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Sum H, Brewer AC. Epigenetic modifications as therapeutic targets in atherosclerosis: a focus on DNA methylation and non-coding RNAs. Front Cardiovasc Med 2023; 10:1183181. [PMID: 37304954 PMCID: PMC10248074 DOI: 10.3389/fcvm.2023.1183181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Significant progress in the diagnosis and treatment of cardiovascular disease (CVD) has been made in the past decade, yet it remains a leading cause of morbidity and mortality globally, claiming an estimated 17.9 million deaths per year. Although encompassing any condition that affects the circulatory system, including thrombotic blockage, stenosis, aneurysms, blood clots and arteriosclerosis (general hardening of the arteries), the most prevalent underlying hallmark of CVD is atherosclerosis; the plaque-associated arterial thickening. Further, distinct CVD conditions have overlapping dysregulated molecular and cellular characteristics which underlie their development and progression, suggesting some common aetiology. The identification of heritable genetic mutations associated with the development of atherosclerotic vascular disease (AVD), in particular resulting from Genome Wide Association Studies (GWAS) studies has significantly improved the ability to identify individuals at risk. However, it is increasingly recognised that environmentally-acquired, epigenetic changes are key factors associated with atherosclerosis development. Increasing evidence suggests that these epigenetic changes, most notably DNA methylation and the misexpression of non-coding, microRNAs (miRNAs) are potentially both predictive and causal in AVD development. This, together with their reversible nature, makes them both useful biomarkers for disease and attractive therapeutic targets potentially to reverse AVD progression. We consider here the association of aberrant DNA methylation and dysregulated miRNA expression with the aetiology and progression of atherosclerosis, and the potential development of novel cell-based strategies to target these epigenetic changes therapeutically.
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Wronska A. The Role of microRNA in the Development, Diagnosis, and Treatment of Cardiovascular Disease: Recent Developments. J Pharmacol Exp Ther 2023; 384:123-132. [PMID: 35779862 DOI: 10.1124/jpet.121.001152] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/13/2023] Open
Abstract
Since their discovery in 1993, microRNAs (miRNAs) have emerged as important regulators of many crucial cellular processes, and their dysregulation have been shown to contribute to multiple pathologic conditions, including cardiovascular disease (CVD). miRNAs have been found to regulate the expression of various genes involved in cardiac development and function and in the development and progression of CVD. Many miRNAs are master regulators fine-tuning the expression of multiple, often interrelated, genes involved in inflammation, apoptosis, fibrosis, senescence, and other processes crucial for the development of different forms of CVD. This article presents a review of recent developments in our understanding of the role of miRNAs in the development of CVD and surveys their potential applicability as therapeutic targets and biomarkers to facilitate CVD diagnosis, prognosis, and treatment. There are currently multiple potential miRNA-based therapeutic agents in different stages of development, which can be grouped into two classes: miRNA mimics (replicating the sequence and activity of their corresponding miRNAs) and antagomiRs (antisense inhibitors of specific miRNAs). However, in spite of promising preliminary data and our ever-increasing knowledge about the mechanisms of action of specific miRNAs, miRNA-based therapeutics and biomarkers have yet to be approved for clinical applications. SIGNIFICANCE STATEMENT: Over the last few years microRNAs have emerged as crucial, specific regulators of the cardiovascular system and in the development of cardiovascular disease, by posttranscriptional regulation of their target genes. The minireview presents the most recent developments in this area of research, including the progress in diagnostic and therapeutic applications of microRNAs. microRNAs seem very promising candidates for biomarkers and therapeutic agents, although some challenges, such as efficient delivery and unwanted effects, need to be resolved.
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Affiliation(s)
- Anetta Wronska
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York
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Yu X, Li D, Xue L, Li R. Power-enhanced simultaneous test of high-dimensional mean vectors and covariance matrices with application to gene-set testing. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2061354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | | | | | - Runze Li
- The Pennsylvania State University
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Integrative Analysis of Deregulated miRNAs Reveals Candidate Molecular Mechanisms Linking H. pylori Infected Peptic Ulcer Disease with Periodontitis. DISEASE MARKERS 2022; 2022:1498525. [PMID: 35132337 PMCID: PMC8817886 DOI: 10.1155/2022/1498525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022]
Abstract
Objective Periodontitis is a highly prevalent oral infectious disease and has been increasingly associated with H. pylori infection, gastric inflammation, and gastric cancer but little is known about epigenetic machinery underlying this potentially bidirectional association. The present study is aimed at identifying key deregulated miRNA, their associated genes, signaling pathways, and compounds linking periodontitis with H. pylori-associated peptic ulcer disease. Methods miRNA expression datasets for periodontitis-affected and H. pylori-associated peptic ulcer disease-affected tissues were sought from the GEO database. Differentially expressed miRNA (DEmiRNAs) were identified and the overlapping, shared-DEmiRNA between both datasets were determined. Shared-DEmiRNA-target networks construction and functional analyses were constructed using miRNet 2.0, including shared-DEmiRNA-gene, shared-DEmiRNA-transcription factor (TF), and shared-DEmiRNA-compound networks. Functional enrichment analysis for shared DEmiRNA-gene and shared DEmiRNA-TF networks was performed using the KEGG, Reactome, and Geno Ontology (GO) pathways. Results 11 shared-DEmiRNAs were identified, among which 9 showed similar expression patterns in both diseases, and 7 were overexpressed. miRNA hsa-hsa-mir-155-5p and hsa-mir-29a-3p were top miRNA nodes in both gene and TF networks. The topmost candidate miRNA-deregulated genes were PTEN, CCND1, MDM2, TNRC6A, and SCD while topmost deregulated TFs included STAT3, HIF1A, EZH2, CEBPA, and RUNX1. Curcumin, 5-fluorouracil, and the gallotanin 1,2,6-Tri-O-galloyl-beta-D-glucopyranose emerged as the most relevant linkage compound targets. Functional analyses revealed multiple cancer-associated pathways, PI3K pathways, kinase binding, and transcription factor binding among as enriched by the network-associated genes and TFs. Conclusion Integrative analysis of deregulated miRNAs revealed candidate molecular mechanisms comprising of top miRNA, their gene, and TF targets linking H. pylori-infected peptic ulcer disease with periodontitis and highlighted compounds targeting both diseases. These findings provide basis for directing future experimental research.
