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).

本研究涵盖了一项临床试验的研究成果，该试验旨在监测个体对肺炎球菌疫苗接种的个性化应答。我们对一名受试者在疫苗接种前后的外周血单个核细胞（peripheral blood mononuclear cells, PBMC）与唾液样本开展了整合组学分析。据我们所知，这是目前规模最庞大的以唾液为核心的个体组学数据集，在为期一年的周期内覆盖了100个采样时间点。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先天免疫与适应性免疫的应答变化。每个时间点均提取了唾液与PBMC中的蛋白质与RNA：其中唾液样本共计100个时间点，PBMC样本共计25个时间点；并对所有样本实施非靶向全面组学分析，涵盖质谱蛋白质组学与RNA测序技术。

具体而言，我们对一名38岁男性受试者在健康阶段及肺炎球菌疫苗（PPSV23）接种后的多个时间点进行了组学分析。初始免疫前样本采集阶段包含一段24小时的每小时采样周期（样本编号P1052515H07至P1052615H08），以建立可用于比对的基线数据。随后我们开展了第二段24小时时间序列采样，在疫苗接种前后同样进行每小时采样（样本编号P1060715H07至P1060815H06）。PPSV23肺炎球菌疫苗于P1060715H11数据点前约上午10:30完成接种。接种后及24小时监测阶段结束后，我们连续约一个月每日采集样本（直至样本P1070715H08），以捕获唾液中的先天与适应性免疫应答信号。后续又采集了两周的周度样本，随后改为月度采样直至研究结束。与此同时，我们同步采集了周度或月度的PBMC样本。

组学样本分析内容包括：唾液与PBMC中总RNA的RNA测序、唾液中小RNA测序、唾液与PBMC的蛋白质组学分析，以及唾液细胞外囊泡中的小RNA测序。

样本命名说明：样本标识符/名称格式为P1MMDDYYHhh，其中P1代表受试者编号，MMDDYY为采样日期，H后紧跟的hh为采用24小时制的采样小时数。

本研究共计在一年周期内完成了100个唾液样本的采集，同时获得了30份PBMC样本。

研究整体设计：外周血单个核细胞（PBMC）RNA测序概述：分析单一个体PBMC中的基因表达动态变化，在为期一年的周期内采集25个周度/月度时间点样本，涵盖肺炎球菌疫苗（PPSV23）接种前后的免疫应答变化阶段。