2-miR-1 to arrest transfected cells on a G2/M state while annexin staining exemplified an apoptotic effect. BAX and PTEN expression levels were affected following the overexpression with the new miRNA. The in vivo expression level was assessed in 35 breast tumor tissues and their paired nonmalignant marginal part. A fourfold downregulation in the tumor specimens compared to their marginal controls could be observed. It can be concluded that the sequence of the hub gene CDH1 harbors at least one miRNA but eventually even more relevant for the pathophysiology of breast cancer.
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Affiliation(s)
- Sedigheh Gharbi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zahra Mohammadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Saedi Dezaki
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sadat Dokanehiifard
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shahriar Dabiri
- Department of Pathology, Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
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22
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Eisa NH, Sudharsan PT, Herrero SM, Herberg SA, Volkman BF, Aguilar-Pérez A, Kondrikov D, Elmansi AM, Reitman C, Shi X, Fulzele S, McGee-Lawrence ME, Isales CM, Hamrick MW, Johnson MH, Chen J, Hill WD. Age-associated changes in microRNAs affect the differentiation potential of human mesenchymal stem cells: Novel role of miR-29b-1-5p expression. Bone 2021; 153:116154. [PMID: 34403754 PMCID: PMC8935397 DOI: 10.1016/j.bone.2021.116154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/01/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022]
Abstract
Age-associated osteoporosis is widely accepted as involving the disruption of osteogenic stem cell populations and their functioning. Maintenance of the local bone marrow (BM) microenvironment is critical for regulating proliferation and differentiation of the multipotent BM mesenchymal stromal/stem cell (BMSC) population with age. The potential role of microRNAs (miRNAs) in modulating BMSCs and the BM microenvironment has recently gained attention. However, miRNAs expressed in rapidly isolated BMSCs that are naïve to the non-physiologic standard tissue culture conditions and reflect a more accurate in vivo profile have not yet been reported. Here we directly isolated CD271 positive (+) BMSCs within hours from human surgical BM aspirates without culturing and performed microarray analysis to identify the age-associated changes in BMSC miRNA expression. One hundred and two miRNAs showed differential expression with aging. Target prediction and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the up-regulated miRNAs targeting genes in bone development pathways were considerably enriched. Among the differentially up-regulated miRNAs the novel passenger strand miR-29b-1-5p was abundantly expressed as a mature functional miRNA with aging. This suggests a critical arm-switching mechanism regulates the expression of the miR-29b-1-5p/3p pair shifting the normally degraded arm, miR-29b-1-5p, to be the dominantly expressed miRNA of the pair in aging. The normal guide strand miR-29b-1-3p is known to act as a pro-osteogenic miRNA. On the other hand, overexpression of the passenger strand miR-29b-1-5p in culture-expanded CD271+ BMSCs significantly down-regulated the expression of stromal cell-derived factor 1 (CXCL12)/ C-X-C chemokine receptor type 4 (SDF-1(CXCL12)/CXCR4) axis and other osteogenic genes including bone morphogenetic protein-2 (BMP-2) and runt-related transcription factor 2 (RUNX2). In contrast, blocking of miR-29b-1-5p function using an antagomir inhibitor up-regulated expression of BMP-2 and RUNX2 genes. Functional assays confirmed that miR-29b-1-5p negatively regulates BMSC osteogenesis in vitro. These novel findings provide evidence of a pathogenic anti-osteogenic role for miR-29b-1-5p and other miRNAs in age-related defects in osteogenesis and bone regeneration.
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Affiliation(s)
- Nada H Eisa
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29403, United States of America; Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Periyasamy T Sudharsan
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, United States of America; Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Sergio Mas Herrero
- Universitat de Barcelona, Unitat Farmacologia, Dpt. Fonaments Clínics, 08036 Barcelona, Spain
| | - Samuel A Herberg
- Departments of Ophthalmology and Visual Sciences, and Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, United States of America
| | - Brian F Volkman
- Biochemistry Department, Medical College of Wisconsin, Milwaukee, WI 53226, United States of America
| | - Alexandra Aguilar-Pérez
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Anatomy and Cell Biology, Indiana University School of Medicine in Indianapolis, IN, United States of America; Department of Cellular and Molecular Biology, School of Medicine, Universidad Central del Caribe, Bayamon 00956, Puerto Rico
| | - Dmitry Kondrikov
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29403, United States of America
| | - Ahmed M Elmansi
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29403, United States of America
| | - Charles Reitman
- Department of Orthopaedics and Physical Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America
| | - Xingming Shi
- Department of Orthopaedics and Physical Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Department of Orthopaedic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Sadanand Fulzele
- Department of Orthopaedic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Meghan E McGee-Lawrence
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Orthopaedic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Carlos M Isales
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Orthopaedic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Division of Endocrinology, Diabetes and Metabolism, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Mark W Hamrick
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Orthopaedic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Maribeth H Johnson
- Department of Population Health Sciences, Division of Biostatistics and Data Science Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - Jie Chen
- Department of Population Health Sciences, Division of Biostatistics and Data Science Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America
| | - William D Hill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29403, United States of America; Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America; Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA 30912, United States of America.
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Kuo MC, Liu SCH, Hsu YF, Wu RM. The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways. J Biomed Sci 2021; 28:78. [PMID: 34794432 PMCID: PMC8603508 DOI: 10.1186/s12929-021-00775-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.
