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Wang T, Zheng J, Pan Y, Zhuang Z, Zeng Y. Investigation of key miRNAs and Target-mRNA in Kaposi's sarcoma using bioinformatic methods. Heliyon 2024; 10:e29502. [PMID: 38660282 PMCID: PMC11041027 DOI: 10.1016/j.heliyon.2024.e29502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Kaposi's sarcoma (KS) is the second most common tumor in human immunodeficiency virus (HIV) infected patients worldwide. While many miRNAs have been confirmed to be involved in KS biological processes, no relevant studies have combined miRNA and mRNA expression profiles using KS patient tissue biopsies. In this study, we performed transcriptome sequencing on tumor and normal tissues from four KS patients and identified differentially expressed mRNA and miRNA, further performed target gene prediction and enrichment analysis. 19,551 target-mRNAs were identified by predicting 106 miRNAs, with 553 overlapping with 571 significantly differentially expressed mRNAs. Enrichment analysis showed significant involvement of the Ubiquitin-mediated proteolysis pathway. Additionally, the miRNA-mRNA interaction network was established, and the topological score of Cytohubba's algorithm was calculated for comparison with three other datasets. The Mutual Clustering Coefficient (MCC) scoring ranking placed ZBTB34, NFIB, and RORA as the top three mRNAs, while hsa-miR-16-5p, hsa-miR-27a-3p, hsa-miR-340-5p, hsa-miR-182-5p, and hsa-miR-186-5p ranked as the top five miRNAs. Hsa-miR-101-3p is the only miRNA that appears both in the top 10 MCC scores and at the intersection of the other two datasets. Finally, qRT-PCR was used to validate the findings at the cellular level. In summary, the miRNA analysis results indicated that hsa-miR-101-3p could be used as a potential diagnostic or therapeutic marker in future studies. Moreover, the mRNA analysis results suggested that the histone binding pathways involved in mRNAs and ubiquitin-related biological processes were closely associated with KS and could serve as promising biomarkers for the diagnosis and treatment of this disease.
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Affiliation(s)
- Tianye Wang
- Precision Clinical Laboratory, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Jun Zheng
- Precision Clinical Laboratory, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yangyang Pan
- Precision Clinical Laboratory, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Zhaowei Zhuang
- Precision Clinical Laboratory, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yan Zeng
- Precision Clinical Laboratory, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
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2
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Kazemi S, Mirzaei R, Karampoor S, Hosseini-Fard SR, Ahmadyousefi Y, Soltanian AR, Keramat F, Saidijam M, Alikhani MY. Circular RNAs in tuberculosis: From mechanism of action to potential diagnostic biomarker. Microb Pathog 2023; 185:106459. [PMID: 37995882 DOI: 10.1016/j.micpath.2023.106459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/01/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), continues to be a major global health concern. Understanding the molecular intricacies of TB pathogenesis is crucial for developing effective diagnostic and therapeutic approaches. Circular RNAs (circRNAs), a class of single-stranded RNA molecules characterized by covalently closed loops, have recently emerged as potential diagnostic biomarkers in various diseases. CircRNAs have been demonstrated to modulate the host's immunological responses against TB, specifically by reducing monocyte apoptosis, augmenting autophagy, and facilitating macrophage polarization. This review comprehensively explores the roles and mechanisms of circRNAs in TB pathogenesis. We also discuss the growing body of evidence supporting their utility as promising diagnostic biomarkers for TB. By bridging the gap between fundamental circRNA biology and TB diagnostics, this review offers insights into the exciting potential of circRNAs in combatting this infectious disease.
