MicroRNA profiling in Marek's disease virus induced lymphoma and infected spleen by deep sequencing
ABSTRACT: To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR. Four samples examined: MDV-infected tumorous spleen, MD lymphoma from liver, Non-infected spleen, Non-infected lymphocytes
Project description:To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR. Overall design: Four samples examined: MDV-infected tumorous spleen, MD lymphoma from liver, Non-infected spleen, Non-infected lymphocytes
Project description:To gain more insight into the molecular mechanisms of the tumorigenesis of MDV, we used microarrays to screen host and viral miRNAs that were sensitive to infection by MDV. Microarray analysis showed significant differential expression of 79 miRNAs, To determine whether miRNAs were involved in the MDV-induced tumorigenesis, miRNA microarray analysis was performed on GA-infected splenic tumors, GA-infected non-tumorous spleen tissues, and control spleen tissues at 28 dpi.
Project description:In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon. Examination of 3 different small RNA expression profilings in self-grafted and grafted watermelon
Project description:BACKGROUND:Marek's disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without lesions after MDV infection, and five spleens from noninfected chickens (NS), to explore the underlying mechanism of host resistance in Marek's disease (MD). RESULTS:By using a precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed (DE) mRNAs, putative lncRNAs, and known lncRNAs were profiled among three groups. We found that several specific intergroup differentially expressed genes were involved in important biological processes and pathways, including B cell activation and the Wnt signaling pathway; some of these genes were also found to be the hub genes in the co-expression network analyzed by WGCNA. Network analysis depicted both intergenic correlation and correlation between genes and MD traits. Five DE lncRNAs including MSTRG.360.1, MSTRG.6725.1, MSTRG.6754.1, MSTRG.15539.1, and MSTRG.7747.5 strongly correlated with MD-resistant candidate genes, such as IGF-I, CTLA4, HDAC9, SWAP70, CD72, JCHAIN, CXCL12, and CD8B, suggesting that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their target genes. CONCLUSIONS:Our results provide both transcriptomic and epigenetic insights on MD resistance and its pathological mechanism. The comprehensive lncRNA and mRNA transcriptomes in MDV-infected chicken spleens were profiled. Co-expression analysis identified integrated lncRNA-mRNA and gene-gene interaction networks, implying that hub genes or lncRNAs exert critical influence on MD resistance and tumorigenesis.
Project description:Marek’s disease (MD) is a viral neoplastic disease in chickens caused by the MD virus (MDV). Successful vaccination strategies against MD have resulted in a progressive increase in the virulence of MDV and therefore, the understanding of genetic resistance to MD is considered crucial to the long-term control of the disease. Here we examine whether MDV infection induces changes in the epigenetic status of genes and whether this response is dependent on the host genotype. We generated genome-wide histone 3 lysine 4 (H3K4) and histone 3 lysine 27 (H3K27) trimethylation maps in thymus tissues from chicken lines with varying resistance to MD. Differential chromatin marks were observed on several genes previously implicated in MD such as MX1, MMP2 and CTLA-4 and also on novel genes such as EAF2, IGF2BP1 and GAL. We also detected bivalent domains on transcriptional regulators such as BCL6, CITED2 and EGR1 that have particular functions in immune response. Moreover, novel putative roles for GAL and CITED2 in the mechanism of MD progression were uncovered. We also found tissue-specific effects of MDV infection with certain genes exhibiting differential marks only in spleen. Our results suggest widespread epigenetic changes are induced by MDV infection extent of which is determined by the level of MD resistance of the host. 8 samples examined: 2 histone modifications X 2 chicken lines with varying resistance to MD X 2 groups - infected and control.
