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Avila-Bonilla RG, Salas-Benito JS. Computational Screening to Predict MicroRNA Targets in the Flavivirus 3' UTR Genome: An Approach for Antiviral Development. Int J Mol Sci 2024; 25:10135. [PMID: 39337625 PMCID: PMC11432202 DOI: 10.3390/ijms251810135] [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: 08/27/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
MicroRNAs (miRNAs) are molecules that influence messenger RNA (mRNA) expression levels by binding to the 3' untranslated region (3' UTR) of target genes. Host miRNAs can influence flavivirus replication, either by inducing changes in the host transcriptome or by directly binding to viral genomes. The 3' UTR of the flavivirus genome is a conserved region crucial for viral replication. Cells might exploit this well-preserved region by generating miRNAs that interact with it, ultimately impacting viral replication. Despite significant efforts to identify miRNAs capable of arresting viral replication, the potential of all these miRNAs to interact with the flavivirus 3' UTR is still poorly characterised. In this context, bioinformatic tools have been proposed as a fundamental part of accelerating the discovery of interactions between miRNAs and the 3' UTR of viral genomes. In this study, we performed a computational analysis to reveal potential miRNAs from human and mosquito species that bind to the 3' UTR of flaviviruses. In humans, miR-6842 and miR-661 were found, while in mosquitoes, miR-9-C, miR-2945-5p, miR-11924, miR-282-5p, and miR-79 were identified. These findings open new avenues for studying these miRNAs as antivirals against flavivirus infections.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Laboratorio de Genómica y Biología Molecular de ARNs, Departamento de Genética y Biología Molecular, Cinvestav, Av. IPN 2508, Mexico City 07360, Mexico
| | - Juan Santiago Salas-Benito
- Laboratorio de Biomedicina Molecular 3, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico
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Georgoulis V, Koumpis E, Hatzimichael E. The Role of Non-Coding RNAs in Myelodysplastic Neoplasms. Cancers (Basel) 2023; 15:4810. [PMID: 37835504 PMCID: PMC10571949 DOI: 10.3390/cancers15194810] [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: 08/27/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia, and increased risk of evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs, serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review presents a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS.
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Affiliation(s)
- Vasileios Georgoulis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Epameinondas Koumpis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Eleftheria Hatzimichael
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19 107, USA
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Extracellular Vesicles and MicroRNA in Myelodysplastic Syndromes. Cells 2023; 12:cells12040658. [PMID: 36831325 PMCID: PMC9955013 DOI: 10.3390/cells12040658] [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: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The bone marrow niche plays an increasing role in the pathophysiogenesis of myelodysplastic syndromes. More specifically, mesenchymal stromal cells, which can secrete extracellular vesicles and their miRNA contents, modulate the fate of hematopoietic stem cells leading to leukemogenesis. Extracellular vesicles can mediate their miRNA and protein contents between nearby cells but also in the plasma of the patients, being potent tools for diagnosis and prognostic markers in MDS. They can be targeted by antisense miRNA or by modulators of the secretion of extracellular vesicles and could lead to future therapeutic directions in MDS.
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DNA methylation changes and increased mRNA expression of coagulation proteins, factor V and thrombomodulin in Fuchs endothelial corneal dystrophy. Cell Mol Life Sci 2023; 80:62. [PMID: 36773096 PMCID: PMC9922242 DOI: 10.1007/s00018-023-04714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Late-onset Fuchs endothelial corneal dystrophy (FECD) is a disease affecting the corneal endothelium (CE), associated with a cytosine-thymine-guanine repeat expansion at the CTG18.1 locus in the transcription factor 4 (TCF4) gene. It is unknown whether CTG18.1 expansions affect global methylation including TCF4 gene in CE or whether global CE methylation changes at advanced age. Using genome-wide DNA methylation array, we investigated methylation in CE from FECD patients with CTG18.1 expansions and studied the methylation in healthy CE at different ages. The most revealing DNA methylation findings were analyzed by gene expression and protein analysis. 3488 CpGs had significantly altered methylation pattern in FECD though no substantial changes were found in TCF4. The most hypermethylated site was in a predicted promoter of aquaporin 1 (AQP1) gene, and the most hypomethylated site was in a predicted promoter of coagulation factor V (F5 for gene, FV for protein). In FECD, AQP1 mRNA expression was variable, while F5 gene expression showed a ~ 23-fold increase. FV protein was present in both healthy and affected CE. Further gene expression analysis of coagulation factors interacting with FV revealed a ~ 34-fold increase of thrombomodulin (THBD). THBD protein was detected only in CE from FECD patients. Additionally, we observed an age-dependent hypomethylation in elderly healthy CE.Thus, tissue-specific genome-wide and gene-specific methylation changes associated with altered gene expression were discovered in FECD. TCF4 pathological methylation in FECD because of CTG18.1 expansion was ruled out.
