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Multi-omic profiling of pathogen-stimulated primary immune cells
Renee Salz1,2, Emil E Vorsteveld2,3, Caspar I van der Made2,3,4
1Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
Iscience
|August 2, 2024
Summary
Long-read sequencing reveals novel immune cell transcripts and isoform changes during pathogen responses. While RNA and secreted protein levels didn't always correlate, new insights into immune mechanisms were uncovered.
Area of Science:
- Immunology
- Genomics
- Proteomics
Background:
- Immune responses involve complex gene and protein expression changes.
- Traditional sequencing methods may miss certain transcript isoforms.
Purpose of the Study:
- To discover novel transcript and protein isoforms in pathogen-stimulated immune cells using long-read sequencing.
- To investigate isoform switching and intron retention during immune responses.
Main Methods:
- Long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs).
- Analysis of novel sequences, isoform switching, and intron retention.
- Clustering analysis of RNA and protein expression data.
Main Results:
- Identification of novel transcript sequences and isoform switching, including transcripts missed by short-read sequencing.
- Observed widespread loss of intron retention across various pathogen stimulations.
- Highlighted novel transcripts for NFKB1 and CASP1, potentially indicating new immunological mechanisms.
- Found no direct correlation between RNA expression differences and secreted protein amounts, but noted correlations for chemokine expression.
Conclusions:
- Long-read sequencing provides a more comprehensive view of the immune cell transcriptome.
- Isoform-specific analysis is crucial for understanding complex immune responses.
- Novel transcripts and isoform dynamics offer new avenues for exploring immunological mechanisms.
