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Yousfi FZE, Haroun AE, Nebhani C, Belayachi J, Askander O, Fahime EE, Fares H, Ennibi K, Abouqal R, Razine R, Bouhouche A. Prevalence of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans: implications for a North African Neanderthal connection. Arch Virol 2024; 169:109. [PMID: 38658463 PMCID: PMC11043147 DOI: 10.1007/s00705-024-06038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
The clinical presentation of COVID-19 shows high variability among individuals, which is partly due to genetic factors. The OAS1/2/3 cluster has been found to be strongly associated with COVID-19 severity. We examined this locus in the Moroccan population for the occurrence of the critical variant rs10774671 and its respective haplotype blocks. The frequency of single-nucleotide polymorphisms (SNPs) in the cluster of OAS immunity genes in 157 unrelated individuals of Moroccan origin was determined using an in-house exome database. OAS1 exon 6 of 71 SARS-CoV-2-positive individuals with asymptomatic/mild disease and 74 with moderate/severe disease was sequenced by the Sanger method. The genotypic, allelic, and haplotype frequencies of three SNPs were compared between these two groups. Finally, males in our COVID-19 series were genotyped for the Berber-specific marker E-M81. The prevalence of the OAS1 rs10774671-G allele in present-day Moroccans was found to be 40.4%, which is similar to that found in Europeans. However, it was found equally in both the Neanderthal GGG haplotype and the African GAC haplotype, with a frequency of 20% each. These two haplotypes, and hence the rs10774671-G allele, were significantly associated with protection against severe COVID-19 (p = 0.034, p = 0.041, and p = 0.008, respectively). Surprisingly, in men with the Berber-specific uniparental markers, the African haplotype was absent, while the prevalence of the Neanderthal haplotype was similar to that in Europeans. The protective rs10774671-G allele of OAS1 was found only in the Neanderthal haplotype in Berbers, the indigenous people of North Africa, suggesting that this region may have served as a stepping-stone for the passage of hominids to other continents.
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Affiliation(s)
- Fatima Zahra El Yousfi
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Abbas Ermilo Haroun
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Chaimae Nebhani
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Jihane Belayachi
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Acute Medical Unit, Ibn Sina University Hospital, Rabat, Morocco
| | - Omar Askander
- Faculty of Medical Science, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Elmostafa El Fahime
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
| | - Hakima Fares
- Intensive Care Department, Cheikh Zaid International Universitary Hospital, Rabat, Morocco
| | - Khalid Ennibi
- Virology, Infectious and Tropical Diseases Center, Hopital Militaire d'Instruction Mohammed V, Rabat, Morocco
| | - Redouane Abouqal
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Rachid Razine
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Ahmed Bouhouche
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco.
- Genomic Center of the Cheikh Zaid Foundation, Abulcasis International University of Health Sciences, Rabat, Morocco.
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Yang R, Du Y, Zhang M, Liu Y, Feng H, Liu R, Yang B, Xiao J, He P, Niu F. Multi-omics analysis reveals interferon-stimulated gene OAS1 as a prognostic and immunological biomarker in pan-cancer. Front Immunol 2023; 14:1249731. [PMID: 37928544 PMCID: PMC10623006 DOI: 10.3389/fimmu.2023.1249731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction OAS1(2'-5'-oligoadenylate synthetase 1) is a member of the Interferon-Stimulated Genes which plays an important role in the antiviral process. In recent years, the role of OAS1 in tumors has attracted attention, and it was found to be associated with prognosis in several tumors. However, the mechanism by which OAS1 affects tumors is unclear and pan-cancer study of OAS1 is necessary to better understand its implication in cancers. Methods The expression, prognostic value, genetic alteration, alternative splicing events of OAS1 in pan-cancers were analyzed using TCGA, GTEx, HPA, GEPIA and OncoSplicing databases. OAS1 associated immune cell infiltration was evaluated using the ESTIMATE, xCell, CIBERSORT and QUANTISEQ algorithm. Single cell transcriptome data download using TISH database. Finally, the roles of the OAS1 on apoptosis, migration and invasion were investigated in two pancreatic cancer cells. Results Our results revealed significant differences in OAS1 expression among various tumors, which had prognostic implications. In addition, we investigated the impact of OAS1 on genomic stability, methylation status, and other factors across different types of cancer, and the effects of these factors on prognosis. Notably, our study also demonstrated that OAS1 overexpression can contribute to CTL dysfunction and macrophage M2 polarization. In addition, cell experiments showed that the knockdown of OAS1 could reduce the invasive ability and increased the apoptosis rate of PAAD cells. Discussion These results confirmed that OAS1 could be a prognostic biomarker and therapeutic target for its potential role in CTL dysfunction and macrophage M2 polarization.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pengcheng He
- Department of Hematology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Fan Niu
- Department of Hematology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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Reghupaty SC, Kanwal S, Mendoza RG, Davis E, Li H, Lai Z, Dozmorov MG, Faison MO, Siddiqui RA, Sarkar D. Dysregulation of Type I Interferon (IFN-I) Signaling: A Potential Contributor to Racial Disparity in Hepatocellular Carcinoma (HCC). Cancers (Basel) 2023; 15:4283. [PMID: 37686559 PMCID: PMC10486472 DOI: 10.3390/cancers15174283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
African-American (AA)/Black hepatocellular carcinoma (HCC) patients have increased incidence and decreased survival rates compared to non-Hispanic (White) patients, the underlying molecular mechanism of which is not clear. Analysis of existing RNA-sequencing (RNA-seq) data in The Cancer Genome Atlas (TCGA) and in-house RNA-sequencing of 14 White and 18 AA/Black HCC patients revealed statistically significant activation of type I interferon (IFN-I) signaling pathway in AA/Black patients. A four-gene signature of IFN-stimulated genes (ISGs) showed increased expression in AA/Black HCC tumors versus White. HCC is a disease of chronic inflammation, and IFN-Is function as pro-inflammatory cytokines. We tested efficacy of ginger extract (GE), a dietary compound known for anti-inflammatory properties, on HCC cell lines derived from White (HepG2), AA/Black (Hep3B and O/20) and Asian (HuH-7) patients. GE exhibited a significantly lower IC50 on Hep3B and O/20 cells than on HepG2 and HuH-7 cells. The GE treatment inhibited the activation of downstream mediators of IFN-I signaling pathways and expression of ISGs in all four HCC cells. Our data suggest that ginger can potentially attenuate IFN-I-mediated signaling pathways in HCC, and cells from AA/Black HCC patients may be more sensitive to ginger. AA/Black HCC patients might benefit from a holistic diet containing ginger.
