A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells

Mihai, I. S.; Nunez-Carpintero, I.; Cirillo, D.; Trygg, J.; Forsell, M. N.; Selinger, M.

doi:10.1101/2025.11.25.687998

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bioRxiv · 10.1101/2025.11.25.687998

A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells

Mihai, I. S.·Nunez-Carpintero, I.·Cirillo, D.·Trygg, J.·Forsell, M. N.·Selinger, M.

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Abstract

CD4+ T cells are components of the adaptive immune system with a plethora of subtype-specific functions. In order to further dissect the activation and differentiation regulatory program(s) of individual CD4+ T cell subsets, we performed an in vitro activation and differentiation of human primary naive CD4+ T cells towards Th1, Th2, Th17 and Treg subtypes followed by the single-cell RNA-seq and ATAC-seq (multiome) analysis. Resulting multiome data were used for constructing the subtype-specific gene regulatory networks, which were next assessed for their differences/similarities among the subtypes. Surprisingly, a conserved set of 8 "backbone" transcription factors (TFs) was identified as highly central in all subtypes, however, with unique differentiation-driven rewiring tendency. Subtype-specific "driver" TFs were identified in the case of Th1-Th1_17-Th17 lineage (EOMES, HLF), naive Tregs (ESR1, DACH1), and memory Tregs (SOX13). Finally, we applied community detection algorithms to identify potential non-obvious groups of genes that regulate diverse molecular functions within the differentiated subtypes, linked to the backbone TFs. Our atlas aims at providing a high resolution understanding of the gene regulatory networks and their rewiring in human primary CD4+ T cells, upon activation and differentiation.

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Mihai, I. S., Nunez-Carpintero, I., Cirillo, D., Trygg, J., Forsell, M. N., Selinger, M.. 2025-11-27. A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells. https://doi.org/10.1101/2025.11.25.687998

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