Abstract
JAK/STAT pathway has been widely acknowledged in the development of human cancers. However, the role of different phosphorylated STAT proteins translocating into nucleus in transcription activation of target genes is not fully understood. In present research, ChIP-seq was carried on to investigate the genome-wide distribution of the activated STAT1, STAT2, STAT3, STAT5 and STAT6 in colorectal cancer HCT-116 cells. Our observations indicated that the homodimers rather than heterodimers of STAT protein predominantly occupied on genomic DNA. STAT3 accounted for the largest proportion among all STAT proteins HCT-116 cells. Furthermore, the biased binding motif targeted by different STAT homodimers suggested the distinct biological functions. Here, we noticed that NR5A2 was a specific co-activator of STAT3 by DNA motif analysis. Co-IP assay determined that NR5A2 indeed interacted with STAT3 homodimer rather than other homodimers or heterodimers. NR5A2 knockdown resulted in a reduced binding affinity of STAT3 homodimer in the original regions. Taken together, we characterize the genome-wide landscape of activated STAT proteins, and reveal the differences of binding patterns as well as the target genes and associated functions between homodimer and heterodimer of STAT proteins in HCT-116 cells. We also present some new findings and possible mechanisms regarding the role of NR5A2 on STAT3 in CRC. Our findings may provide new insights into the design of STAT inhibitors to treat CRC and other diseases.
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Acknowledgements
This work was supported by Science and Technology Development Plan of Suzhou (Medical and Health Science and Technology Innovation) (SKYD2022023), Start-up Funding of Suzhou Ninth People’s Hospital, Youth Program of Develo** Public Health through Science and Education of Suzhou (KJXW2019069), Program of Develo** Public Health through Science and Education of Wujiang District (wwk201811), The People’s Livelihood Science and Technology of Suzhou (SYSD2020043), Suzhou science and technology planning project (SKJY2021016), Joint Co-construction Project of Henan Medical Science and Technology Research Plan (LHGJ20210199), Key R & D and promotion projects in Henan Province of 2020 (scientific and technical program) (222102310266). We are grateful for the assistance from Shanghai Genefund Biotech Co. Ltd. in the generation and analysis of high-throughput sequencing data. We are also grateful for Coweldgen Scientific Co. Ltd. for STR authentication of cell lines.
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HY and SYF performed the cellular and molecular experiments and analyzed data. HY and ZY provided the clinical samples. TY and GY helped cell culture and molecular experiments. LC helped bioinformatic analysis. YT provided the major financial support for the project. SYH designed the research route, and was responsible for quality control of all raw data, and drafted and revised the manuscript.
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The authors declared that they have no conflicts of interest to this work. The datasets and supporting materials generated during and/or analysis during the current study are available from the corresponding author on reasonable request.
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The research protocol was approved by Ethics Committee of Henan Cancer Hospital (2022-KY-0073-001). The experiments were conducted in accordance with the Declaration of Helsinki (2000 version).
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13577_2022_815_MOESM1_ESM.xlsx
Supplementary file1 Table S1-5. The genomic annotation of STAT1 (S1), STAT2 (S2), STAT3 (S3), STAT5 (S4) and STAT6 (S5) in HCT116 cells. Column E lists the nearby gene element if exists. Column I-K list the information of probable typical enhancer (TE) and super-enhancer (SE) of HCT116 cells based from SEdbV1.05 Database. (XLSX 5445 KB)
13577_2022_815_MOESM6_ESM.xlsx
Supplementary file6 Table S6. The genomic annotation of binding areas with probable dimers with different STAT combinations. In Column D-H, the positive (“1”) and negative (“0”) abundance of the given protein are listed. In Column I, number means how many kind of STAT proteins bind on this area. In Column J to AD, difference of binding abundance between two STAT proteins are compared and shown by fold change and FDR. (XLSX 5909 KB)
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Hu, Y., Shen, Y., Zhao, Y. et al. Genomic distribution of signal transducer and activator of transcription (STAT) family in colorectal cancer. Human Cell 36, 286–295 (2023). https://doi.org/10.1007/s13577-022-00815-0
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DOI: https://doi.org/10.1007/s13577-022-00815-0