Introduction

Neurodegenerative diseases (NDs) are characterized by progressive neuron loss, resulting in severe motor impairments, cognitive decline, and dementia. The global incidence of NDs exceeds 40 million individuals and is strongly associated with advanced age [1]. The most common NDs include Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease, and amyotrophic lateral sclerosis. Shared pathological features include neuronal dysfunction, aberrant protein aggregation, oxidative stress, programmed cell death, and neuroinflammation [2]. The molecular mechanisms underlying ND pathogenesis remain unclear, limiting therapeutic options for symptomatic relief. Consequently, understanding these mechanisms is crucial for the development of effective treatments.

Neuroinflammation is the central nervous system’s response to homeostatic imbalance and involves numerous cell types, such as microglia, astrocytes, and oligodendrocytes, the blood–brain barrier, cytokines, and cytokine signaling pathways [3]. Depending on the specific context triggering the inflammatory response, neuroinflammation can have either beneficial or detrimental effects. AD and PD are characterized by microglial and astrocytic activation and elevated levels of inflammatory mediators [4]. Genetic studies have also highlighted the association between inflammation-regulating genes and NDs [5,6,7,8,9,10], emphasizing the important role of neuroinflammation in disease pathogenesis.

Microglia, as the primary innate immune cells in the central nervous system, are essential for brain development, the maintenance of homeostasis, and response to infections. Under pathological conditions associated with aging and NDs, microglia undergo excessive activation and functional dysregulation, resulting in impaired degradation, heightened inflammatory responses, production of proinflammatory cytokines [11, 12], generation of reactive oxygen species [13, 14], and neurotoxicity, thereby exacerbating ND pathologies [15, 16]. Investigating the regulatory mechanisms of microglial inflammatory responses is crucial for a deeper understanding of ND pathogenesis.

Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from acetylated lysine residues on histone and nonhistone proteins. HDAC1/2 can form four classical transcriptional co-repressor complexes, and the Sin3/HDAC complex is one of the classical multiprotein complexes formed by HDAC1/2 [17]. In mammalian cells, the core components of the Sin3/HDAC complex include paired amphipathic helix protein Sin3A/B (Sin3A/B), HDAC1/2, the Sin3 histone deacetylase corepressor complex component SDS3 (SDS3), retinoblastoma-binding protein 4/7 (RBBP4/7), 30-kDa Sin3-associated polypeptide (SAP30), and 18-kDa Sin3-associated polypeptide (SAP18). The Sin3/HDAC complex plays a critical role in processes such as the cell cycle, cell proliferation, and cellular senescence [18, 19]. The classical view is that Sin3/HDAC represses transcription through histone deacetylase activity and is therefore referred to as a transcriptional co-repressor complex [20, 21].

Some existing studies have revealed the regulatory role of Sin3/HDAC in inflammatory responses. In ovarian clear cell carcinoma cells with PIK3CA mutations, knockdown of ARID1A impedes recruitment of the Sin3A/HDAC complex to the promoters of cytokines genes, such as IL6 and IL8, releasing transcriptional repression and promoting cytokine production and cancer progression [22]. In mouse macrophages, lipopolysaccharide (LPS) treatment induces recruitment of the Sin3A/HDAC complex to the promoter region of the gene encoding inducible nitric oxide synthase (iNOS), thereby inhibiting iNOS expression [23]. In human macrophages, the Sin3A/HDAC complex can bind to the promoter regions of interferon (IFN) response genes, such as IFNB1 and IRF7, as well as proinflammatory genes, such as TNFS and CCL3. After LPS treatment, the binding of Sin3A to these promoter regions is reduced, resulting in upregulated gene expression [24]. Together, these studies suggest that the Sin3/HDAC complex negatively regulates inflammatory responses through transcriptional repression in different contexts.

