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. * BIIR : Baylor Institute for Immunology Research COPD : Chronic Obstructive Pulmonary Disease CRP : C-Reactive Protein Ct : Cycle threshold FC : Fold Change FDR : False Discovery Rate GO_BP : Gene Ontology Biologic Process GO_MF : Gene Ontology Molecular Function HIV : Human Immunodeficiency Virus IFN : Interferon IRB : Institutional Review Board KEGG : Kyoto Encyclopedia of Genes and Genomes MS : Multiple Sclerosis PCA : Principle Component Analysis PCR : Polymerase Chain Reaction PID : Primary Immune Deficiency RF : Random Forest ROC : Receiver Operating Characteristic RSV : Respiratory Syncytial Virus SLE : Systemic Lupus Erythematosus SLEDAI : SLE Disease Activity Index SOJIA : Systemic onset Juvenile Idiopathic Arthritis TB : Tuberculosis TBD : To Be Determined TFA : Transcriptome Fingerprinting Assay