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Fan Y, Tang Z, Sun J, Zhao X, Li Z, Zheng Y, Zeng X, Feng J. MicroRNA-29a promotes the proliferation of human nasal epithelial cells and inhibits their apoptosis and promotes the development of allergic rhinitis by down-regulating FOS expression. PLoS One 2021; 16:e0255480. [PMID: 34383804 PMCID: PMC8360612 DOI: 10.1371/journal.pone.0255480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To explore the regulation of microRNA-29a (miR-29a) on FOS in human nasal epithelial cells and its molecular mechanism, as well as the effects of miR-29a on the cell proliferation and apoptosis. METHODS By cell transfection, gene silencing, quantitative real-time polymerase chain reaction (qRT-PCR), flow cytometry and TUNEL assay (for cell apoptosis), CCK-8 assay (for cell proliferation), dual-luciferase reporter gene assay and Western Blot, it was validated that miR-29a promoted the proliferation of human nasal epithelial cells and inhibited their apoptosis by down-regulating FOS expression in RPMI2650 and HNEpC cell lines. RESULTS ①Compared with healthy controls, miR-29a expression was up-regulated and FOS mRNA expression was down-regulated in the nasal tissues from the patients with allergic rhinitis (AR). ②MiR-29a over-expression promoted the proliferation of RPMI2650 cells and HNEpC cells but inhibited their apoptosis. ③MiR-29a targeted at FOS. ④MiR-29a over-expression and FOS silencing both significantly promoted cell proliferation and inhibited cell apoptosis. After transfection with both miR-29a and FOS, there was a decrease in the proliferation but an increase in the apoptosis of cells.⑤MiR-29a promoted the proliferation of human nasal epithelial cells and inhibited their apoptosis by down-regulating FOS expression. CONCLUSION MiR-29a-/FOS axis can be regarded as a potential marker and a new therapy for AR.
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Affiliation(s)
- Yuqin Fan
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyuan Tang
- Department of Otorhinolaryngology, Shenzhen Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T., Institute of E.N.T., Shenzhen, Guangdong, China
| | - Jie Sun
- Department of Otorhinolaryngology, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiaorui Zhao
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhen Li
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Yiqing Zheng
- Department of Otolaryngology, Sun Yat-Sen Memorial Hospital, Guangzhou, Guangdong, P.R. China
| | - Xianhai Zeng
- Department of Otorhinolaryngology, Shenzhen Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T., Institute of E.N.T., Shenzhen, Guangdong, China
| | - Juan Feng
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
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Meliț LE, Mărginean CO, Mărginean CD, Săsăran MO. The Peculiar Trialogue between Pediatric Obesity, Systemic Inflammatory Status, and Immunity. BIOLOGY 2021; 10:biology10060512. [PMID: 34207683 PMCID: PMC8229553 DOI: 10.3390/biology10060512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
Pediatric obesity is not only an energetic imbalance, but also a chronic complex multisystem disorder that might impair both the life length and quality. Its pandemic status should increase worldwide awareness regarding the long-term life-threatening associated complications. Obesity related complications, such as cardiovascular, metabolic, or hepatic ones, affect both short and long-term wellbeing, and they do not spare pediatric subjects, defined as life-threatening consequences of the systemic inflammatory status triggered by the adipose tissue. The energetic imbalance of obesity clearly results in adipocytes hypertrophy and hyperplasia expressing different degrees of chronic inflammation. Adipose tissue might be considered an immune organ due to its rich content in a complex array of immune cells, among which the formerly mentioned macrophages, neutrophils, mast cells, but also eosinophils along with T and B cells, acting together to maintain the tissue homeostasis in normal weight individuals. Adipokines belong to the class of innate immunity humoral effectors, and they play a crucial role in amplifying the immune responses with a subsequent trigger effect on leukocyte activation. The usefulness of complete cellular blood count parameters, such as leukocytes, lymphocytes, neutrophils, erythrocytes, and platelets as predictors of obesity-triggered inflammation, was also proved in pediatric patients with overweight or obesity. The dogma that adipose tissue is a simple energy storage tissue is no longer accepted since it has been proved that it also has an incontestable multifunctional role acting like a true standalone organ resembling to endocrine or immune organs.
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Affiliation(s)
- Lorena Elena Meliț
- Department of Pediatrics I, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Gheorghe Marinescu Street No 38, 540136 Târgu Mureș, Romania; (L.E.M.); (C.D.M.)
| | - Cristina Oana Mărginean
- Department of Pediatrics I, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Gheorghe Marinescu Street No 38, 540136 Târgu Mureș, Romania; (L.E.M.); (C.D.M.)
- Correspondence: ; Tel.: +40-723-278543
| | - Cristian Dan Mărginean
- Department of Pediatrics I, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Gheorghe Marinescu Street No 38, 540136 Târgu Mureș, Romania; (L.E.M.); (C.D.M.)
| | - Maria Oana Săsăran
- Department of Pediatrics III, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Gheorghe Marinescu Street No 38, 540136 Târgu Mureș, Romania;
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Epigenetic alterations in skin homing CD4 +CLA + T cells of atopic dermatitis patients. Sci Rep 2020; 10:18020. [PMID: 33093567 PMCID: PMC7582180 DOI: 10.1038/s41598-020-74798-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
T cells expressing the cutaneous lymphocyte antigen (CLA) mediate pathogenic inflammation in atopic dermatitis (AD). The molecular alterations contributing to their dysregulation remain unclear. With the aim to elucidate putative altered pathways in AD we profiled DNA methylation levels and miRNA expression in sorted T cell populations (CD4+, CD4+CD45RA+ naïve, CD4+CLA+, and CD8+) from adult AD patients and healthy controls (HC). Skin homing CD4+CLA+ T cells from AD patients showed significant differences in DNA methylation in 40 genes compared to HC (p < 0.05). Reduced DNA methylation levels in the upstream region of the interleukin-13 gene (IL13) in CD4+CLA+ T cells from AD patients correlated with increased IL13 mRNA expression in these cells. Sixteen miRNAs showed differential expression in CD4+CLA+ T cells from AD patients targeting genes in 202 biological processes (p < 0.05). An integrated network analysis of miRNAs and CpG sites identified two communities of strongly interconnected regulatory elements with strong antagonistic behaviours that recapitulated the differences between AD patients and HC. Functional analysis of the genes linked to these communities revealed their association with key cytokine signaling pathways, MAP kinase signaling and protein ubiquitination. Our findings support that epigenetic mechanisms play a role in the pathogenesis of AD by affecting inflammatory signaling molecules in skin homing CD4+CLA+ T cells and uncover putative molecules participating in AD pathways.