SDS3 is one of the core components of the Sin3/HDAC complex and plays a critical role in maintaining the integrity and histone deacetylase activity of the complex [25, Full size table

ChIP-seq identified SDS3 target genes, and siSDS3_DEP were labeled on the GO enrichment analysis results of siSDS3_DEG (Fig. 3C). Genes that were increased in expression that were related to neuroinflammation, including Ptgs2 (also known as COX-2, prostaglandin G/H synthase 2) and Tlr6 (Toll-like receptor 6), as well as the downregulated gene Ffar4 (free fatty acid receptor 4) are all SDS3 target genes. Among them, COX-2 and Tlr6 were transcriptionally inhibited by SDS3. IL-1β and iNOS were not identified as SDS3 target genes, suggesting that their regulation by SDS3 may be indirect. Our proteomic results showed that the change in COX-2 protein expression due to SDS3 knockout (COX-2 ratio of 1.2) did not reach statistical significance. Similarly, in untreated BV2 cells, due to the low basal expression level of COX-2, no significant changes in COX-2 expression were observed between BV2ctrl and BV2SDS3 − KD cells (Fig. 1F and G). However, after LPS induction, COX-2 expression changed significantly, suggesting that the expression of COX-2 is regulated not only by SDS3 through negative regulation but also by other regulatory mechanisms.

Further analysis of the data in Fig. 3C revealed that SDS3 downstream genes, including Map3k5, Met, and Xdh, are involved in the regulation of the p38 MAPK signaling cascade. The corresponding protein levels of mitogen-activated protein kinase kinase kinase 5 (MAP3K5) and xanthine dehydrogenase/oxidase (XDH) were also significantly upregulated (Table 1; Fig. 3B). The p38 MAPK signaling pathway can be activated by various stimuli, both inside and outside the cell, and it is a key signaling pathway involved in the regulation of inflammatory responses [34, 35]. XDH plays a critical role in purine degradation and can influence cell activity by regulating the production of reactive oxygen species [36]. MAP3K5, also known as apoptosis signal-regulating kinase 1 (ASK1), is one of the upstream kinases of p38 MAPK. ASK1 can be activated by a range of intracellular and extracellular stimuli and, through signal transduction, activates the downstream p38 MAPK signaling pathway. SDS3 may regulate the expression of genes related to the p38 MAPK signaling pathway and thereby modulate inflammatory responses.

SDS3 regulates the activation of p38 MAPK

Activation of p38 MAPK can be assessed by the phosphorylation of Thr180 and Tyr182 (referred to as p-p38). In BV2 cells, SDS3 knockdown was performed, and changes in p-p38 before and after LPS treatment were examined. In the absence of LPS treatment, SDS3 knockdown led to an upregulation in p-p38 compared with that observed in the control group (Control siRNA). After LPS treatment, there was a significant increase in p-p38 in microglia, and SDS3 knockdown further enhanced this process, resulting in the highest level of p-p38. This suggests that SDS3 knockdown promotes activation of the p38 MAPK pathway in microglia.

SB203580 is an inhibitor of p38 MAPK kinase activity that negatively regulates the p38 MAPK signaling pathway and its downstream effects. We treated BV2 cells with SB203580 or DMSO followed by LPS and assessed the expression of inflammatory factors by Western blotting. Inhibiting p38 MAPK activity resulted in decreased expression of LPS-induced inflammatory factors (Fig. 4B and Supplemental Fig. S4A, quantitative bar graph), indicating that the p38 MAPK signaling pathway can regulate the LPS-induced inflammatory response in microglia.

Fig. 4
figure 4

SDS3 knockdown enhances lipopolysaccharide (LPS)-induced p38 MAPK activation. (A) BV2 cells transfected with SDS3 or Control siRNA were treated with 1 μg/mL LPS for 1 h to assess p38 phosphorylation. The Control siRNA group served as the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05. (B) BV2 cells were treated with 20 μM SB203580 (p38 MAPK inhibitor) or DMSO for 1 h, followed by treatment with 1 μg/mL LPS for 6 h, and protein levels of iNOS, COX-2, and IL-1β were measured. β-Actin was used as the internal reference protein. For protein band quantification information, refer to Supplemental Fig. S4A

SDS3 regulates the expression of ASK1

To validate the transcriptional regulation of ASK1 by SDS3, three primer pairs were designed in the ASK1 promoter approximately 0, 500, and 800 bp upstream of the first exon. ChIP experiments were then conducted in BV2 cells using anti-SDS3 or IgG control antibody to enrich DNA fragments bound by SDS3 and assess the DNA content of the ASK1 promoter by qPCR, thereby determining the ability of SDS3 to bind the ASK1 promoter. Pulldown with anti-SDS3 demonstrated enrichment of the ASK1 promoter region compared with pulldown with IgG control (Fig. 5A), indicating that SDS3 can bind to the ASK1 promoter. SDS3 knockdown was then performed in BV2 cells, and the expression of ASK1 was examined. Consistent with the proteomic and RNA-seq results, SDS3 knockdown resulted in a significant upregulation in ASK1 expression (Fig. 5B), indicating that SDS3 knockdown can enhance the expression of ASK1 in microglia, thus confirming ASK1 as a downstream gene that is negatively regulated by SDS3.