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Affiliation(s)
- Sima Kazemi
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaghoub Ahmadyousefi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Reza Soltanian
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Iran
| | - Fariba Keramat
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Yousef Alikhani
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran; Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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3
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Vuillier F, Li Z, Black I, Cruciani M, Rubino E, Michel F, Pellegrini S. IFN-I inducible miR-3614-5p targets ADAR1 isoforms and fine tunes innate immune activation. Front Immunol 2022; 13:939907. [PMID: 35935998 PMCID: PMC9354889 DOI: 10.3389/fimmu.2022.939907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of innate immune responses is essential for maintenance of immune homeostasis and development of an appropriate immunity against microbial infection. We show here that miR-3614-5p, product of the TRIM25 host gene, is induced by type I interferon (IFN-I) in several human non-immune and immune cell types, in particular in primary myeloid cells. Studies in HeLa cells showed that miR-3614-5p represses both p110 and p150 ADAR1 and reduces constitutive and IFN-induced A-to-I RNA editing. In line with this, activation of innate sensors and expression of IFN-β and the pro-inflammatory IL-6 are promoted. MiR-3614-5p directly targets ADAR1 transcripts by binding to one specific site in the 3’UTR. Moreover, we could show that endogenous miR-3614-5p is associated with Ago2 and targets ADAR1 in IFN-stimulated cells. Overall, we propose that, by reducing ADAR1, IFN-I-induced miR-3614-5p contributes to lowering the activation threshold of innate sensors. Our findings provide new insights into the role of miR-3614-5p, placing it as a potential fine tuner of dsRNA metabolism, cell homeostasis and innate immunity.
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Affiliation(s)
- Françoise Vuillier
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Zhi Li
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Iain Black
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Melania Cruciani
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Erminia Rubino
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Frédérique Michel
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Sandra Pellegrini
- Cytokine Signaling Unit, Department of Immunology, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
- *Correspondence: Sandra Pellegrini,
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4
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Kitsou K, Iliopoulou M, Spoulou V, Lagiou P, Magiorkinis G. Viral Causality of Human Cancer and Potential Roles of Human Endogenous Retroviruses in the Multi-Omics Era: An Evolutionary Epidemiology Review. Front Oncol 2021; 11:687631. [PMID: 34778024 PMCID: PMC8586426 DOI: 10.3389/fonc.2021.687631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Being responsible for almost 12% of cancers worldwide, viruses are among the oldest known and most prevalent oncogenic agents. The quality of the evidence for the in vivo tumorigenic potential of microorganisms varies, thus accordingly, viruses were classified in 4 evidence-based categories by the International Agency for Research on Cancer in 2009. Since then, our understanding of the role of viruses in cancer has significantly improved, firstly due to the emergence of high throughput sequencing technologies that allowed the “brute-force” recovery of unknown viral genomes. At the same time, multi-omics approaches unravelled novel virus-host interactions in stem-cell biology. We now know that viral elements, either exogenous or endogenous, have multiple sometimes conflicting roles in human pathophysiology and the development of cancer. Here we integrate emerging evidence on viral causality in human cancer from basic mechanisms to clinical studies. We analyze viral tumorigenesis under the scope of deep-in-time human-virus evolutionary relationships and critically comment on the evidence through the eyes of clinical epidemiology, firstly by reviewing recognized oncoviruses and their mechanisms of inducing tumorigenesis, and then by examining the potential role of integrated viruses in our genome in the process of carcinogenesis.
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Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Iliopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Gono T, Okazaki Y, Kuwana M. Antiviral proinflammatory phenotype of monocytes in anti-MDA5 antibody-associated interstitial lung disease. Rheumatology (Oxford) 2021; 61:806-814. [PMID: 33890985 DOI: 10.1093/rheumatology/keab371] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/17/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To evaluate upstream and downstream regulators leading to macrophage activation and subsequent cytokine storm in patients with anti-melanoma differentiation-associated gene 5 (MDA5) antibody-associated interstitial lung disease (ILD). METHODS We conducted an integrated miRNA-mRNA association analysis using circulating monocytes from 3 patients with anti-MDA5-associated ILD and 3 healthy controls and identified disease pathways and a regulator effect network by Ingenuity Pathway Analysis (IPA). The expression of relevant genes and proteins was verified using an independent validation cohort, including 6 patients with anti-MDA5-associated ILD, 5 with anti-aminoacyl tRNA synthetase antibody-associated ILD, and 6 healthy controls. RESULTS IPA identified 26 matched pairs of downregulated miRNA and upregulated mRNAs and revealed that canonical pathways mediated by type I IFN signaling and C-C motif ligand 2 (CCL2) were responsible for the pathogenic process (P < 0.05 for all pathways). The regulatory network model identified IFN-β; Toll-like receptors 3, 7, and 9; and PU.1 as upstream regulators, while the downstream effect of this network converged at the inhibition of viral infection. mRNA and protein expression analysis using validation cohort showed a trend towards the increased expression of relevant molecules identified by IPA in patients with anti-MDA5-associated ILD compared with those with anti-aminoacyl tRNA synthetase antibody-associated ILD or healthy controls. The expression of all relevant genes in monocytes and serum levels of CCL2 and IFN-β declined after treatment in survivors with anti-MDA5-associated ILD. CONCLUSION An antiviral proinflammatory network orchestrated primarily by activated monocytes/macrophages might be responsible for cytokine storm in anti-MDA5-associated ILD.