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Nozari E, Moradi A, Samadi M. Effect of Atorvastatin, Curcumin, and Quercetin on miR-21 and miR-122 and their correlation with TGFβ1 expression in experimental liver fibrosis. Life Sci 2020; 259:118293. [DOI: 10.1016/j.lfs.2020.118293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/09/2020] [Accepted: 08/14/2020] [Indexed: 02/08/2023]
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Huang YA, Hu P, Chan KCC, You ZH. Graph convolution for predicting associations between miRNA and drug resistance. Bioinformatics 2020; 36:851-858. [PMID: 31397851 DOI: 10.1093/bioinformatics/btz621] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION MicroRNA (miRNA) therapeutics is becoming increasingly important. However, aberrant expression of miRNAs is known to cause drug resistance and can become an obstacle for miRNA-based therapeutics. At present, little is known about associations between miRNA and drug resistance and there is no computational tool available for predicting such association relationship. Since it is known that miRNAs can regulate genes that encode specific proteins that are keys for drug efficacy, we propose here a computational approach, called GCMDR, for finding a three-layer latent factor model that can be used to predict miRNA-drug resistance associations. RESULTS In this paper, we discuss how the problem of predicting such associations can be formulated as a link prediction problem involving a bipartite attributed graph. GCMDR makes use of the technique of graph convolution to build a latent factor model, which can effectively utilize information of high-dimensional attributes of miRNA/drug in an end-to-end learning scheme. In addition, GCMDR also learns graph embedding features for miRNAs and drugs. We leveraged the data from multiple databases storing miRNA expression profile, drug substructure fingerprints, gene ontology and disease ontology. The test for performance shows that the GCMDR prediction model can achieve AUCs of 0.9301 ± 0.0005, 0.9359 ± 0.0006 and 0.9369 ± 0.0003 based on 2-fold, 5-fold and 10-fold cross validation, respectively. Using this model, we show that the associations between miRNA and drug resistance can be reliably predicted by properly introducing useful side information like miRNA expression profile and drug structure fingerprints. AVAILABILITY AND IMPLEMENTATION Python codes and dataset are available at https://github.com/yahuang1991polyu/GCMDR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yu-An Huang
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Pengwei Hu
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Keith C C Chan
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China
| | - Zhu-Hong You
- Department of Computing, Hong Kong Polytechnic University, Hong Kong SAR, 999077, China.,Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, China
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Correlation between miR-223 and IL-35 and their regulatory effect in children with allergic rhinitis. Clin Immunol 2020; 214:108383. [PMID: 32169441 DOI: 10.1016/j.clim.2020.108383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 12/29/2022]
Abstract
The relationship between microRNA (miR) and immune activity in allergic rhinitis (AR) remains unclear. 37 children with AR and 30 healthy children were enrolled to study the correlation of miR-223 and IL-35. There was a significant inverse correlation between plasma levels of IL-35 and serum eosinophil cationic protein (ECP) levels and eosinophils counts, while there was a positive correlation between serum miR-223 level and ECP levels and eosinophils counts. Besides, the serum levels of IL-35 or miR-223 were found to be negatively or positively correlated with TNSS respectively. The serum level of miR-223 was increased, while IL-35 level was decreased. Moreover, the expression of miRNA-223 was inversely correlated with expression of IL-35. Finally, the levels of miR-223 and IL-35 were related to Th1/Th2 cytokines, eosinophils count as well as the clinical severity. Our study suggests the potential of miR-223 and IL-35 as a molecular target for the treatment of AR.
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Transcription Factor and miRNA Interplays Can Manifest the Survival of ccRCC Patients. Cancers (Basel) 2019; 11:cancers11111668. [PMID: 31661791 PMCID: PMC6895828 DOI: 10.3390/cancers11111668] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) still remains a higher mortality rate in worldwide. Obtaining promising biomakers is very crucial for improving the diagnosis and prognosis of ccRCC patients. Herein, we firstly identified eight potentially prognostic miRNAs (hsa-miR-144-5p, hsa-miR-223-3p, hsa-miR-365b-3p, hsa-miR-3613-5p, hsa-miR-9-5p, hsa-miR-183-5p, hsa-miR-335-3p, hsa-miR-1269a). Secondly, we found that a signature containing these eight miRNAs showed obviously superior to a single miRNA in the prognostic effect and credibility for predicting the survival of ccRCC patients. Thirdly, we discovered that twenty-two transcription factors (TFs) interact with these eight miRNAs, and a signature combining nine TFs (TFAP2A, KLF5, IRF1, RUNX1, RARA, GATA3, IKZF1, POU2F2, and FOXM1) could promote the prognosis of ccRCC patients. Finally, we further identified eleven genes (hsa-miR-365b-3p, hsa-miR-223-3p, hsa-miR-1269a, hsa-miR-144-5p, hsa-miR-183-5p, hsa-miR-335-3p, TFAP2A, KLF5, IRF1, MYC, IKZF1) that could combine as a signature to improve the prognosis effect of ccRCC patients, which distinctly outperformed the eight-miRNA signature and the nine-TF signature. Overall, we identified several new prognosis factors for ccRCC, and revealed a potential mechanism that TFs and miRNAs interplay cooperatively or oppositely regulate a certain number of tumor suppressors, driver genes, and oncogenes to facilitate the survival of ccRCC patients.
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Wei Y, Chen S, Sun D, Li X, Wei R, Li X, Nian H. miR-223-3p promotes autoreactive T h17 cell responses in experimental autoimmune uveitis (EAU) by inhibiting transcription factor FOXO3 expression. FASEB J 2019; 33:13951-13965. [PMID: 31645142 DOI: 10.1096/fj.201901446r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pathogenic T helper (Th)17 cells are key mediators of autoimmune diseases such as uveitis and its animal model, experimental autoimmune uveitis (EAU). However, the contribution of microRNAs (miRs) to the intrinsic control of pathogenic Th17 cells in EAU remains largely unknown. Here, we have reported that miR-223-3p was significantly up-regulated in interphotoreceptor retinoid-binding protein-specific Th17 cells, and its expression was enhanced by IL-23-signal transducer and activator of transcription 3 signaling. Knockdown of miR-223-3p decreased the pathogenicity of Th17 cells in a T-cell transfer model of EAU. Mechanistic studies showed that miR-223-3p directly repressed the expression of forkhead box O3 (FOXO3), and FOXO3 negatively regulated pathogenic Th17 cell responses partially via suppression of IL-23 receptor expression. Thus, our results reveal an important role for miR-223-3p in autoreactive Th17 cell responses and suggest a potential therapeutic avenue for uveitis.-Wei, Y., Chen, S., Sun, D., Li, X., Wei, R., Li, X., Nian, H. miR-223-3p promotes autoreactive Th17 cell responses in experimental autoimmune uveitis (EAU) by inhibiting transcription factor FOXO3 expression.