Project description:Introduction:Marek's disease virus (MDV) can cause malignant T-cell lymphomas and immunosuppression in chickens. Macrophage migration inhibitory factor (MIF) not only plays a critical role in inhibiting T-cell responses, but also contributes to multiple aspects of tumour progression. The aim of this study was to reveal the potential role of MIF in the pathogenesis of MDV infection. Material and Methods:MIF gene expression levels were measured by using real-time PCR. Expression was assayed at different times in chicken embryo fibroblast (CEF) cells and tissue samples of SPF chickens infected with different MDV strains and fold change was calculated by the 2-??CT method. Results:The expression of MIF was significantly downregulated (p < 0.05 and FC > 2) in CEF cells infected with the very virulent MDV RB1B strain at 48 h post infection (hpi) and in the skin and spleen at 14 days post infection (dpi). The reduction of MIF expression was also found in CEF cells infected by reticuloendotheliosis virus (REV), avian leukosis virus subgroup J (ALV-J), and MDV vaccine strain CVI988 or in HD11 cells stimulated with TLR2, 3, 4, and 7 ligands. Interestingly, MIF expression decreased continuously from 7 to 28 dpi in the thymus after RB1B virus infection while it increased after CVI988 virus infection. Upregulated expression of MIF was found in CEF infected with RB1B at 96 hpi and in the spleen and skin at 21 and 28 dpi. Conclusion:The present study revealed the different expression pattern of MIF in response to MDV infection and indicated that MIF level may be associated with MDV pathogenesis.
Project description:Marek's disease virus (MDV), an alpha herpes virus, causes a lymphoproliferative state in chickens known as Marek's disease (MD), resulting in severe monetary losses to the poultry industry. Because lymphocytes of bursa of Fabricius and spleen are prime targets of MDV replication during the early cytolytic phase of infection, the immune response in bursa and spleen should be the foundation of late immunity induced by MDV. However, the mechanism of the MDV-mediated host immune response in lymphocytes in the early stage is poorly understood. The present study is primarily aimed at identifying the crucial genes and significant pathways involved in the immune response of chickens infected with MDV CVI988 and the very virulent RB1B (vvRB1B) strains. Using the RNA sequencing approach, we analyzed the generated transcriptomes from lymphocytes isolated from chicken bursa and spleen. Our findings validated the expression of previously characterized genes; however, they also revealed the expression of novel genes during the MDV-mediated immune response. The results showed that after challenge with CVI988 or vvRB1B strains, 634 and 313 differentially expressed genes (DEGs) were identified in splenic lymphocytes, respectively. However, 58 and 47 DEGs were observed in bursal lymphocytes infected with CVI988 and vvRB1B strains, respectively. Following MDV CVI988 or vvRB1B challenge, the bursal lymphocytes displayed changes in IL-6 and IL-4 gene expression. Surprisingly, splenic lymphocytes exhibited an overwhelming alteration in the expression of cytokines and cytokine receptors involved in immune response signaling. On the other hand, there was no distinct trend between infection with CVI988 and vvRB1B and the expression of cytokines and chemokines, such as IL-10, IFN-?, STAT1, IRF1, CCL19, and CCL26. However, the expression profiles of IL-1?, IL-6, IL8L1, CCL4 (GGCL1), and CCL5 were significantly upregulated in splenic lymphocytes from chickens infected with CVI988 compared with those of chickens infected with vvRB1B. Because these cytokines and chemokines are considered to be associated with B cell activation and antigenic signal transduction to T cells, they may indicate differences of immune responses initiated by vaccinal and virulent strains during the early phase of infection. Collectively, our study provides valuable data on the transcriptional landscape using high-throughput sequencing to understand the different mechanism between vaccine-mediated protection and pathogenesis of virulent MDV in vivo.