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Affiliation(s)
- Takahisa Gono
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Yuka Okazaki
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
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6
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Zhang Y, Xia S, Wang T, Wang S, Yuan D, Li F, Wang X. Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat. BMC Genomics 2020; 21:430. [PMID: 32586272 PMCID: PMC7318507 DOI: 10.1186/s12864-020-06799-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Background During goat embryonic morphogenesis and postnatal initiation of hair follicle (HF) regeneration, dermal papilla (DP) cells play a vital role in hair formation. Growing evidence shows that microRNAs (miRNAs) participate in HF development and DP cell proliferation. However, the molecular mechanisms have not been thoroughly investigated. Result In this study, we utilized miRNA sequencing (miRNA-Seq) to identify differentially expressed miRNAs at different HF cycling stages (anagen and telogen). MiRNA-Seq has identified 411 annotated miRNAs and 130 novel miRNAs in which 29 miRNAs were up-regulated and 32 miRNAs were down-regulated in the anagen phase compared to the telogen phase. Target gene prediction and functional enrichment analysis indicated some major biological pathways related to hair cycling, such as Wnt signaling pathways, ECM-receptor interaction, VEGF signaling pathway, biosynthesis of amino acids, metabolic pathways, ribosome and oxidative phosphorylation. Also, we explored the function of chi-miR-30b-5p in regulating hair growth cycle. Similar to the HF cycling, DP cells were isolated from skin and used to investigate miRNA functions. The MTT and EdU assays showed that the viability and proliferation of DP cells were inhibited or promoted after the transfection of chi-miR-30b-5p mimic or inhibitor, respectively. Bioinformatics analysis revealed CaMKIIδ as a candidate target gene of chi-miR-30b-5p, and the dual-luciferase and western blot assay demonstrated that chi-miR-30b-5p bound to the 3’UTR of CaMKIIδ and further inhibited its translation. Conclusion Chi-miR-30b-5p was found to be highly expressed in the telogen than that in the anagen phase and could inhibit the proliferation of DP cells by targeting CaMKIIδ. Our study provides new information on the regulatory functions of miRNAs during HF development.
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Affiliation(s)
- Yuelang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Present address: College of Animal Science & Technology, Northwest A&F University, No.3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Sizhe Xia
- The College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Tianci Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shanhe Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dan Yuan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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7
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Zhang X, Zhang Q, Wu Q, Tang H, Ye L, Zhang Q, Hua D, Zhang Y, Li F. Integrated analyses reveal hsa_circ_0028883 as a diagnostic biomarker in active tuberculosis. INFECTION GENETICS AND EVOLUTION 2020; 83:104323. [PMID: 32305357 DOI: 10.1016/j.meegid.2020.104323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are known to be closely involved in various diseases progression. Nevertheless, their function and underlying mechanisms in tuberculosis (TB) remain largely unknown. The aim of the present study was to explore their potential diagnostic values in TB. We downloaded the gene expression datasets of circRNA (GSE117563 and GSE106953), microRNA (miRNA, dataset GSE29190) and mRNA (GSE54992) from Gene Expression Omnibus (GEO) database. A competing endogenous RNAs (ceRNA) network was constructed based on circRNA-miRNA-mRNA potential interaction. We also constructed a circRNA-miRNA-hub gene regulatory module by using the Cytohubba. Gene ontology (GO) as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to predict their biological functions. By further validation, the expression level of hsa_circ_0028883 and hsa-miR-409-5p were detected by qRT-PCR in 20 active TB patients and 20 healthy donors. Then, Receiver Operating Characteristic (ROC) was constructed to evaluate the diagnostic values of hsa_circ_0028883. 1 differentially expressed circRNA (DE-circRNA), 1 differentially expressed miRNA (DE-miRNA), and 44 differentially expressed mRNAs (DE-mRNAs) were selected for the construction of ceRNA network in TB. A circRNA-miRNA-hub gene (mRNA) sub-network was constructed based on 1 DE-circRNA, 1 DE-miRNA, and 8 DE-mRNAs. Hsa_circ_0028883/hsa-miR-409-5p/mRNA interactions may provide some novel mechanisms for active TB. GO and KEGG pathway analysis indicated the possible function of hsa_circ_0028883 with TB. ROC analysis revealed that hsa_circ_0028883 had potential value for TB diagnosis. Hsa_circ_0028883 is a potentially reliable biomarker to diagnose active TB, but there remains a need to further study the mechanism in TB.