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Affiliation(s)
- Yankai Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Sisi Chen
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Deming Sun
- Department of Ophthalmology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA.,Doheny Eye Institute, Los Angeles, California, USA
| | - Xue Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Ruihua Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xiaorong Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Nian
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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Vastrad C, Vastrad B. Investigation into the underlying molecular mechanisms of non-small cell lung cancer using bioinformatics analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wang X, Yang C, Liu X, Yang P. Ghrelin Alleviates Angiotensin II-Induced H9c2 Apoptosis: Impact of the miR-208 Family. Med Sci Monit 2018; 24:6707-6716. [PMID: 30244257 PMCID: PMC6178878 DOI: 10.12659/msm.908096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Ghrelin is a novel peptide with abundant cardioprotective effects. The miR-208 family, consisting of cardiac-specifically expressed microRNAs, are not only involved in hypertrophy and fibrosis, but are also closely related with myocyte apoptosis. This study explored the role of the miR-208 family in the protective effect of ghrelin on angiotensin II (Ang II)-induced apoptosis. MATERIAL AND METHODS H9c2 cells were exposed to Ang II with or without ghrelin. Cell viability was detected by MTT assay and the percentage of apoptotic cells was confirmed by flow cytometry. miRNAs expression levels were measured by qRT-PCR. Then, cells transfected with miR-208 negative control, mimics, and inhibitors were treated with Ang II and ghrelin, followed by flow cytometry. PCR array was performed to explore the pathways affected by miR-208. RESULTS The miR-208 level was reduced in Ang II-treated H9c2 cells, accompanied with increased cell apoptosis, which were both reversed by ghrelin administration. Flow cytometry revealed that miR-208 inhibitors clearly upregulated the apoptotic percentage, whereas miR-208 mimics showed the opposite effects in the Ang II group. miR-208a further alleviated apoptosis when treated with ghrelin. miR-208 mainly affected caspase, inflammatory-related genes, and several signaling pathways. CONCLUSIONS We provide new evidence that the miR-208 family is regulated by Ang II and ghrelin. Overexpression of miR-208 family alleviated Ang II-induced cell apoptosis and miR-208a assisted in the protective effect of ghrelin. Several apoptosis pathways affected by miR-208 family were found. These findings suggest the pathogenesis of cardiomyocyte apoptosis and the protective mechanism of ghrelin.
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Affiliation(s)
- Xiaotong Wang
- Department of Cardiololgy, China-Japan Union Hospital, Jilin University, Changchun, Jilin, China (mainland)
| | - Chunyan Yang
- Department of Cardiology, China-Japan Union Hospital, Jilin University, Changchun, Jilin, China (mainland)
| | - Xueyan Liu
- Department of Cardiology, China-Japan Union Hospital, Jilin University, Changchun, Jilin, China (mainland)
| | - Ping Yang
- Department of Cardiology, China-Japan Union Hospital, Jilin University, Changchun, Jilin, China (mainland)
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Lin Z, Yang F, Sun L, Gao J, Cao Y, Qiu H, Zhan X. Systematically analyses of the common dysregulated networks to understand the common pathologies between T2D and atherosclerosis. Gene X 2018; 671:110-116. [DOI: 10.1016/j.gene.2018.04.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 11/27/2022] Open
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Schoen C, Aschrafi A, Thonissen M, Poelmans G, Von den Hoff JW, Carels CEL. MicroRNAs in Palatogenesis and Cleft Palate. Front Physiol 2017; 8:165. [PMID: 28420997 PMCID: PMC5378724 DOI: 10.3389/fphys.2017.00165] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/06/2017] [Indexed: 01/01/2023] Open
Abstract
Palatogenesis requires a precise spatiotemporal regulation of gene expression, which is controlled by an intricate network of transcription factors and their corresponding DNA motifs. Even minor perturbations of this network may cause cleft palate, the most common congenital craniofacial defect in humans. MicroRNAs (miRNAs), a class of small regulatory non-coding RNAs, have elicited strong interest as key regulators of embryological development, and as etiological factors in disease. MiRNAs function as post-transcriptional repressors of gene expression and are therefore able to fine-tune gene regulatory networks. Several miRNAs are already identified to be involved in congenital diseases. Recent evidence from research in zebrafish and mice indicates that miRNAs are key factors in both normal palatogenesis and cleft palate formation. Here, we provide an overview of recently identified molecular mechanisms underlying palatogenesis involving specific miRNAs, and discuss how dysregulation of these miRNAs may result in cleft palate.
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Affiliation(s)
- Christian Schoen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of HealthBethesda, MD, USA
| | - Michelle Thonissen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegen, Netherlands.,Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud UniversityNijmegen, Netherlands
| | - Johannes W Von den Hoff
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Oral Health Sciences, University Hospitals-KU LeuvenLeuven, Belgium
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17
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Olsen LC, O'Reilly KC, Liabakk NB, Witter MP, Sætrom P. MicroRNAs contribute to postnatal development of laminar differences and neuronal subtypes in the rat medial entorhinal cortex. Brain Struct Funct 2017; 222:3107-3126. [PMID: 28260163 PMCID: PMC5585308 DOI: 10.1007/s00429-017-1389-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/13/2017] [Indexed: 01/23/2023]
Abstract
The medial entorhinal cortex (MEC) is important in spatial navigation and memory formation and its layers have distinct neuronal subtypes, connectivity, spatial properties, and disease susceptibility. As little is known about the molecular basis for the development of these laminar differences, we analyzed microRNA (miRNA) and messenger RNA (mRNA) expression differences between rat MEC layer II and layers III–VI during postnatal development. We identified layer and age-specific regulation of gene expression by miRNAs, which included processes related to neuron specialization and locomotor behavior. Further analyses by retrograde labeling and expression profiling of layer II stellate neurons and in situ hybridization revealed that the miRNA most up-regulated in layer II, miR-143, was enriched in stellate neurons, whereas the miRNA most up-regulated in deep layers, miR-219-5p, was expressed in ependymal cells, oligodendrocytes and glia. Bioinformatics analyses of predicted mRNA targets with negatively correlated expression patterns to miR-143 found that miR-143 likely regulates the Lmo4 gene, which is known to influence hippocampal-based spatial learning.
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Affiliation(s)
- Lene C Olsen
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kally C O'Reilly
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University for Science and Technology, Trondheim, Norway
| | - Nina B Liabakk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University for Science and Technology, Trondheim, Norway
| | - Pål Sætrom
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway. .,Department of Computer and Information Science, Norwegian University for Science and Technology, Trondheim, Norway. .,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway.
