Multi-omic profiling of pathogen-stimulated primary immune cells

Renee Salz; Emil E Vorsteveld; Caspar I van der Made; Simone Kersten; Merel Stemerdink; Tabea V Riepe; Tsung-Han Hsieh; Musa Mhlanga; Mihai G Netea; Pieter-Jan Volders; Alexander Hoischen; Peter A C 't Hoen

doi:10.1016/j.isci.2024.110471

Multi-omic profiling of pathogen-stimulated primary immune cells

iScience. 2024 Jul 6;27(8):110471. doi: 10.1016/j.isci.2024.110471. eCollection 2024 Aug 16.

Authors

Renee Salz^{1

2}, Emil E Vorsteveld^{2

3}, Caspar I van der Made^{2

3

4}, Simone Kersten^{2

3}, Merel Stemerdink^{2

5}, Tabea V Riepe^{1

2

3}, Tsung-Han Hsieh⁶, Musa Mhlanga^{2

6}, Mihai G Netea^{3

4}, Pieter-Jan Volders^{7

8}, Alexander Hoischen^{2

3

4}, Peter A C 't Hoen^{1

2}

Affiliations

¹ Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
² RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
³ Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
⁴ Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands.
⁵ Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
⁶ Department of Cell Biology, Radboud University, 6500 HB Nijmegen, the Netherlands.
⁷ Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
⁸ Laboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium.

Abstract

We performed long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors to discover new transcript and protein isoforms expressed during immune responses to diverse pathogens. Long-read transcriptome profiling reveals novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. Widespread loss of intron retention occurs as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. RNA expression differences did not result in differences in the amounts of secreted proteins. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and poly(I:C)-stimulated PBMCs. Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.

Keywords: Immunology; Proteomics; Transcriptomics.