Chromatin accessibility and transcriptome integrative analysis revealed AP-1-mediated genes potentially modulate histopathology features in psoriasis
Background Psoriasis is a chronic and hyperproliferative skin disease featured by hyperkeratosis with parakeratosis, Munro micro-abscess, elongation of rete pegs, granulosa thinning, and lymphocyte infiltration. We previously profiled gene expression and chromatin accessibility of psoriatic skins by transcriptome sequencing and ATAC-seq. However, integrating both of these datasets to unravel gene expression regulation is lacking. Here, we integrated transcriptome and ATAC-seq of the same psoriatic and normal skin tissues, trying to leverage the potential role of chromatin accessibility and their function in histopathology features. Results By inducing binding and expression target analysis (BETA) algorithms, we explored the target prediction of transcription factors binding in 15 psoriatic and 19 control skins. BETA identified 408 upregulated genes (rank product < 0.01) and 133 downregulated genes linked with chromatin accessibility. We noticed that cumulative fraction of genes in upregulation group was statistically higher than background, while that of genes in downregulation group was not significant. KEGG pathway analysis showed that the upregulated 408 genes were enriched in TNF, NOD, and IL-17 signaling pathways. In addition, the motif module in BETA suggested the 57 upregulated genes are targeted by transcription factor AP-1, indicating that increased chromatin accessibility facilitated the binding of AP-1 to the target regions and further induced expression of relevant genes. Among these genes, SQLE, STRN, EIF4, and MYO1B expression was increased in patients with hyperkeratosis, parakeratosis, and acanthosis thickening. Conclusions In summary, with the advantage of BETA, we identified a series of genes that contribute to the disease pathogenesis, especially in modulating histopathology features, providing us with new clues in treating psoriasis..
| Medienart: |
Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:14 |
|---|---|
| Enthalten in: |
Clinical epigenetics - 14(2022), 1 vom: 11. März |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Xu, Xiaoqing [VerfasserIn] |
|---|
| Links: |
Volltext [lizenzpflichtig] |
|---|
| Themen: |
AP-1 |
|---|
| Anmerkungen: |
© The Author(s) 2022 |
|---|
| doi: |
10.1186/s13148-022-01250-6 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
OLC2129727719 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | OLC2129727719 | ||
| 003 | DE-627 | ||
| 005 | 20230505235700.0 | ||
| 007 | tu | ||
| 008 | 230505s2022 xx ||||| 00| ||eng c | ||
| 024 | 7 | |a 10.1186/s13148-022-01250-6 |2 doi | |
| 035 | |a (DE-627)OLC2129727719 | ||
| 035 | |a (DE-He213)s13148-022-01250-6-p | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 082 | 0 | 4 | |a 610 |q VZ |
| 082 | 0 | 4 | |a 610 |q VZ |
| 100 | 1 | |a Xu, Xiaoqing |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Chromatin accessibility and transcriptome integrative analysis revealed AP-1-mediated genes potentially modulate histopathology features in psoriasis |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ohne Hilfsmittel zu benutzen |b n |2 rdamedia | ||
| 338 | |a Band |b nc |2 rdacarrier | ||
| 500 | |a © The Author(s) 2022 | ||
| 520 | |a Background Psoriasis is a chronic and hyperproliferative skin disease featured by hyperkeratosis with parakeratosis, Munro micro-abscess, elongation of rete pegs, granulosa thinning, and lymphocyte infiltration. We previously profiled gene expression and chromatin accessibility of psoriatic skins by transcriptome sequencing and ATAC-seq. However, integrating both of these datasets to unravel gene expression regulation is lacking. Here, we integrated transcriptome and ATAC-seq of the same psoriatic and normal skin tissues, trying to leverage the potential role of chromatin accessibility and their function in histopathology features. Results By inducing binding and expression target analysis (BETA) algorithms, we explored the target prediction of transcription factors binding in 15 psoriatic and 19 control skins. BETA identified 408 upregulated genes (rank product < 0.01) and 133 downregulated genes linked with chromatin accessibility. We noticed that cumulative fraction of genes in upregulation group was statistically higher than background, while that of genes in downregulation group was not significant. KEGG pathway analysis showed that the upregulated 408 genes were enriched in TNF, NOD, and IL-17 signaling pathways. In addition, the motif module in BETA suggested the 57 upregulated genes are targeted by transcription factor AP-1, indicating that increased chromatin accessibility facilitated the binding of AP-1 to the target regions and further induced expression of relevant genes. Among these genes, SQLE, STRN, EIF4, and MYO1B expression was increased in patients with hyperkeratosis, parakeratosis, and acanthosis thickening. Conclusions In summary, with the advantage of BETA, we identified a series of genes that contribute to the disease pathogenesis, especially in modulating histopathology features, providing us with new clues in treating psoriasis. | ||
| 650 | 4 | |a Psoriasis | |
| 650 | 4 | |a AP-1 | |
| 650 | 4 | |a BETA | |
| 650 | 4 | |a ATAC-seq | |
| 650 | 4 | |a Integrated analysis | |
| 650 | 4 | |a Histopathology | |
| 650 | 4 | |a Gene expression | |
| 700 | 1 | |a Tang, Xianfa |4 aut | |
| 700 | 1 | |a Zhang, Yuxi |4 aut | |
| 700 | 1 | |a Pan, Zhaobing |4 aut | |
| 700 | 1 | |a Wang, Qingping |4 aut | |
| 700 | 1 | |a Tang, Lili |4 aut | |
| 700 | 1 | |a Zhu, Caihong |4 aut | |
| 700 | 1 | |a Cheng, Hui |4 aut | |
| 700 | 1 | |a Zhou, Fusheng |0 (orcid)0000-0003-4195-2801 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Clinical epigenetics |d BioMed Central, 2010 |g 14(2022), 1 vom: 11. März |w (DE-627)640572596 |w (DE-600)2582204-4 |w (DE-576)341090573 |x 1868-7075 |7 nnns |
| 773 | 1 | 8 | |g volume:14 |g year:2022 |g number:1 |g day:11 |g month:03 |
| 856 | 4 | 1 | |u https://doi.org/10.1186/s13148-022-01250-6 |z lizenzpflichtig |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a SYSFLAG_A | ||
| 912 | |a GBV_OLC | ||
| 951 | |a AR | ||
| 952 | |d 14 |j 2022 |e 1 |b 11 |c 03 | ||