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. 2022 May 16;18(5):e1009973.
doi: 10.1371/journal.pgen.1009973. eCollection 2022 May.

Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis

Amy A Eapen  1   2   3 , Sreeja Parameswaran  3 , Carmy Forney  3 , Lee E Edsall  3 , Daniel Miller  3 , Omer Donmez  3 , Katelyn Dunn  3 , Xiaoming Lu  3 , Marissa Granitto  3 , Hope Rowden  3 , Adam Z Magier  1 , Mario Pujato  3 , Xiaoting Chen  3 , Kenneth Kaufman  3   4   5   6 , David I Bernstein  7 , Ashley L Devonshire  1   5 , Marc E Rothenberg  1   5 , Matthew T Weirauch  3   4   5 , Leah C Kottyan  1   3   5
Affiliations

Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis

Amy A Eapen et al. PLoS Genet. .

Abstract

Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Study Design.
Figure created in BioRender.
Fig 2
Fig 2. Differential chromatin accessibility and transcription factor (TF) motif enrichment in atopic dermatitis (AD) subjects vs. matched controls.
Assay for transposase-accessible chromatin sequencing (ATAC-seq) peaks were identified for all cases and controls and compared for all subject pairs. (A) Differential chromatin accessibility analysis. For each matched pair of subjects, we identified shared, control-specific, and AD-specific peaks (see METHODS). A representative subject pair is shown in (A). Each row represents a single genomic locus where an ATAC-seq peak was identified in either the AD or control subject. The center of each row corresponds to the center of the ATAC-seq peak. Heatmap colors indicate the normalized ATAC-seq read count within the AD1 (right) or CTL1 (control) (left) subject–see key on the right. (B) Differential transcriptional factor (TF) motif enrichment analysis. Comparison of TF motif enrichment results within a representative AD-specific and control-specific matched subject pair. Each dot represents the enrichment of a particular motif (corrected negative log10 p-value). Select motif families are color-coded (see key on the upper left side). (C and D) Nuclear factor kappa B (NFKB) motif enrichment comparison between consistently AD-specific and consistently control-specific ATAC-seq peaks. “Consistently specific” peaks were defined as those peaks that were AD- or control-specific in at least three AD or control subjects, respectively. Results are shown for representative Cis-BP NFKB motif, M05887_2.00. Full results are provided in S5 Table.
Fig 3
Fig 3. Shared peaks in ATAC-seq and chromatin immunoprecipitation with sequencing (ChIP-seq) experiments between paired subjects.
Percentage of shared peaks between paired samples in ATAC-seq compared to NFKB1 ChIP-seq experiments.
Fig 4
Fig 4. Differential NFKB1 binding and TF motif enrichment in AD subjects vs. matched controls.
NFKB1 ChIP-seq peaks were identified for all case and control subjects and compared between matched subject pairs. (A) Differential NFKB1 binding analysis. For each matched pair of subjects, we identified the shared peaks, control-specific peaks, and AD-specific peaks (see METHODS). A representative subject pair is shown in (A). Each row represents a single genomic locus, where an NFKB1 ChIP-seq peak was identified in either the AD or control subject. The center of each row corresponds to the center of the ChIP-seq peak. Heatmap colors indicate the normalized ChIP-seq read counts within the AD2 (right) or CTL2 (left) subject–see key on the right. (B) Differential TF motif enrichment analysis. Comparison of TF motif enrichment results within a representative AD-specific and control-specific matched subject pair. Each dot represents the enrichment of a particular motif (corrected negative log10 p-value). Select motif families are color-coded (see key on the upper right side). (C and D) NFKB motif enrichment comparison between consistently AD-specific and consistently control-specific NFKB1 ChIP-seq peaks. “Consistently specific” peaks were defined as those peaks that were AD- or control-specific in at least three case or control subjects, respectively. Results are shown for representative Cis-BP NF-κB motif, M05887_2.00. All results are listed in S7 and S9 Tables.
Fig 5
Fig 5. Overlap of genes expressed in an AD-dependent manner with Control-specific and AD-specific ATAC-seq and ChIP-seq peaks.
AD-dependent genes can be upregulated in AD (Up in AD) or downregulated in AD (Down in AD). Overlap with of these gene sets with Control-specfic and AD-specific ATAC and ChIP-seq peaks is shown.
Fig 6
Fig 6. Allele-dependent chromatin accessibility at AD risk loci.
(A) AD-associated genetic risk variants with allele-dependent ATAC-seq peaks in CD4+ T cells. Each variant is heterozygous and located within an ATAC-seq peak in the indicated individual, facilitating measurement of allelic ratios informatics operator (MARIO) analysis to identify allele-dependent behavior. Red tick marks indicate allelic accessibility in a subject who with AD. Complete data are presented in S12 Table. All results shown have MARIO allelic reproducibility score (ARS) values ≥ 0.4, and hence, are allele-dependent. In the cutout, the participant identifier and reads under the ATAC-seq peak overlapping rs10791824 mapping to the strong and weak bases are provided.
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References

    1. Paller AS, Spergel JM, Mina-Osorio P, Irvine AD. The atopic march and atopic multimorbidity: Many trajectories, many pathways. J Allergy Clin Immunol. 2019;143(1):46–55. Epub 2018/11/21. doi: 10.1016/j.jaci.2018.11.006 . - DOI - PubMed
    1. Silverberg JI, Hanifin JM. Adult eczema prevalence and associations with asthma and other health and demographic factors: a US population-based study. J Allergy Clin Immunol. 2013;132(5):1132–8. Epub 2013/10/08. doi: 10.1016/j.jaci.2013.08.031 . - DOI - PubMed
    1. Margolis JS, Abuabara K, Bilker W, Hoffstad O, Margolis DJ. Persistence of mild to moderate atopic dermatitis. JAMA Dermatol. 2014;150(6):593–600. Epub 2014/04/04. doi: 10.1001/jamadermatol.2013.10271 ; PubMed Central PMCID: PMC4352328. - DOI - PMC - PubMed
    1. Czarnowicki T, He H, Krueger JG, Guttman-Yassky E. Atopic dermatitis endotypes and implications for targeted therapeutics. J Allergy Clin Immunol. 2019;143(1):1–11. Epub 2019/01/08. doi: 10.1016/j.jaci.2018.10.032 . - DOI - PubMed
    1. Otsuka A, Nomura T, Rerknimitr P, Seidel JA, Honda T, Kabashima K. The interplay between genetic and environmental factors in the pathogenesis of atopic dermatitis. Immunol Rev. 2017;278(1):246–62. Epub 2017/06/29. doi: 10.1111/imr.12545 . - DOI - PubMed

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