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Affiliation(s)
| | - Sadia Kanwal
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Rachel G. Mendoza
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Eva Davis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Haiwen Li
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA;
| | - Mikhail G. Dozmorov
- Department of Biostatistics and Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Milton Omar Faison
- Department of Biology, Virginia State University, Petersburg, VA 23806, USA;
| | - Rafat Ali Siddiqui
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Massey Cancer Center, VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
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Taravella Oill AM, Buetow KH, Wilson MA. The role of Neanderthal introgression in liver cancer. BMC Med Genomics 2022; 15:255. [PMID: 36503519 PMCID: PMC9743633 DOI: 10.1186/s12920-022-01405-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk. METHODS Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population. RESULTS We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population. CONCLUSION Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.
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Affiliation(s)
- Angela M Taravella Oill
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Kenneth H Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Li X, Zhou W, Wang D. Integrative bioinformatic analysis identified IFIT3 as a novel regulatory factor in psoriasis. J Cell Biochem 2022; 123:2066-2078. [PMID: 36169003 DOI: 10.1002/jcb.30332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/18/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022]
Abstract
Psoriasis is an autoimmune skin disease with poor prognosis. Currently, there is no cure for psoriasis and the pathogenic mechanism of psoriasis remains unclear. Our study aims to explore key regulators underlying psoriasis and potential targets for psoriasis treatment. RNA-seq data of psoriasis and normal tissues were extracted from Gene Expression Omnibus database to screen differentially expressed genes (DEGs). Weighted correlation network analysis (WGCNA) was conducted to identify key gene modules correlated with psoriasis. Enrichment analysis was used to characterize identified genes. The expression of identified genes was verified in a data set with various types of psoriasis lesion tissues and six psoriasis and healthy control tissues by quantitative polymerase chain reaction and immunohistochemistry assays. And the biological functions of IFIT3 in keratinocytes were determined by colony formation assays, Cell Counting Kit-8, and enzyme-linked immunosorbent assays. A total of 594 overlapped genes (370 upregulated and 224 downregulated) were selected as DEGs between psoriasis and normal tissues in three independent data sets. These genes were enriched in interferon-related pathway and cytokine-related pathway. Weighted correlation network analysis identified several gene modules that were associated with psoriasis. Overlapped genes between gene modules and DEGs were associated with interferon-related pathway and T cell activities. Among these genes, OAS1, USP18, and IFIT3 had higher expression levels in psoriasis vulgaris (PV) and nonpustular palmoplantar psoriasis (NPPP) tissues but not Palmoplantar Pustular Psoriasis (PPPP). Meanwhile, these results were confirmed in our independent psoriasis tissue cohort. And results of in vitro experiments showed that inhibition of IFIT3 significantly impaired the proliferation capacity and CXCL1, CCL20, IL-1β, and IL-6 secretion of keratinocytes. Our study identified key genes and pathways underlying the pathogenesis of psoriasis through the conduct of integrated analysis. OAS1, USP18, and IFIT3 could be potential targets for the treatment of psoriasis. IFIT3 can promote the proliferation and immune activation of keratinocytes and facilitates the development of psoriasis.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis and Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Wolong Zhou
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis and Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Dan Wang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
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Lu L, Wang H, Fang J, Zheng J, Liu B, Xia L, Li D. Overexpression of OAS1 Is Correlated With Poor Prognosis in Pancreatic Cancer. Front Oncol 2022; 12:944194. [PMID: 35898870 PMCID: PMC9309611 DOI: 10.3389/fonc.2022.944194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background OAS1 expression in pancreatic cancer has been confirmed by many studies. However, the prognostic value and mechanism of OAS1 in pancreatic cancer have not been analyzed. Methods The RNA-seq in pancreatic cancer were obtained by UCSC XENA and GEO database. In addition, immunohistochemical validation and analysis were performed using samples from the 900th hospital. The prognosis of OAS1 was evaluated by timeROC package, Cox regression analysis, and Kaplan-Meier survival curves. Then, the main functional and biological signaling pathways enrichment and its relationship with the abundance of immune cells were analyzed by bioinformatics. Results OAS1 was highly expressed in pancreatic cancer compared with normal pancreatic tissue. High OAS1 expression was associated with poor overall survival (p<0.05). The OAS1 was significantly correlated to TNM staging (p=0.014). The timeROC analysis showed that the AUC of OAS1 was 0.734 for 3-year OS. In addition, the expression of OAS1 was significantly correlated with the abundance of a variety of immune markers. GSEA showed that enhanced signaling pathways associated with OAS1 include Apoptosis, Notch signaling pathway, and P53 signaling pathway. Conclusions OAS1 is a valuable prognostic factor in pancreatic cancer. Moreover, it may be a potential immunotherapeutic target.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Huaxiang Wang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jiaolong Zheng
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lei Xia
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
- *Correspondence: Dongliang Li,
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Schwartz SL, Dey D, Tanquary J, Bair CR, Lowen AC, Conn GL. Role of helical structure and dynamics in oligoadenylate synthetase 1 (OAS1) mismatch tolerance and activation by short dsRNAs. Proc Natl Acad Sci U S A 2022; 119:e2107111119. [PMID: 35017296 PMCID: PMC8784149 DOI: 10.1073/pnas.2107111119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
The 2'-5'-oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection. How these proteins are able to avoid aberrant activation by cellular RNAs is not fully understood, but adenosine-to-inosine (A-to-I) editing has been proposed to limit accumulation of endogenous RNAs that might otherwise cause stimulation of the OAS/RNase L pathway. Here, we aim to uncover whether and how such sequence modifications can restrict the ability of short, defined dsRNAs to activate the single-domain form of OAS, OAS1. Unexpectedly, we find that all tested inosine-containing dsRNAs have an increased capacity to activate OAS1, whether in a destabilizing (I•U) or standard Watson-Crick-like base pairing (I-C) context. Additional variants with strongly destabilizing A•C mismatches or stabilizing G-C pairs also exhibit increased capacity to activate OAS1, eliminating helical stability as a factor in the relative ability of the dsRNAs to activate OAS1. Using thermal difference spectra and molecular dynamics simulations, we identify both increased helical dynamics and specific local changes in helical structure as important factors in the capacity of short dsRNAs to activate OAS1. These helical features may facilitate more ready adoption of the distorted OAS1-bound conformation or stabilize important structures to predispose the dsRNA for optimal binding and activation of OAS1. These studies thus reveal the molecular basis for the greater capacity of some short dsRNAs to activate OAS1 in a sequence-independent manner.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Julia Tanquary