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Affiliation(s)
- Ming-Che Kuo
- Department of Medicine, Section of Neurology, Cancer Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sam Chi-Hao Liu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
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24
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Ross K. MiR equal than others: MicroRNA enhancement for cutaneous wound healing. J Cell Physiol 2021; 236:8050-8059. [PMID: 34160067 DOI: 10.1002/jcp.30485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
Keratinocyte migration is vital in the re-epithelialisation of the skin during wound healing. Multiple factors conspire to impair closure of chronic wounds such as diabetic foot ulcers, venous leg ulcers and pressure wounds. Despite deep mechanistic understanding of microRNA (miRNA) biogenesis and function, the translational potential of these small genetic molecules has not been exploited to promote wound repair. In this review, I focus on miRNAs whose importance for wound healing stems from their impact on epidermal keratinocyte behaviour. These include miR-21-5p, miR-31-5p, miR-132-3p, miR-19b, miR-20a, miR-184, miR-129-5p and miR-335-5p which regulate diverse aspect of keratinocyte biology such as migration, proliferation, differentiation, inflammation and wound closure. A combinatorial approach where two or more miRNA mimics targeting distinct but complementary wound healing processes is proposed as this may enhance wound repair more effectively than any single miRNA mimic alone.
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Affiliation(s)
- Kehinde Ross
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, England, UK
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25
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Soltani N, Staton M, Gwinn KD. Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective. PLoS One 2021; 16:e0244364. [PMID: 33621238 PMCID: PMC7901783 DOI: 10.1371/journal.pone.0244364] [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: 09/10/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa to Cucumber mosaic virus (CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties × +/- CMV × 1 or 4 days after inoculation × 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In 'Red Head' (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.
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Affiliation(s)
- Nourolah Soltani
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kimberly D. Gwinn
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
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26
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Weiss JBW, Wagner AE, Eberherr C, Häberle B, Vokuhl C, von Schweinitz D, Kappler R. High expression of IGF2-derived intronic miR-483 predicts outcome in hepatoblastoma. Cancer Biomark 2021; 28:321-328. [PMID: 32390604 DOI: 10.3233/cbm-191390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The role of microRNAs (miRs) as biomarkers to predict outcome in hepatoblastoma (HB), the most common malignant liver tumor in childhood, has still to be determined. Recently, the so-called four-miR signature has been described to efficiently stratify HB patients according to their prognosis. OBJECTIVE We examined the recently described four-miR signature for its clinical relevance in an independent validation cohort of HB patients and tried to optimize its predictive value by analyzing four additional miRs involved in HB biology. METHODS Expression of eight miR was determined in 29 tumor and 10 normal liver samples by TaqMan assays and association studies and Kaplan-Meier estimators determined their clinical relevance. RESULTS Stratifying HB patients by the four-miR signature showed no difference in patients' outcome, which was also reflected by the lack of association with any clinical risk parameter. Adding miR-23b-5p and miR-23b-3p did also not increase its discriminating power. However, the integration of miR-483-5p and miR-483-3p into the four-miR signature could predict patients with poor outcome that were associated with large tumors and vessel invasive growth with high accuracy. CONCLUSIONS The expansion of the four-miR signature by miR-483 serves as a useful biomarker to predict outcome of HB patients.
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Affiliation(s)
- Jakob Benjamin Wilhelm Weiss
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Department of Plastic and Hand Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Alexandra Elisabeth Wagner
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Corinna Eberherr
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Beate Häberle
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | | | - Dietrich von Schweinitz
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
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27
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Pawlick JS, Zuzic M, Pasquini G, Swiersy A, Busskamp V. MiRNA Regulatory Functions in Photoreceptors. Front Cell Dev Biol 2021; 8:620249. [PMID: 33553155 PMCID: PMC7858257 DOI: 10.3389/fcell.2020.620249] [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: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. These small, non-coding RNAs post-transcriptionally silence messenger RNAs (mRNAs) in a sequence-specific manner. In this way, miRNAs control important regulatory functions, also in the retina. If dysregulated, these molecules are involved in several retinal pathologies. For example, several miRNAs have been linked to essential photoreceptor functions, including light sensitivity, synaptic transmission, and modulation of inflammatory responses. Mechanistic miRNA knockout and knockdown studies further linked their functions to degenerative retinal diseases. Of note, the type and timing of genetic manipulation before, during, or after retinal development, is important when studying specific miRNA knockout effects. Within this review, we focus on miR-124 and the miR-183/96/182 cluster, which have assigned functions in photoreceptors in health and disease. As a single miRNA can regulate hundreds of mRNAs, we will also discuss the experimental validation and manipulation approaches to study complex miRNA/mRNA regulatory networks. Revealing these networks is essential to understand retinal pathologies and to harness miRNAs as precise therapeutic and diagnostic tools to stabilize the photoreceptors’ transcriptomes and, thereby, function.
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Affiliation(s)
- Julia Sophie Pawlick
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Marta Zuzic
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Giovanni Pasquini
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Anka Swiersy
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Volker Busskamp
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
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28
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Zhang Q, Liu S, Zhang J, Ma X, Dong M, Sun B, Xin Y. Roles and regulatory mechanisms of miR-30b in cancer, cardiovascular disease, and metabolic disorders (Review). Exp Ther Med 2021; 21:44. [PMID: 33273973 PMCID: PMC7706387 DOI: 10.3892/etm.2020.9475] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs 21-23 nucleotides in length that regulate gene expression, and thereby modulate signaling pathways and protein synthesis in both physiological and pathogenic processes. miR-30b inhibits cell proliferation, migration, invasion and epithelial-mesenchymal transformation in multiple types of cancer. In addition to its role in several types of neoplasias, miR-30b has been shown to exhibit essential roles in cardiovascular and metabolic diseases. In the present review, an overview of the biological functions of miR-30b and its role in the pathogenesis of neoplastic, cardiovascular and metabolic diseases is provided. miR-30b is a potential candidate for clinical development as a diagnostic and prognostic biomarker, therapeutic agent and drug target. However, further research is required to elucidate its role in health and disease and to harness its potential clinical utility.
