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
Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
iScience. 2024 Jul 6;27(8):110471. doi: 10.1016/j.isci.2024.110471. eCollection 2024 Aug 16.
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 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 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.
我们对来自健康供体的病原体刺激外周血单核细胞（PBMC）进行了长读长转录组和蛋白质组分析，以发现对多种病原体免疫应答过程中表达的新转录本和蛋白质异构体。长读长转录组分析揭示了病原体刺激后诱导产生的新序列和异构体切换，包括使用传统短读长测序难以检测到的转录本。所有病原体刺激的一个常见结果是内含子保留普遍减少。我们重点介绍了可能指示新免疫机制的新转录本。RNA表达差异并未导致分泌蛋白量的差异。对分泌蛋白的聚类分析揭示了在病毒和聚肌苷酸-聚胞苷酸（poly(I:C)）刺激的PBMC中，趋化因子（受体）在RNA和蛋白质水平上表达之间的相关性。对病原体刺激的免疫细胞进行异构体识别长读长测序突出了这些方法识别新转录本的潜力，揭示了比以前认识到的更复杂的转录组格局。
