A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination

Abstract

Listen

Translate article

Background Our understanding of the human immune system’s response to viral respiratory tract infections (VRTIs) and vaccines, including the molecular mechanisms and correlates of protection, remains incomplete. Extensive transcriptomic data from inoculation and vaccination studies have been deposited in publicly available databases. However, these studies are often separate and difficult to locate. Methods To bridge this research gap, we have systematically searched and reviewed publicly available datasets from NCBI Gene Expression Omnibus (GEO), Archive of Functional Genomics Data (ArrayExpress), Immunology Database and Analysis Portal (ImmPort), and Google using targeted queries. Inoculation study queries included terms related to humans, blood, PBMCs, nasal, respiratory challenges, and respiratory viral inoculations; while vaccination study queries focused on humans, blood, PBMCs, transcriptomes, and respiratory viral vaccines or vaccinations. Results This collection includes 18 datasets from inoculation of 5 respiratory viruses: H1N1, H3N2, RSV, HRV, and SARS-CoV-2 (14 from blood and 4 from nasal swabs) with 429 participants (ages 18 to 55 years) and 37 datasets from vaccination of influenza and COVID-19 with 2,084 participants (ages 0.5 to over 89 years). The duration and number of post-immunization time points range from 14 days before to 28 days after inoculation (1 to 20 time points) and from 28 days before to 360 days after vaccination (1 to 13 time points). Conclusion We provide a curated compendium of public gene expression data repositories for researchers to reanalyze transcriptomes from human whole blood, peripheral blood mononuclear cells (PBMCs), and nasal swab samples. This will facilitate studies of transcriptional responses to respiratory viral inoculation or vaccination.