biostudies-arrayexpressQui MartinHomo sapiensSeurathttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15436The goal of this experiment is to compare the transcriptomic profile of CD8+ T cells isolated from the nasal cavity and whole blood at two different state, baseline and CD3/28 activated. This will allow us to characterise the unique features of CD8+ T cells in the nasal cavity. We isolated CD8+CD45RO+ T cells from fresh nasal turbinate samples and PBMCs of four healthy donors (1 Females, 45 years old; 3 Males, 24, 40 and 41 years old). Single-cell RNA sequencing was performed on both nasal and blood CD8+ CD45RO+ T cells, either directly or following overnight TCR-mediated stimulation with anti-CD3/CD28 beads.biostudies-arrayexpressSequencing - Libraries were quantified using a qPCR machine (Bio-Rad) and assessed for quality using a bioanalyzer (Agilent Technologies), then sequenced on an Illumina NovaSeq 6000 platform.Sample Collection - Freshly isolated nasal cells and PBMCs were rested in culture medium (AIM-V supplemented with 2% AB serum) for 2 hours at 37 °C. Following the resting period, half of the cells were stimulated with anti-CD3/CD28 Dynabeads at a 1:1 cell-to-bead ratio, while the remaining half were left unstimulated as controls. Cells were cultured overnight in 96-well U-bottom tissue culture plates under standard incubation conditions (37 °C, 5% CO2). After 24 hours, both nasal and blood T cells were washed with PBS and subsequently stained with surface markers (NIR, CD3, CD4, CD8, CD45RO) and sorted using FACS (BD FACSAria III). Specifically, NIR-CD3+CD4-CD8+CD45RO+ cells were sorted from each sample for the single-cell RNA sequencing experiment. The sorted cells were labeled with distinct Hash Tag Oligonucleotides (HTOs) for multiplexing.Nucleic Acid Extraction - Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller for partitioning into Gel Bead-In-Emulsion (GEMs) using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics). Reverse transcription was performed within the GEMs, followed by amplification and library construction. HTO libraries were constructed following the TotalSeq™ protocol.Library Construction - Reverse transcription was performed within the GEMs, followed by amplification and library construction. HTO libraries were constructed following the TotalSeq™ protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data were processed using the Cell Ranger pipeline (10x Genomics, v6.0.1), and HTO demultiplexing was performed using the HTODemux function in Seurat (v4.0). For data analysis and quality control, Seurat (v4.0) was used. Low-quality cells and potential doublets were excluded based on quality control metrics. Normalized gene expression data were obtained using Seurat, followed by PCA, clustering using the Louvain algorithm, and visualization using UMAP. MAIT cells (SLC4A10, TRAV1-2 and KLRB1) were excluded from the analysis. Differential expression analysis was performed for each donor, and the overlapping differentially expressed genes were used to generate the volcano plots.UnknownTranscriptomicsGenomicsProteomicsFLOQSwab (Copan)Chromium Single Cell 5' Library & Gel Bead Kit v210x Genomics Chromium ControllerIllumina NovaSeq 6000Local workstationThe nasal cavity is the entry site for respiratory viruses. Understanding how the nasal cavity sustains memory CD8+ T cell is essential for improving respiratory virus management and vaccine development. Here, we sampled CD8+ T cells from the upper nasal turbinate and peripheral blood of healthy adults. We analysed their transcriptomic profile and antigen specificity for respiratory (SARS-CoV-2, Influenza A) and non-respiratory (HCMV) viruses. Transcriptomic analysis revealed that nasal CD8+ T cells failed to upregulate STAT1 following TCR stimulation, potentially enabling clonal expansion despite the antiproliferative effects of IFN signalling. They also exhibited a cytotoxic, Th1-like profile with tissue-residency markers but lacked TCF7 expression, suggesting limited self-renewal capacity. The CD8+ T cell analysis of antigen specificity demonstrates that local nasal exposure is indispensable for virus-specific CD8+ T cell detection. Only SARS-CoV-2 and influenza-specific but not HCMV-specific CD8+ T cells were detected in the nasal compartment. However, their persistence over time in the nasal cavity appears linked to repetitive viral exposure. Our findings provide insights into the adaptations of nasal-resident CD8+ T cells and highlight challenges in eliciting durable nasal T cell immunity, with important implications for vaccine strategies against respiratory pathogens.RNA-seq of coding RNA from single cellsHomo sapiensDynamics of virus-specific CD8+ T cells in the human nasal cavityQui MartinJoey Ming Er Lim, Sabrina Ottolini, Shou Kit Hang, Martin Daniel Qui, Adeline Chia, Jenny Guek Hong Low, Nina Le Bert, Anthony Tanoto Tan, Antonio BertolettiJoey Ming Er LimfalseDynamics of Virus-specific CD8+ T cells in the Human Nasal CavityThe goal of this experiment is to compare the transcriptomic profile of CD8+ T cells isolated from the nasal cavity and whole blood at two different state, baseline and CD3/28 activated. This will allow us to characterise the unique features of CD8+ T cells in the nasal cavity. We isolated CD8+CD45RO+ T cells from fresh nasal turbinate samples and PBMCs of four healthy donors (1 Females, 45 years old; 3 Males, 24, 40 and 41 years old). Single-cell RNA sequencing was performed on both nasal and blood CD8+ CD45RO+ T cells, either directly or following overnight TCR-mediated stimulation with anti-CD3/CD28 beads.2025-08-23T00:00:00Z2025-08-04T09:53:53.479Z2025-08-04T09:53:53.479ZE-MTAB-15436ERP177766EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_000418410.1016/j.mucimm.2025.07.007