In-silico cell sorting revealed granulocyte-specific single-cell-type gene expression from peripheral blood bulk expression data and its application as host response biomarkers to discriminate bacterial and viral infections

Abstract

Peripheral Blood transcriptome analysis evaluated the bulk transcript abundance (TA) covering all leukocyte cell populations. However, there are 2 main problems in using bulk expression as biomarkers: (1) A long list of differential expression genes (DEGs) was found, and (2) DEGs cannot be attributed to a host response of any specific cell-type. TA assays after conventional cell sorting, as the gold-standard method, is too tedious for routine use. Recently, we showed that by using a ratio-based biomarker, RBB (ratio of two stringently selected genes), it is feasible to interrogate the gene expression of a single cell-type (monocyte and B lymphocyte) in peripheral whole blood (WB) directly. Here, we apply this in-silico cell sorting algorithm (DIRECT LS-TA, Direct Leukocyte Single cell-type Transcript Abundance) to granulocytes in WB samples to reveal RBBs specific to granulocytes. This DIRECT LS-TA approach without the need for cell-sorting was applied to public datasets to differentiate the 2 types of infection (bacterial vs viral infection). The following RBBs measured in WB correlate with the expression of target (numerator) genes in purified granulocytes, thus cell-sorting can be avoided by using these RBBs: ARG1/SRGN, ANXA3/SRGN, RSAD2/SRGN. Together with monocyte DIRECT LS-TA biomarkers, IFI27/PSAP, direct quantification of 4 genes provided optimal differentiation of viral from bacterial infection. Meta-analysis and unsupervised machine learning classification confirmed the superior performance of DIRECT LS-TA biomarkers. These RBBs found by prior In-silico cell-sorting identified pairs of genes that are used to formulate as ratio-based biomarkers (RBBs) to represent gene expression of granulocytes inside whole blood cell-mixture samples which was useful to triage febrile patients into two major categories of febrile diseases between viral and bacterial infection with high degree of sensitivity and specificity.