Author:
Hoffmann Markus,Willruth Lina-Liv,Dietrich Alexander,Lee Hye Kyung,Knabl Ludwig,Trummer Nico,Baumbach Jan,Furth Priscilla A.,Hennighausen Lothar,List Markus
Abstract
AbstractBulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we propose that RNA-seq should be considered a diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers insights into a patient’s immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 196 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that—combined with sequence alignments and BLASTp—they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.
Funder
Technical University Munich – Institute for Advanced Study
Intramural Research Programs (IRPs) of the National Institute of Diabetes and Digestive and Kidney Diseases
Deutsche Forschungsgemeinschaft
VILLUM Young Investigator Grant
German Federal Ministry of Education and Research (BMBF) within the framework of the *e:Med* research and funding concept
European Union’s Horizon 2020 research and innovation program
Technische Universität München
Publisher
Springer Science and Business Media LLC