Project description:Aim:The aim of this work was to detect chicken B-cell marker 6 (ChB6) gene in some native breeds in Egypt and find the relationship between founded genes in these different breeds to determine the resistance of native Egyptian breeds of chicken to Marek's disease (MD). Materials and Methods:A total of 14 different chicken breeds (30 each) including ten native breeds in addition to SPF Lohmann, High Line, Bovans, and Roodiland were used. Blood samples were collected for the detection of (ChB6) by polymerase chain reaction (PCR) assay and sequenced to determine the presence or absence of ChB6 gene. Experimental infection was done using local field isolated MD virus (MDV) of 11 (1 day old) unvaccinated chick breeds having no maternal antibodies against MDV. Ten breeds of them carry ChB6 gene, eight breeds were native, and the rest two breeds were SPF Lohmann and High Line in addition to a group of ChB6 gene-lacking breed (Bovans) were infected. Spleen samples were collected from all infected breeds at 20th, 25th, 30th, 35th, and 40th weeks post-infection and tested by PCR assay for the detection of MDV. Furthermore, at 40th week post-infection, tumorized spleen sample of Bovans breed was collected and prepared for examination by transmission electron microscope (TEM) to confirm the presence of MDV. Results:Our results revealed the positivity of 10 out of 14 breeds (Gimmizah, Sinai, Dandarawi, Fayoumi, Golden Montazah, Matrouh, Beheri, Dokki, SPF Lohmann, and High Line) to the presence of ChB6 gene and resistance to MDV infection, while the Bovans, Mandarah, Inshas and Roodiland breeds lack the ChB6 gene and are susceptible to MDV infection. The collected spleen samples revealed negative for the presence of challenged MDV by PCR in 10 breeds (Gimmizah, Sinai, Dandarawi, Fayoumi, Golden Montazah, Matrouh, Beheri, Dokki, SPF Lohmann, and High Line) and positive for Bovans breed. TEM is used to confirm MDV infection in Bovans group which demonstrated tumors. Conclusion:The study confirms the relationship between the presence of ChB6 gene in our native breeds and the absence of tumors.
Project description:Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that causes immunosuppression, paralysis, and deadly lymphomas in chickens. In infected animals, B cells are efficiently infected and are thought to amplify the virus and transfer it to T cells. MDV subsequently establishes latency in T cells and transforms CD4+ T cells, resulting in fatal lymphomas. Despite many years of research, the exact role of the different B and T cell subsets in MDV pathogenesis remains poorly understood, mostly due to the lack of reverse genetics in chickens. Recently, Ig heavy chain J gene segment knockout (JH-KO) chickens lacking mature and peripheral B cells have been generated. To determine the role of these B cells in MDV pathogenesis, we infected JH-KO chickens with the very virulent MDV RB1B strain. Surprisingly, viral load in the blood of infected animals was not altered in the absence of B cells. More importantly, disease and tumor incidence in JH-KO chickens was comparable to wild-type animals, suggesting that both mature and peripheral B cells are dispensable for MDV pathogenesis. Intriguingly, MDV efficiently replicated in the bursa of Fabricius in JH-KO animals, while spread of the virus to the spleen and thymus was delayed. In the absence of B cells, MDV readily infected CD4+ and CD8+ T cells, allowing efficient virus replication in the lymphoid organs and transformation of T cells. Taken together, our data change the dogma of the central role of B cells, and thereby provide important insights into MDV pathogenesis.
Project description:Marek's disease (MD) is a highly contagious viral neoplastic disease caused by Marek's disease virus (MDV), which can lead to huge economic losses in the poultry industry. Recently, microRNAs (miRNAs) have been found in various cancers and tumors. In recent years, 994 mature miRNAs have been identified through deep sequencing in chickens, but only a few miRNAs have been investigated further in terms of their function. Previously, gga-miR-103-3p was found downregulated in MDV-infected samples by using Solexa deep sequencing. In this study, we further verified the expression of gga-miR-103-3p among MDV-infected spleen, MD lymphoma from liver, noninfected spleen, and noninfected liver, by qPCR. The results showed that the expression of gga-miR-103-3p was decreased in MDV-infected tissues, which was consistent with our previous study. Furthermore, two target genes of gga-miR-103-3p, cyclin E1 (CCNE1) and transcription factor Dp-2 (E2F dimerization partner 2) (TFDP2), were predicted and validated by luciferase reporter assay, qPCR, and western blot analysis. The results suggested that CCNE1 and TFDP2 are direct targets of gga-miR-103-3p in chickens. Subsequent cell proliferation and migration assay showed that gga-miR-103-3p suppressed MDCC-MSB1 migration, but did not obviously modulate MDCC-MSB1 cell proliferation. In conclusion, gga-miR-103-3p targets the CCNE1 and TFDP2 genes, and suppresses cell migration, which indicates that it might play an important role in MD tumor transformation.