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Affiliation(s)
- Qing Zhang
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
| | - Shousheng Liu
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
- Digestive Disease Key Laboratory of Qingdao, Qingdao, Shandong 266071, P.R. China
| | - Jie Zhang
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
| | - Xuefeng Ma
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
| | - Mengzhen Dong
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
| | - Baokai Sun
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
| | - Yongning Xin
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
- Digestive Disease Key Laboratory of Qingdao, Qingdao, Shandong 266071, P.R. China
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong 266011, P.R. China
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Todd LA, Bui-Marinos MP, Katzenback BA. Post-transcriptional regulation of frog innate immunity: discovery of frog microRNAs associated with antiviral responses and ranavirus infection using a Xenopus laevis skin epithelial-like cell line. Facets (Ott) 2021. [DOI: 10.1139/facets-2021-0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Post-transcriptional regulators such as microRNAs are emerging as conserved regulators of innate antiviral immunity in vertebrates, yet their roles in amphibian antiviral responses remain uncharacterized. We profiled changes in microRNA expressions in the Xenopus laevis skin epithelial-like cell line Xela DS2 in response to poly(I:C)—an analogue of viral double-stranded RNA and inducer of type I interferons—or frog virus 3 (FV3), an immunoevasive virus associated with amphibian mortality events. Small RNA libraries generated from untreated, poly(I:C)-treated, and FV3-infected cells were sequenced. We detected 136 known X. laevis microRNAs and discovered 133 novel X. laevis microRNAs. Sixty-five microRNAs were differentially expressed in response to poly(I:C), many of which were predicted to target regulators of antiviral pathways such as cGAS-STING, RIG-I/MDA-5, TLR signaling, and type I interferon signaling, as well as products of these pathways (NF-ĸB-induced and interferon-stimulated genes). In contrast, only 49 microRNAs were altered by FV3 infection, fewer of which were predicted to interact with antiviral pathways. Interestingly, poly(I:C) treatment or FV3 infection downregulated transcripts encoding factors of the host microRNA biogenesis pathway. Our study is the first to suggest that host microRNAs regulate innate antiviral immunity in frogs and sheds light on microRNA-mediated mechanisms of immunoevasion by FV3.
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Affiliation(s)
- Lauren A. Todd
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Maxwell P. Bui-Marinos
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Barbara A. Katzenback
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
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Chen L, Huang K, Yi K, Huang Y, Tian X, Kang C. Premature MicroRNA-Based Therapeutic: A "One-Two Punch" against Cancers. Cancers (Basel) 2020; 12:cancers12123831. [PMID: 33353171 PMCID: PMC7766154 DOI: 10.3390/cancers12123831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The current understanding of miRNA biology is greatly derived from studies on the guide strands and the passenger strands, also called miRNAs*, which are considered as carriers with no sense for long periods. As such, various studies alter the expression of guide strands by manipulating the expression of their primary transcripts or precursors, both of which are premature miRNAs. In this situation, the regulatory miRNA* species may interfere with the phenotypic interpretation against the target miRNA. However, such methods could manipulate the expression of two functionally synergistic miRNAs of the same precursor, leading to therapeutic potential against various diseases, including cancers. Premature miRNAs represent an underappreciated target reservoir and provide molecular targets for “one-two punch” against cancers. Examples of targetable miRNA precursors and available targeting strategies are provided in this review. Abstract Up-to-date knowledge regarding the biogenesis and functioning of microRNAs (miRNAs) has provided a much more comprehensive and concrete view of miRNA biology than anyone ever expected. Diverse genetic origins and biogenesis pathways leading to functional miRNAs converge on the synthesis of ≈21-nucleotide RNA duplex, almost all of which are processed from long premature sequences in a DICER- and/or DROSHA-dependent manner. Formerly, it was assumed that one mature strand of the duplex is preferentially selected for entry into the silencing complex, and the paired passenger strands (miRNA*) are subjected to degradation. However, given the consolidated evidence of substantial regulatory activity of miRNA* species, currently, this preconception has been overturned. Here, we see the caveat and opportunity toward exogenously manipulating the expression of premature miRNA, leading to simultaneous upregulation or downregulation of dual regulatory strands due to altered expressions. The caveat is the overlooked miRNA* interference while manipulating the expression of a target miRNA at the premature stage, wherein lies the opportunity. If the dual strands of a pre-miRNA function synergistically, the overlooked miRNA* interference may inversely optimize the therapeutic performance. Insightfully, targeting the premature miRNAs may serve as the “one-two punch” against diseases, especially cancers, and this has been discussed in detail in this review.
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Affiliation(s)
- Luyue Chen
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, China;
| | - Kaikai Yi
- Laboratory of Neuro-Oncology, Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China;
| | - Yanlin Huang
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
| | - Xinhua Tian
- Department of Neurosurgery, Zhongshan Hospital Xiamen University, Xiamen 361004, China; (L.C.); (Y.H.)
- Correspondence: (X.T.); (C.K.); Tel.: +86-0592-229-2941 (X.T.); +86-022-6081-7499 (C.K.)
| | - Chunsheng Kang
- Laboratory of Neuro-Oncology, Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China;
- Correspondence: (X.T.); (C.K.); Tel.: +86-0592-229-2941 (X.T.); +86-022-6081-7499 (C.K.)