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Hao R, Ge J, Li M, Song X, Jiang Y, Li F, Sun‐Waterhouse D, Li D. Caffeic acid phenethyl ester mitigates cadmium‐induced damage via the Hsa_circ_0010039/miR‐661/Caspase9 axis–mediated apoptosis. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.95] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Rili Hao
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Junlin Ge
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Meiqi Li
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Xinyu Song
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Yang Jiang
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Feng Li
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
| | - Dongxiao Sun‐Waterhouse
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
- School of Chemical Sciences The University of Auckland Auckland New Zealand
| | - Dapeng Li
- College of Food Science and Engineering Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian People's Republic of China
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Veryaskina YA, Titov SE, Kovynev IB, Fedorova SS, Pospelova TI, Zhimulev IF. MicroRNAs in the Myelodysplastic Syndrome. Acta Naturae 2021; 13:4-15. [PMID: 34377552 PMCID: PMC8327150 DOI: 10.32607/actanaturae.11209] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
The myelodysplastic syndrome (MDS) holds a special place among blood cancers, as it represents a whole spectrum of hematological disorders with impaired differentiation of hematopoietic precursors, bone marrow dysplasia, genetic instability and is noted for an increased risk of acute myeloid leukemia. Both genetic and epigenetic factors, including microRNAs (miRNAs), are involved in MDS development. MicroRNAs are short non-coding RNAs that are important regulators of normal hematopoiesis, and abnormal changes in their expression levels can contribute to hematological tumor development. To assess the prognosis of the disease, an international assessment system taking into account a karyotype, the number of blast cells, and the degree of deficiency of different blood cell types is used. However, the overall survival and effectiveness of the therapy offered are not always consistent with predictions. The search for new biomarkers, followed by their integration into the existing prognostic system, will allow for personalized treatment to be performed with more precision. Additionally, this paper explains how miRNA expression levels correlate with the prognosis of overall survival and response to the therapy offered.
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Affiliation(s)
- Y. A. Veryaskina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090 Russia
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090 Russia
| | - S. E. Titov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090 Russia
- Vector-Best, Novosibirsk, 630117 Russia
| | - I. B. Kovynev
- Novosibirsk State Medical University, Novosibirsk, 630091 Russia
| | - S. S. Fedorova
- Novosibirsk State Medical University, Novosibirsk, 630091 Russia
| | - T. I. Pospelova
- Novosibirsk State Medical University, Novosibirsk, 630091 Russia
| | - I. F. Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090 Russia
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Unravelling the Epigenome of Myelodysplastic Syndrome: Diagnosis, Prognosis, and Response to Therapy. Cancers (Basel) 2020; 12:cancers12113128. [PMID: 33114584 PMCID: PMC7692163 DOI: 10.3390/cancers12113128] [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: 09/11/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Myelodysplastic syndrome (MDS) is a type of blood cancer that mostly affects older individuals. Invasive tests to obtain bone samples are used to diagnose MDS and many patients do not respond to therapy or stop responding to therapy in the short-term. Less invasive tests to help diagnose, prognosticate, and predict response of patients is a felt need. Factors that influence gene expression without changing the DNA sequence (epigenetic modifiers) such as DNA methylation, micro-RNAs and long-coding RNAs play an important role in MDS, are potential biomarkers and may also serve as targets for therapy. Abstract Myelodysplastic syndrome (MDS) is a malignancy that disrupts normal blood cell production and commonly affects our ageing population. MDS patients are diagnosed using an invasive bone marrow biopsy and high-risk MDS patients are treated with hypomethylating agents (HMAs) such as decitabine and azacytidine. However, these therapies are only effective in 50% of patients, and many develop resistance to therapy, often resulting in bone marrow failure or leukemic transformation. Therefore, there is a strong need for less invasive, diagnostic tests for MDS, novel markers that can predict response to therapy and/or patient prognosis to aid treatment stratification, as well as new and effective therapeutics to enhance patient quality of life and survival. Epigenetic modifiers such as DNA methylation, long non-coding RNAs (lncRNAs) and micro-RNAs (miRNAs) are perturbed in MDS blasts and the bone marrow micro-environment, influencing disease progression and response to therapy. This review focusses on the potential utility of epigenetic modifiers in aiding diagnosis, prognosis, and predicting treatment response in MDS, and touches on the need for extensive and collaborative research using single-cell technologies and multi-omics to test the clinical utility of epigenetic markers for MDS patients in the future.