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18
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Rayner S, Bruhn S, Vallhov H, Andersson A, Billmyre RB, Scheynius A. Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis. Sci Rep 2017; 7:39742. [PMID: 28051166 PMCID: PMC5209728 DOI: 10.1038/srep39742] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/25/2016] [Indexed: 12/21/2022] Open
Abstract
Malassezia is the dominant fungus in the human skin mycobiome and is associated with common skin disorders including atopic eczema (AE)/dermatitis. Recently, it was found that Malassezia sympodialis secretes nanosized exosome-like vesicles, designated MalaEx, that carry allergens and can induce inflammatory cytokine responses. Extracellular vesicles from different cell-types including fungi have been found to deliver functional RNAs to recipient cells. In this study we assessed the presence of small RNAs in MalaEx and addressed if the levels of these RNAs differ when M. sympodialis is cultured at normal human skin pH versus the elevated pH present on the skin of patients with AE. The total number and the protein concentration of the released MalaEx harvested after 48 h culture did not differ significantly between the two pH conditions nor did the size of the vesicles. From small RNA sequence data, we identified a set of reads with well-defined start and stop positions, in a length range of 16 to 22 nucleotides consistently present in the MalaEx. The levels of small RNAs were not significantly differentially expressed between the two different pH conditions indicating that they are not influenced by the elevated pH level observed on the AE skin.
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Affiliation(s)
- Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Sören Bruhn
- Translational Immunology Unit, Department of Medicine Solna, Karolinska Institutet and University Hospital Stockholm, Sweden
| | - Helen Vallhov
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden
| | - Anna Andersson
- Translational Immunology Unit, Department of Medicine Solna, Karolinska Institutet and University Hospital Stockholm, Sweden
| | - R Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden
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19
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Ruddy JM, Ikonomidis JS, Jones JA. Multidimensional Contribution of Matrix Metalloproteinases to Atherosclerotic Plaque Vulnerability: Multiple Mechanisms of Inhibition to Promote Stability. J Vasc Res 2016; 53:1-16. [PMID: 27327039 PMCID: PMC7196926 DOI: 10.1159/000446703] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/07/2016] [Indexed: 12/17/2022] Open
Abstract
The prevalence of atherosclerotic disease continues to increase, and despite significant reductions in major cardiovascular events with current medical interventions, an additional therapeutic window exists. Atherosclerotic plaque growth is a complex integration of cholesterol penetration, inflammatory cell infiltration, vascular smooth muscle cell (VSMC) migration, and neovascular invasion. A family of matrix-degrading proteases, the matrix metalloproteinases (MMPs), contributes to all phases of vascular remodeling. The contribution of specific MMPs to endothelial cell integrity and VSMC migration in atherosclerotic lesion initiation and progression has been confirmed by the increased expression of these proteases in plasma and plaque specimens. Endogenous blockade of MMPs by the tissue inhibitors of metalloproteinases (TIMPs) may attenuate proteolysis in some regions, but the progression of matrix degeneration suggests that MMPs predominate in atherosclerotic plaque, precipitating vulnerability. Plaque neovascularization also contributes to instability and, coupling the known role of MMPs in angiogenesis to that of atherosclerotic plaque growth, interest in targeting MMPs to facilitate plaque stabilization continues to accumulate. This article aims to review the contributions of MMPs and TIMPs to atherosclerotic plaque expansion, neovascularization, and rupture vulnerability with an interest in promoting targeted therapies to improve plaque stabilization and decrease the risk of major cardiovascular events.
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Affiliation(s)
- Jean Marie Ruddy
- Division of Vascular Surgery, Department of Surgery, Medical University of South Carolina, Charleston, S.C., USA
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20
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Magner WJ, Weinstock-Guttman B, Rho M, Hojnacki D, Ghazi R, Ramanathan M, Tomasi TB. Dicer and microRNA expression in multiple sclerosis and response to interferon therapy. J Neuroimmunol 2016; 292:68-78. [PMID: 26943961 PMCID: PMC4779496 DOI: 10.1016/j.jneuroim.2016.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/06/2016] [Accepted: 01/14/2016] [Indexed: 12/11/2022]
Abstract
Dysregulation of microRNA expression has been shown in multiple sclerosis (MS); however, the mechanisms underlying these changes, their response to therapy and the impact of microRNA changes in MS are not completely understood. Dicer mediates the cleavage of precursor microRNAs to mature microRNAs and is dysregulated in multiple pathologies. Having shown that interferons regulate Dicer in vitro, we hypothesized that MS patient IFNβ1a treatment could potentially alter Dicer expression. Dicer mRNA and protein levels, as well as microRNA expression, were determined in MS patient and healthy control PBL. Acute responses to IFNβ1a were assessed in 50 patients. We found that Dicer protein but not mRNA levels decreases in MS patients while both are selectively induced in patients responding well to IFNβ1a. Potential microRNA biomarkers for relapsing remitting multiple sclerosis (RRMS), secondary progressive multiple sclerosis (SPMS) and IFNβ1a response are described. Contrasts in Dicer and microRNA expression levels between patient populations may offer insight into mechanisms underlying disease courses and responses to IFNβ1a therapy. This work identifies Dicer regulation as both a potential mediator of MS pathology and a therapeutic target.
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Affiliation(s)
- William J Magner
- Laboratory of Molecular Medicine, Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA; Department of Microbiology and Immunology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
| | - Bianca Weinstock-Guttman
- Jacobs Neurological Institute, Buffalo, NY, USA; Department of Neurology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
| | - Mina Rho
- Division of Computer Science and Engineering, Hanyang University, Seoul, Republic of Korea.
