biostudies-arrayexpressCarolin TurnerHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14687We used the tuberculin skin test (TST) as human challenge model to study the temporal evolution of the immune response to Mycobacterium tuberculosis (Mtb) antigens in vivo. Study participants comprised healthy HIV seronegative adults, 18-60 years of age. Latent tuberculosis (TB) infection was defined as immune memory for Mtb-specific antigens identified by positive peripheral blood IFNg release assays, but no clinical or radiological evidence of active TB. Two units tuberculin each were injected intradermally into the contralateral forearms of participants. After 2 days (n=216) or 7 days (n=158), 3 mm skin punch biopsies were taken from the injection sites and processed for whole genome transcriptional profiling by bulk RNA sequencing. The time points reflect maximum clinical inflammation (day 2) and maximum T cell infiltration (day 7) of the TST. TST samples were compared to skin biopsies taken two days after control injection of saline in a separate group of individuals (n=33), comprising healthy volunteers as well as patients with active or latent TB, ranging from 18-75 years of age. This submission includes 407 samples from 256 individuals (n=33 saline, n=223 with Day 2 and/or Day 7 TST).biostudies-arrayexpressSample Collection - Tuberculin skin tests were performed by intradermal injection of 2U Tuberculin (Serum Statens Institute) into the forearm. Controls received an equivalent volume of saline. On day 2 or day 7, 3-mm punch skin biopsies were taken and collected into RNAlater (Qiagen) for RNA extraction.Library Construction - The KAPA mRNA HyperPrep Kit (Roche Diagnostics) was used to construct stranded mRNA-Seq libraries from up to 500 ng intact total RNA.Sequencing - Paired-end sequencing was performed on the Illumina Nextseq using the Nextseq 500/550 High Output 75 cycle kit (Illumina). Runs were demultiplexed using bcl2fastq by Illumina.Nucleic Acid Extraction - Total RNA from skin biopsies was obtained with the Precellys Evolution homogenizer (Bertin Instruments) and Qiagen RNeasy mini kit. RNA was subjected to DNase treatment to remove contaminating genomic DNA using a TURBO DNA-free kit (Ambion, Life Technologies).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - RNAseq data were mapped to the reference transcriptome (Ensembl Human GRCh38 release 111) using Kallisto. Transcript-level counts were summed on gene level, and annotated with Ensembl gene ID, gene name and gene biotype using the R/Bioconductor packages tximport and BioMart. Genes annotated as pseudogenes were removed from analysis.Data Transformation - RNAseq counts were normalised within-sample into TPM (transcripts per million) to remove feature-length and library-size effects, and log2-transformed following the addition of a pseudocount of 0.001.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500T cells contribute to immune protection and pathogenesis in tuberculosis, but measurements of polyclonal responses have failed to resolve correlates of outcome. We report the temporal evaluation of the human in vivo clonal repertoire of Mycobacterium tuberculosis (Mtb)-reactive T cell responses, by T cell receptor (TCR) sequencing at the site of the tuberculin skin test, as a model for a standardised antigenic challenge. Initial non-selective recruitment of T cells is followed by enrichment of Mtb-reactive clones arising from oligoclonal T cell proliferation. We introduce a modular computational pipeline, Metaclonotypist, to sensitively cluster distinct TCRs with shared epitope specificity, which we apply here to establish a catalogue of public Mtb-reactive HLA-restricted T cell metaclones. Although most in vivo Mtb-reactive T cells are private, 10 metaclones were sufficient to identify Mtb-T cell reactivity across our study population (N≥128), indicating striking population level immunodominance of specific TCR-peptide interactions that may inform patient stratification and vaccine development.RNA-seq of coding RNAHomo sapiensEvolution of the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones.Turner, C.T., Tiffeau-Mayer, A., Rosenheim, J. et al.Carolin TurnerfalseBulk RNA sequencing of day 2 and day 7 biopsies from the tuberculin skin test in people with latent tuberculosisWe used the tuberculin skin test (TST) as human challenge model to study the temporal evolution of the immune response to Mycobacterium tuberculosis (Mtb) antigens in vivo. Study participants comprised healthy HIV seronegative adults, 18-60 years of age. Latent tuberculosis (TB) infection was defined as immune memory for Mtb-specific antigens identified by positive peripheral blood IFNg release assays, but no clinical or radiological evidence of active TB. Two units tuberculin each were injected intradermally into the contralateral forearms of participants. After 2 days (n=216) or 7 days (n=158), 3 mm skin punch biopsies were taken from the injection sites and processed for whole genome transcriptional profiling by bulk RNA sequencing. The time points reflect maximum clinical inflammation (day 2) and maximum T cell infiltration (day 7) of the TST. TST samples were compared to skin biopsies taken two days after control injection of saline in a separate group of individuals (n=33), comprising healthy volunteers as well as patients with active or latent TB, ranging from 18-75 years of age. This submission includes 407 samples from 256 individuals (n=33 saline, n=223 with Day 2 and/or Day 7 TST).2025-12-18T00:00:00Z2026-02-26T09:58:03.35Z2024-12-10T21:51:04.237ZE-MTAB-1468741565657EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184