Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [Saliva RNA-sequencing]. Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [Saliva RNA-sequencing]

The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling assessment of 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 were produced at each timepoint (100 timepoints), 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 samples till the end of the investigation. Omics sample analysis includes: RNA-sequencing of total RNA, small RNA sequencing in saliva extracellular vesicles and saliva mass spectrometry proteomics. Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24 hour enumeration. Overall design: Saliva RNA-sequencing summary: Examination of saliva gene expression dynamics in a single individual in saliva over multiple timepoints. 100 total timepoints spanning two 24-hour periods, one without vaccination, and the second with vaccination. 30 daily samples follow and multiple monthly samples over the course of 1 year total.

本研究调查涵盖了本团队临床试验的相关发现，聚焦个体对肺炎球菌疫苗接种的个体化应答监测，针对单一受试者在疫苗接种前后的唾液样本开展了整合组学表征分析。据我们所知，该数据集是目前针对单一个体的最全面的唾液聚焦型组学数据集，在为期一年的周期内覆盖了100个时间点。该时间跨度既包含健康状态阶段，也全面监测了肺炎球菌疫苗接种后的先天免疫与适应性免疫应答。每个时间点均采集了唾液中的蛋白质与RNA，并对全部样本开展了非靶向全面组学分析，涵盖质谱蛋白质组学与RNA测序。具体而言，本研究针对一名38岁男性受试者，在健康阶段及接种肺炎球菌疫苗（PPSV23）后多个时间点开展了组学表征。最初采集了预免疫样本，其中包含一段24小时的每小时采样周期（样本编号为P1052515H07至P1052615H08），以提供对照基线。后续又开展了一段24小时的时间序列采样，在疫苗接种前后同样每小时采集样本（P1060715H07至P1060815H06）。PPSV23肺炎球菌疫苗于样本P1060715H11采集前约上午10:30完成接种。疫苗接种及24小时监测结束后，连续约一个月每日采集样本（直至样本P1070715H08），以捕捉唾液中的先天与适应性免疫应答。后续又追加了两周的每周采样，随后改为每月采样直至研究结束。组学样本分析涵盖：总RNA测序、唾液细胞外囊泡小RNA测序以及唾液质谱蛋白质组学。关于样本命名的说明：样本标识符/名称P1MMDDYYHhh的对应规则为：受试者编号P1、日期MMDDYY、以H为前缀的24小时制采样小时hh。整体实验设计：唾液RNA测序研究概述：对单一个体唾液中的基因表达动态开展跨多时间点分析。共计100个时间点，覆盖两段24小时采样周期，一段未接种疫苗，另一段完成疫苗接种。后续采集了30份每日样本，并在总计一年的周期内采集了多份月度样本。