AUTHOR=Soni Jyoti , Chattopadhyay Partha , Mehta Priyanka , Mohite Ramakant , Tardalkar Kishore , Joshi Meghnad , Pandey Rajesh 

TITLE=Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics

JOURNAL=Frontiers in Medicine

VOLUME=11

YEAR=2024

URL=https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2024.1297001

DOI=10.3389/fmed.2024.1297001

ISSN=2296-858X

ABSTRACT=<sec id="sec1001"><title>Introduction</title><p>Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins.</p></sec><sec id="sec2001"><title>Methods</title><p>We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state.</p></sec><sec id="sec3001"><title>Results</title><p>We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, <italic>CD3E</italic>, <italic>CD4</italic>, <italic>CD8A</italic>, <italic>CD5</italic>, <italic>CD7</italic>, <italic>GITR</italic>, and <italic>KLRB1</italic> in healthy individuals, whereas markers related to cell activation, <italic>CD38</italic>, <italic>CD28</italic>, <italic>CD69</italic>, <italic>CD62L</italic>, <italic>CD14</italic>, and <italic>CD16</italic> elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (<italic>CCR5, CCR7, CCR4, CXCR3</italic>, and <italic>PTGRD2</italic>). We also observed variations in the expression of markers within cell populations under different states.</p></sec><sec id="sec4001"><title>Discussion</title><p>Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.</p></sec>