Next Generation Sequencing to determine HHV-6B Transcriptome in HCT patients with a recent viral reactivation
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ABSTRACT:
PROVIDER: PRJNA475279 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7281473_1.fastq.gz | Fastqsanger.gz | |||
| SRR7281473_2.fastq.gz | Fastqsanger.gz | |||
| SRR7281474.fastq.gz | Fastqsanger.gz | |||
| SRR7281474_1.fastq.gz | Fastqsanger.gz | |||
| SRR7281474_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study is to determine the expression profile of HHV-6B in whole blood samples from transplant patients with HHV-6B genomes detected in plasma Methods: Viral mRNA profiles in whole blood samples of different transplant patients were generated by deep sequencing using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation for U38 expression was performed using TaqMan Results: Hierarchical clustering uncovered systematic detection of U38 mRNA transcripts in whole blood samples from all patients with a detectable HHV-6B reactivation in their plasma Conclusions: Our study represents the first detailed analysis of viral transcriptomes associated with HHV-6B reactivation in whole blood samples generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate qualitative evaluation of mRNA content within a whole blood sample.
2018-09-08 | GSE115533 | GEO
Project description:Limited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplantation (HCT). We conducted a prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT. We tested blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and performed RNA-seq on paired blood. Among 116 participants, HHV-6B DNA was detected in 37% of BALs, 49% of which had HHV-6B mRNA detection. We established an HHV-6B DNA threshold (≥2.3 log10copies/ml in BALF) that was highly predictive of HHV-6B mRNA detection and increased risk for death from respiratory failure (adjusted HR, 2.35; 95% CI, 1.08-5.11). Participants with HHV-6B DNA in BALF exhibited distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.
2023-12-18 | GSE244210 | GEO
Project description:Roseolovirus, or human herpesvirus 6 (HHV-6) is a ubiquitous human pathogen infecting over 95% of the population by the age of two years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived micro (mi)RNAs in modulating both cellular and viral gene expression. An initial report, which computed the likelihood of various viruses to encode for miRNAs, did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6 encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant 60-65 nucleotide RNA of unknown function derived from the lytic origin of replication (OriLyt) that gave rise to smaller RNA species of 18-19 nucleotides in length. In addition, we identified four pre-miRNAs, whose mature forms accumulated in Argonaute 2. In contrast to other beta-herpesviruses, HHV-6B miRNAs are expressed from direct repeat regions (DRL and DRR) located at either side of the genome. All miRNAs are conserved in the closely related HHV-6A variant, and one of them is a seed ortholog of the human miR-582-5p. Similar to alpha-herpesvirus miRNAs, they are expressed antisense to immediate early ORFs and thus have the potential to regulate key viral regulators. Small RNA sequencing from total RNA or Ago2 associated small RNAs extracted from HHV-6 infected Sup-T-1 cells
2012-01-01 | E-GEOD-34196 | biostudies-arrayexpress
Project description:Roseolovirus, or human herpesvirus 6 (HHV-6) is a ubiquitous human pathogen infecting over 95% of the population by the age of two years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived micro (mi)RNAs in modulating both cellular and viral gene expression. An initial report, which computed the likelihood of various viruses to encode for miRNAs, did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6 encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant 60-65 nucleotide RNA of unknown function derived from the lytic origin of replication (OriLyt) that gave rise to smaller RNA species of 18-19 nucleotides in length. In addition, we identified four pre-miRNAs, whose mature forms accumulated in Argonaute 2. In contrast to other beta-herpesviruses, HHV-6B miRNAs are expressed from direct repeat regions (DRL and DRR) located at either side of the genome. All miRNAs are conserved in the closely related HHV-6A variant, and one of them is a seed ortholog of the human miR-582-5p. Similar to alpha-herpesvirus miRNAs, they are expressed antisense to immediate early ORFs and thus have the potential to regulate key viral regulators.
2012-01-01 | GSE34196 | GEO
Project description:HHV-6A is a human herpesvirus that integrates into human sub telomeric regions to acquire latency. This latent virus frequently reactivates causing numerous diseases. The project was aimed to understand changes in host cell prteomics upon virus reactivation, which might helpin understanding the pathophysiology of virus reactivation.
2020-04-07 | PXD016211 | Pride
Project description:In order to understand the effect of HHV-6A reactivation on host cell, U2-OS bone osteosarcoma cells were generated carrying latent HHV-6A genome. These cells were either treated with DMSO (solvent control) or Trichostatin-A (TSA) for viral reactivation. As a control cells carrying no HHV-6A were used and treated similarly. Two biological replicates of each sample were processed for small RNA transcriptomics (small RNAseq). Furthermore, HeLa (cervical epithelial cells) were generated carrying lentiviral insertions of one of the small non-coding RNA from HHV-6A (sncRNA-U14). These cells could be transiently induced for sncRNA-U14 transcription using Doxycycline. HeLa cells having a mock lentiviral backbone was used as a control and was treated similarly. Two biological replicates of each sample were processed for small RNA transcriptomics (small RNAseq).
2022-02-15 | GSE134215 | GEO
Project description:Human herpesvirus 6B (HHV-6B) detection and genome-wide host expression profiles implicate HHV-6B as a pulmonary pathogen after hematopoietic cell transplantation
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Project description:Background: Diverticular disease is a significant healthcare burden in the United States. Younger diverticulitis patients are at increased risk for recurrence. How the molecular pathophysiology differs from those that develop disease at an older age is not understood. We aimed to profile the colonic transcriptome from younger versus older diverticulitis patients to identify differential biological pathways contributing to disease. Methods: We performed RNA-seq on full-thickness sigmoid colon tissue obtained at the time of surgery on diverticulitis patients (n=26) diagnosed at a younger age (<42 years old) or at an older age (>65 years old). Viral reads were identified from the RNA-seq dataset and associated with clinical metadata and the host transcriptome. HHV-6 positivity was evaluated in diverticulitis patients by PCR and immunofluorescence. Patient sera was profiled for HHV-6 using qPCR and ELISA to detect anti-HHV-6 antibodies. Results: Using RNA-seq, diverticulitis patients were profiled for differential expression associated with age of diagnosis. A subset of younger diverticulitis patients (diverticulitis colonic transcriptome-viral signature (DCT-VS)) demonstrated increased expression of anti-viral response genes. We identified viral transcripts in the RNA-seq dataset and found HHV-6 transcripts negatively correlated with DCT-VS. Younger patients more frequently displayed evidence of HHV-6 infection through DNA analysis and immunofluorescence of colonic tissue. During acute disease, HHV-6 DNA was detected in the serum but was absent during disease quiescence. Conclusions: Patients diagnosed with diverticulitis at a younger age demonstrate reactivation of HHV-6 in the sigmoid colon that remains persistent. Future studies to assess the role of pathogenicity and the use of anti-virals for acute uncomplicated diverticulitis should be considered.
2019-02-05 | GSE111819 | GEO
Project description:Transcriptomics of small RNAs upon HHV-6A reactivation
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Project description:Identification of MHC-II naturally processed and presented peptides derived from HHV-6B (strain Z29). MHC-II-peptide complexes were immuno-affinity purified from the total membrane fraction obtained from a T lymphoblastoid cell line infected with HHV-6B (Z29). Peptides were eluted off the purified complexes by acid treatment and separated from protein subunits using C4 columns. LC-MS/MS was used for analysis of the peptide mix and identification of eluted peptides sequences
2019-03-08 | MSV000083546 | MassIVE