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Camden R Bair
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322;
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
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Yan S, Fang J, Zhu Y, Xie Y, Fang F. Comprehensive analysis of prognostic immune-related genes associated with the tumor microenvironment of pancreatic ductal adenocarcinoma. Oncol Lett 2020; 20:366. [PMID: 33133266 PMCID: PMC7590433 DOI: 10.3892/ol.2020.12228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor with a specific tumor immune microenvironment (TIME). Therefore, investigating prognostic immune-related genes (IRGs) that are closely associated with TIME to predict PDAC clinical outcomes is necessary. In the present study, 459 samples of PDAC from the Genotype-Tissue Expression database, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) were included and a survival-associated module was identified using weighted gene co-expression network analysis. Based on the Cox regression analysis and least absolute shrinkage and selection operator analysis, four IRGs (2′-5′-oligoadenylate synthetase 1, MET proto-oncogene, receptor tyrosine kinase, interleukin 1 receptor type 2 and interleukin 20 receptor subunit β) were included in the prognostic model to calculate the risk score (RS), and patients with PDAC were divided into high- and low-RS groups. Kaplan-Meier survival and receiver operating characteristic curve analyses demonstrated that the low-RS group had significantly improved survival conditions compared with the high-RS group in TCGA training set. The prognostic function of the model was also validated using ICGC and GEO cohorts. To investigate the mechanism of different overall survival between the high- and low-RS groups, the present study included Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data and Cell Type Identification by Estimating Relative Subset of Known RNA Transcripts algorithms to investigate the state of the tumor microenvironment and immune infiltration inpatients in the cohort from TCGA. In summary, four genes associated with the TIME of PDAC were identified, which may provide a reference for clinical treatment.
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Affiliation(s)
- Shibai Yan
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Juntao Fang
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Yuanqiang Zhu
- Department of Infertility and Sexual Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yong Xie
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Feng Fang
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
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Schwartz SL, Park EN, Vachon VK, Danzy S, Lowen AC, Conn GL. Human OAS1 activation is highly dependent on both RNA sequence and context of activating RNA motifs. Nucleic Acids Res 2020; 48:7520-7531. [PMID: 32678884 PMCID: PMC7367156 DOI: 10.1093/nar/gkaa513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
2′-5′-Oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) and play a critical role in limiting viral infection. dsRNA binding induces allosteric structural changes in OAS1 that reorganize its catalytic center to promote synthesis of 2′-5′-oligoadenylate and thus activation of endoribonuclease L. Specific RNA sequences and structural motifs can also enhance activation of OAS1 through currently undefined mechanisms. To better understand these drivers of OAS activation, we tested the impact of defined sequence changes within a short dsRNA that strongly activates OAS1. Both in vitro and in human A549 cells, appending a 3′-end single-stranded pyrimidine (3′-ssPy) can strongly enhance OAS1 activation or have no effect depending on its location, suggesting that other dsRNA features are necessary for correct presentation of the motif to OAS1. Consistent with this idea, we also find that the dsRNA binding position is dictated by an established consensus sequence (WWN9WG). Unexpectedly, however, not all sequences fitting this consensus activate OAS1 equivalently, with strong dependence on the identity of both partially conserved (W) and non-conserved (N9) residues. A picture thus emerges in which both specific RNA features and the context in which they are presented dictate the ability of short dsRNAs to activate OAS1.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
| | - Esther N Park
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Virginia K Vachon
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
| | - Shamika Danzy
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Anice C Lowen
- Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, USA.,Graduate Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Emory University, USA
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Yaping LI, Song Z, Wenjun W, Huiling D, Mei LI, Xiaoli J, Shuangsuo D. [ OAS1 gene polymorphism is associated with central nervous system involvement in children with enterovirus 71 infection]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:381-386. [PMID: 31068279 PMCID: PMC6744003 DOI: 10.12122/j.issn.1673-4254.2019.04.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE We investigated the association between OAS1 gene polymorphism and susceptibility to central nervous system (CNS) involvement of enterovirus (EV)71 infection. METHODS This case-control study was conducted among 180 children with EV71 infection, including 72 with mild infections without any complications and 108 with severe infections and CNS involvement; 201 children undergoing routine physical examination served as the healthy controls. For all the participants, the single nucleotide polymorphisms (SNPs) at OAS1 rs2660 and rs1131454 were analyzed using SNPscan multiple SNP typing methods. RESULTS No significant differences were found between the case and control groups in genotype or allele distributions of rs2660 and rs1131454. OAS1 rs2660 polymorphism was significantly different between the children with CNS involvement and those with mild EV71 infection, and the genotype AG frequency was higher and the genotype GG frequency was lower in children with CNS involvement. No significant difference was found in the distribution of genotypes or alleles of rs1131454 between the children with CNS involvement and those with mild EV71 infection. CONCLUSIONS OAS1 gene rs2660 and rs1131454 SNPs are not associated with the susceptibility to or CNS involvement of EV71 infection, but OAS1 rs2660 SNPs are significantly correlated with the susceptibility to CNS involvement in EV71 infection. Children carrying OAS1 rs2660 AG genotype are more likely to have CNS involvement after EV71 infection.
