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Haddad-Mashadrizeh A, Mirahmadi M, Taghavizadeh Yazdi ME, Gholampour-Faroji N, Bahrami A, Zomorodipour A, Moghadam Matin M, Qayoomian M, Saebnia N. Introns and Their Therapeutic Applications in Biomedical Researches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3316. [PMID: 38269198 PMCID: PMC10804063 DOI: 10.30498/ijb.2023.334488.3316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/23/2023] [Indexed: 01/26/2024]
Abstract
Context Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms. Evidence Acquisition In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included. Results & Conclusions The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Mirahmadi
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Nazanin Gholampour-Faroji
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmadreza Bahrami
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Maryam Moghadam Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Qayoomian
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Saebnia
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Machado HC, Bispo S, Dallagiovanna B. miR-6087 Might Regulate Cell Cycle–Related mRNAs During Cardiomyogenesis of hESCs. Bioinform Biol Insights 2023; 17:11779322231161918. [PMID: 37020502 PMCID: PMC10069004 DOI: 10.1177/11779322231161918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 04/03/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.
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Affiliation(s)
- Hellen Cristine Machado
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
| | - Saloe Bispo
- Laboratory of Molecular and Systems
Biology of Trypanosomatids, Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba,
Brazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
- Bruno Dallagiovanna, Laboratory of Basic
Stem-Cell Biology, Instituto Carlos Chagas – FIOCRUZ-PR, Rua Professor Algacyr
Munhoz Mader, 3775, Curitiba 81350-010, Brazil.
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Lázár B, Szabadi NT, Anand M, Tóth R, Ecker A, Urbán M, Aponte MTS, Stepanova G, Hegyi Z, Homolya L, Várkonyi EP, Pain B, Gócza E. Effect of miR-302b MicroRNA Inhibition on Chicken Primordial Germ Cell Proliferation and Apoptosis Rate. Genes (Basel) 2021; 13:genes13010082. [PMID: 35052421 PMCID: PMC8774308 DOI: 10.3390/genes13010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
The primordial germ cells (PGCs) are the precursors for both the oocytes and spermatogonia. Recently, a novel culture system was established for chicken PGCs, isolated from embryonic blood. The possibility of PGC long-term cultivation issues a new advance in germ cell preservation, biotechnology, and cell biology. We investigated the consequence of gga-miR-302b-5P (5P), gga-miR-302b-3P (3P) and dual inhibition (5P/3P) in two male and two female chicken PGC lines. In treated and control cell cultures, the cell number was calculated every four hours for three days by the XLS Imaging system. Comparing the cell number of control and treated lines on the first day, we found that male lines had a higher proliferation rate independently from the treatments. Compared to the untreated ones, the proliferation rate and the number of apoptotic cells were considerably reduced at gga-miR-302b-5P inhibition in all PGC lines on the third day of the cultivation. The control PGC lines showed a significantly higher proliferation rate than 3P inhibited lines on Day 3 in all PGC lines. Dual inhibition of gga-miR-302b mature miRNAs caused a slight reduction in proliferation rate, but the number of apoptotic cells increased dramatically. The information gathered by examining the factors affecting cell proliferation of PGCs can lead to new data in stem cell biology.
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Affiliation(s)
- Bence Lázár
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Godollo, Hungary;
| | - Nikolett Tokodyné Szabadi
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Mahek Anand
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Roland Tóth
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - András Ecker
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Martin Urbán
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Maria Teresa Salinas Aponte
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Ganna Stepanova
- Faculty of Medicine, Institute of Translational Medicine, Semmelweis University, 1089 Budapest, Hungary;
| | - Zoltán Hegyi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Z.H.); (L.H.)
| | - László Homolya
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Z.H.); (L.H.)
