Uncovering Hidden Consistency in Cellular Research Models
COS/BioE Professor Meni Wanunu and BioE Associate Professor Sara Rouhanifard’s research on “Pseudouridine reprogramming in the human T cell epitranscriptome: from primary to immortalized states” was published in RNA. In their study comparing pseudouridine (ψ) profiles in primary human T cells and Jurkat cell lines, they found that while 87% of core RNA modification patterns are conserved, the remaining 13% differ in biologically significant ways, suggesting immortalized cells are a surprisingly consistent yet imperfect model for study.
Abstract:
Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T cell signaling, activation, and immune responses. However, the immortalization process can alter key cellular properties, and researchers widely believe this process could significantly change RNA modification machinery and modification sites. In this study, we focus on pseudouridine (ψ), one of the most abundant mRNA modifications, and compare ψ profiles in mRNA from primary and immortalized T cells using direct RNA sequencing (DRS). Surprisingly, 87% of ψ-sites were shared between the two cell types, primarily in transcripts encoding proteins involved in essential cellular processes, including RNA-modification regulation. Furthermore, the analysis of the 13% of sites unique to each cell type reveals that Jurkat cells contained transcripts linked to immune activation and oncogenesis, while primary T cells contained transcripts associated with calcium signaling and intracellular trafficking. We provide a list of these genes, which should be considered when using immortalized cells to study RNA modifications in immunology contexts. Most differences were driven by whether the mRNA was present or absent in the immortalized or primary cell type. Interestingly, RNA-modification enzyme expression levels were highly conserved in both cell types. This suggests that site-specific differences in ψ levels arise from regulatory processes acting in trans rather than differences in modification enzyme levels.