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Affiliation(s)
- L I Yaping
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Zhai Song
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Wang Wenjun
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Deng Huiling
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China.,Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an 710003, China
| | - L I Mei
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Jia Xiaoli
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Dang Shuangsuo
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
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Schwartz SL, Conn GL. RNA regulation of the antiviral protein 2'-5'-oligoadenylate synthetase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1534. [PMID: 30989826 DOI: 10.1002/wrna.1534] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/25/2022]
Abstract
The innate immune system is a broad collection of critical intra- and extra-cellular processes that limit the infectivity of diverse pathogens. The 2'-5'-oligoadenylate synthetase (OAS) family of enzymes are important sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection by activating the latent ribonuclease (RNase L) to halt viral replication and establish an antiviral state. Attesting to the importance of the OAS/RNase L pathway, diverse viruses have developed numerous distinct strategies to evade the effects of OAS activation. How OAS proteins are regulated by viral or cellular RNAs is not fully understood but several recent studies have provided important new insights into the molecular mechanisms of OAS activation by dsRNA. Other studies have revealed unanticipated features of RNA sequence and structure that strongly enhance activation of at least one OAS family member. While these discoveries represent important advances, they also underscore the fact that much remains to be learned about RNA-mediated regulation of the OAS/RNase L pathway. In particular, defining the full complement of RNA molecular signatures that activate OAS is essential to our understanding of how these proteins maximize their protective role against pathogens while still accurately discriminating host molecules to avoid inadvertent activation by cellular RNAs. A more complete knowledge of OAS regulation may also serve as a foundation for the development of novel antiviral therapeutic strategies and lead the way to a deeper understanding of currently unappreciated cellular functions of the OAS/RNase L pathway in the absence of infection. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
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12
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Wang K, Li L, Fu L, Yuan Y, Dai H, Zhu T, Zhou Y, Yuan F. Integrated Bioinformatics Analysis the Function of RNA Binding Proteins (RBPs) and Their Prognostic Value in Breast Cancer. Front Pharmacol 2019; 10:140. [PMID: 30881302 PMCID: PMC6405693 DOI: 10.3389/fphar.2019.00140] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background and Purpose: Breast cancer is one of the leading causes of death among women. RNA binding proteins (RBPs) play a vital role in the progression of many cancers. Functional investigation of RBPs may contribute to elucidating the mechanisms underlying tumor initiation, progression, and invasion, therefore providing novel insights into future diagnosis, treatment, and prognosis. Methods: We downloaded RNA sequencing data from the cancer genome atlas (TCGA) by UCSC Xena and identified relevant RBPs through an integrated bioinformatics analysis. We then analyzed biological processes of differentially expressed genes (DEGs) by DAVID, and established their interaction networks and performed pathway analysis through the STRING database to uncover potential biological effects of these RBPs. We also explored the relationship between these RBPs and the prognosis of breast cancer patients. Results: In the present study, we obtained 1092 breast tumor samples and 113 normal controls. After data analysis, we identified 90 upregulated and 115 downregulated RBPs in breast cancer. GO and KEGG pathway analysis indicated that these significantly changed genes were mainly involved in RNA processing, splicing, localization and RNA silencing, DNA transposition regulation and methylation, alkylation, mitochondrial gene expression, and transcription regulation. In addition, some RBPs were related to histone H3K27 methylation, estrogen response, inflammatory mediators, and translation regulation. Our study also identified five RBPs associated with breast cancer prognosis. Survival analysis found that overexpression of DCAF13, EZR, and MRPL13 showed worse survival, but overexpression of APOBEC3C and EIF4E3 showed better survival. Conclusion: In conclusion, we identified key RBPs of breast cancer through comprehensive bioinformatics analysis. These RBPs were involved in a variety of biological and molecular pathways in breast cancer. Furthermore, we identified five RBPs as a potential prognostic biomarker of breast cancer. Our study provided novel insights to understand breast cancer at a molecular level.
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Affiliation(s)
- Ke Wang
- Clinical Laboratory, Yongchuan People's Hospital of Chongqing, Chongqing, China
| | - Ling Li
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Liang Fu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yongqiang Yuan
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hongying Dai
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Tianjin Zhu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxi Zhou
- Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, China
| | - Fang Yuan
- Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, China
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13
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Matveeva OV, Chumakov PM. Defects in interferon pathways as potential biomarkers of sensitivity to oncolytic viruses. Rev Med Virol 2018; 28:e2008. [PMID: 30209859 PMCID: PMC6906582 DOI: 10.1002/rmv.2008] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/26/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022]
Abstract
Increased sensitivity of cancer cells to viruses is a prerequisite for the success of oncolytic virotherapy. One of the major causes of such a phenotype is the disruption of innate antiviral defenses associated with dysfunction of type 1 interferons (IFNs) that permits unlimited replication of viruses in cancer cells. Defects in IFN pathways help cancer progression by providing additional advantages to tumor cells. However, while these defects promote the survival and accelerated proliferation of malignant cells, they facilitate viral replication and thus enhance the efficiency of viral oncolysis. This review describes a broad spectrum of defects in genes that participate in IFN induction and IFN response pathways. Expression levels and/or functional activities of these genes are frequently low or absent in cancer cells, making them sensitive to virus infection. Therefore, certain specific defects in IFN signaling cascades might serve as potential biomarkers to help in identifying individual cancer patients who are likely to benefit from oncolytic virotherapy.
