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Aharon-Yariv A, Wang Y, Ahmed A, Delgado-Olguín P. Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart. BMC Genomics 2023; 24:709. [PMID: 37996818 PMCID: PMC10668469 DOI: 10.1186/s12864-023-09801-8] [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: 08/01/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases in a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome-wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. RESULTS Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis demonstrated that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progressed. Moreover, we found that downregulated targets of upregulated miRNAs, including hsa-let-7b, miR-1-3p, miR-133a-3p, miR-143-3p, miR-499a-5p, and miR-30a-5p predominantly control cell cycle progression. In contrast, upregulated targets of downregulated miRNAs, including hsa-miR-1276, miR-183-5p, miR-1229-3p, miR-615-3p, miR-421, miR-200b-3p and miR-18a-3p, are linked to energy sensing and oxidative metabolism. Furthermore, integrating miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets and their associated metabolites mediate fatty acid oxidation and are enriched as the heart develops. CONCLUSIONS This study presents the first comprehensive analysis of the small RNAome of the maturing human fetal heart. Our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart. Our results provide novel insights into the molecular control of metabolic maturation of the human fetal heart.
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Affiliation(s)
- Adar Aharon-Yariv
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yaxu Wang
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Abdalla Ahmed
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul Delgado-Olguín
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada.
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Heart & Stroke, Richard Lewar Centre of Excellence, Toronto, Ontario, Canada.
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Sweef O, Zaabout E, Bakheet A, Halawa M, Gad I, Akela M, Tousson E, Abdelghany A, Furuta S. Unraveling Therapeutic Opportunities and the Diagnostic Potential of microRNAs for Human Lung Cancer. Pharmaceutics 2023; 15:2061. [PMID: 37631277 PMCID: PMC10459057 DOI: 10.3390/pharmaceutics15082061] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Lung cancer is a major public health problem and a leading cause of cancer-related deaths worldwide. Despite advances in treatment options, the five-year survival rate for lung cancer patients remains low, emphasizing the urgent need for innovative diagnostic and therapeutic strategies. MicroRNAs (miRNAs) have emerged as potential biomarkers and therapeutic targets for lung cancer due to their crucial roles in regulating cell proliferation, differentiation, and apoptosis. For example, miR-34a and miR-150, once delivered to lung cancer via liposomes or nanoparticles, can inhibit tumor growth by downregulating critical cancer promoting genes. Conversely, miR-21 and miR-155, frequently overexpressed in lung cancer, are associated with increased cell proliferation, invasion, and chemotherapy resistance. In this review, we summarize the current knowledge of the roles of miRNAs in lung carcinogenesis, especially those induced by exposure to environmental pollutants, namely, arsenic and benzopyrene, which account for up to 1/10 of lung cancer cases. We then discuss the recent advances in miRNA-based cancer therapeutics and diagnostics. Such information will provide new insights into lung cancer pathogenesis and innovative diagnostic and therapeutic modalities based on miRNAs.
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Affiliation(s)
- Osama Sweef
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44109, USA
- Department of Zoology, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Elsayed Zaabout
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ahmed Bakheet
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44109, USA
| | - Mohamed Halawa
- Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ibrahim Gad
- Department of Statistics and Mathematics, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Mohamed Akela
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ehab Tousson
- Department of Zoology, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Ashraf Abdelghany
- Biomedical Research Center of University of Granada, Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
| | - Saori Furuta
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44109, USA
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Shi M, Lu Q, Zhao Y, Ding Z, Yu S, Li J, Ji M, Fan H, Hou S. miR-223: a key regulator of pulmonary inflammation. Front Med (Lausanne) 2023; 10:1187557. [PMID: 37465640 PMCID: PMC10350674 DOI: 10.3389/fmed.2023.1187557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Small noncoding RNAs, known as microRNAs (miRNAs), are vital for the regulation of diverse biological processes. miR-223, an evolutionarily conserved anti-inflammatory miRNA expressed in cells of the myeloid lineage, has been implicated in the regulation of monocyte-macrophage differentiation, proinflammatory responses, and the recruitment of neutrophils. The biological functions of this gene are regulated by its expression levels in cells or tissues. In this review, we first outline the regulatory role of miR-223 in granulocytes, macrophages, endothelial cells, epithelial cells and dendritic cells (DCs). Then, we summarize the possible role of miR-223 in chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), coronavirus disease 2019 (COVID-19) and other pulmonary inflammatory diseases to better understand the molecular regulatory networks in pulmonary inflammatory diseases.
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Affiliation(s)
- Mingyu Shi
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Qianying Lu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Yanmei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Ziling Ding
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Sifan Yu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Junfeng Li
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Mengjun Ji
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Haojun Fan
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, China
| | - Shike Hou
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, China
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Aryankalayil M, Bylicky MA, Chopra S, Dalo J, Scott K, Ueda Y, Coleman CN. Biomarkers for Biodosimetry and Their Role in Predicting Radiation Injury. Cytogenet Genome Res 2023; 163:103-109. [PMID: 37285811 PMCID: PMC10946629 DOI: 10.1159/000531444] [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: 03/11/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
Radiation-related normal tissue injury sustained during cancer radiotherapy or in a radiological or mass casualty nuclear incident is a major health concern. Reducing the risk and mitigating consequences of radiation injury could have a broad impact on cancer patients and citizens. Efforts to discover biomarkers that can determine radiation dose, predict tissue damage, and aid medical triage are underway. Exposure to ionizing radiation causes changes in gene, protein, and metabolite expression that needs to be understood to provide a holistic picture for treating acute and chronic radiation-induced toxicities. We present evidence that both RNA (mRNA, microRNA, long noncoding RNA) and metabolomic assays may provide useful biomarkers of radiation injury. RNA markers may provide information on early pathway alterations after radiation injury that can predict damage and implicate downstream targets for mitigation. In contrast, metabolomics is impacted by changes in epigenetics, genetics, and proteomics and can be considered a downstream marker that incorporates all these changes to provide an assessment of what is currently happening within an organ. We highlight research from the past 10 years to understand how biomarkers may be used to improve personalized medicine in cancer therapy and medical decision-making in mass casualty scenarios.