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31
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Lam NT, Gartz M, Thomas L, Haberman M, Strande JL. Influence of microRNAs and exosomes in muscle health and diseases. J Muscle Res Cell Motil 2020; 41:269-284. [PMID: 31564031 PMCID: PMC7101267 DOI: 10.1007/s10974-019-09555-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
microRNAs are short, (18-22 nt) non-coding RNAs involved in important cellular processes due to their ability to regulate gene expression at the post-transcriptional level. Exosomes are small (50-200 nm) extracellular vesicles, naturally secreted from a variety of living cells and are believed to mediate cell-cell communication through multiple mechanisms, including uptake in destination cells. Circulating microRNAs and exosome-derived microRNAs can have key roles in regulating muscle cell development and differentiation. Several microRNAs are highly expressed in muscle and their regulation is important for myocyte homeostasis. Changes in muscle associated microRNA expression are associated with muscular diseases including muscular dystrophies, inflammatory myopathies, and congenital myopathies. In this review, we aim to highlight the biology of microRNAs and exosomes as well as their roles in muscle health and diseases. We also discuss the potential crosstalk between skeletal and cardiac muscle through exosomes and their contents.
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Affiliation(s)
- Ngoc Thien Lam
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melanie Gartz
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah Thomas
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Margaret Haberman
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jennifer L Strande
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA.
- Medical College of Wisconsin, CVC/MEB 4679, 8701 Watertown Plank Rd, Milwaukee, WI, 53226, USA.
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Saikia M, Paul S, Chakraborty S. Role of microRNA in forming breast carcinoma. Life Sci 2020; 259:118256. [DOI: 10.1016/j.lfs.2020.118256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/19/2022]
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Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, Li C, Baril T, Wong AYP, Swale T, Chan TF, Hayward A, Ngai SM, Hui JHL. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol 2020; 18:e3000636. [PMID: 32991578 PMCID: PMC7523956 DOI: 10.1371/journal.pbio.3000636] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 08/24/2020] [Indexed: 01/27/2023] Open
Abstract
The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs—including species-specific microRNA arm switching—providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes—and in particular the reconstruction of the myriapod ancestral situation—for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes. This study describes the genome sequences of two millipedes, Helicorthomorpha holstii and Trigoniulus corallinus, revealing unique adaptations not found in other arthropods.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tom Barton-Owen
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas C. N. Leung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Chade Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Annette Y. P. Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, California, United States of America
| | - Ting-Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Sai-Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Jerome H. L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
- * E-mail:
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Lin W, Liu H, Tang Y, Wei Y, Wei W, Zhang L, Chen J. The development and controversy of competitive endogenous RNA hypothesis in non-coding genes. Mol Cell Biochem 2020; 476:109-123. [PMID: 32975695 DOI: 10.1007/s11010-020-03889-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
As a momentous post-transcriptional regulator, microRNAs (miRNAs) are attracting more and more attention. The classical miRNAs regulated mechanism shows it binds to the targets' 3'UTR thus play the role in post-transcription. Meanwhile, single miRNA can target multiple genes, so those should compete to bind that miRNA. Vice versa, single gene can sponge mass of miRNAs as well. Thus the competitive endogenous RNAs (ceRNAs) hypothesis was put forward in 2011. The ceRNA hypothesis has made huge achievements, in particular in non-coding genes, which including long non-coding RNAs (lncRNAs), circle RNAs (circRNAs) and pseudogenes, even viral transcripts. It also contributed greatly to epigenetics development. However, an increasing number of controversies have occurred with applause. Based on this situation, this review introduces something in detail about the ceRNAs hypothesis achieved in lncRNAs, circRNAs, pseudogenes and viral transcripts, respectively. Meanwhile, it also covers controversy of the ceRNAs hypothesis.
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Affiliation(s)
- Weimin Lin
- Nanjing Agricultural University, Nanjing, China
| | | | | | - Yuchen Wei
- Nanjing Agricultural University, Nanjing, China
| | - Wei Wei
- Nanjing Agricultural University, Nanjing, China
| | - Lifan Zhang
- Nanjing Agricultural University, Nanjing, China
| | - Jie Chen
- Nanjing Agricultural University, Nanjing, China.