| | - David Hojnacki
- Jacobs Neurological Institute, Buffalo, NY, USA; Department of Neurology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
| | - Rabia Ghazi
- Jacobs Neurological Institute, Buffalo, NY, USA; Department of Neurology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
| | - Murali Ramanathan
- Jacobs Neurological Institute, Buffalo, NY, USA; Department of Neurology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA; Department of Pharmaceutical Sciences, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
| | - Thomas B Tomasi
- Laboratory of Molecular Medicine, Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA; Department of Microbiology and Immunology, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA; Department of Medicine, State University of New York, School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
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21
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Benson M. Clinical implications of omics and systems medicine: focus on predictive and individualized treatment. J Intern Med 2016; 279:229-40. [PMID: 26891944 DOI: 10.1111/joim.12412] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many patients with common diseases do not respond to treatment. This is a key challenge to modern health care, which causes both suffering and enormous costs. One important reason for the lack of treatment response is that common diseases are associated with altered interactions between thousands of genes, in combinations that differ between subgroups of patients who do or do not respond to a given treatment. Such subgroups, or even distinct disease entities, have been described recently in asthma, diabetes, autoimmune diseases and cancer. High-throughput techniques (omics) allow identification and characterization of such subgroups or entities. This may have important clinical implications, such as identification of diagnostic markers for individualized medicine, as well as new therapeutic targets for patients who do not respond to existing drugs. For example, whole-genome sequencing may be applied to more accurately guide treatment of neurodevelopmental diseases, or to identify drugs specifically targeting mutated genes in cancer. A study published in 2015 showed that 28% of hepatocellular carcinomas contained mutated genes that potentially could be targeted by drugs already approved by the US Food and Drug Administration. A translational study, which is described in detail, showed how combined omics, computational, functional and clinical studies could identify and validate a novel diagnostic and therapeutic candidate gene in allergy. Another important clinical implication is the identification of potential diagnostic markers and therapeutic targets for predictive and preventative medicine. By combining computational and experimental methods, early disease regulators may be identified and potentially used to predict and treat disease before it becomes symptomatic. Systems medicine is an emerging discipline, which may contribute to such developments through combining omics with computational, functional and clinical studies. The aims of this review are to provide a brief introduction to systems medicine and discuss how it may contribute to the clinical implementation of individualized treatment, using clinically relevant examples.
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Affiliation(s)
- M Benson
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Health Sciences, Linköping University, Linköping, Sweden
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22
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Reversal of MicroRNA Dysregulation in an Animal Model of Pulmonary Hypertension. PLoS One 2016; 11:e0147827. [PMID: 26815432 PMCID: PMC4731388 DOI: 10.1371/journal.pone.0147827] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 01/08/2016] [Indexed: 11/19/2022] Open
Abstract
Background Animals models have played an important role in enhancing our understanding of the pathogenesis of pulmonary arterial hypertension (PAH). Dysregulation of the profile of microRNAs (miRNAs) has been demonstrated in human tissues from PAH patients and in animal models. In this study, we measured miRNA levels in the monocrotaline (MCT) rat model of PAH and examined whether blocking a specific dysregulated miRNA not previously reported in this model, attenuated PAH. We also evaluated changes in miRNA expression in lung specimens from MCT PAH rats overexpressing human prostacyclin synthase, which has been shown to attenuate MCT PAH. Methods Expression levels of a panel of miRNAs were measured in MCT-PAH rats as compared to naïve (saline) control rats. Subsequently, MCT PAH rats were injected with a specific inhibitor (antagomiR) for miR-223 (A223) or a nonspecific control oligonucleotide (A-control) 4 days after MCT administration, then weekly. Three weeks later, RV systolic pressure and RV mass were measured. Total RNA, isolated from the lungs, microdissected pulmonary arteries, and right ventricle, was reverse transcribed and real-time quantitative PCR was performed. MiRNA levels were also measured in RNA isolated from paraffin sections of MCT-PAH rats overexpressing prostacyclin synthase. Results MiRs 17, 21, and 223 were consistently upregulated, whereas miRs 126, 145, 150, 204, 424, and 503 were downregulated in MCT PAH as compared to vehicle control. A223 significantly reduced levels of miR-223 in PA and lungs of MCT PAH rats as compared to levels measured in A-control or control MCT PAH rats, but A223 did not attenuate MCT PAH. Right ventricular mass and right ventricular systolic pressure in rats treated with A223 were not different from values in A-control or MCT PAH rats. In contrast, analysis of total RNA from lung specimens of MCT PAH rats overexpressing human prostacyclin synthase (hPGIS) demonstrated reversal of MCT-induced upregulation of miRs 17, 21, and 223 and an increase in levels of miR-424 and miR-503. Reduction in bone morphogenetic receptor 2 (BMPR2) messenger (m)RNA expression was not altered by A223, whereas human prostacyclin synthase overexpression restored BMPR2 mRNA to levels in MCT PAH to levels measured in naive controls. Conclusions Inhibition of miR-223 did not attenuate MCT PAH, whereas human prostacyclin synthase overexpression restored miRNA levels in MCT PAH to levels detected in naïve rats. These data may establish a paradigm linking attenuation of PAH to restoration of BMPR2 signaling.
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23
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Fan SJ, Li HB, Cui G, Kong XL, Sun LL, Zhao YQ, Li YH, Zhou J. miRNA-149* promotes cell proliferation and suppresses apoptosis by mediating JunB in T-cell acute lymphoblastic leukemia. Leuk Res 2015; 41:62-70. [PMID: 26725775 DOI: 10.1016/j.leukres.2015.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/03/2015] [Accepted: 11/28/2015] [Indexed: 12/29/2022]
Abstract
MicroRNA-149* (miRNA-149*) functions as an oncogenic regulator in human melanoma. However, the effect of miRNA-149* on T-cell acute lymphoblastic leukemia (T-ALL) is unclear. Here we aimed to analyze the effects of miRNA-149* on in vitro T-ALL cells and to uncover the target for miRNA-149* in these cells. The miRNA-149* level was determined in multiple cell lines and bone marrow cells derived from patients with T-ALL, B acute lymphoblastic leukemia (B-ALL), acute myelocytic leukemia (AML), and healthy donors. We found that miRNA-149* was highly expressed in T-ALL cell lines and T-ALL patients' bone marrow samples. JunB was identified as a direct target of miR-149*. miRNA-149* mimics downregulated JunB levels in Molt-4 and Jurkat cells, while miRNA-149* inhibitors dramatically upregulated JunB expression in these cells. miRNA-149* mimics promoted proliferation, decreased the proportion of cells in G1 phase, and reduced cell apoptosis in T-ALL cells, while miRNA-149* inhibitors prevented these effects. miRNA-149* mimics downregulated p21 and upregulated cyclinD1, 4EBP1, and p70s6k in Molt-4 and Jurkat cells. Again, inhibitors prevented these effects. Our findings demonstrate that miRNA-149* may serve as an oncogenic regulator in T-ALL by negatively regulating JunB.
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Affiliation(s)
- Sheng-Jin Fan
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Hui-Bo Li
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Gang Cui
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Xiao-Lin Kong
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Li-Li Sun
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Yan-Qiu Zhao
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Ying-Hua Li
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
| | - Jin Zhou
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
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24
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Diener Y, Walenda T, Jost E, Brümmendorf TH, Bosio A, Wagner W, Bissels U. MicroRNA expression profiles of serum from patients before and after chemotherapy. GENOMICS DATA 2015; 6:125-7. [PMID: 26697352 PMCID: PMC4664708 DOI: 10.1016/j.gdata.2015.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 11/11/2022]
Abstract
Recovery of the blood and immune system after chemotherapy requires proliferation of hematopoietic stem and progenitor cells (HPSCs). It has been shown that systemically released factors in serum after chemotherapy stimulate HSPC expansion in vitro. We wondered if microRNAs (miRNAs) circulating in serum could account for this effect. Therefore, we compared the miRNA expression profiles of serum from patients with hematologic malignancies before and after chemotherapy. In addition to a general decrease in miRNA expression after chemotherapy, we found 23 miRNAs to be significantly differentially expressed in serum before versus after chemotherapy. The miRNA microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series accession number GSE57570. Here, we provide a detailed protocol of the miRNA microarray and data analysis.