Fig. 5
figure 5

Regulation of ASK1 expression by SDS3 and HDAC1. (A) Binding of SDS3 to the promoter region of ASK1. ChIP experiments were performed using anti-SDS3 or negative-control IgG on chromatin fractions from formaldehyde cross-linked BV2 cells. Quantitative PCR (qPCR) analysis was conducted to assess the binding of SDS3 to the promoter region of ASK1. Results are presented as a percentage of input. IgG was used as the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; **p < 0.01. (B) Upregulation of ASK1 expression after SDS3 knockdown. BV2 cells were transfected with SDS3 or Control siRNA, and changes in SDS3 and ASK1 mRNA and protein expression were measured. β-Actin was used as the internal reference. The Control siRNA group served as the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05; **p < 0.01; ***p < 0.001. (C) Binding of HDAC1 to the ASK1 promoter. ChIP experiments were performed using anti-HDAC1 or negative-control IgG on chromatin fractions from formaldehyde cross-linked BV2 cells. qPCR analysis was conducted to assess the binding of HDAC1 to the ASK1 promoter region. Results are presented as a percentage of input. IgG was used as the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05; **p < 0.01. (D) Upregulation of ASK1 expression after HDAC1 knockdown. BV2 cells were transfected with HDAC1 or Control siRNA, and changes in HDAC1 and ASK1 mRNA and protein expression were measured. β-Actin was used as the internal reference. The Control siRNA group served as the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05; **p < 0.01; ***p < 0.001

In addition, SDS3 forms a complex with HDAC1 in microglia (Fig. 1A), and ChIP-qPCR experiments showed that the ASK1 promoter region is enriched following pulldown with anti-HDAC1 (Fig. 5C). Similarly, knockdown of HDAC1 in BV2 cells also increased ASK1 expression (Fig. 5D). These results suggest that HDAC1 also binds to the ASK1 promoter region, indicating that SDS3 may inhibit the expression of ASK1 by forming the Sin3/HDAC transcriptional co-repressor complex.

ASK1 regulates microglial inflammatory processes through the p38 MAPK signaling pathway

ASK1, as an upstream kinase of the p38 MAPK, plays a crucial role in regulating the inflammatory response in microglia. To investigate the role of ASK1 in inflammation, ASK1 was knocked out using CRISPR-Cas9 technology in BV2 cells (BV2ASK1 − KO; Fig. 6A). Compared with normal cells (BV2WT), p-p38 was significantly decreased in BV2ASK1 − KO cells (Fig. 6B). After LPS stimulation, p-p38 levels were significantly increased in both cell groups; however, p-p38 was lower in BV2ASK1 − KO cells than in BV2WT cells (Fig. 6B). Following LPS stimulation, the expression of iNOS, COX-2, and IL-1β was significantly upregulated in both BV2WT and BV2ASK1 − KO cells compared with untreated cells; however, expression in BV2ASK1 − KO cells was lower than in BV2WT cells (Fig. 6C and D and Supplemental Fig. S4B, quantitative bar graph). Accordingly, BV2WT and BV2ASK1 − KO cells exhibited an increase in nitric oxide production after LPS treatment; however, nitric oxide production in BV2ASK1 − KO cells was lower than in BV2WT cells (Fig. 6E). Together, these results suggest that knocking out ASK1 can partially inhibit activation of p38 MAPK induced by LPS, thereby reducing the expression of the inflammatory factors iNOS, COX2, and IL-1β and inhibiting nitric oxide production in microglia.

