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An efficient framework to decipher microRNA regulatory programs in functionally divergent naïve T cell subsets [smallRNAseq_adultNeoTNVM]

ABSTRACT: Naïve CD8+ T cells are heterogenous, with subsets exhibiting divergent kinetics and functions post-activation. MicroRNAs (miRNAs) are post-transcriptional regulators, and certain miRNAs contribute to specification of different naïve T cell subsets. However, the microRNA regulatory circuits mediating functional specialization of naïve subsets have not been identified. In this work, we profiled microRNA expression in diverse subsets of naïve CD8+ T cells, revealing significant differences in their microRNA expression landscapes. We developed a novel framework, miR-Inf, to decipher microRNA regulatory programs. MiR-Inf has two key components: (i) an efficient method for estimating gene decay rates from the RNA seq profiles to better capture microRNA regulatory effects, and (ii) identification of functional microRNA targets by integrating decay rate data and microRNA expression data. We applied this framework to identify consequential miRNAs in naïve CD8+ T cell subsets and predicted their context-specific targets. Our analyses revealed that miR-29, a microRNA known to be important in CD8+ T cells, likely functions by modulating transcripts encoding epigenetic factors. Collectively, our data and framework defined microRNA regulatory circuits across diverse naïve CD8+ T cell subsets.

ORGANISM(S): Mus musculus

PROVIDER: GSE280664 | GEO | 2025/08/25

REPOSITORIES: GEO

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Project description:MicroRNAs (miRNAs) have emerged as important players in the regulation of T-cell functionality. However, comprehensive insight into the extent of age-related miRNA changes in T cells is lacking. We established miRNA expression patterns of CD45RO- naïve and CD45RO+ memory T-cell subsets isolated from peripheral blood cells from young and elderly individuals. Unsupervised clustering of the miRNA expression data revealed an age-related clustering in the CD45RO- T cells, while CD45RO+ T cells clustered based on expression of CD4 and CD8. Seventeen miRNAs showed an at least 2-fold up- or downregulation in CD45RO- T cells obtained from young as compared to old donors. Validation on the same and independent samples revealed a statistically significant age-related upregulation of miR-21, miR-223 and miR-15a. In a T-cell subset analysis focusing on known age-related phenotypic changes, we showed significantly higher miR-21 and miR-223 levels in CD8+CD45RO-CCR7- TEMRA compared to CD45RO-CCR7+ TNAIVE-cells. Moreover, miR-21 but not miR-223 levels were significantly increased in CD45RO-CD31- post-thymic TNAIVE cells as compared to thymic CD45RO-CD31+ TNAIVE cells. Upon activation of CD45RO- TNAIVE cells we observed a significant induction of miR-21 especially in CD4+ T cells, while miR-223 levels significantly decreased only in CD4+ T cells. Besides composition and activation, we showed a borderline significant increase in miR-21 levels upon an increasing number of population doublings in CD4+ T-cell clones. Together, our results show that ageing related changes in miRNA expression are dominant in the CD45RO- T-cell compartment. The differential expression patterns can be explained by age related changes in T-cell composition, i.e. accumulation of CD8+ TEMRA and CD4+ post thymic expanded CD31- T cells and by cellular ageing, as demonstrated in a longitudinal clonal culture model. MicroRNA profiling was performed in eight T cell subsets: CD4 naive (CD3+CD4+CD45RO-), CD8 naive (CD3+CD4-CD45RO-), CD4 memory (CD3+CD4+CD45RO+) and CD8 memory (CD3+CD4-CD45RO+) T cells derived from 5 healthy young and 5 healthy old participants.

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An efficient framework to decipher microRNA regulatory programs in functionally divergent naïve T cell subsets [smallRNAseq_adultNeoTNVM]

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