Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study

Abstract

Saliva omics, a rapidly developing field for non-invasive diagnostics, may be utilized for monitoring very young or elderly populations, as well as individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over 100 timepoints, over three periods involving: (i) hourly sampling over 24 hours without intervention, (ii) hourly sampling over 24 hours including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (iii) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome were profiled, and salivary extracellular vesicles were derived, from which small-RNA sequencing was used to determine RNA, miRNA, piRNA and bacterial RNA components. The two 24-hour periods were used in a paired analysis to reveal vaccination responses. Temporal trends were classified and collective behavior revealed broad immune-responses captured in saliva, both at the innate as well as the adaptive response time frames. 1 Year Vaccination 24 hourly samples TFH2 24 hourly samples TFH1 P P S V 2 3 Results Samples and AssaysWe followed a single individual (m, 38, Caucasian), in general good health (has reported chronic sinusitis) over the span of a year. To observe whether the effects of perturbation can be profiled in saliva we carried out the profiling over 3 time frames. In the first 24 hr time frame (TFH1) we established a baseline, obtaining a saliva sample from the subject hourly without perturbation over his standard routine. In the second 24 hr time frame (TFH2), the subject was vaccinated with pneumococcal polysaccharide vaccine (PPSV23) within 3.5 hrs of waking up (at 10.30 am), while otherwise maintaining a similar routine as in the first period (including food intake and meal timing), and again saliva samples were taken hourly. We should note here that the subject reported fever ∼7.5 hours post the vaccination (between timepoints at 5 and 6 pm), lasting for about 4 hrs (10 pm). The two time periods, TFH1 and TFH2, were treated as paired and combined in the analysis below (TF∆) to identify changes induced by the vaccination, by effectively removing daily normal routine effects for this individual. Additionally, in the third time frame (TFD) we monitored the subject daily for over a month, pre-and post-vaccination to identify potential immune changes over both innate and adaptive time frames, Fig. 1.The daily samples were all taken at 8 am, to limit variability. Saliva was sampled both for downstream total RNA profiling, mass spectrometry proteomics, as well as for extraction of extracellular vesicles which were profiled for a variate of small RNA 2/19

Visibility graph based temporal community detection with applications in biological time series

“…Saliva Set (DS1) We used a saliva RNA-sequencing dataset we generated, that was obtained from a clinical trial monitoring individualized response to the standard 23-valent pneumococcal polysaccharide vaccine (PPSV23) 50 . The saliva was sampled from a healthy individual.…”