Fig. 6
figure 6

ASK1 knockout inhibits LPS-induced p38 MAPK activation and downregulates the expression of LPS-induced inflammatory factors. (A) Protein expression levels of ASK1 in ASK1-knockout monoclonal cells (ASK1-KO) and control cells (WT). (B) Inhibition of LPS-induced p38 MAPK activation by ASK1 knockout. ASK1-KO and WT BV2 cells were treated with 1 μg/mL LPS for 1 h, and p38 phosphorylation was detected. Statistical analysis was performed on the relative levels of p38 phosphorylation, with the WT group (untreated with LPS) as the reference group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; **p < 0.01. (C) Downregulation of inflammatory factor gene expression after ASK1 knockout. ASK1-KO and WT BV2 cells were treated with 1 μg/mL LPS for 6 h, and the mRNA levels of iNOS, COX-2, and IL-1β were measured. ACTB was used as the reference gene, with the untreated WT BV2 as the reference group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05; ***p < 0.001. (D) Downregulation of inflammatory factor protein expression by ASK1 knockout. ASK1-KO and WT BV2 cells were treated with 1 μg/mL LPS for 6 h, and the protein levels of iNOS, COX-2, and IL-1β were measured. Protein band quantification information can be found in Supplemental Fig. S4B. (E) Reduction of nitric oxide generation by ASK1 knockout. ASK1-KO and WT BV2 cells were treated with 1 μg/mL LPS for 24 h, and the concentration of nitrite in the culture medium was measured using the Griess Reagent method to assess nitric oxide production; n = 3. Error bars represent mean ± SEM. Data were analyzed by one-way analysis of variance and a Tukey’s multiple comparisons post hoc test; *p < 0.05

ASK1 knockout affects the regulation of SDS3 and the inflammatory response

LPS stimulation downregulates SDS3 expression (Fig. 1), and knockdown of SDS3 can upregulate the expression of LPS-induced inflammatory factors (Fig. 2). To investigate whether ASK1 knockout affects the regulation of SDS3 and the expression of inflammatory factors, BV2ASK1 − KO and BV2WT cells were transfected with SDS3 siRNA (SDS3-KD) or Control siRNA (ctrl). After 6 h of LPS treatment, compared with the control group (BV2WT + ctrl), the expression of SDS3 was significantly downregulated in BV2WT + SDS3−KD cells, indicating successful knockdown of SDS3 expression (Fig. 7A and B). Moreover, the expression of COX-2 and IL-1β was significantly upregulated in BV2WT + SDS3−KD cells compared to in BV2WT + ctrl cells, indicating that knocking down SDS3 significantly increases the expression of COX-2 and IL-1β in BV2WT + SDS3−KD cells (Fig. 7A and B). In BV2ASK1 − KO cells, after LPS treatment, SDS3 expression was similarly decreased in BV2ASK1 − KO + SDS3−KD and BV2ASK1 − KO + ctrl cells. However, because of a lack of ASK1 in these cells, there were no significant changes in the expression of COX-2 and IL-1β between BV2ASK1 − KO + SDS3−KD and BV2ASK1 − KO + ctrl cells even after LPS stimulation (Fig. 7A and B and Supplemental Fig. S4C, quantitative bar graph). These results indicate that knocking out ASK1 affects the regulation of SDS3 on the expression of inflammatory mediators. Additionally, the regulation of microglial inflammation by SDS3, to some extent, depends on its inhibition of the downstream gene ASK1.

Fig. 7
figure 7

Analysis of SDS3 regulation of the inflammatory response after ASK1 knockout. (A) In ASK1-KO cells, SDS3 no longer regulates the transcription of inflammatory factors. ASK1 KO and WT BV2 cells were transfected with SDS3 or Control siRNA, followed by treatment with 1 μg/mL LPS for 6 h. The mRNA expression levels of SDS3, COX-2, and IL-1β were measured, and ACTB was used as the internal reference gene. WT BV2 cells transfected with Control siRNA represents the control group; n = 3. Error bars represent mean ± SEM. Data were analyzed by Student’s t-test; *p < 0.05; **p < 0.01; ***p < 0.001. (B) After knocking out ASK1, SDS3 no longer regulates the protein expression of inflammatory factors. ASK1-KO and WT BV2 cells were transfected with SDS3 or Control siRNA, followed by treatment with 1 μg/mL LPS for 6 h. The protein levels of SDS3, COX-2, and IL-1β were measured. “Long exp” indicates a long exposure of the same band. Protein band quantification information can be found in Supplemental Fig. S4C. (C) Schematic of the molecular mechanism of SDS3 regulation in the microglial inflammatory response