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Affiliation(s)
- Molykutty Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle A Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA,
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan Dalo
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin Scott
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuki Ueda
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
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Ibáñez-Cabellos JS, Pallardó FV, García-Giménez JL, Seco-Cervera M. Oxidative Stress and Epigenetics: miRNA Involvement in Rare Autoimmune Diseases. Antioxidants (Basel) 2023; 12:antiox12040800. [PMID: 37107175 PMCID: PMC10135388 DOI: 10.3390/antiox12040800] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Autoimmune diseases (ADs) such as Sjögren’s syndrome, Kawasaki disease, and systemic sclerosis are characterized by chronic inflammation, oxidative stress, and autoantibodies, which cause joint tissue damage, vascular injury, fibrosis, and debilitation. Epigenetics participate in immune cell proliferation and differentiation, which regulates the development and function of the immune system, and ultimately interacts with other tissues. Indeed, overlapping of certain clinical features between ADs indicate that numerous immunologic-related mechanisms may directly participate in the onset and progression of these diseases. Despite the increasing number of studies that have attempted to elucidate the relationship between miRNAs and oxidative stress, autoimmune disorders and oxidative stress, and inflammation and miRNAs, an overall picture of the complex regulation of these three actors in the pathogenesis of ADs has yet to be formed. This review aims to shed light from a critical perspective on the key AD-related mechanisms by explaining the intricate regulatory ROS/miRNA/inflammation axis and the phenotypic features of these rare autoimmune diseases. The inflamma-miRs miR-155 and miR-146, and the redox-sensitive miR miR-223 have relevant roles in the inflammatory response and antioxidant system regulation of these diseases. ADs are characterized by clinical heterogeneity, which impedes early diagnosis and effective personalized treatment. Redox-sensitive miRNAs and inflamma-miRs can help improve personalized medicine in these complex and heterogeneous diseases.
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Affiliation(s)
| | - Federico V. Pallardó
- U733, Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029 Madrid, Spain
- Mixed Unit for Rare Diseases INCLIVA-CIPF, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Correspondence: (F.V.P.); (J.L.G.-G.); (M.S.-C.); Tel.: +34-963-864-646 (F.V.P.)
| | - José Luis García-Giménez
- U733, Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029 Madrid, Spain
- Mixed Unit for Rare Diseases INCLIVA-CIPF, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Correspondence: (F.V.P.); (J.L.G.-G.); (M.S.-C.); Tel.: +34-963-864-646 (F.V.P.)
| | - Marta Seco-Cervera
- Hospital Dr. Peset, Fundación para la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO, 46010 Valencia, Spain
- Correspondence: (F.V.P.); (J.L.G.-G.); (M.S.-C.); Tel.: +34-963-864-646 (F.V.P.)
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Leng Q, Ding J, Dai M, Liu L, Fang Q, Wang DW, Wu L, Wang Y. Insights Into Platelet-Derived MicroRNAs in Cardiovascular and Oncologic Diseases: Potential Predictor and Therapeutic Target. Front Cardiovasc Med 2022; 9:879351. [PMID: 35757325 PMCID: PMC9218259 DOI: 10.3389/fcvm.2022.879351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022] Open
Abstract
Non-communicable diseases (NCDs), represented by cardiovascular diseases and cancer, have been the leading cause of death globally. Improvements in mortality from cardiovascular (CV) diseases (decrease of 14%/100,000, United States) or cancers (increase 7.5%/100,000, United States) seem unsatisfactory during the past two decades, and so the search for innovative and accurate biomarkers of early diagnosis and prevention, and novel treatment strategies is a valuable clinical and economic endeavor. Both tumors and cardiovascular system are rich in angiological systems that maintain material exchange, signal transduction and distant regulation. This pattern determines that they are strongly influenced by circulating substances, such as glycolipid metabolism, inflammatory homeostasis and cyclic non-coding RNA and so forth. Platelets, a group of small anucleated cells, inherit many mature proteins, mRNAs, and non-coding RNAs from their parent megakaryocytes during gradual formation and manifest important roles in inflammation, angiogenesis, atherosclerosis, stroke, myocardial infarction, diabetes, cancer, and many other diseases apart from its classical function in hemostasis. MicroRNAs (miRNAs) are a class of non-coding RNAs containing ∼22 nucleotides that participate in many key cellular processes by pairing with mRNAs at partially complementary binding sites for post-transcriptional regulation of gene expression. Platelets contain fully functional miRNA processors in their microvesicles and are able to transport their miRNAs to neighboring cells and regulate their gene expression. Therefore, the importance of platelet-derived miRNAs for the human health is of increasing interest. Here, we will elaborate systematically the roles of platelet-derived miRNAs in cardiovascular disease and cancer in the hope of providing clinicians with new ideas for early diagnosis and therapeutic strategies.
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