Epigenetic aging of classical monocytes from healthy individuals

Shchukina, I.; Bagaitkar, J.; Shpynov, O.; Loginicheva, E.; Porter, S.; Mogilenko, D. A.; Wolin, E.; Collins, P.; Demidov, G.; Artomov, M.; Zaitsev, K.; Sidorov, S.; Camell, C.; Bambouskova, M.; Arthur, L.; Swain, A.; Panteleeva, A.; Dievskii, A.; Kurbatsky, E.; Tsurinov, P.; Chernyatchik, R.; Dixit, V. D.; Jovanovic, M.; Stewart, S. A.; Daly, M. J.; Dmitriev, S.; Oltz, E. M.; Artyomov, M. N.

doi:10.1101/2020.05.10.087023

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bioRxiv · 10.1101/2020.05.10.087023

Epigenetic aging of classical monocytes from healthy individuals

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Abstract

The impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older individuals (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) - a novel, cell-type specific signature of aging in DNA methylome. Optimized ultra-low-input ChIP-seq (ULI-ChIP-seq) data acquisition and analysis pipelines applied to 5 chromatin marks for each individual revealed lack of large-scale age-associated changes in chromatin modifications and allowed us to link hypo- and hypermethylated DMRs to distinct chromatin modification patterns. Specifically, hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with normal pattern of expression. Furthermore, hypo- and hypermethylated DMRs followed distinct functional and genetic association patterns. Hypomethylation events were associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells. Furthermore, these locations were also enriched in genetic regions associated by GWAS with asthma, total blood protein, hemoglobin levels and MS. On the other side, acceleration of epigenetic age in HIV and asthma stems only from changes in hypermethylated DMRs but not from hypomethylated loci.

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Shchukina, I., Bagaitkar, J., Shpynov, O., Loginicheva, E., Porter, S., Mogilenko, D. A., Wolin, E., Collins, P., Demidov, G., Artomov, M., Zaitsev, K., Sidorov, S., Camell, C., Bambouskova, M., Arthur, L., Swain, A., Panteleeva, A., Dievskii, A., Kurbatsky, E., Tsurinov, P., Chernyatchik, R., Dixit, V. D., Jovanovic, M., Stewart, S. A., Daly, M. J., Dmitriev, S., Oltz, E. M., Artyomov, M. N.. 2020-05-11. Epigenetic aging of classical monocytes from healthy individuals. https://doi.org/10.1101/2020.05.10.087023

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