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Bauer M, Vaxevanis C, Heimer N, Al-Ali HK, Jaekel N, Bachmann M, Wickenhauser C, Seliger B. Expression, Regulation and Function of microRNA as Important Players in the Transition of MDS to Secondary AML and Their Cross Talk to RNA-Binding Proteins. Int J Mol Sci 2020; 21:ijms21197140. [PMID: 32992663 PMCID: PMC7582632 DOI: 10.3390/ijms21197140] [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: 08/24/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndromes (MDS), heterogeneous diseases of hematopoietic stem cells, exhibit a significant risk of progression to secondary acute myeloid leukemia (sAML) that are typically accompanied by MDS-related changes and therefore significantly differ to de novo acute myeloid leukemia (AML). Within these disorders, the spectrum of cytogenetic alterations and oncogenic mutations, the extent of a predisposing defective osteohematopoietic niche, and the irregularity of the tumor microenvironment is highly diverse. However, the exact underlying pathophysiological mechanisms resulting in hematopoietic failure in patients with MDS and sAML remain elusive. There is recent evidence that the post-transcriptional control of gene expression mediated by microRNAs (miRNAs), long noncoding RNAs, and/or RNA-binding proteins (RBPs) are key components in the pathogenic events of both diseases. In addition, an interplay between RBPs and miRNAs has been postulated in MDS and sAML. Although a plethora of miRNAs is aberrantly expressed in MDS and sAML, their expression pattern significantly depends on the cell type and on the molecular make-up of the sample, including chromosomal alterations and single nucleotide polymorphisms, which also reflects their role in disease progression and prediction. Decreased expression levels of miRNAs or RBPs preventing the maturation or inhibiting translation of genes involved in pathogenesis of both diseases were found. Therefore, this review will summarize the current knowledge regarding the heterogeneity of expression, function, and clinical relevance of miRNAs, its link to molecular abnormalities in MDS and sAML with specific focus on the interplay with RBPs, and the current treatment options. This information might improve the use of miRNAs and/or RBPs as prognostic markers and therapeutic targets for both malignancies.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Christoforos Vaxevanis
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Haifa Kathrin Al-Ali
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Nadja Jaekel
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Michael Bachmann
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, 01328 Dresden, Germany;
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
- Correspondence: ; Tel.: +49-345-557-4054
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Prognostic Markers of Myelodysplastic Syndromes. ACTA ACUST UNITED AC 2020; 56:medicina56080376. [PMID: 32727068 PMCID: PMC7466347 DOI: 10.3390/medicina56080376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/26/2022]
Abstract
Myelodysplastic syndrome (MDS) is a clonal disease characterized by multilineage dysplasia, peripheral blood cytopenias, and a high risk of transformation to acute myeloid leukemia. In theory, from clonal hematopoiesis of indeterminate potential to hematologic malignancies, there is a complex interplay between genetic and epigenetic factors, including miRNA. In practice, karyotype analysis assigns patients to different prognostic groups, and mutations are often associated with a particular disease phenotype. Among myeloproliferative disorders, secondary MDS is a group of special entities with a typical spectrum of genetic mutations and cytogenetic rearrangements resembling those in de novo MDS. This overview analyzes the present prognostic systems of MDS and the most recent efforts in the search for genetic and epigenetic markers for the diagnosis and prognosis of MDS.
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