Underrepresentation of activating KIR gene expression in single-cell RNA-seq data is due to KIR gene misassignment

Eric Alves; Abha Chopra; Ramesh Ram; Jennifer Currenti; Spyros A Kalams; Simon A Mallal; Elizabeth J Phillips; Silvana Gaudieri

doi:10.1002/eji.202350590

Underrepresentation of activating KIR gene expression in single-cell RNA-seq data is due to KIR gene misassignment

Eur J Immunol. 2024 Jan;54(1):e2350590. doi: 10.1002/eji.202350590. Epub 2023 Nov 20.

Authors

Eric Alves^{1

2}, Abha Chopra³, Ramesh Ram³, Jennifer Currenti^{2

4}, Spyros A Kalams⁵, Simon A Mallal^{3

5}, Elizabeth J Phillips^{3

5}, Silvana Gaudieri^{1

3

5}

Affiliations

¹ School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia.
² Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.
³ Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia.
⁴ School of Medicine, Curtin University, Bentley, Western Australia, Australia.
⁵ Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.

PMID: 37944995
DOI: 10.1002/eji.202350590

Abstract

Standard single-cell RNA-sequencing alignment pipelines exhibit a propensity for misassigning killer immunoglobulin-like receptor (KIR) transcripts, thereby giving rise to inaccuracies in quantifying KIR expression. Alves et al. elucidated that these default workflows frequently misclassify activating KIR transcripts as inhibitory KIR expression, resulting in a skewed representation of the KIR repertoire.

MeSH terms

Gene Expression
Genotype
Killer Cells, Natural* / metabolism
Receptors, KIR / genetics
Receptors, KIR / metabolism
Single-Cell Gene Expression Analysis*

Substances

Receptors, KIR

Abstract

MeSH terms

Substances

Grants and funding