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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: 73] [Impact Index Per Article: 18.3] [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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Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics 2020; 36:698-703. [PMID: 31504201 DOI: 10.1093/bioinformatics/btz675] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. RESULTS To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification. AVAILABILITY AND IMPLEMENTATION https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Karen Eilbeck
- University of Utah, Biomedical Informatics, Salt Lake City, UT 84108, USA
| | - Jeffery Ma
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Gianvito Urgese
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ernesto Aparicio-Puerta
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Victor Barrera
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roderic Espín
- Universitat Oberta de Catalunya, Barcelona 08018, Spain
| | - Florian Thibord
- Sorbonne Université, Pierre Louis Doctoral School of Public Health, Paris 75006, France.,Institut National pour la Santé et la Recherche Médicale (INSERM) Unité Mixte de Recherche en Santé (UMR_S), University of Bordeaux, Bordeaux 33076, France
| | - Xavier Bofill-De Ros
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | | | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Michael Hackenberg
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Ioannis S Vlachos
- Non-coding Research Lab, Department of Pathology, Cancer Research Institute, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lorena Pantano
- Bioinformatics Core, The Picower Institute for Learning and Memory, Cambridge, MA 02139, USA
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Hepatic miR-192-3p reactivation alleviates steatosis by targeting glucocorticoid receptor. JHEP Rep 2020; 2:100179. [PMID: 33134908 PMCID: PMC7588854 DOI: 10.1016/j.jhepr.2020.100179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Background & Aims The paradox of hepatic insulin resistance describes the inability for liver to respond to bioenergetics hormones in suppressing gluconeogenesis whilst maintaining lipid synthesis. Here, we report the deficiency of miR-192-3p in the livers of mice with diabetes and its role in alleviating hepatic steatosis. Methods As conventional pre-microRNA (miRNA) stem-loop overexpression only boosts guiding strand (i.e. miR-192-5p) expression, we adopted an artificial AAV(DJ)-directed, RNA Pol III promoter-driven miRNA hairpin construct for star-strand-specific overexpression in the liver. Liver steatosis and insulin resistance markers were evaluated in primary hepatocytes, mice with diabetes, and mice with excessive carbohydrate consumption. Results Functional loss of miR-192-3p in liver exacerbated hepatic micro-vesicular steatosis and insulin resistance in either mice with diabetes or wild-type mice with excessive fructose consumption. Liver-specific overexpression of miR-192-3p effectively halted hepatic steatosis and ameliorated insulin resistance in these mice models. Likewise, hepatocytes overexpressing miR-192-3p exhibited improved lipid accumulation, accompanied with decreases in lipogenesis and lipid-accumulation-related transcripts. Mechanistically, glucocorticoid receptor (GCR, also known as nuclear receptor subfamily 3, group C, member 1 [NR3C1]) was demonstrated to be negatively regulated by miR-192-3p. The effect of miR-192-3p on mitigating micro-vesicular steatosis was ablated by the reactivation of NR3C1. Conclusions The star strand miR-192-3p was an undermined glycerolipid regulator involved in controlling fat accumulation and insulin sensitivity in liver through blockade of hepatic GCR signalling; this miRNA may serve as a potential therapeutic option for the common co-mobility of diabetic mellitus and fatty liver disease. Lay summary The potential regulatory activity of star strand microRNA (miRNA) species has been substantially underestimated. In this study, we investigate the role and mechanism of an overlooked star strand miRNA (miR-192-3p) in regulating hepatic steatosis and insulin signalling in the livers of mice with diabetes and mice under excessive carbohydrate consumption. Liver-specific knockdown of miR-192-3p recapitulated functional loss of the miRNA as in mice with diabetes. This knockdown was characterised by pronounced hepatic micro-vesicular steatosis coupled to insulin resistance. In vivo overexpression of miR-192-3p alleviated hepatic steatosis in mice with diabetes and wild-type mice with excessive fructose consumption. Glucocorticoid receptor (also known as NR3C1) was discovered as the immediate target of miR-192-3p in regulating hepatic lipid turnover and storage.
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Key Words
- 3′-UTR, 3′-untranslated region
- AAV, adeno-associated virus
- CPT, carnitine palmitoyl transferase
- DEG, differentially expressed gene
- DEX, dexamethasone
- DM, diabetes mellitus
- DNL, de novo lipogenesis
- Diabetes mellitus
- FA, fatty acid
- FAO, fatty acid oxidation
- FASN, fatty acid synthase
- GCR, glucocorticoid receptor
- Glucocorticoid receptor
- HFD, high-fat diet
- HFrD, high-fructose drink
- HOMA-IR, homeostatic model assessment of insulin resistance
- Hepatic steatosis
- High carbohydrate consumption
- MicroRNA
- NAFLD, non-alcoholic fatty liver disease
- NR3C1, nuclear receptor subfamily 3, group C, member 1
- NT, non-targeting
- OA, oleic acid
- OGTT, oral glucose tolerance test
- SCD1, stearoyl-CoA desaturase-1
- T2DM, type 2 diabetes mellitus
- TAG, triacylglyceride/triglyceride
- Transcription repressor
- VAT, visceral adipose tissue
- miRNA, microRNA
- shRNA, short hairpin RNA
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MicroRNAs as Guardians of the Prostate: Those Who Stand before Cancer. What Do We Really Know about the Role of microRNAs in Prostate Biology? Int J Mol Sci 2020; 21:ijms21134796. [PMID: 32645914 PMCID: PMC7370012 DOI: 10.3390/ijms21134796] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Prostate cancer is the second leading cause of cancer-related deaths of men in the Western world. Despite recent advancement in genomics, transcriptomics and proteomics to understand prostate cancer biology and disease progression, castration resistant metastatic prostate cancer remains a major clinical challenge and often becomes incurable. MicroRNAs (miRNAs), about 22-nucleotide-long non-coding RNAs, are a group of regulatory molecules that mainly work through post-transcriptional gene silencing via translational repression. Expression analysis studies have revealed that miRNAs are aberrantly expressed in cancers and have been recognized as regulators of prostate cancer progression. In this critical review, we provide an analysis of reported miRNA functions and conflicting studies as they relate to expression levels of specific miRNAs and prostate cancer progression; oncogenic and/or tumor suppressor roles; androgen receptor signaling; epithelial plasticity; and the current status of diagnostic and therapeutic applications. This review focuses on select miRNAs, highly expressed in normal and cancer tissue, to emphasize the current obstacles faced in utilizing miRNA data for significant impacts on prostate cancer therapeutics.
