Analyzing Lack of Concordance Between the Proteome and Transcriptome in Paired scRNA-Seq and Multiplexed Spatial Proteomics

TL;DR

This paper investigates the persistent discordance between gene transcripts and proteins in immune cells using paired single-cell RNA sequencing and spatial proteomics data, revealing key immune markers with sustained expression.

Contribution

It provides novel insights into the complex regulation of gene expression and protein function, highlighting persistent immune markers across different cell types.

Findings

CD45-RO is consistently expressed in memory T cells

Ki67 shows sustained expression related to proliferation

HLA-DR demonstrates continuous expression in antigen-presenting cells

Abstract

In this study, we analyze discordance between the transcriptome and proteome using paired scRNA-Seq and multiplexed spatial proteomics data from HuBMAP. Our findings highlight persistent transcripts in key immune markers, including CD45-RO, Ki67, CD45, CD20, and HLA-DR. CD45-RO is consistently expressed in memory T cells, while Ki67, associated with cell proliferation, also displays sustained expression. Furthermore, HLA-DR, part of the MHC class II molecules, demonstrates continuous expression, possibly crucial for APCs to trigger an effective immune response. This investigation provides novel insights into the complexity of gene expression regulation and protein function.