Direct Measurement of B Lymphocyte Gene Expression Biomarkers in Peripheral Blood Transcriptomics Enables Early Prediction of Vaccine Seroconversion

Abstract

Peripheral blood transcriptome is a highly promising area for biomarker development. However, transcript abundances (TA) in these cell mixture samples are confounded by proportions of the component leukocyte subpopulations. This poses a challenge to clinical applications, as the cell of origin of any change in TA is not known without prior cell separation procedure. We developed a framework to develop a cell-type informative TA biomarkers which enable determination of TA of a single cell-type (B lymphocytes) directly in cell mixture samples of peripheral blood (e.g., peripheral blood mononuclear cells, PBMC) without the need for subpopulation separation. It is applicable to a panel of genes called B cell informative genes. Then a ratio of two B cell informative genes (a target gene and a stably expressed reference gene) obtained in PBMC was used as a new biomarker to represent the target gene expression in purified B lymphocytes. This approach, which eliminates the tedious procedure of cell separation and directly determines TA of a leukocyte subpopulation in peripheral blood samples, is called the Direct LS-TA method. This method is applied to gene expression datasets collected in influenza vaccination trials as early predictive biomarkers of seroconversion. By using TNFRSF17 or TXNDC5 as the target genes and TNFRSF13C or FCRLA as the reference genes, the Direct LS-TA B cell biomarkers were determined directly in the PBMC transcriptome data and were highly correlated with TA of the corresponding target genes in purified B lymphocytes. Vaccination responders had almost a 2-fold higher Direct LS-TA biomarker level of TNFRSF17 (log 2 SMD = 0.84, 95% CI = 0.47–1.21) on day 7 after vaccination. The sensitivity of these Direct LS-TA biomarkers in the prediction of seroconversion was greater than 0.7 and area-under curves (AUC) were over 0.8 in many datasets. In this paper, we report a straightforward approach to directly estimate B lymphocyte gene expression in PBMC, which could be used in a routine clinical setting. Moreover, the method enables the practice of precision medicine in the prediction of vaccination response. More importantly, seroconversion could now be predicted as early as day 7. As the acquired immunology pathway is common to vaccination against influenza and COVID-19, these biomarkers could also be useful to predict seroconversion for the new COVID-19 vaccines.

Blood leukocyte transcriptional modules and differentially expressed genes associated with disease severity and age in COVID-19 patients

“…The plasmatic levels of this protein are markedly elevated in septic patients, and it has been considered a therapeutic target for attenuating inflammatory responses 91 . Additionally, it was shown that TXND5 is hyper-expressed in B cells after COVID-19 vaccination, being a marker for seroconversion 92 . Therefore, the three genes are potential candidates for monitoring disease severity in COVID-19.…”

Interferon response and profiling of interferon response genes in peripheral blood of vaccine-naive COVID-19 patients

“…Secondly, outlier samples (i.e. individuals in pseudobulks) were excluded based on Mahalanobis distance metrics that were computed using 19 selected housekeeping genes ( 39 – 41 ). Finally, for datasets with batches (e.g.…”

The role and mechanism of TXNDC5 in disease progression

“…Atorvastatin inhibits ROS production and Nox2 activity by promoting the membrane translocation of TXNDC5 in lipid rafts and enhancing the colocalization of TXNDC5 and Nox2, thus exerting antioxidant effects ( 162 ). Moreover, direct B lymphocyte LS-TA of TXNDC5 is an early biomarker of vaccine response in novel coronavirus pneumonia (COVID-19) ( 163 ).…”