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Affiliation(s)
- Xiaolin Zhang
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Qian Zhang
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Qingguo Wu
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Haicheng Tang
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Linxiong Ye
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Qilong Zhang
- Department of Critical Care Medicine, Jiangxi Chest Hospital, Nanchang 330006, China
| | - Demi Hua
- Department of Tuberculosis, The Third People's Hospital of Tibet Autonomous Region, Lhasa 850000, China
| | - Yunbin Zhang
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Feng Li
- Department of Respirology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
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Zhang J, Pu XM, Xiong Y. kshv-mir-k12-1-5p promotes cell growth and metastasis by targeting SOCS6 in Kaposi's sarcoma cells. Cancer Manag Res 2019; 11:4985-4995. [PMID: 31213914 PMCID: PMC6549767 DOI: 10.2147/cmar.s198411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/07/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Kaposi’s sarcoma (KS) is a highly disseminated angiogenic tumour of endothelial cells. Many deregulated miRNAs, including kshv-mir-k12-1-5p, have been identified in KS. kshv-mir-k12-1-5p plays important roles in KS. However, the underlying mechanism is not fully understood. The aim of this study was to investigate the exact functions of kshv-mir-k12-1-5p in KS cells. Materials and methods: The biological functions of kshv-mir-k12-1-5p were studied using CCK-8, apoptosis, migration and invasion assays. Bioinformatics software was used to identify the target gene (SOCS6) of kshv-mir-k12-1-5p. A dual luciferase assay, Western blot (WB) and quantitative real-time polymerase chain reaction (q-PCR) were performed to further verify the target gene. The underlying molecular mechanisms of kshv-mir-k12-1-5p in KS cells were also explored. Results: kshv-mir-k12-1-5p can promote the proliferation, migration and invasion of KS cells and inhibit cell apoptosis. Suppressor of cytokine signalling 6 (SOCS6) was identified as a direct target of kshv-mir-k12-1-5p, and kshv-mir-k12-1-5p can downregulate SOCS6 expression. In addition, knockdown of SOCS6 rescued the effects of kshv-mir-k12-1-5p inhibitor. Hence, a direct relationship between kshv-mir-k12-1-5p and SOCS6 was confirmed. Conclusions: kshv-mir-k12-1-5p promotes the malignant phenotype of KS cells by targeting SOCS6, suggesting that kshv-mir-k12-1-5p could be a potential therapeutic target for KS.
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Affiliation(s)
- Jing Zhang
- Postgraduate College of Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China.,Department of Pathology, Affiliated Traditional Chinese Medicine Hospital, Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China
| | - Xiong-Ming Pu
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, People's Republic of China
| | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing, People's Republic of China
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Wu J, Yang J, Ding J, Guo X, Zhu XQ, Zheng Y. Exosomes in virus-associated cancer. Cancer Lett 2018; 438:44-51. [PMID: 30219505 DOI: 10.1016/j.canlet.2018.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 12/13/2022]
Abstract
Exosomes are phospholipid bilayer membrane-enclosed vesicles in a size from 30 to 150 nm, carrying a variety of active components, such as proteins, mRNA and miRNAs, and are involved in intercellular communication. Exosomes are released by almost all living cells and detected in various biological fluids. Viruses especially oncogenic viruses have been reported to influence the formation of virus-associated cancer through reshaping the tumor microenvironment via exosomes. In this review, a role of exosomes released by oncogenic virus-infected cells in promoting or inhibiting cancer formation is outlined. Moreover, the prospects and challenges of exosome applications in cancer therapies are critically discussed.
