A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring
bioRxiv(2019)
摘要
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
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关键词
human immunology,transcriptome,gene expression,systems biology,systemic lupus erythematosus,pregnancy
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