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RNA sequencing of Chlamydia trachomatis-stimulated HIV-1-infected CD4 T cells

ABSTRACT: RNA sequencing of Chlamydia trachomatis-stimulated HIV-1-infected CD4 T cells

PROVIDER: PRJNA689763 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13358622.fastq.gz	Fastqsanger.gz
	SRR13358623.fastq.gz	Fastqsanger.gz
	SRR13358624.fastq.gz	Fastqsanger.gz
	SRR13358625.fastq.gz	Fastqsanger.gz
	SRR13358626.fastq.gz	Fastqsanger.gz

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RNA sequencing of Chlamydia trachomatis-stimulated HIV-1-infected CD4 T cells

Project description:Sexually transmitted infections (STIs) are commonly reported among HIV-1 infected patients. The increasing prevalence of the most common STI, Chlamydia trachomatis (CT), among HIV-1 infected people suggests a role in HIV-1 infectivity. However, the mechanisms modulating the enhancement of HIV-1 infectivity during HIV-1/STIs coinfection remain elusive. The stimulation of CD4 T cells during CT infection may modulate the expression of specific genes, which in turn enhance the susceptibility and infectivity of CT-specific CD4 T cells to HIV-1 infection. After three days of CT stimulation of PBMCs followed by 3 days of HIV-1 infection, we observed a significant increase in HIV-1 p24 levels among clinically diagnosed C. trachomatis-infected patients as compared to cells from healthy donors. Similarly, ex vivo CT antigen-stimulated PBMCs from healthy donors showed enhanced susceptibility to HIV-1 as compared to unstimulated PBMCs. CT-specific CD4 T cells also harbour more HIV-1 copy numbers as compared to healthy unstimulated CD4 T cells. RNA-seq data revealed the upregulation of CCR chemokine receptors and cytokines in CD4 T cells from CT-stimulated CD4 T cells infected with HIV-1.

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Project description:Chlamydia trachomatis is the most common sexually transmitted infection and the bacterial agent of trachoma globally. C. trachomatis undergoes a biphasic developmental cycle involving an infectious elementary body and a replicative reticulate body. Little is currently known about the expression of host cell mRNAs, lncRNAs, and miRNAs at different stages of C. trachomatis development. Here, we performed RNA-seq and miR-seq on HeLa cells infected with C. trachomatis serovar E at 20 hpi and 44 hpi with or without IFN-γ treatment. Our study identified and validated differentially expressed host cell mRNAs, lncRNAs, and miRNAs during infection. Infection at 20 hpi showed the most differential upregulation of both coding and non-coding genes while infection at 44 hpi in the presence of IFN-γ resulted in a dramatic downregulation of a large proportion of genes. Using RT-qPCR, we validated the top 5 stage-specific upregulated mRNAs and miRNAs. One of the commonly expressed miRNAs at all three stages, miR-193b-5p, showed significant expression in clinical serum samples of C. trachomatis-infected patients as compared to sera from healthy controls and HIV-1-infected patients. Furthermore, at 20 hpi we observed significant upregulation of antigen processing and presentation, and T helper cell differentiation pathways whereas T cell receptor, mTOR, and Rap1 pathways were modulated at 44 hpi. Treatment with IFN-γ at 44 hpi showed the regulation of cytokine-cytokine receptor interaction, FoxO signaling, and Ras signaling pathways. Our study documents a role for the stage-specific transcriptional manipulation of the host cell genome and important signaling pathways that are necessary for the survival of pathogen and could serve as potential biomarkers in the diagnosis and management of the disease.

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