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Szabó MR, Gáspár R, Pipicz M, Zsindely N, Diószegi P, Sárközy M, Bodai L, Csont T. Hypercholesterolemia Interferes with Induction of miR-125b-1-3p in Preconditioned Hearts. Int J Mol Sci 2020; 21:ijms21113744. [PMID: 32466450 PMCID: PMC7312064 DOI: 10.3390/ijms21113744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022] Open
Abstract
Ischemic preconditioning (IPre) reduces ischemia/reperfusion (I/R) injury in the heart. The non-coding microRNA miR-125b-1-3p has been demonstrated to play a role in the mechanism of IPre. Hypercholesterolemia is known to attenuate the cardioprotective effect of preconditioning; nevertheless, the exact underlying mechanisms are not clear. Here we investigated, whether hypercholesterolemia influences the induction of miR-125b-1-3p by IPre. Male Wistar rats were fed with a rodent chow supplemented with 2% cholesterol and 0.25% sodium-cholate hydrate for 8 weeks to induce high blood cholesterol levels. The hearts of normo- and hypercholesterolemic animals were then isolated and perfused according to Langendorff, and were subjected to 35 min global ischemia and 120 min reperfusion with or without IPre (3 × 5 min I/R cycles applied before index ischemia). IPre significantly reduced infarct size in the hearts of normocholesterolemic rats; however, IPre was ineffective in the hearts of hypercholesterolemic animals. Similarly, miR-125b-1-3p was upregulated by IPre in hearts of normocholesterolemic rats, while in the hearts of hypercholesterolemic animals IPre failed to increase miR-125b-1-3p significantly. Phosphorylation of cardiac Akt, ERK, and STAT3 was not significantly different in any of the groups at the end of reperfusion. Based on these results we propose here that hypercholesterolemia attenuates the upregulation of miR-125b-1-3p by IPre, which seems to be associated with the loss of cardioprotection.
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Affiliation(s)
- Márton R. Szabó
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
| | - Renáta Gáspár
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
| | - Márton Pipicz
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
| | - Nóra Zsindely
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary;
| | - Petra Diószegi
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
| | - Márta Sárközy
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary;
| | - Tamás Csont
- Metabolic Diseases and Cell Signaling (MEDICS) Research Group, Department of Biochemistry, Faculty of Medicine, University of Szeged, Dóm tér 9., H-6720 Szeged, Hungary; (M.R.S.); (R.G.); (M.P.); (P.D.); (M.S.)
- Interdisciplinary Centre of Excellence, University of Szeged, Dugonics tér 13., H-6720 Szeged, Hungary
- Correspondence: ; Tel.: +36-62-545-096
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Tian C, Hu G, Gao L, Hackfort BT, Zucker IH. Extracellular vesicular MicroRNA-27a* contributes to cardiac hypertrophy in chronic heart failure. J Mol Cell Cardiol 2020; 143:120-131. [PMID: 32370947 DOI: 10.1016/j.yjmcc.2020.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/17/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023]
Abstract
Under stress, the heart undergoes extensive remodeling resulting in cardiac fibrosis and hypertrophy, ultimately contributing to chronic heart failure (CHF). Alterations in microRNA levels are associated with dysfunctional gene expression profiles involved in the pathogenesis of heart failure. We previously showed that myocardial infarction-induced microRNA-enriched extracellular vesicles (EVs) contribute to the reduction in antioxidant enzymes by targeting Nrf2 signaling in CHF. MicroRNA-27a (miRNA-27a) is the predominant microRNA contained in cardiac fibroblast-derived EVs contributing to oxidative stress along with hypertrophic gene expression in cardiomyocytes. In the present study, we observed that miRNA-27a passenger strand (miRNA-27a*) was markedly upregulated in the non-infarcted area of the left ventricle of rats with CHF and encapsulated into EVs and secreted into the circulation. Bioinformatic analysis revealed that PDZ and LIM domain 5 (PDLIM5) is one of the major targets of miRNA-27a*, playing a major role in cardiac structure and function, and potentially contributing to the progression of cardiac hypertrophy. Our in vivo data demonstrate that PDLIM5 is down-regulated in the progression of heart failure, accompanied with the upregulation of hypertrophic genes and consistent with alterations in miRNA-27a*. Moreover, exogenous administration of miRNA27a* mimics inhibit PDLIM5 translation in cardiomyocytes whereas a miRNA27a* inhibitor enhanced PDLIM5 expression. Importantly, we confirmed that infarcted hearts have higher abundance of miRNA-27a* in EVs compared to normal hearts and further demonstrated that cultured cardiac fibroblasts secrete miRNA27a*-enriched EVs into the extracellular space in response to Angiotensin II stimulation, which inhibited PDLIM5 translation, leading to cardiomyocyte hypertrophic gene expression. In vivo studies suggest that the administration of a miRNA-27a* inhibitor in CHF rats partially blocks endogenous miR-27a* expression, prevents hypertrophic gene expression and improves myocardial contractility. These findings suggest that cardiac fibroblast-secretion of miRNA27a*-enriched EVs may act as a paracrine signaling mediator of cardiac hypertrophy that has potential as a novel therapeutic target.
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Affiliation(s)
- Changhai Tian
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198-5850, United States of America.
| | - Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, United States of America
| | - Lie Gao
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198-5850, United States of America
| | - Bryan T Hackfort
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198-5850, United States of America
| | - Irving H Zucker
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198-5850, United States of America
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Zaporozhchenko IA, Rykova EY, Laktionov PP. The Fundamentals of miRNA Biology: Structure, Biogenesis, and Regulatory Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202001015x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Affiliation(s)
- Hervé Seitz
- IGH, CNRS-University of Montpellier, Montpellier, France
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43
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Gao Q, Lei F, Zeng Q, Gao Z, Niu P, Junnan, Ning, Li J, Zhang J. Functional Passenger-Strand miRNAs in Exosomes Derived from Human Colon Cancer Cells and Their Heterogeneous Paracrine Effects. Int J Biol Sci 2020; 16:1044-1058. [PMID: 32140072 PMCID: PMC7053335 DOI: 10.7150/ijbs.40787] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
Exosome-mediated microRNAs (miRNAs) are closely related to the occurrence, development, invasion, metastasis, therapeutic resistance, diagnosis and treatment of malignant tumors. Guide-strand miRNA and passenger-strand miRNA (miRNA*) exist in miRNA processing, but the function of passenger-strand miRNA is often overlooked. In this study, we attempted to identify functional miRNA*s in exosomes derived from human colon cancer SW620 cells. miRNA expression profiles of human normal colonic epithelial cells NCM460 and colon cancer cells SW620 were compared by high-throughput sequencing. According to the sequencing results, we defined two sets of differentially expressed miRNAs: "high in exosome and high in cell" (HEHC) and "high in exosome but low in cell" (HELC). As passenger-strand miRNAs, miR-2277-3p and miR-26b-3p, which belong to different sets, have diametrically opposite functions. MiR-2277-3p promotes proliferation, migration, and invasion of SW620 cells by targeting NUPR1L, while miR-26b-3p exerts an inhibitory effect by targeting PFDN1. Using exosomes as transport vectors, the effect of exosomes rich in miR-2277-3p on cells is consistent with the effect of liposome-transfected overexpressed miR-2277-3p, resulting in a cancer-promoting effect. However, exosomes rich in miR-26b-3p did not have a tumor suppressor effect. Further analysis revealed that exosomes rich in miR-2277-3p also had a high abundance of integrin β4. Altering the abundance of integrin β4 in exosomes changes the ability of exosomes to be taken up by cells, thereby altering the paracrine effects of exosomes. In summary, we revealed the fact that a large number of passenger-strand miRNAs exist in exosomes of colon cancer cells, these miRNAs are preliminarily categorized into two sets, and miR-2277-3p and miR-26b-3p, as representatives of each set, showed opposite functions. In addition, we revealed that integrin β4 is a marker of exosome heterogeneity in colon cancer cells, which directly correlates with the ability of exosomes to be uptaken by cells of the same kind, thus regulating the paracrine effect of exosomes.
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Affiliation(s)
- Qingkun Gao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing 100050. China
| | - Fuming Lei
- Department of General Surgery, Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Qingmin Zeng
- Department of General Surgery, Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Zhaoya Gao
- Department of General Surgery, Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Pengfei Niu
- Department of General Surgery, Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Junnan
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing 100050. China.,Department of General Surgery, Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China.,Research Department, Genex Health Co., Ltd, Beijing 100195, China
| | - Ning
- Research Department, Genex Health Co., Ltd, Beijing 100195, China
| | - Jie Li
- Research Department, Genex Health Co., Ltd, Beijing 100195, China
| | - Jun Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing 100050. China
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ADAR1p150 regulates the biosynthesis and function of miRNA-149* in human melanoma. Biochem Biophys Res Commun 2020; 523:900-907. [PMID: 31959472 DOI: 10.1016/j.bbrc.2019.12.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/17/2019] [Indexed: 11/20/2022]
Abstract
Melanoma is an aggressive malignant skin tumor. Study found that miR-149* was abnormally expressed in melanoma. Adenosine deaminases acting on the RNA1 (ADAR1) is an RNA editing enzyme. It can change the structure and function of miRNA. In this study, we investigate the role of ADAR1 in regulation of miRNA-149* in melanoma. Western-blot analysis was used to analyze the expression of ADAR1p150, ADAR1p110 and GSK3α at protein level. The expression of ADAR1p150, miR-149* and GSK3α at mRNA level were detected using qRT-PCR. Co-immunoprecipitation test was then performed to determine the interaction between ADAR1 and Dicer. Target verification of miRNA-149*/GSK3α was carried out using luciferase reporter assay. CCK-8 was used to detect cell proliferation. Cell apoptosis was tested using Tunel assays. The expression level of ADAR1p150 was found to be increased in human melanoma tissues, but not ADAR1p110. There was a direct interaction between ADAR1p150 and Dicer in melanoma cells. MiRNA-149* was significantly up-regulated in melanoma tissues and melanoma cells. Luciferase reporter assay suggested that GSK3α was a directly target of miR-149*. The expression level of miR-149* showed a positive correlation with ADAR1p150. At the same time, ADAR1p150 expression was negatively correlated with the expression of GSK3α. ADAR1p150 promoted proliferation of melanoma cells and inhibited cell apoptosis. ADAR1p150 can promote the biosynthesis and function of miRNA-149* in melanoma cells which makes it be considered as both a bio-marker and a therapeutic target for treatment of melanoma.
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MicroRNAs as Potential Biomarkers in Atherosclerosis. Int J Mol Sci 2019; 20:ijms20225547. [PMID: 31703274 PMCID: PMC6887712 DOI: 10.3390/ijms20225547] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Atherosclerosis is a complex multifactorial disease that, despite advances in lifestyle management and drug therapy, remains to be the major cause of high morbidity and mortality rates from cardiovascular diseases (CVDs) in industrialized countries. Therefore, there is a great need in reliable diagnostic/prognostic biomarkers and effective treatment alternatives to reduce its burden. It was established that microRNAs (miRNAs/miRs), a class of non-coding single-stranded RNA molecules, can regulate the expression of genes at the post-transcriptional level and, accordingly, coordinate the cellular protein expression. Thus, they are involved not only in cell-specific physiological functions but also in the cellular and molecular mechanisms of human pathologies, including atherosclerosis. MiRNAs may be significant in the dysregulation that affects endothelial integrity, the function of vascular smooth muscle and inflammatory cells, and cellular cholesterol homeostasis that drives the initiation and growth of an atherosclerotic plaque. Besides, distinct expression patterns of several miRNAs are attributed to atherosclerotic and cardiovascular patients. In this article, the evidence indicating the multiple critical roles of miRNAs and their relevant molecular mechanisms related to atherosclerosis development and progression was reviewed. Moreover, the effects of miRNAs on atherosclerosis enabled to exploit them as novel diagnostic biomarkers and therapeutic targets that may lead to better management of atherosclerosis and CVDs.