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Affiliation(s)
| | - Peter M Chumakov
- Engelhardt Institute of Molecular Biology, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia
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14
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Jeong G, Bae H, Jeong D, Ham J, Park S, Kim HW, Kang HS, Kim SJ. A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway. Sci Rep 2018; 8:12922. [PMID: 30150751 PMCID: PMC6110865 DOI: 10.1038/s41598-018-31306-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022] Open
Abstract
In our previous study, the Kelch domain-containing 7B (KLHDC7B) was revealed to be hypermethylated at the promoter but upregulated in breast cancer. In this study, we identified a long non-coding RNA, ST8SIA6-AS1 (STAR1), whose expression was significantly associated with KLHDC7B in breast cancer (R2 = 0.3466, P < 0.01). Involvement of the two genes in tumorigenesis was examined via monitoring their effect on cellular as well as molecular events after each gene dysregulation in cultured mammary cell lines. Apoptosis of MCF-7 decreased by 49.5% and increased by 33.1%, while proliferation noted increase and decrease by up- and downregulation of KLHDC7B, respectively, suggesting its oncogenic property. STAR1, however, suppressed cell migration and increased apoptosis. Network analysis identified many target genes that appeared to have similar regulation, especially in relation to the interferon signaling pathway. Concordantly, expression of genes such as IFITs, STATs, and IL-29 in that pathway was affected by KLHDC7B and STAR1. Taken together, KLHDC7B and STAR1 are both overexpressed in breast cancer and significantly associated with gene modulation activity in the interferon signaling pathway during breast tumorigenesis.
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Affiliation(s)
- Gookjoo Jeong
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
- PanGen Biotech Inc, Suwon, 16675, Republic of Korea
| | - Hansol Bae
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Dawoon Jeong
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Juyeon Ham
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Sungbin Park
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Hyeon Woo Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Han-Sung Kang
- Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Sun Jung Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea.
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15
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ALEX RANI, RAMESHA KP, SINGH UMESH, KUMAR SUSHIL, ALYETHODI RAFEEQUER, DEB RAJIB, SHARMA SHEETAL, SENGAR GYANENDRAS, ASHISH ASHISH, PRAKASH B. Genomic variations in the 2'-5' oligoadenylate synthetase 1 (OAS1) gene in zebu cattle and its crossbreds of Indian origin. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2017. [DOI: 10.56093/ijans.v87i11.75889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In the antiviral host defense mechanisms, the role of mammalian OAS/RNASEL pathway is very significant. These enzymes are interferon-inducible and activated by binding to double-stranded RNA (dsRNA) which are present in virus infected cells. The OAS proteins functions through its receptor, the 2-5Adependent ribonuclease (RNaseL) and activated OAS-RNaseL system degrades viral and cellular RNA and subsequently inhibits protein synthesis. Polymorphisms in the human and equine OAS gene cluster have been previously utilized for casecontrol analysis of virus-induced disease. But no polymorphisms have yet been identified in the bovine OAS1 genes for use in similar case-control studies. The promoter and coding regions of the OAS1 gene was amplified and screened for polymorphisms by PCR-SSCP and sequencing in Sahiwal and Frieswal animals. Two SNPs have been identified in the promoter region of OAS1 gene, which have predicted to create/delete sites for transcription factors. Specific amplification of the exonic regions of the OAS1 gene have identified 26 SNPs and one dinucleotide repeats, among them 14 are mis-sense variants. These polymorphisms are the first to be reported in OAS1 gene and will facilitate future case-control studies of cattle susceptibility to infectious diseases.
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16
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Elkhateeb E, Tag-El-Din-Hassan HT, Sasaki N, Torigoe D, Morimatsu M, Agui T. The role of mouse 2',5'-oligoadenylate synthetase 1 paralogs. INFECTION GENETICS AND EVOLUTION 2016; 45:393-401. [PMID: 27663720 DOI: 10.1016/j.meegid.2016.09.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/30/2016] [Accepted: 09/19/2016] [Indexed: 10/21/2022]
Abstract
The interferon-induced oligoadenylate synthetase (OAS) family is one of the most important immune response proteins to the viral infection. The OAS protein binds dsRNA and is activated to produce 2',5'-oligoadenylates, which lead to the activation of latent form of RNase L, resulting in degradation of cellular and viral RNA and inhibition of viral replication. In mice, the Oas gene family locates on chromosome 5. The mouse Oas gene locus undergoes a recent series of duplication event, leading to the presence of eight paralogs of Oas1 genes (Oas1a through Oas1h) that forms Oas gene cluster with the Oas2, Oas3 and two OasL (OasL1 and OasL2) genes. Previous studies demonstrated that the mouse Oas1b gene conferred resistance to the flavivirus infection in mice; however, the antiviral activity of other mouse Oas1 gene family is still unknown. Therefore, in the present study, we have evaluated the mouse Oas1 paralogs regarding the enzymatic activity and antiviral activity against the two neurotropic flaviviruses, West Nile virus and tick-borne encephalitis virus. The mouse Oas1 genes were cloned from C57BL/6J (B6) as well as the Oas1b derived from feral mouse strain, MSM. The obtained results demonstrated that only Oas1a and Oas1g showed enzymatic activity. Although MSM-derived Oas1b showed antiviral activity to both viruses, all B6-derived OAS paralogs did not show antiviral activity. These results suggest that Oas1a and Oas1g play a role in potentiating viral RNA-induced interferon response in the cell, whereas the Oas1b works as a specific anti-flavivirus factor unless it is mutated. However, the role of other paralogs is unknown and should wait for further investigation.