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Affiliation(s)
- Jin'en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China
| | - Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China
| | - Juntao Ding
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, 225009, China
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, 225009, China.
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10
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Isaac C, Patel TR, Zovoilis A. Non-coding RNAs in virology: an RNA genomics approach. Biotechnol Genet Eng Rev 2018; 34:90-106. [PMID: 29865927 DOI: 10.1080/02648725.2018.1471642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advances in sequencing technologies and bioinformatic analysis techniques have greatly improved our understanding of various classes of RNAs and their functions. Despite not coding for proteins, non-coding RNAs (ncRNAs) are emerging as essential biomolecules fundamental for cellular functions and cell survival. Interestingly, ncRNAs produced by viruses not only control the expression of viral genes, but also influence host cell regulation and circumvent host innate immune response. Correspondingly, ncRNAs produced by the host genome can play a key role in host-virus interactions. In this article, we will first discuss a number of types of viral and mammalian ncRNAs associated with viral infections. Subsequently, we also describe the new possibilities and opportunities that RNA genomics and next-generation sequencing technologies provide for studying ncRNAs in virology.
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Affiliation(s)
- Christopher Isaac
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
| | - Trushar R Patel
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases , Cumming School of Medicine, University of Calgary , Calgary , Canada.,c DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada
| | - Athanasios Zovoilis
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
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11
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Kabekkodu SP, Shukla V, Varghese VK, D' Souza J, Chakrabarty S, Satyamoorthy K. Clustered miRNAs and their role in biological functions and diseases. Biol Rev Camb Philos Soc 2018; 93:1955-1986. [PMID: 29797774 DOI: 10.1111/brv.12428] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 04/20/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs known to regulate expression of protein-coding genes. A large proportion of miRNAs are highly conserved, localized as clusters in the genome, transcribed together from physically adjacent miRNAs and show similar expression profiles. Since a single miRNA can target multiple genes and miRNA clusters contain multiple miRNAs, it is important to understand their regulation, effects and various biological functions. Like protein-coding genes, miRNA clusters are also regulated by genetic and epigenetic events. These clusters can potentially regulate every aspect of cellular function including growth, proliferation, differentiation, development, metabolism, infection, immunity, cell death, organellar biogenesis, messenger signalling, DNA repair and self-renewal, among others. Dysregulation of miRNA clusters leading to altered biological functions is key to the pathogenesis of many diseases including carcinogenesis. Here, we review recent advances in miRNA cluster research and discuss their regulation and biological functions in pathological conditions.
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Affiliation(s)
- Shama P Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Vinay K Varghese
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jeevitha D' Souza
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
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12
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Li Z, Rouse R. Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury. BMC Genomics 2018; 19:297. [PMID: 29699496 PMCID: PMC5922017 DOI: 10.1186/s12864-018-4657-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
Background Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology. RNAs were derived from pancreatic tissues obtained in experiments characterizing the serum levels of candidate miRNA biomarkers in response to acute pancreatic injury in rats. Results No correlation was discovered between tissue and serum levels of the miRNAs. A combination of differential gene expression, novel delayed anti-correlation analysis and experimental database interrogation was used to identify messenger RNAs and miRNAs that experienced significant expression change across the time series, that were negatively correlated, that were complementary in sequence, and that had experimentally supported relationships. This approach yielded a complex signaling network for future investigation and a link for the specific candidate miRNA biomarkers, miR-216a-5p and miR-217-5p, to cellular processes that were in fact the prominent histopathology observations in the same experimental samples. RNA quality bias by treatment was observed in the study samples and a statistical correction was applied. The relevance and impact of that correction on significant results is discussed. Conclusion The described approach allowed extraction of miRNA function from genomic data and defined a mechanistic anchor for these miRNAs as biomarkers. Functional and mechanistic conclusions are supported by histopathology findings. Electronic supplementary material The online version of this article (10.1186/s12864-018-4657-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhihua Li