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Inhibiting microRNA-144 potentiates Nrf2-dependent antioxidant signaling in RPE and protects against oxidative stress-induced outer retinal degeneration. Redox Biol 2019; 28:101336. [PMID: 31590045 PMCID: PMC6812120 DOI: 10.1016/j.redox.2019.101336] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/11/2019] [Accepted: 09/26/2019] [Indexed: 01/03/2023] Open
Abstract
The retinal pigment epithelium (RPE) is consistently exposed to high levels of pro-oxidant and inflammatory stimuli. As such, under normal conditions the antioxidant machinery in the RPE cell is one of the most efficient in the entire body. However, antioxidant defense mechanisms are often impacted negatively by the process of aging and/or degenerative disease leaving RPE susceptible to damage which contributes to retinal dysfunction. Thus, understanding better the mechanisms governing antioxidant responses in RPE is critically important. Here, we evaluated the role of the redox sensitive microRNA miR-144 in regulation of antioxidant signaling in human and mouse RPE. In cultured human RPE, miR-144-3p and miR-144-5p expression was upregulated in response to pro-oxidant stimuli. Likewise, overexpression of miR-144-3p and -5p using targeted miR mimics was associated with reduced expression of Nrf2 and downstream antioxidant target genes (NQO1 and GCLC), reduced levels of glutathione and increased RPE cell death. Alternately, some protection was conferred against the above when miR-144-3p and miR-144-5p expression was suppressed using antagomirs. Expression analyses revealed a higher conservation of miR-144-3p expression across species and additionally, the presence of two potential Nrf2 binding sites in the 3p sequence compared to only one in the 5p sequence. Thus, we evaluated the impact of miR-144-3p expression in the retinas of mice in which a robust pro-oxidant environment was generated using sodium iodate (SI). Subretinal injection of miR-144-3p antagomir in SI mice preserved retinal integrity and function, decreased oxidative stress, limited apoptosis and enhanced antioxidant gene expression. Collectively, the present work establishes miR-144 as a potential target for preventing and treating degenerative retinal diseases in which oxidative stress is paramount and RPE is prominently affected (e.g., age-related macular degeneration and diabetic retinopathy).
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Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nat Commun 2019; 10:3682. [PMID: 31417090 PMCID: PMC6695490 DOI: 10.1038/s41467-019-11610-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic mutations in the RNase IIIb domain of DICER1 arise in cancer and disrupt the cleavage of 5' pre-miRNA arms. Here, we characterize an unstudied, recurrent, mutation (S1344L) in the DICER1 RNase IIIa domain in tumors from The Cancer Genome Atlas (TCGA) project and MSK-IMPACT profiling. RNase IIIa/b hotspots are absent from most cancers, but are notably enriched in uterine cancers. Systematic analysis of TCGA small RNA datasets show that DICER1 RNase IIIa-S1344L tumors deplete 5p-miRNAs, analogous to RNase IIIb hotspot samples. Structural and evolutionary coupling analyses reveal constrained proximity of RNase IIIa-S1344 to the RNase IIIb catalytic site, rationalizing why mutation of this site phenocopies known hotspot alterations. Finally, examination of DICER1 hotspot endometrial tumors reveals derepression of specific miRNA target signatures. In summary, comprehensive analyses of DICER1 somatic mutations and small RNA data reveal a mechanistic aspect of pre-miRNA processing that manifests in specific cancer settings.
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Affiliation(s)
- Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Walid K Chatila
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bülent Arman Aksoy
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Immunology and Microbiology Department, Medical University of South Carolina, Charleston, SC, 29412, USA
| | - Sonali Majumdar
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Anders Jacobsen Skanderup
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Emek Demir
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Oregon Health and Science University, Computational Biology Program, Portland, OR, 97239, USA
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,cBio Center, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
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Abstract
microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successive releases. A further consideration is that each new miRBase release contains entries that have had limited review and which may subsequently be removed in a future release to ensure the quality of annotation. To aid the miRBase user, we developed a software tool, miRBaseMiner, for investigating miRBase annotation and generating custom annotation sets. We apply the tool to characterize each release from v9.2 to v22 to examine how annotation has changed across releases and highlight some of the annotation features that users should keep in mind when using for miRBase for data analysis. These include: (1) entries with identical or very similar sequences; (2) entries with multiple annotated genome locations; (3) hairpin precursor entries with extremely low-estimated minimum free energy; (4) entries possessing reverse complementary; (5) entries with 3ʹ poly(A) ends. As each of these factors can impact the identification of dysregulated features and subsequent clinical or biological conclusions, miRBaseMiner is a valuable resource for any user using miRBase as a reference source.
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Affiliation(s)
- Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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Ravichandran S, Ragupathy R, Edwards T, Domaratzki M, Cloutier S. MicroRNA-guided regulation of heat stress response in wheat. BMC Genomics 2019; 20:488. [PMID: 31195958 PMCID: PMC6567507 DOI: 10.1186/s12864-019-5799-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. Results Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins. Conclusion The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5799-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sridhar Ravichandran
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Raja Ragupathy
- Plant Science Department, University of Manitoba, Winnipeg, Manitoba, Canada.,Present address: Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Tara Edwards
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada.
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