| | - Eszter Patakiné Várkonyi
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Godollo, Hungary;
| | - Bertrand Pain
- Stem-Cell and Brain Research Institute, USC1361 INRA, U1208 INSERM, 69675 Bron, France;
| | - Elen Gócza
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
- Correspondence:
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Hashemzadeh MR, Taghavizadeh Yazdi ME, Amiri MS, Mousavi SH. Stem cell therapy in the heart: Biomaterials as a key route. Tissue Cell 2021; 71:101504. [PMID: 33607524 DOI: 10.1016/j.tice.2021.101504] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/19/2022]
Abstract
Cardiovascular diseases are one of the main concerns, nowadays causing a high rate of mortality in the world. The majority of conventional treatment protects the heart from failure progression. As a novel therapeutic way, Regenerative medicine in the heart includes cellular and noncellular approaches. Despite the irrefutable privileges of noncellular aspects such as administration of exosomes, utilizing of miRNAs, and growth factors, they cannot reverse necrotic or ischemic myocardium, hence recruiting of stem cells to help regenerative therapy in the heart seems indispensable. Stem cell lineages are varied and divided into two main groups namely pluripotent and adult stem cells. Not only has each of which own regenerative capacity, benefits, and drawbacks, but their turnover also close correlates with the target organ and/or tissue as well as the stage and level of failure. In addition to inefficient tissue integration due to the defects in delivering methods and poor retention of transplanted cells, the complexity of the heart and its movement also make more rigorous the repair process. Hence, utilizing biomaterials can make a key route to tackle such obstacles. In this review, we evaluate some natural products which can help stem cells in regenerative medicine of the cardiovascular system.
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Affiliation(s)
- Mohammad Reza Hashemzadeh
- Department of Stem Cells and Regenerative Medicine, Royesh Stem Cell Biotechnology Institute, Mashhad, Iran; Medical Toxicology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | | | | | - Seyed Hadi Mousavi
- Medical Toxicology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Huang C, Luo WF, Ye YF, Lin L, Wang Z, Luo MH, Song QD, He XP, Chen HW, Kong Y, Tang YK. Characterization of inflammatory factor-induced changes in mesenchymal stem cell exosomes and sequencing analysis of exosomal microRNAs. World J Stem Cells 2019; 11:859-890. [PMID: 31692888 PMCID: PMC6828590 DOI: 10.4252/wjsc.v11.i10.859] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/24/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Treatments utilizing stems cells often require stem cells to be exposed to inflammatory environments, but the effects of such environments are unknown. AIM To examine the effects of inflammatory cytokines on the morphology and quantity of mesenchymal stem cell exosomes (MSCs-exo) as well as the differential expression of microRNAs (miRNAs) in the exosomes. METHODS MSCs were isolated from human umbilical tissue by enzymatic digestion. Exosomes were then collected after a 48-h incubation period in a serum-free medium with one of the following the inflammatory cytokines: None (control), vascular cell adhesion molecule-1 (VCAM-1), tumor necrosis factor (TNF) α, and interleukin (IL) 6. The morphology and quantity of each group of MSC exosomes were observed and measured. The miRNAs in MSCs-exo were sequenced. We compared the sequenced data with the miRBase and other non-coding databases in order to detect differentially expressed miRNAs and explore their target genes and regulatory mechanisms. In vitro tube formation assays and Western blot were performed in endothelial cells which were used to assess the angiogenic potential of MSCs-exo after inflammatory cytokine stimulation. RESULTS MSCs-exo were numerous, small, and regularly shaped in the VCAM-1 group. TNFα stimulated MSCs to secrete larger and irregular exosomes. IL6 led to a reduced quantity of MSCs-exo. Compared to the control group, the TNFα and IL6 groups had more downregulated differentially expressed miRNAs, particularly angiogenesis-related miRNAs. The angiogenic potential of MSCs-exo declined after IL6 stimulation. CONCLUSION TNFα and IL6 may influence the expression of miRNAs that down-regulate the PI3K-AKT, MAPK, and VEGF signaling pathways; particularly, IL6 significantly down-regulates the PI3K-AKT signaling pathway. Overall, inflammatory cytokines may lead to changes in exosomal miRNAs that abnormally impact cellular components, molecular function, and biological processes.
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Affiliation(s)
- Chen Huang
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Wen-Feng Luo
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Yu-Feng Ye
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Li Lin
- Jinan University Biomedical Translational Research Institute, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Zhe Wang
- Department of Pharmacy, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, Guangdong Province, China
| | - Ming-Hua Luo
- Department of Radiology, Shiyan People's Hospital, Shenzhen 518108, Guangdong Province, China
| | - Qi-De Song
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Xue-Ping He
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Han-Wei Chen
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China
| | - Yi Kong
- Department of Pharmacy, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, Guangdong Province, China
| | - Yu-Kuan Tang
- Department of Minimally Invasive Interventional Radiology, Guangzhou Panyu Central Hospital, Guangzhou 511400, Guangdong Province, China.
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