- U. S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, Division of Applied Regulatory Science, HFD-910, White Oak Federal Research Center, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Rodney Rouse
- U. S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, Division of Applied Regulatory Science, HFD-910, White Oak Federal Research Center, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
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13
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Screening of miRNA profiles and construction of regulation networks in early and late lactation of dairy goat mammary glands. Sci Rep 2017; 7:11933. [PMID: 28931951 PMCID: PMC5607250 DOI: 10.1038/s41598-017-12297-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/06/2017] [Indexed: 01/12/2023] Open
Abstract
In recent years, studies related to the expression profiles of miRNAs in the dairy goat mammary gland were performed, but regulatory mechanisms in the physiological environment and the dynamic homeostasis of mammary gland development and lactation are not clear. In the present study, sequencing data analysis of early and late lactation uncovered a total of 1,487 unique miRNAs, including 45 novel miRNA candidates and 1,442 known and conserved miRNAs, of which 758 miRNAs were co-expressed and 378 differentially expressed with P < 0.05. Moreover, 76 non-redundant target genes were annotated in 347 GO consortiums, with 3,143 candidate target genes grouped into 33 pathways. Additionally, 18 predicted target genes of 214 miRNAs were directly annotated in mammary gland development and used to construct regulatory networks based on GO annotation and the KEGG pathway. The expression levels of seven known miRNAs and three novel miRNAs were examined using quantitative real-time PCR. The results showed that miRNAs might play important roles in early and late lactation during dairy goat mammary gland development, which will be helpful to obtain a better understanding of the genetic control of mammary gland lactation and development.
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14
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Herpesvirus microRNAs for use in gene therapy immune-evasion strategies. Gene Ther 2017; 24:385-391. [PMID: 28485720 DOI: 10.1038/gt.2017.37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/26/2017] [Accepted: 05/04/2017] [Indexed: 01/12/2023]
Abstract
Transplantation of allogeneic cells as well as of genetically corrected autologous cells are potent approaches to restore cellular functions in patients suffering from genetic diseases. The recipient's immune responses against non-self-antigens may compromise the survival of the grafted cells. Recipients of the graft may therefore require lifelong treatment with immunosuppressive drugs. An alternative approach to reduce graft rejection could involve the use of immune-evasion molecules. Expression of such molecules in cells of the graft may subvert recognition by the host's immune system. Viruses in particular are masters of exploitation and modulation of their hosts immune response. The Herpesviridae family provides a proof of concept for this as these viruses are capable to establish latency and a lifelong persistence in the infected hosts. While several viral proteins involved in immune evasion have been characterized, the Herpesviridae also encode a multitude of viral microRNA (miRNAs). Several of these miRNAs have been demonstrated to reduce the sensitivity of the infected cells to the destructive action of the host's immune cells. In this review, the miRNAs of some common herpesviruses that are associated with immune modulation will be discussed with a focus on their potential use in strategies aiming at generating non-immunogenic cells for transplantation.
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Viollet C, Davis DA, Tekeste SS, Reczko M, Ziegelbauer JM, Pezzella F, Ragoussis J, Yarchoan R. RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature. PLoS Pathog 2017; 13:e1006143. [PMID: 28046107 PMCID: PMC5234848 DOI: 10.1371/journal.ppat.1006143] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/13/2017] [Accepted: 12/19/2016] [Indexed: 01/09/2023] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) causes several tumors and hyperproliferative disorders. Hypoxia and hypoxia-inducible factors (HIFs) activate latent and lytic KSHV genes, and several KSHV proteins increase the cellular levels of HIF. Here, we used RNA sequencing, qRT-PCR, Taqman assays, and pathway analysis to explore the miRNA and mRNA response of uninfected and KSHV-infected cells to hypoxia, to compare this with the genetic changes seen in chronic latent KSHV infection, and to explore the degree to which hypoxia and KSHV infection interact in modulating mRNA and miRNA expression. We found that the gene expression signatures for KSHV infection and hypoxia have a 34% overlap. Moreover, there were considerable similarities between the genes up-regulated by hypoxia in uninfected (SLK) and in KSHV-infected (SLKK) cells. hsa-miR-210, a HIF-target known to have pro-angiogenic and anti-apoptotic properties, was significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Interestingly, expression of KSHV-encoded miRNAs was not affected by hypoxia. These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and that a substantial portion of hypoxia-induced changes in cellular gene expression are induced by KSHV infection. Therefore, targeting hypoxic pathways may be a useful way to develop therapeutic strategies for KSHV-related diseases.
