Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Box 480, Gothenburg, 40530, Sweden.
Rheumatology Clinic, Sahlgrenska University Hospital, Gröna Stråket 16, Gothenburg, 41346, Sweden.
Cell Commun Signal. 2024 Sep 11;22(1):440. doi: 10.1186/s12964-024-01814-4.
Bivalent regions of chromatin (BvCR) are characterized by trimethylated lysine 4 (H3K4me3) and lysine 27 on histone H3 (H3K27me3) deposition which aid gene expression control during cell differentiation. The role of BvCR in post-transcriptional DNA damage response remains unidentified. Oncoprotein survivin binds chromatin and mediates IFNγ effects in CD4 cells. In this study, we explored the role of BvCR in DNA damage response of autoimmune CD4 cells in rheumatoid arthritis (RA).
We performed deep sequencing of the chromatin bound to survivin, H3K4me3, H3K27me3, and H3K27ac, in human CD4 cells and identified BvCR, which possessed all three histone H3 modifications. Protein partners of survivin on chromatin were predicted by integration of motif enrichment analysis, computational machine-learning, and structural modeling, and validated experimentally by mass spectrometry and peptide binding array. Survivin-dependent change in BvCR and transcription of genes controlled by the BvCR was studied in CD4 cells treated with survivin inhibitor, which revealed survivin-dependent biological processes. Finally, the survivin-dependent processes were mapped to the transcriptome of CD4 cells in blood and in synovial tissue of RA patients and the effect of modern immunomodulating drugs on these processes was explored.
We identified that BvCR dominated by H3K4me3 (H3K4me3-BvCR) accommodated survivin within cis-regulatory elements of the genes controlling DNA damage. Inhibition of survivin or JAK-STAT signaling enhanced H3K4me3-BvCR dominance, which improved DNA damage recognition and arrested cell cycle progression in cultured CD4 cells. Specifically, BvCR accommodating survivin aided sequence-specific anchoring of the BRG1/SWI chromatin-remodeling complex coordinating DNA damage response. Mapping survivin interactome to BRG1/SWI complex demonstrated interaction of survivin with the subunits anchoring the complex to chromatin. Co-expression of BRG1, survivin and IFNγ in CD4 cells rendered complete deregulation of DNA damage response in RA. Such cells possessed strong ability of homing to RA joints. Immunomodulating drugs inhibited the anchoring subunits of BRG1/SWI complex, which affected arthritogenic profile of CD4 cells.
BvCR execute DNA damage control to maintain genome fidelity in IFN-activated CD4 cells. Survivin anchors the BRG1/SWI complex to BvCR to repress DNA damage response. These results offer a platform for therapeutic interventions targeting survivin and BRG1/SWI complex in autoimmunity.
染色质的二价区域（BvCR）的特征是组蛋白 H3 上的赖氨酸 4（H3K4me3）和赖氨酸 27 的三甲基化（H3K27me3）沉积，这有助于细胞分化过程中的基因表达调控。BvCR 在转录后 DNA 损伤反应中的作用尚不清楚。癌蛋白存活素与染色质结合，并在 CD4 细胞中介导 IFNγ 的作用。在这项研究中，我们探讨了 BvCR 在类风湿关节炎（RA）患者自身免疫性 CD4 细胞中 DNA 损伤反应中的作用。
我们对人类 CD4 细胞中与存活素、H3K4me3、H3K27me3 和 H3K27ac 结合的染色质进行了深度测序，并鉴定了具有所有三种组蛋白 H3 修饰的 BvCR。通过 motif 富集分析、计算机器学习和结构建模的整合，预测了存活素在染色质上的蛋白质伴侣，并通过质谱和肽结合阵列实验进行了验证。用存活素抑制剂处理 CD4 细胞后，研究了存活素依赖性 BvCR 变化和受 BvCR 控制的基因转录，揭示了存活素依赖性的生物学过程。最后，将存活素依赖性过程映射到 RA 患者血液中的 CD4 细胞和滑膜组织中的转录组中，并探索了现代免疫调节药物对这些过程的影响。
我们发现，由 H3K4me3 主导的 BvCR（H3K4me3-BvCR）容纳了控制 DNA 损伤的基因中的存活素。抑制存活素或 JAK-STAT 信号增强了 H3K4me3-BvCR 的优势，从而改善了培养的 CD4 细胞中的 DNA 损伤识别和细胞周期停滞。具体而言，容纳存活素的 BvCR 有助于 BRG1/SWI 染色质重塑复合物协调 DNA 损伤反应的序列特异性锚定。将存活素相互作用组映射到 BRG1/SWI 复合物上，证明了存活素与将复合物锚定到染色质的亚基相互作用。在 CD4 细胞中共表达 BRG1、存活素和 IFNγ 会导致 RA 中 DNA 损伤反应完全失调。这样的细胞具有强烈的归巢到 RA 关节的能力。免疫调节药物抑制了 BRG1/SWI 复合物的锚定亚基，这影响了 CD4 细胞的关节炎表型。
BvCR 在 IFN 激活的 CD4 细胞中执行 DNA 损伤控制以维持基因组保真度。存活素将 BRG1/SWI 复合物锚定到 BvCR 以抑制 DNA 损伤反应。这些结果为针对自身免疫中的存活素和 BRG1/SWI 复合物的治疗干预提供了一个平台。
