Computational protocol: Patients with Tuberculosis Disease Have Mycobacterium tuberculosis-Specific CD8 T Cells with a Pro-Apoptotic Phenotype and Impaired Proliferative Capacity, Which Is Not Restored following Treatment

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Protocol publication

[…] All flow cytometry data were acquired using a BD LSRII flow cytometer with FACSDiva software (v6.0; BD Biosciences), and analyzed using FlowJo (v9.5.2; TreeStar). Lymphocytes were gated by morphological parameters (forward scatter and side scatter). T cells were identified as CD3+ lymphocytes; live cells were identified as Vividlo cells; proliferating cells were identified as OGlo cells. In ICS phenotyping assays, CFP-10/ESAT-6-specific CD8 T cells were defined as Vividl°CD3+CD8+IFN-γ+ T cells following stimulation with CFP-10 or ESAT-6 peptide pools. As confirmed in a separate PBMC ICS assay, >90% of CD3+CD8−IFN-γ+ T cells following stimulation with CFP-10 or ESAT-6 peptide pools were found to be CD4+ (), and are thus referred to as CFP-10/ESAT-6-specific CD4 T cells. Co-expression patterns of phenotypic markers were analyzed using Pestle v1.7 (Mario Roederer, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health) and Spice v5.22 . […]

Pipeline specifications

Software tools FlowJo, SPICE
Application Flow cytometry
Organisms Mycobacterium tuberculosis, Homo sapiens