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Loss of CD4 T cell responses to prior vaccines associate with inflammation and altered transcriptional signatures in HIV infection

GSE273967 Homo sapiens (human) RNA-seq (gene expression) 174 samples Submitted 2024/10/16 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 174 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
174 samples: 10 conditions, mostly with about 18 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Chronic inflammation degrades CD4 T cell immunity to prior vaccines in treated HIV infectionNature communications · 2024
Summary (written by the submitters)
The preference of HIV to infect activated CD4 T cells has been proposed to contribute to a numerical reduction of antigen-specific T cells and the loss of T cell-mediated immunity. To date, our understanding of how HIV impact on vaccine-induced cellular immunity is limited. Moreover, the influence of chronic inflammation, that persist in treated HIV infection, is still unclear.
Read the full summary ↓
Here, we investigated inflammation, immune activation and antigen-specific T cell responses in HIV-uninfected and cART-treated HIV people with prior measles virus and tetanus toxoid immunity. Our findings highlight lower antigen-induced T cell activation and lower cytokine production of antigen-specific CD4 T cells in the HIV group. These lower recall CD4 T cell responses associated with high plasma levels of multiple cytokines and with T cell hyperactivation. Transcriptome analysis of sorted antigen-specific CD4 T cells revealed that upon antigen reencounter, HIV people on cART had a reduced expression of gene sets previously reported to associate with vaccine-induced protective immunity against various pathogens. We further identified a consistent impairment of the IFN and IFN signaling pathways as a mechanism for the functional loss of antigen-specific CD4 T cell responses in cART-treated people with HIV. Together, our findings suggest that vaccine-induced cellular immunity may benefit from strategies to counteract inflammation in HIV infection.pecific
Published in
Chronic inflammation degrades CD4 T cell immunity to prior vaccines in treated HIV infection
Kießling M, Cole JJ, Kübel S et al. · Nature communications 2024 · PMID 39587133 · doi:10.1038/s41467-024-54605-3
This dataset
Open GSE273967 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE273967_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1144374 and SRA study SRP524629. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39587133) ↗
Study design
10 conditions, mostly with about 18 replicates each
Med45RO_HU ×18 MV154_HU ×18 MV45RO_HU ×18 TT154_HU ×18 TT45RO_HU ×18 MV154_HIV ×17 MV45RO_HIV ×17 TT154_HIV ×17 +2 more

Supports a between-group comparison across 174 samples.

How we read this: 10 replicated groups read from 174 sample titles; they account for 174 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 134 more — browse all 174 samples with per-sample file links →

Datasets on a similar topic

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