Longitudinal saliva omics responses to immune perturbation: a case study

Abstract

Saliva omics has immense potential for non-invasive diagnostics, including monitoring very young or elderly populations, or individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over three periods (100 timepoints) involving: (1) hourly sampling over 24 h without intervention, (2) hourly sampling over 24 h including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (3) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome, and small RNA from salivary extracellular vesicles were profiled, including mRNA, miRNA, piRNA and bacterial RNA. The two 24-h periods were used in a paired analysis to remove daily variation and reveal vaccination responses. Over 18,000 omics longitudinal series had statistically significant temporal trends compared to a healthy baseline. Various immune response and regulation pathways were activated following vaccination, including interferon and cytokine signaling, and MHC antigen presentation. Immune response timeframes were concordant with innate and adaptive immunity development, and coincided with vaccination and reported fever. Overall, mRNA results appeared more specific and sensitive (timewise) to vaccination compared to other omics. The results suggest saliva omics can be consistently assessed for non-invasive personalized monitoring and immune response diagnostics.

Differential Network Analysis of Longitudinal Gene Expression in Response to Perturbations

“…Interferon signaling is crucial in antiviral defense, cell regulation and growth, and immune response modulation [50]. Our Reactome pathway analysis results are consistent with the results of our saliva multi-omics study [15], which observed that vaccination activates various immune response and regulation pathways, which are also identified in our present results, including ER-Phagosome pathway, Interferon alpha/beta and gamma signaling, cytokine signaling, and MHC antigen presentation.…”

“…Our RNA-seq time series raw data were retrieved from the Gene Expression Omnibus database under accessions GSE108664 and GSE100441 for the saliva and B cell experiments, respectively. The study of the immune response to the PPSV23 vaccine in saliva probed the expression of a potential 84647 gene identifiers (GENCODE annotation [36]) at 24 time points [15]. The other study of drug activation by Rituximab in B cells provided a dataset for 6 time points.…”

“…In our assessment we focused on the vaccine’s potential pathways of action. Our initial saliva investigation in PPSV23 established that an immune response to the vaccination can be detected utilizing non-invasive saliva monitoring at the molecular level [15]. Since aggregate saliva was sampled, we expected that multiple the multiple immune cells contained therein are involved in the observed patterns and associated immune responses.…”

“…The saliva dataset was obtained from our previous study of immune responses to the PPSV23 vaccine (GSE108664) [15]. In this study, hourly saliva samples were collected from a healthy individual over two 24 hour periods and profiled with RNA-seq every hour.…”

“…In the present study, we applied a DN approach to RNA-seq time series datasets retrieved from two longitudinal TC RNA-seq experiments: (i) The 40 first dataset (GSE108664) was generated from saliva samples from a healthy individual before and after the administration of the Pneumococcal Polysaccharide Vaccine (PPSV23) [15]. The primary goal of this study was to gain insights on the adaptive immune responses to PPSV23 through saliva profiling.…”