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Frontiers of Medicine

ISSN 2095-0217

ISSN 2095-0225(Online)

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Front. Med.    2022, Vol. 16 Issue (3) : 483-495    https://doi.org/10.1007/s11684-021-0872-3
RESEARCH ARTICLE
Characterization of chromatin accessibility in psoriasis
Zheng Zhang1, Lu Liu2, Yanyun Shen1, Ziyuan Meng2, Min Chen2,3, Zhong Lu1(), Xuejun Zhang1,2,3()
1. Department of Dermatology, Huashan Hospital, Fudan University. Shanghai 200040, China
2. Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei 230032, China
3. Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou 215123, China
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Abstract

The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
Keywords psoriasis      ATAC-seq      epigenetics      transcription factor     
Corresponding Author(s): Zhong Lu,Xuejun Zhang   
Just Accepted Date: 09 September 2021   Online First Date: 18 October 2021    Issue Date: 18 July 2022
 Cite this article:   
Zheng Zhang,Lu Liu,Yanyun Shen, et al. Characterization of chromatin accessibility in psoriasis[J]. Front. Med., 2022, 16(3): 483-495.
 URL:  
https://academic.hep.com.cn/fmd/EN/10.1007/s11684-021-0872-3
https://academic.hep.com.cn/fmd/EN/Y2022/V16/I3/483
Fig.1  Epigenomic signature of psoriasis. (A) Schematic of the sample processing pipeline. Immune cells from 13 healthy controls and 12 patients were sorted through flow cytometry, activated, and subjected to ATAC-seq and RNA-seq. (B) The flow cytometry of memory Th and memory Treg cells. (C) Principal component analysis of Th1, Th17, Th1-17, Th2, Treg, and naïve T cells in two psoriasis patients and three normal controls.
Fig.2  Epigenomic signature of memory Th/Treg cells in psoriasis. (A) Major functional state annotation of memory Th/Treg cells. (B) Heatmap of 3086 regulatory elements in patients with psoriasis and normal controls. (C) Normalized ATAC-seq profiles at genes CXCL2, IL1RN, and IL17REL with differential peaks.
Fig.3  Gene expression analysis. (A) Differential expression genes analyses in memory Th and memory Treg cells. Plots representing log2 (fold change) of patients with psoriasis and normal controls. (B) Gene Ontology (GO) analysis in memory Th cells. (C) GO analysis in memory Treg cells. (D) Expression of peak associated genes.
Fig.4  TF occupancy in memory Th/Treg cells in psoriasis. (A) TF motifs enriched in memory Th and Treg cell peaks, with P values estimated from HOMER v3.12. (B and C) Predicted TFs that may regulate the pathogenesis of psoriasis, the color of each circle representing the expression levels of genes that encode corresponding TFs, and the size of the circle representing the enrichment of the motifs. (D) The visualization of ATAC-seq footprint for motif of NFKB1, ATF3, RORC, and FOSL1.
Fig.5  Merged memory Th/Treg TF regulatory network originating from 10 cases and 10 controls. TFs are organized from the center to the periphery. The node color represents the fold change of TFs, whereas a weighted edge defines the regulatory relationship between TFs.
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