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Affiliation(s)
- Coralie Viollet
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David A. Davis
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shewit S. Tekeste
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martin Reczko
- Institute of Molecular Oncology, Alexander Fleming Biomedical Sciences Research Center, Vari, Greece
| | - Joseph M. Ziegelbauer
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Francesco Pezzella
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Jiannis Ragoussis
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Institute of Molecular Oncology, Alexander Fleming Biomedical Sciences Research Center, Vari, Greece
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Wang L, Wang JK, Han LX, Zhuo JS, Du X, Liu D, Yang XQ. Characterization of miRNAs involved in response to poly(I:C) in porcine airway epithelial cells. Anim Genet 2016; 48:182-190. [PMID: 27878834 DOI: 10.1111/age.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) have been implicated in a variety of pathological conditions including infectious diseases. Knowledge of the miRNAs affected by poly(I:C), a synthetic analog of viral double-stranded RNA, in porcine airway epithelial cells (PAECs) contributes to understanding the mechanisms of swine viral respiratory diseases, which bring enormous economic loss worldwide every year. In this study, we used high throughput sequencing to profile miRNA expression in PAECs treated with poly(I:C) as compared to the untreated control. This approach revealed 23 differentially expressed miRNAs (DEMs), five of which have not been implicated in viral infection before. Nineteen of the 23 miRNAs were down-regulated including members of the miR-17-92 cluster, a well-known polycistronic oncomir and extensively involved in viral infection in humans. Target genes of DEMs, predicted using bioinformatic methods and validated by luciferase reporter analysis on two representative DEMs, were significantly enriched in several pathways including transforming growth factor-β signaling. A large quantity of sequence variations (isomiRs) were found including a substitution at position 5, which was verified to redirect miRNAs to a new spectrum of targets by luciferase reporter assay together with bioinformatics analysis. Twelve novel porcine miRNAs conserved in other species were identified by homology analysis together with cloning verification. Furthermore, the expression analysis revealed the potential importance of three novel miRNAs in porcine immune response to viruses. Overall, our data contribute to clarifying the mechanisms underlying the host immune response against respiratory viruses in pigs, and enriches the repertoire of porcine miRNAs.
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Affiliation(s)
- L Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - J K Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - L X Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - J S Zhuo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - X Du
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - D Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - X Q Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
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Purushothaman P, Uppal T, Sarkar R, Verma SC. KSHV-Mediated Angiogenesis in Tumor Progression. Viruses 2016; 8:E198. [PMID: 27447661 PMCID: PMC4974533 DOI: 10.3390/v8070198] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/18/2016] [Accepted: 07/07/2016] [Indexed: 12/14/2022] Open
Abstract
Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), is a malignant human oncovirus belonging to the gamma herpesvirus family. HHV-8 is closely linked to the pathogenesis of Kaposi's sarcoma (KS) and two other B-cell lymphoproliferative diseases: primary effusion lymphoma (PEL) and a plasmablastic variant of multicentric Castleman's disease (MCD). KS is an invasive tumor of endothelial cells most commonly found in untreated HIV-AIDS or immuno-compromised individuals. KS tumors are highly vascularized and have abnormal, excessive neo-angiogenesis, inflammation, and proliferation of infected endothelial cells. KSHV directly induces angiogenesis in an autocrine and paracrine fashion through a complex interplay of various viral and cellular pro-angiogenic and inflammatory factors. KS is believed to originate due to a combination of KSHV's efficient strategies for evading host immune systems and several pro-angiogenic and pro-inflammatory stimuli. In addition, KSHV infection of endothelial cells produces a wide array of viral oncoproteins with transforming capabilities that regulate multiple host-signaling pathways involved in the activation of angiogenesis. It is likely that the cellular-signaling pathways of angiogenesis and lymph-angiogenesis modulate the rate of tumorigenesis induction by KSHV. This review summarizes the current knowledge on regulating KSHV-mediated angiogenesis by integrating the findings reported thus far on the roles of host and viral genes in oncogenesis, recent developments in cell-culture/animal-model systems, and various anti-angiogenic therapies for treating KSHV-related lymphoproliferative disorders.
