Particulate pollutant-induced trained immunity is mediated by
H3K27ac in circulating monocytes
Next, we asked whether pollution-induced trained immunity is
specifically mediated by H3K27ac modifications. Epigenomic ChIP Seq
profiling of pollutant (SRM-1648a) versus media trained circulating
monocytes, freshly purified from a healthy donor, revealed H3K27
acetylation patterns, depending on the training type, throughout the
genomic regions that include promoter-transcription start sites (TSS)
(Fig. 5A-B). In promoters, operationally defined as regions within 3 kb
of a TSS, we identified H3K27ac marks that specifically associate with
pollutant exposure, 6 days post training (Fig. 5C). In line with the
inflammatory signature (Fig. 3-4), we detected an enhanced H3K27ac in
the promoter-TSS of the genes encoding inflammatory mediators such as
IL-1β, IL-6, IL-8, and MIP-1α upon pollutant training, arguing that this
training drives a pro-inflammatory transcriptional program in monocytes
(Fig. 5D). Training with pollutant enhanced H3K27ac marks in the
promoter-TSS of IRF 8 and AHR , which encode essential
transcription factors, Interferon Regulatory Factor 8 and Aryl
Hydrocarbon Receptor. Furthermore, the strongest H3K27ac signal among
transcription factors was detected upstream of TCF3 , encoding
transcription factor 3. Finally, pollution-induced training of monocytes
increased H3K27ac in promoter-TSS of SETD1A encoding SET Domain
Containing 1A, a dedicated H3K4 methyltransferase (Fig. 5D). To
understand the biological pathways affected during pollutant-induced
trained immunity, we performed a gene ontology (GO) and KEGG pathway
analysis using clusterProfiler R package (21 ). As shown in Fig.
5E, H3K27ac was highly enriched in the promoter-TSS of genes involved in
inflammatory responses such as chemokine and TNF signaling, consistent
with increased secretion of inflammatory mediators such as IL-8, and
TNF. Interestingly, other inflammatory pathways relevant to asthma
immunopathogenesis such as MAPK signaling, TCR activation, Fcγ
receptor-mediated phagocytosis, autophagy, NOD-like receptor signaling
were found among the pathways with highest H3K27ac mark specifically
activated by particulate pollutants in circulating monocytes. The
comprehensive list of genes, peaks, and pathways specific to
pollutant-induced training have been summarized in Supplementary Table
2-4, respectively. In addition, untrained monocytes, baseline control
group, possess a specific H3K27ac pattern of specific genes and peaks as
well as biological pathways, e.g. tight junctions, cell adhesion,
and insulin secretion as shown in Fig. 5E and Supplementary Table 5-7.
Finally, monocytes underwent training with β-glucan, served as positive
control, for 6 days (Table 8). Collectively, pollution training leaves
H3K27ac scars in specific genome regions that are not affected in the
control untrained monocytes.