Interplay between T-bet and HIF-1a is required for proper epigenomic and transcriptomic reprogramming of monocyte subsets

Background: Monocyte subsets, classified into classical, intermediate, and non-classical, have distinct specific functions. Despite increasing reports describing changes in monocyte subsets in a wide range of pathological inflammatory conditions, such as autoimmune and infectious diseases, the regulatory mechanisms underlying their differentiation are poorly understood. This information could be essential to understand their contribution to pathology. Methods: In this study, we obtained the DNA methylomes and transcriptomes from classical, intermediate, and non-classical monocytes using MethylationEPIC BeadChip arrays and RNA-seq from matching samples. Regulon analysis, in vitro induction experiments, and integration with single-cell transcriptomics were used to study the impact on the myeloid compartment of a patient with Mendelian susceptibility to mycobacterial disease (MSMD). Results: DNA methylome and transcriptome profiling of the three monocyte subsets revealed progressive changes associated with pathways and transcription factors related to their properties. Specifically, HIF-1α and T-bet stand out as major factors in the transition from classical to non-classical subsets. While HIF-1α and its partner ARNT, as well as their targets, undergo a decrease in their expression levels in the transition to non-classical monocytes, T-bet and its targets become prominent in the non-classical compartment. Analysis of monocytes from single-cell RNA-seq data of a patient with a homozygous mutation for T-bet, which leads to MSMD, reveals a decrease in non-classical monocyte subsets, a strong effect on HIF-1α signalling, as well as impairment of the TNF/NF-κB pathway. Conclusion: Altogether, these findings support the interplay between T-bet and HIF-1α for the proper differentiation of monocyte subsets.