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Affiliation(s)
- Enas Elkhateeb
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Hassan T Tag-El-Din-Hassan
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan; Poultry Production Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Daisuke Torigoe
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Masami Morimatsu
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan.
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17
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Bhosle SM, Hunt A, Chaudhary J. A Modified Coupled Spectrophotometric Method to Detect 2-5 Oligoadenylate Synthetase Activity in Prostate Cell Lines. Biol Proced Online 2016; 18:9. [PMID: 26997919 PMCID: PMC4797170 DOI: 10.1186/s12575-016-0038-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/07/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND 2'-5' oligoadenylate synthetases (OAS) are interferon inducible enzymes that polymerizes ATP to 2'-5'-linked oligomers of adenylate (2-5As). As part of the innate immune response, these enzymes are activated by viral double stranded RNA or mRNAs with significant double stranded structure. The 2-5As in turn activate RNaseL that degrade single stranded RNAs. Three distinct forms of OAS exist in human cells (OAS1, 2 and 3) with each form having multiple spliced variants. The OAS enzymes and their spliced variants have different enzyme activities. OAS enzymes also play a significant role in regulating multiple cellular processes such as proliferation and apoptosis. Moreover, Single nucleotide polymorphisms that alter OAS activity are also associated with viral infection, diabetes and cancer. Thus detection of OAS enzyme activity with a simple spectrophotometric method in cells will be important in clinical research. RESULTS Here we propose a modified coupled spectrophotometric assay to detect 2-5 oligoadenylate synthetase (OAS) enzyme activity in prostate cell lines as a model system. The OAS enzyme from prostate cancer cell lysates was purified using Polyinosinic: polycytidylic acid (poly I:C) bound activated sepharose beads. The activated OAS enzyme eluted from Sepharose beads showed expression of p46 isoform of OAS1, generally considered the most abundant OAS isoform in elutes from DU14 cell line but not in other prostate cell line. In this assay the phosphates generated by the OAS enzymatic reaction is coupled with conversion of the substrate 2-amino-6-mercapto-7-methylpurine ribonucleoside (methylthioguanosine, a guanosine analogue; MESG) to a purine base product, 2-amino-6-mercapto-7-methylpurine and ribose1-phosphate via a catalyst purine nucleoside phosphorylase (phosphorylase) using a commercially available pyrophosphate kit. The absorbance of the purine base product is measured at 360 nm. The higher levels of phosphates detected in DU145 cell line indicates more activity of OAS in this prostate cancer cell line. CONCLUSION The modified simple method detected OAS enzyme activity with sensitivity and specificity, which could help in detection of OAS enzymes avoiding the laborious and radioactive methods.
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Affiliation(s)
- Sushma M. Bhosle
- Department of Biological Sciences, Centre for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314 USA
| | - Aisha Hunt
- Department of Biological Sciences, Centre for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314 USA
| | - Jaideep Chaudhary
- Department of Biological Sciences, Centre for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314 USA
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18
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Activation of RNase L is dependent on OAS3 expression during infection with diverse human viruses. Proc Natl Acad Sci U S A 2016; 113:2241-6. [PMID: 26858407 DOI: 10.1073/pnas.1519657113] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The 2',5'-oligoadenylate (2-5A) synthetase (OAS)-RNase L system is an IFN-induced antiviral pathway. RNase L activity depends on 2-5A, synthesized by OAS. Although all three enzymatically active OAS proteins in humans--OAS1, OAS2, and OAS3--synthesize 2-5A upon binding dsRNA, it is unclear which are responsible for RNase L activation during viral infection. We used clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) technology to engineer human A549-derived cell lines in which each of the OAS genes or RNase L is knocked out. Upon transfection with poly(rI):poly(rC), a synthetic surrogate for viral dsRNA, or infection with each of four viruses from different groups (West Nile virus, Sindbis virus, influenza virus, or vaccinia virus), OAS1-KO and OAS2-KO cells synthesized amounts of 2-5A similar to those synthesized in parental wild-type cells, causing RNase L activation as assessed by rRNA degradation. In contrast, OAS3-KO cells synthesized minimal 2-5A, and rRNA remained intact, similar to infected RNase L-KO cells. All four viruses replicated to higher titers in OAS3-KO or RNase L-KO A549 cells than in parental, OAS1-KO, or OAS2-KO cells, demonstrating the antiviral effects of OAS3. OAS3 displayed a higher affinity for dsRNA in intact cells than either OAS1 or OAS2, consistent with its dominant role in RNase L activation. Finally, the requirement for OAS3 as the major OAS isoform responsible for RNase L activation was not restricted to A549 cells, because OAS3-KO cells derived from two other human cell lines also were deficient in RNase L activation.
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19
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Larsen S, Kawamoto S, Tanuma SI, Uchiumi F. The hematopoietic regulator, ELF-1, enhances the transcriptional response to Interferon-β of the OAS1 anti-viral gene. Sci Rep 2015; 5:17497. [PMID: 26643049 PMCID: PMC4672336 DOI: 10.1038/srep17497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 10/30/2015] [Indexed: 12/11/2022] Open
Abstract
Interferon (IFN) therapy is effective in treating cancers, haematological and virus induced diseases. The classical Jak/Stat pathway of IFN signal transduction leading to changes in transcriptional activity is well established but alone does not explain the whole spectrum of cellular responses to IFN. Gene promoters contain cis-acting sequences that allow precise and contextual binding of transcription factors, which control gene expression. Using the transcriptional response to IFN as a starting point we report a high frequency of tandem GGAA motifs in the proximal promoters of Interferon stimulated genes, suggesting a key regulatory action. Utilizing the well-characterized anti-viral gene, OAS1, as an example Interferon stimulated gene promoter containing such a duplicated GGAA motif, we have demonstrated a regulatory role of this promoter in response to IFN by mutation analysis. Furthermore, we identified ELF-1 as a direct binding factor at this motif. Additionally, recruitment of RB1 and SP1 factors to the promoter following IFN stimulation is shown. ELF-1 overexpression enhanced and knockdown of ELF-1 inhibited full activation of OAS1 by IFN stimulation. Collectively, ELF-1 binds an important duplicated GGAA cis-acting element at the OAS1 promoter and in cooperation with RB1 and SP1 recruitment contributes to regulation in response to IFN stimulation.