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Affiliation(s)
| | - Thomas Walenda
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Edgar Jost
- Department for Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Tim H Brümmendorf
- Department for Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Ute Bissels
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
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25
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Liu Y, Shi J, Chen X. Identification of novel targets for seasonal allergic rhinitis during and outside the pollen season by microarray analysis. Acta Otolaryngol 2015; 135:1330-6. [PMID: 26189617 DOI: 10.3109/00016489.2015.1067906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONCLUSION FOS, JUN, and DUSP1 could be used as candidate targets for the treatment of seasonal allergic rhinitis (SAR) during the pollen season, while KLF4 and CD163 could be used as candidate targets outside the pollen season. OBJECTIVES The aim of this study is to screen novel genes related to SAR during and outside the pollen season, by using microarray analysis. METHODS The mRNA expression profile (GSE50101) of CD4(+) T cells from SAR and healthy controls during and outside the pollen season was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were then screened with the cut-off criteria of fold change larger than 1.5 and p-value less than 0.05. RESULTS A total of 47 DEGs were identified. Ten DEGs were shared by SAR patient samples during and outside the pollen season, while four and 23 DEGs were specific to during and outside the pollen season, respectively. Five miRNAs were screened in this study. Among these miRNAs, miR-139, miR-101, miR-29A, and miR-181 could target FOS; miR-200 and miR-29A could target KLF4; miR-101 and miR-200 could target DUSP1; miR-139 and miR-181 could target JUN and CD163, respectively.
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26
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Walenda T, Diener Y, Jost E, Morin-Kensicki E, Goecke TW, Bosio A, Rath B, Brümmendorf TH, Bissels U, Wagner W. MicroRNAs and Metabolites in Serum Change after Chemotherapy: Impact on Hematopoietic Stem and Progenitor Cells. PLoS One 2015; 10:e0128231. [PMID: 26024523 PMCID: PMC4449031 DOI: 10.1371/journal.pone.0128231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/24/2015] [Indexed: 11/21/2022] Open
Abstract
Hematopoietic regeneration after high dose chemotherapy necessitates activation of the stem cell pool. There is evidence that serum taken after chemotherapy comprises factors stimulating proliferation and self-renewal of CD34+ hematopoietic stem and progenitor cells (HSPCs) – however, the nature of these feedback signals is yet unclear. Here, we addressed the question if specific microRNAs (miRNAs) or metabolites are affected after high dose chemotherapy. Serum taken from the same patients before and after chemotherapy was supplemented for in vitro cultivation of HSPCs. Serum taken after chemotherapy significantly enhanced HSPC proliferation, better maintained a CD34+ immunophenotype, and stimulated colony forming units. Microarray analysis revealed that 23 miRNAs changed in serum after chemotherapy – particularly, miRNA-320c and miRNA-1275 were down-regulated whereas miRNA-3663-3p was up-regulated. miRNA-320c was exemplarily inhibited by an antagomiR, which seemed to increase proliferation. Metabolomic profiling demonstrated that 44 metabolites were less abundant, whereas three (including 2-hydroxybutyrate and taurocholenate sulphate) increased in serum upon chemotherapy. Nine of these metabolites were subsequently tested for effects on HSPCs in vitro, but none of them exerted a clear concentration dependent effect on proliferation, immunophenotype and colony forming unit formation. Taken together, serum profiles of miRNAs and metabolites changed after chemotherapy. Rather than individually, these factors may act in concert to recruit HSPCs into action for hematopoietic regeneration.
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Affiliation(s)
- Thomas Walenda
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Edgar Jost
- Department for Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Tamme W. Goecke
- Department of Obstetrics and Gynecology, RWTH Aachen University Medical School, Aachen, German
| | | | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen, Germany
| | - Tim H. Brümmendorf
- Department for Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Ute Bissels
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
- * E-mail:
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and, therefore, biological processes in different tissues. A major function of miRNAs in adipose tissue is to stimulate or inhibit the differentiation of adipocytes, and to regulate specific metabolic and endocrine functions. Numerous miRNAs are present in human adipose tissue; however, the expression of only a few is altered in individuals with obesity and type 2 diabetes mellitus or are differentially expressed in various adipose depots. In humans, obesity is associated with chronic low-grade inflammation that is regulated by signal transduction networks, in which miRNAs, either directly or indirectly (through regulatory elements such as transcription factors), influence the expression and secretion of inflammatory proteins. In addition to their diverse effects on signalling, miRNAs and transcription factors can interact to amplify the inflammatory effect. Although additional miRNA signal networks in human adipose tissue are not yet known, similar regulatory circuits have been described in brown adipose tissue in mice. miRNAs can also be secreted from fat cells into the circulation and serve as markers of disturbed adipose tissue function. Given their role in regulating transcriptional networks, miRNAs in adipose tissue might offer tangible targets for treating metabolic disorders.
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Affiliation(s)
- Peter Arner
- Lipid Laboratory, Department of Medicine Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Agné Kulyté
- Lipid Laboratory, Department of Medicine Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
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28
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Hou B, Murata M, Said AS, Sakaida H, Masuda S, Takahashi T, Zhang Z, Takeuchi K. Changes of micro-RNAs in asymptomatic subjects sensitized to Japanese cedar pollen after prophylactic sublingual immunotherapy. ALLERGY & RHINOLOGY 2015; 6:33-8. [PMID: 25675113 PMCID: PMC4388874 DOI: 10.2500/ar.2015.6.0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Japanese cedar pollinosis is the predominant seasonal allergic rhinitis in Japan, and it has increased in prevalence during the past 10 years. Sublingual immunotherapy (SLIT) is considered a safe and effective treatment for pollinosis. Micro-RNAs (miRNAs) are a class of short single-stranded RNA molecules that posttranscriptionally silence gene expression and may mediate allergic immune responses. The aim of this study was to investigate the miRNA alteration in asymptomatic subjects sensitized to Japanese cedar pollen under prophylactic SLIT under part of a randomized, double-blind, placebo-controlled, multiple-center trial. Analysis was undertaken in 15 asymptomatic subjects sensitized to Japanese cedar pollen–specific IgE (ImmunoCAP class ≥2) who participated in 2013. The SLIT group (n = 6) received standardized Japanese cedar pollen extract and the placebo group (n = 9) received an inactive placebo for 5 months covering the cedar pollen season. Changes in serum miRNAs were measured by real-time quantitative polymerase chain reaction to determine whether SLIT had effects on profiles of circulating miRNA. Seven subjects in the placebo group developed pollinosis symptoms, whereas no subjects in the SLIT group did (p = 0.007). Serum hsa-miR-223 was significantly up-regulated in postseason compared with preseason samples. The hsa-let-7b was significantly more down-regulated in postseason than in preseason samples from the placebo group; however, no significant differences were observed in those from the SLIT group. A significant decrease in circulating let-7b was also observed in the subjects who developed symptoms. Prophylactic SLIT was effective in preventing the development of pollinosis. Alterations in miRNA expression occurred in asymptomatic, sensitized subjects during cedar pollen season.
