Translation of scRNA-seq to a clinical blood test for infection diagnostics

INTRODUCTION: Early and accurate triage of patients with febrile illness is crucial for appropriate treatment. While standard inflammatory biomarkers are often nonspecific, transcriptome analysis of peripheral blood has diagnostic potential. However, bulk gene expression data is often confounded by changes in cell count proportions, a more robust quantification of gene expression in specific single-cell types, such as monocytes, is required to serve as a reliable clinical biomarker. AREAS COVERED: Various methods to obtain single-cell-type gene expression results, including the gold standard of gene expression analysis after cell sorting and single-cell RNA sequencing, which are difficult to implement in the routine settings are discussed. Other method to interrogate gene expression of a single cell-type is needed. Finally, monocyte cell-type specific ratio-based biomarker (RBB, called Direct Leukocyte Single cell-type Transcript Abundance, or DIRECT LS-TA) which can estimate single cell-type (monocyte) specific gene expression without cell sorting is introduced. EXPERT OPINION: Traditional diagnostic test for differentiating infection has several limitations requiring breakthrough including turn-around time and cost. DIRECT LS-TA provides a reliable way to quantify monocyte-specific gene expression that strongly correlates with gold-standard methods. It is more affordable than single-cell RNA sequencing and can be readily implemented in clinical laboratories using widely available quantitative PCR or digital PCR machines.