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Title: | Multi-omic profiling of pathogen-stimulated primary immune cells | Authors: | Salz, Renee Vorsteveld, Emil E. van der Made, Caspar I. Kersten, Simone Stemerdink, Merel Riepe, Tabea, V Hsieh, Tsung-han Mhlanga, Musa Netea, Mihai G. VOLDERS, Pieter-Jan Hoischen, Alexander 't Hoen, Peter A. C. |
Issue Date: | 2024 | Publisher: | CELL PRESS | Source: | iScience (Cambridge), 27 (8) (Art N° 110471) | 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. | Notes: | 't Hoen, PAC (corresponding author), Radboud Univ Nijmegen, Med Ctr, Dept Med BioSci, NL-6525 GA Nijmegen, Netherlands.; Hoischen, A; 't Hoen, PAC (corresponding author), Radboud Univ Nijmegen, RadboudUMC Res Inst Med Innovat, Med Ctr, NL-6525 GA Nijmegen, Netherlands.; Hoischen, A (corresponding author), Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6525 GA Nijmegen, Netherlands.; Hoischen, A (corresponding author), Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, NL-6525 GA Nijmegen, Netherlands.; Hoischen, A (corresponding author), Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, NL-6525 GA Nijmegen, Netherlands. alexander.hoischen@radboudumc.nl; peter-bram.thoen@radboudumc.nl |
Keywords: | Immunology;Proteomics;Transcriptomics | Document URI: | http://hdl.handle.net/1942/43569 | ISSN: | 2589-0042 | e-ISSN: | 2589-0042 | DOI: | 10.1016/j.isci.2024.110471 | ISI #: | 001274993300001 | Rights: | 2024 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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