Dataset Information

LncRNA Expression in CD4+ T Cells in Neurosyphilis Patients.

ABSTRACT: Recent studies have shown that several long noncoding RNAs (lncRNAs) are involved in regulating the immune response to cope with pathogenic invasion. To date, the roles of lncRNAs in the CD4+ T cell response to Treponema pallidum (T. pallidum) infection in neurosyphilis patients remain unknown. The mRNA and lncRNA expression profiles of CD4+ T cells that were isolated from neurosyphilis patients and healthy controls were analyzed by microarray. A total of 2258 lncRNAs and 1728 mRNAs were identified as over-expressed or under-expressed, respectively (fold change > 1.5) in the CD4+ T cells of neurosyphilis patients compared to the healthy controls. The lncRNA-mRNA co-expression network showed that 59 lncRNAs showed significant differences along with significantly different mRNAs. Among the 59 gene pairs, the LOC79999 mRNA was positively correlated with the RP11-160E2.16, RP11-160E2.11, and RP11-160E2.19 lncRNAs, and the NKX1-1 mRNA was positively correlated with the RP11-1398P2.1, RP11-160E2.19, and XLOC_003422 lncRNAs. The following five mRNAs were correlated with two differential lncRNAs: DUSP16, AP000349.1, FAM115C, TIMM8A, and SMCHD1. Gene Ontology (GO) analysis revealed that the differentially expressed coding genes were mainly involved in biological processes and the top 4 terms that associated with above-mentioned differentially expressed coding genes were as follows: defense response to fungus, defense response to bacterium, killing of cells of other organism and disruption of cells of another organism. A subsequent pathway analysis was also conducted, and several pathways, including the T cell receptor, MAPK, and TGF-beta signaling pathways, were associated with the differentially expressed mRNAs. This study reveals the differential expression profiles of lncRNAs in the CD4+ T cell response to the T. pallidum infection in neurosyphilis patients. LncRNAs are involved in key biological processes that comprise the CD4+ T cell response to the T. pallidum infection.

SUBMITTER: Liu LL

PROVIDER: S-EPMC5682391 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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LncRNA Expression in CD4+ T Cells in Neurosyphilis Patients.

Liu Li-Li LL Zhu Shao-Gang SG Jiang Xiao-Yong XY Ren Jun J Lin Yong Y Zhang Ning-Ning NN Tong Man-Li ML Zhang Hui-Lin HL Zheng Wei-Hong WH Fu Hua-Jun HJ Luo Hai-Juan HJ Lin Li-Rong LR Yan Jiang-Hua JH Yang Tian-Ci TC

Frontiers in cellular and infection microbiology 20171108

Recent studies have shown that several long noncoding RNAs (lncRNAs) are involved in regulating the immune response to cope with pathogenic invasion. To date, the roles of lncRNAs in the CD4+ T cell response to <i>Treponema pallidum</i> (<i>T. pallidum</i>) infection in neurosyphilis patients remain unknown. The mRNA and lncRNA expression profiles of CD4+ T cells that were isolated from neurosyphilis patients and healthy controls were analyzed by microarray. A total of 2258 lncRNAs and 1728 mRNA ...[more]

PMID: 29167762

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Project description:Objective: To analysis lncRNAs expression profiles and identify differentially expressed lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. Methods: CD4+ T cells were isolated from peripheral blood mononuclear cells. RNA extraction was performed to conduct further experiments. Expression profiles of mRNAs and lncRNAs in CD4+ T cells isolated from neurosyphilis patients and healthy controls were analyzed by using microarray assay. Four lncRNAs were selected to conduct validation by using real time-quantitative polymerase chain reaction and the expression levels of those above mentioned lncRNAs in neurosyphilis patients and healthy controls were compared. Results: In total, 17, 278 lncRNAs and 15, 840 mRNA were found to be differentially expressed when comparing the CD4+ T cells between neurosyphilis patients and healthy control individuals. Of these transcripts, 2258 lncRNAs and 1728 mRNAs were significantly over or under expressed, respectively. Compared with healthy controls, AC068282.3 (fold change: 21.90) and CTD-3064M3.3 (fold change: 23.93) were the most over-expressed and under-expressed lncRNAs in neurosyphilis patients. The majority of differentially expressed lncRNAs are from intergenic regions (~ 57.5%), intronic antisense to protein-coding loci (~ 15.0%), natural antisense to protein-coding loci (~12.1%). It is worth noting that 59 lncRNAs were significant difference along with significantly different mRNA. Among the 59 pairs of genes, LOC7999 mRNA was positively correlated with lncRNA RP11-160E2.16, RP11-160E2.11, RP11-160E2.19, respectively; NKX1-1 mRNA was positively correlated with lncRNA RP11-1398P2.1, RP11-160E2.19, XLOC_003422, respectively. The following five mRNAs were correlated with two differential lncRNAs, namely DUSP16, AP000349.1, FAM115C, TIMM8A, SMCHD1. GO analysis revealed that the differentially expressed coding genes were mainly involved in the biological processes, and among them, the most significant association was observed in defense response to fungus, defense response to bacterium, killing cells of other organism and disruption of cells of other organism. Subsequent pathway analysis was also conducted, and T cell receptor signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway, etc. were found out to be associated with differentially expressed mRNAs. Conclusion: The present study revealed the differential expression profiles of lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. LncRNAs are involved in the key biological process in CD4+ T cell response to T. pallidum infection.

Project description:Background:Elite controller refers to a patient with human immunodeficiency virus infection with an undetected viral load in the absence of highly active antiretroviral therapy. Studies on gene expression and regulation in these individuals are limited but significant, and have helped researchers and clinicians to understand the interrelationships between HIV and its host. Methods:We collected CD4 T-cell samples from two elite controllers (ECs), two HIV-positive infected patients (HPs), and two healthy controls (HCs) to perform second-generation transcriptome sequencing. Using the Cufflinks software, we calculated the Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) and identified differentially expressed (DE) mRNAs and long non-coding RNAs (lncRNAs), with corrected P value < 0.05 (based on a false discovery rate (FDR) < 0.05). We then constructed a protein-protein interaction network using cytoHubba and a long non-coding RNA-mRNA co-expression network based on the Pearson correlation coefficient. Results:In total, 1109 linear correlations of DE lncRNAs targeting DE mRNAs were found and several interesting interactions were identified as being associated with viral infections and immune responses within the networks based on these correlations. Among these lncRNA-mRNA relationships, hub mRNAs including HDAC6, MAPK8, MAPK9, ATM and their corresponding annotated co-expressed lncRNAs presented strong correlations with the MAPK-NF-kappa B pathway, which plays a role in the reactivation and replication of the virus. Conclusions:Using RNA-sequencing, we systematically analyzed the expression profiles of lncRNAs and mRNAs from CD4+ T cells from ECs, HPs, and HCs, and constructed a co-expression network based on the relationships among DE transcripts and database annotations. This was the first study to examine gene transcription in elite controllers and to study their functional relationships. Our results provide a reference for subsequent functional verification at the molecular or cellular level.

Dataset Information

LncRNA Expression in CD4+ T Cells in Neurosyphilis Patients.

Publications

LncRNA Expression in CD4+ T Cells in Neurosyphilis Patients.

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