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Affiliation(s)
- Bo Hou
- Department of Otorhinolaryngology, Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, Japan
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29
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Wronska A, Kurkowska-Jastrzebska I, Santulli G. Application of microRNAs in diagnosis and treatment of cardiovascular disease. Acta Physiol (Oxf) 2015; 213:60-83. [PMID: 25362848 DOI: 10.1111/apha.12416] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/08/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022]
Abstract
Cardiovascular disease (CVD) is a major cause of morbidity and mortality worldwide. Innovative, more stringent diagnostic and prognostic biomarkers and effective treatment options are needed to lessen its burden. In recent years, microRNAs have emerged as master regulators of gene expression - they bind to complementary sequences within the mRNAs of their target genes and inhibit their expression by either mRNA degradation or translational repression. microRNAs have been implicated in all major cellular processes, including cell cycle, differentiation and metabolism. Their unique mode of action, fine-tuning gene expression rather than turning genes on/off, and their ability to simultaneously regulate multiple elements of relevant pathways makes them enticing potential biomarkers and therapeutic targets. Indeed, cardiovascular patients have specific patterns of circulating microRNA levels, often early in the disease process. This article provides a systematic overview of the role of microRNAs in the pathophysiology, diagnosis and treatment of CVD.
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Affiliation(s)
- A. Wronska
- Helen and Clyde Wu Center for Molecular Cardiology; Department of Physiology and Cellular Biophysics; College of Physicians and Surgeons of Columbia University; New York NY USA
| | - I. Kurkowska-Jastrzebska
- Department of Experimental and Clinical Pharmacology; Medical University of Warsaw; Warsaw Poland
- 2nd Department of Neurology; National Institute of Psychiatry and Neurology; Warsaw Poland
| | - G. Santulli
- Helen and Clyde Wu Center for Molecular Cardiology; Department of Physiology and Cellular Biophysics; College of Physicians and Surgeons of Columbia University; New York NY USA
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30
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Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M. Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Med 2014; 6:82. [PMID: 25473422 PMCID: PMC4254417 DOI: 10.1186/s13073-014-0082-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many common diseases, such as asthma, diabetes or obesity, involve
altered interactions between thousands of genes. High-throughput techniques (omics)
allow identification of such genes and their products, but functional understanding
is a formidable challenge. Network-based analyses of omics data have identified
modules of disease-associated genes that have been used to obtain both a systems
level and a molecular understanding of disease mechanisms. For example, in allergy a
module was used to find a novel candidate gene that was validated by functional and
clinical studies. Such analyses play important roles in systems medicine. This is an
emerging discipline that aims to gain a translational understanding of the complex
mechanisms underlying common diseases. In this review, we will explain and provide
examples of how network-based analyses of omics data, in combination with functional
and clinical studies, are aiding our understanding of disease, as well as helping to
prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve
significant problems and limitations, which will be discussed. We also highlight the
steps needed for clinical implementation.
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Affiliation(s)
- Mika Gustafsson
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Colm E Nestor
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Huan Zhang
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Albert-László Barabási
- Department of Physics, Biology and Computer Science, Center for Complex Network Research, Northeastern University, Boston, MA 02115 USA
| | - Sergio Baranzini
- Department of Neurology, University of California, San Francisco, CA 94143 USA
| | - Sören Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark ; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kian Fan Chung
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, SW3 6LY UK
| | - Howard J Federoff
- Department of Neurology and Neuroscience, Georgetown University Medical Center, Washington, DC 20057 USA
| | | | - Richard R Meehan
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Paola Picotti
- Institute of Biochemistry, University of Zürich, 8093 Zürich, Switzerland
| | - Miguel Àngel Pujana
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, 08908 Spain
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Kenneth Gc Smith
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK ; Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, CB2 0QQ UK
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Pablo Villoslada
- Center of Neuroimmunology and Department of Neurology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, 08028 Barcelona, Spain
| | - Mikael Benson
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
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31
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Bruhn S, Fang Y, Barrenäs F, Gustafsson M, Zhang H, Konstantinell A, Krönke A, Sönnichsen B, Bresnick A, Dulyaninova N, Wang H, Zhao Y, Klingelhöfer J, Ambartsumian N, Beck MK, Nestor C, Bona E, Xiang Z, Benson M. A generally applicable translational strategy identifies S100A4 as a candidate gene in allergy. Sci Transl Med 2014; 6:218ra4. [PMID: 24401939 DOI: 10.1126/scitranslmed.3007410] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (TH2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.
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Affiliation(s)
- Sören Bruhn
- The Center for Individualized Medication, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
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The miRNA-mediated cross-talk between transcripts provides a novel layer of posttranscriptional regulation. ADVANCES IN GENETICS 2014; 85:149-99. [PMID: 24880735 DOI: 10.1016/b978-0-12-800271-1.00003-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Endogenously expressed transcripts that are posttranscriptionally regulated by the same microRNAs (miRNAs) will, in principle, compete for the binding of their shared small noncoding RNA regulators and modulate each other's abundance. Recently, the levels of some coding as well as noncoding transcripts have indeed been found to be regulated in this way. Transcripts that engage in such regulatory interactions are referred to as competitive endogenous RNAs (ceRNAs). This novel layer of posttranscriptional regulation has been shown to contribute to diverse aspects of organismal and cellular biology, despite the number of functionally characterized ceRNAs being as yet relatively low. Importantly, increasing evidence suggests that the dysregulation of some ceRNA interactions is associated with disease etiology, most preeminently with cancer. Here we review how posttranscriptional regulation by miRNAs contributes to the cross-talk between transcripts and review examples of known ceRNAs by highlighting the features underlying their interactions and what might be their biological relevance.
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