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Affiliation(s)
- Steven Larsen
- Research Center for RNA Science, RIST, Tokyo University of Science, Noda, Chiba, Japan.,Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Shota Kawamoto
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Sei-ichi Tanuma
- Research Center for RNA Science, RIST, Tokyo University of Science, Noda, Chiba, Japan.,Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Fumiaki Uchiumi
- Research Center for RNA Science, RIST, Tokyo University of Science, Noda, Chiba, Japan.,Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
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Brennan-Laun SE, Ezelle HJ, Li XL, Hassel BA. RNase-L control of cellular mRNAs: roles in biologic functions and mechanisms of substrate targeting. J Interferon Cytokine Res 2015; 34:275-88. [PMID: 24697205 DOI: 10.1089/jir.2013.0147] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNase-L is a mediator of type 1 interferon-induced antiviral activity that has diverse and critical cellular roles, including the regulation of cell proliferation, differentiation, senescence and apoptosis, tumorigenesis, and the control of the innate immune response. Although RNase-L was originally shown to mediate the endonucleolytic cleavage of both viral and ribosomal RNAs in response to infection, more recent evidence indicates that RNase-L also functions in the regulation of cellular mRNAs as an important mechanism by which it exerts its diverse biological functions. Despite this growing body of work, many questions remain regarding the roles of mRNAs as RNase-L substrates. This review will survey known and putative mRNA substrates of RNase-L, propose mechanisms by which it may selectively cleave these transcripts, and postulate future clinical applications.
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Affiliation(s)
- Sarah E Brennan-Laun
- 1 Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland
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21
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Marino N, Collins JW, Shen C, Caplen NJ, Merchant AS, Gökmen-Polar Y, Goswami CP, Hoshino T, Qian Y, Sledge GW, Steeg PS. Identification and validation of genes with expression patterns inverse to multiple metastasis suppressor genes in breast cancer cell lines. Clin Exp Metastasis 2014; 31:771-86. [PMID: 25086928 DOI: 10.1007/s10585-014-9667-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/04/2014] [Indexed: 12/30/2022]
Abstract
Metastasis suppressor genes (MSGs) have contributed to an understanding of regulatory pathways unique to the lethal metastatic process. When re-expressed in experimental models, MSGs block cancer spread to, and colonization of distant sites without affecting primary tumor formation. Genes have been identified with expression patterns inverse to a single MSG, and found to encode functional, druggable signaling pathways. We now hypothesize that common signaling pathways mediate the effects of multiple MSGs. By gene expression profiling of human MCF7 breast carcinoma cells expressing a scrambled siRNA, or siRNAs to each of 19 validated MSGs (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1), we identified genes whose expression was significantly opposite to at least five MSGs. Five genes were selected for further analysis: PDE5A, UGT1A, IL11RA, DNM3 and OAS1. After stable downregulation of each candidate gene in the aggressive human breast cancer cell line MDA-MB-231T, in vitro motility was significantly inhibited. Two stable clones downregulating PDE5A (phosphodiesterase 5A), an enzyme involved in the regulation of cGMP-specific signaling, exhibited no difference in cell proliferation, but reduced motility by 47 and 66 % compared to the empty vector-expressing cells (p = 0.01 and p = 0.005). In an experimental metastasis assay, two shPDE5A-MDA-MB-231T clones produced 47-62 % fewer lung metastases than shRNA-scramble expressing cells (p = 0.045 and p = 0.009 respectively). This study demonstrates that previously unrecognized genes are inversely related to the expression of multiple MSGs, contribute to aspects of metastasis, and may stand as novel therapeutic targets.
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Affiliation(s)
- Natascia Marino
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37/Room 1126, 37 Convent Drive, Bethesda, MD, 20892, USA,
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Glymph S, Mandal S, Knowell AE, Abebe F, Chaudhary J. The myxovirus resistance A (MxA) gene -88G>T single nucleotide polymorphism is associated with prostate cancer. INFECTION GENETICS AND EVOLUTION 2013; 16:186-90. [PMID: 23438650 DOI: 10.1016/j.meegid.2013.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/17/2013] [Accepted: 02/05/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND Myxovirus (influenza virus) resistance A (MxA) is an interferon stimulated antiviral protein that is required for a complete antiviral response. MxA polymorphism (rs2071430) is located within an Interferon Stimulated Response Element (ISRE) at position -88 in the gene's promoter region, and it has been associated with increased susceptibility to infections and various diseases. In general, the low promoter activity genotype (GG) promotes susceptibility, whereas the high promoter activity genotype (TT) confers protection to Hepatitis C viral infection. MxA's role in prostate cancer is not fully understood. Previous literature has shown that MxA may be a mediator of the effect of IFN on normal and tumor cell motility. MxA may act as a tumor suppressor and the level of expression may be a predictor of metastatic potential. Based on this information, in this study we investigated the association of this functional polymorphism (rs2071430) in MxA with prostate cancer. METHODS Sample size and power was calculated using the PGA software. Genomic DNA from a controls (n=140) and prostate cancer patients (n=164) were used for genotyping SNP rs2071430 on all samples. Statistical analysis was performed using logistic regression model. RESULTS A significant association was observed between rs2071430 genotype GG and prostate cancer. Individuals harboring the GG genotype are at an increased risk of prostate cancer. Data stratification reveals that the mutant GT genotype offers either offers some protection against prostate cancer in Caucasians. CONCLUSIONS MxA SNP rs2071430 GG genotype is significantly associated with prostate cancer irrespective of race. However, data stratification also suggests that the GT genotype is under-represented in Caucasian subjects suggesting its role in protection against prostate cancer in Caucasians. Although MxA is primarily implicated in viral infection, but it may be also be associated with prostate cancer. Recent studies have implicated viral and bacterial infections with increased prostate cancer risk. Expression of the high promoter activity genotype may offer resistance to prostate cancer infection and possibly influence clinical outcomes.
