DOI: 10.5281/zenodo.17654509
title: Systems Immunology Dataset: Innate Predictors of TSCM Response to Influenza Vaccination (FluPRINT Cohort)

description: This dataset contains the fully integrated multi-omic profiles of 19 pediatric subjects from the FluPRINT cohort, as analyzed in the paper "Innate antiviral readiness drives the expansion of protective T stem cell memory against influenza" by Tomic et al. The data captures the baseline immunological state (transcriptomic, proteomic, cellular, and serological) and links it to the subsequent expansion of T stem cell-like memory (TSCM) cells following Live Attenuated Influenza Vaccination (LAIV).

These data were used to identify the innate antiviral readiness signature, characterized by a pDC-associated type I interferon profile, that predetermines a robust and functional TSCM response.

Usage This dataset is formatted for systems immunology modeling. It allows reproducing the Structural Equation Models (SEM), Partial Least Squares Discriminant Analysis (PLS-DA), and correlation networks presented in the associated publication. It serves as a reference dataset for investigating the links between baseline innate immunity and adaptive T-cell memory formation.

Citation If you use this dataset, please cite the original publication: Tomic, I., et al. "Innate antiviral readiness drives the expansion of protective T stem cell memory against influenza." (Year). [Journal Name]. DOI: [Insert DOI].
description: Study cohort





Population: 19 healthy children (ages 4–6 years).




Intervention: Single dose of Live Attenuated Influenza Vaccine (LAIV).




Timepoints: Baseline (Day 0) and Post-Vaccination (Day 28).



Data structure The file Full_integrated_data.csv contains 19 rows (one per subject) and 182 columns encompassing five distinct biological layers. All continuous features (transcriptomic scores, protein levels) have been normalized for integrative modeling.

Variable Categories





Clinical Metadata:





subject_id: Unique identifier.




sex, age: Demographic variables.




group: Prior vaccination history (1 = Naive, 2 = 1 prior dose, 3 = ≥2 prior doses).




responder_status: Classification based on TSCM expansion magnitude (Responder vs. Non-Responder).






Cellular Immunity (Mass Cytometry/CyTOF):





tscm: Frequency of CD8+ T stem cell-like memory cells (primary outcome).




clust_1 to clust_12: Frequencies of specific T-cell phenotypic clusters.






Targeted Proteomics (Olink Inflammation Panel):





Plasma concentrations of inflammatory cytokines and chemokines (e.g., cxcl10, il18, ccl4, tnf, ifn_gamma).






Transcriptomics (RNA-Seq & Deconvolution):





isg_score: Composite score of 32 canonical Interferon-Stimulated Genes.




pdc: Plasmacytoid Dendritic Cell enrichment score (derived from xCell deconvolution).




GSVA Pathway Scores: Enrichment scores for key innate immune pathways, including:





Hallmark gene sets (e.g., hallmark_interferon_alpha_response).




Blanco-Melo Viral Signatures (e.g., blanco_melo_bronchial_epithelial_cells_influenza_a_del_ns1_infection_up).




KEGG/Reactome Pathways (e.g., reactome_antiviral_mechanism_by_ifn_stimulated_genes, kegg_cytosolic_dna_sensing_pathway).








Serology:





hai_brisbane, hai_kansas: Baseline Hemagglutination Inhibition (HAI) titers against vaccine strains.