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Affiliation(s)
- Pravinkumar Purushothaman
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, 1664 N Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, 1664 N Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Roni Sarkar
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, 1664 N Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Subhash C Verma
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, 1664 N Virginia Street, MS 320, Reno, NV 89557, USA.
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Bioinformatic analysis of microRNA networks following the activation of the constitutive androstane receptor (CAR) in mouse liver. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1228-1237. [PMID: 27080131 DOI: 10.1016/j.bbagrm.2016.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/01/2016] [Accepted: 04/03/2016] [Indexed: 12/18/2022]
Abstract
The constitutive androstane receptor (CAR; NR1I3) is a member of the nuclear receptor superfamily that functions as a xenosensor, serving to regulate xenobiotic detoxification, lipid homeostasis and energy metabolism. CAR activation is also a key contributor to the development of chemical hepatocarcinogenesis in mice. The underlying pathways affected by CAR in these processes are complex and not fully elucidated. MicroRNAs (miRNAs) have emerged as critical modulators of gene expression and appear to impact many cellular pathways, including those involved in chemical detoxification and liver tumor development. In this study, we used deep sequencing approaches with an Illumina HiSeq platform to differentially profile microRNA expression patterns in livers from wild type C57BL/6J mice following CAR activation with the mouse CAR-specific ligand activator, 1,4-bis-[2-(3,5,-dichloropyridyloxy)] benzene (TCPOBOP). Bioinformatic analyses and pathway evaluations were performed leading to the identification of 51 miRNAs whose expression levels were significantly altered by TCPOBOP treatment, including mmu-miR-802-5p and miR-485-3p. Ingenuity Pathway Analysis of the differentially expressed microRNAs revealed altered effector pathways, including those involved in liver cell growth and proliferation. A functional network among CAR targeted genes and the affected microRNAs was constructed to illustrate how CAR modulation of microRNA expression may potentially mediate its biological role in mouse hepatocyte proliferation. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie.
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Strahan R, Uppal T, Verma SC. Next-Generation Sequencing in the Understanding of Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses 2016; 8:92. [PMID: 27043613 PMCID: PMC4848587 DOI: 10.3390/v8040092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/16/2022] Open
Abstract
Non-Sanger-based novel nucleic acid sequencing techniques, referred to as Next-Generation Sequencing (NGS), provide a rapid, reliable, high-throughput, and massively parallel sequencing methodology that has improved our understanding of human cancers and cancer-related viruses. NGS has become a quintessential research tool for more effective characterization of complex viral and host genomes through its ever-expanding repertoire, which consists of whole-genome sequencing, whole-transcriptome sequencing, and whole-epigenome sequencing. These new NGS platforms provide a comprehensive and systematic genome-wide analysis of genomic sequences and a full transcriptional profile at a single nucleotide resolution. When combined, these techniques help unlock the function of novel genes and the related pathways that contribute to the overall viral pathogenesis. Ongoing research in the field of virology endeavors to identify the role of various underlying mechanisms that control the regulation of the herpesvirus biphasic lifecycle in order to discover potential therapeutic targets and treatment strategies. In this review, we have complied the most recent findings about the application of NGS in Kaposi’s sarcoma-associated herpesvirus (KSHV) biology, including identification of novel genomic features and whole-genome KSHV diversities, global gene regulatory network profiling for intricate transcriptome analyses, and surveying of epigenetic marks (DNA methylation, modified histones, and chromatin remodelers) during de novo, latent, and productive KSHV infections.
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Affiliation(s)
- Roxanne Strahan
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Timsy Uppal
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
| | - Subhash C Verma
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N, Virginia Street, MS 320, Reno, NV 89557, USA.
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