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Affiliation(s)
- Shanora Glymph
- Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA 30314, USA
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Kazma R, Mefford JA, Cheng I, Plummer SJ, Levin AM, Rybicki BA, Casey G, Witte JS. Association of the innate immunity and inflammation pathway with advanced prostate cancer risk. PLoS One 2012; 7:e51680. [PMID: 23272139 PMCID: PMC3522730 DOI: 10.1371/journal.pone.0051680] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/05/2012] [Indexed: 01/13/2023] Open
Abstract
Prostate cancer is the most frequent and second most lethal cancer in men in the United States. Innate immunity and inflammation may increase the risk of prostate cancer. To determine the role of innate immunity and inflammation in advanced prostate cancer, we investigated the association of 320 single nucleotide polymorphisms, located in 46 genes involved in this pathway, with disease risk using 494 cases with advanced disease and 536 controls from Cleveland, Ohio. Taken together, the whole pathway was associated with advanced prostate cancer risk (P = 0.02). Two sub-pathways (intracellular antiviral molecules and extracellular pattern recognition) and four genes in these sub-pathways (TLR1, TLR6, OAS1, and OAS2) were nominally associated with advanced prostate cancer risk and harbor several SNPs nominally associated with advanced prostate cancer risk. Our results suggest that the innate immunity and inflammation pathway may play a modest role in the etiology of advanced prostate cancer through multiple small effects.
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Affiliation(s)
- Rémi Kazma
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Joel A. Mefford
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Iona Cheng
- Epidemiology Program, University of Hawai’i Cancer Center, University of Hawai’i, Honolulu, Hawai’i, United States of America
| | - Sarah J. Plummer
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Albert M. Levin
- Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Benjamin A. Rybicki
- Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Graham Casey
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John S. Witte
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Moerdyk-Schauwecker M, Shah NR, Murphy AM, Hastie E, Mukherjee P, Grdzelishvili VZ. Resistance of pancreatic cancer cells to oncolytic vesicular stomatitis virus: role of type I interferon signaling. Virology 2012; 436:221-34. [PMID: 23246628 DOI: 10.1016/j.virol.2012.11.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/08/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022]
Abstract
Oncolytic virus (OV) therapy takes advantage of common cancer characteristics, such as defective type I interferon (IFN) signaling, to preferentially infect and kill cancer cells with viruses. Our recent study (Murphy et al., 2012. J. Virol. 86, 3073-87) found human pancreatic ductal adenocarcinoma (PDA) cells were highly heterogeneous in their permissiveness to vesicular stomatitis virus (VSV) and suggested at least some resistant cell lines retained functional type I IFN responses. Here we examine cellular responses to infection by the oncolytic VSV recombinant VSV-ΔM51-GFP by analyzing a panel of 11 human PDA cell lines for expression of 33 genes associated with type I IFN pathways. Although all cell lines sensed infection by VSV-ΔM51-GFP and most activated IFN-α and β expression, only resistant cell lines displayed constitutive high-level expression of the IFN-stimulated antiviral genes MxA and OAS. Inhibition of JAK/STAT signaling decreased levels of MxA and OAS and increased VSV infection, replication and oncolysis, further implicating IFN responses in resistance. Unlike VSV, vaccinia and herpes simplex virus infectivity and killing of PDA cells was independent of the type I IFN signaling profile, possibly because these two viruses are better equipped to evade type I IFN responses. Our study demonstrates heterogeneity in the type I IFN signaling status of PDA cells and suggests MxA and OAS as potential biomarkers for PDA resistance to VSV and other OVs sensitive to type I IFN responses.
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Gröger CJ, Grubinger M, Waldhör T, Vierlinger K, Mikulits W. Meta-analysis of gene expression signatures defining the epithelial to mesenchymal transition during cancer progression. PLoS One 2012; 7:e51136. [PMID: 23251436 PMCID: PMC3519484 DOI: 10.1371/journal.pone.0051136] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/29/2012] [Indexed: 12/12/2022] Open
Abstract
The epithelial to mesenchymal transition (EMT) represents a crucial event during cancer progression and dissemination. EMT is the conversion of carcinoma cells from an epithelial to a mesenchymal phenotype that associates with a higher cell motility as well as enhanced chemoresistance and cancer stemness. Notably, EMT has been increasingly recognized as an early event of metastasis. Numerous gene expression studies (GES) have been conducted to obtain transcriptome signatures and marker genes to understand the regulatory mechanisms underlying EMT. Yet, no meta-analysis considering the multitude of GES of EMT has been performed to comprehensively elaborate the core genes in this process. Here we report the meta-analysis of 18 independent and published GES of EMT which focused on different cell types and treatment modalities. Computational analysis revealed clustering of GES according to the type of treatment rather than to cell type. GES of EMT induced via transforming growth factor-β and tumor necrosis factor-α treatment yielded uniformly defined clusters while GES of models with alternative EMT induction clustered in a more complex fashion. In addition, we identified those up- and downregulated genes which were shared between the multitude of GES. This core gene list includes well known EMT markers as well as novel genes so far not described in this process. Furthermore, several genes of the EMT-core gene list significantly correlated with impaired pathological complete response in breast cancer patients. In conclusion, this meta-analysis provides a comprehensive survey of available EMT expression signatures and shows fundamental insights into the mechanisms that are governing carcinoma progression.
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Affiliation(s)
- Christian J. Gröger
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Markus Grubinger
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Thomas Waldhör
- Department of Epidemiology, Centre of Public Health, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang Mikulits
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- * E-mail:
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