A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring

Background While our understanding of the role that the immune system plays in health and disease is growing at a rapid pace, available clinical tools to capture this complexity are lagging. We previously described the construction of a third-generation modular transcriptional repertoire derived from genome-wide transcriptional profiling of blood of 985 subjects across 16 diverse immunologic conditions, which comprises 382 distinct modules. Results Here we describe the use of this modular repertoire framework for the development of a targeted transcriptome fingerprinting assay (TFA). The first step consisted in down-selection of the number of modules to 32, on the basis of similarities in changes in transcript abundance and functional interpretation. Next down-selection took place at the level of each of the 32 modules, with each one of them being represented by four transcripts in the final 128 gene panel. The assay was implemented on both the Fluidigm high throughput microfluidics PCR platform and the Nanostring platform, with the list of assays target probes being provided for both. Finally, we provide evidence of the versatility of this assay to assess numerous immune functions in vivo by demonstrating applications in the context of disease activity assessment in systemic lupus erythematosus and longitudinal immune monitoring during pregnancy. Conclusions This work demonstrates the utility of data-driven network analysis applied to large-scale transcriptional profiling to identify key markers of immune responses, which can be downscaled to a rapid, inexpensive, and highly versatile assay of global immune function applicable to diverse investigations of immunopathogenesis and biomarker discovery.

背景 尽管我们对免疫系统在健康和疾病中所起作用的理解正在迅速增长，但用于捕捉这种复杂性的现有临床工具却相对滞后。我们先前描述了一种第三代模块化转录组库的构建，它源自对16种不同免疫状况下985名受试者的血液进行的全基因组转录谱分析，该转录组库包含382个不同的模块。 结果 在此我们描述了利用这种模块化组库框架来开发一种靶向转录组指纹分析检测法（TFA）。第一步是根据转录本丰度变化的相似性和功能解释，将模块数量向下筛选至32个。接下来在这32个模块中的每一个模块层面进行进一步的向下筛选，最终的128个基因组合中每个模块由4个转录本代表。该检测法在Fluidigm高通量微流体PCR平台和Nanostring平台上均得以实施，并且提供了两个平台的检测目标探针列表。最后，我们通过展示其在系统性红斑狼疮疾病活动评估以及孕期纵向免疫监测中的应用，证明了这种检测法在体内评估多种免疫功能的通用性。 结论 这项工作证明了将数据驱动的网络分析应用于大规模转录谱分析以识别免疫反应关键标志物的实用性，这些标志物可被精简为一种快速、廉价且通用性极强的全球免疫功能检测法，适用于免疫发病机制的多种研究以及生物标志物的发现。