GSE108665
Multi-omics profiling for individualized precision wellness [blood (PBMCs) RNA-seq]
The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling on peripheral blood mononuclear cells (PBMCs) and saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva and PBMCs were produced at each timepoint (100 timepoints for saliva, 25 for PBMCs), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling.    Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly sample till the end of the investigation. Concurrently, weekly or monthly PBMC samples were taken.    Omics sample analysis includes: RNA-sequencing of total RNA in saliva and PBMCs. small RNA sequencing in saliva. Proteomics in saliva and PBMCs. small RNA from extracellular vesicles in saliva.    Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24hour enumeration. Overall the study produced 100 timepoints for saliva in the span of a year, as well as 30 PBMC samples. Overall design: Peripheral Blood Mononuclear Cell (PBMC) RNA-sequencing summary: Examination of gene expression dynamics in a single individual in PBMCs over multiple timepoints. 25 weekly/monthly samples follow the changes in expression in 1 individual over the span of 1 year. The timepoints include pre and post vaccination response, for pneumococcal vaccine (PPSV23).