Phosphoproteome landscape of ARID1A and its implications in DNA damage response and breast cancer pathogenesis

Abstract

ARID1A, a subunit of the SWI/SNF chromatin-remodeling complex, plays a critical role in maintaining genomic stability and regulating estrogen receptor (ER) signaling, yet its phosphorylation dynamics in cancer remain underexplored. This study employed phosphoproteomic analysis to investigate ARID1A phosphorylation in breast cancer, identifying predominant phosphosites-S363, S1184, and S696-regulated by kinases such as MAPK14, CDK16, and MAPK9. Functional enrichment revealed ARID1A interactions with SWI/SNF components (e.g., PBRM1, SMARCC2, BRD9) and DNA damage response (DDR) proteins (e.g., TP53BP1, TOP2A, CHEK2, NBN), underscoring its dual role in chromatin remodeling and double-strand break repair. Notably, phosphorylation at S363 and S1184 was significantly upregulated in breast cancer, suggesting tumour-specific hyperphosphorylation that may disrupt ARID1A tumour-suppressive function and contribute to endocrine resistance. Dysregulation of these phosphorylation events correlated with enhanced MAPK signaling, cancer progression, and poor prognosis. These findings position ARID1A as a molecular hub linking chromatin dynamics to genome integrity, with implications for therapeutic resistance. Targeting ARID1A phosphorylation pathways, potentially via MAPK inhibitors or BRD4/BRD9 antagonists, could restore its suppressive activity and improve treatment outcomes in breast cancer. This study enhances our understanding of ARID1A regulatory mechanisms, highlighting its phosphorylation as a key driver of breast cancer biology. Future research should validate these kinase-substrate interactions and explore their transcriptional and chromatin-level impacts to develop precision therapies for ARID1A-dysregulated cancers.

Keywords: ARID1A; Breast cancer; DNA damage response; Phosphoproteomics.

Fig. 1

The workflow adopted in this study

Fig. 2

-Lollipop plot visualization of ARID1A phosphosite frequency. A Class-1 phosphosites found in ARID1A from quantitative profiling datasets taken globally. B The Y-axis represents the frequency of phosphosites found throughout the differential datasets, while the X-axis shows the phosphosites mapped onto the ARID1A amino acid sequence together with its structural domains. Positive values on the Y-axis indicate upregulation of phosphosite abundance, while negative values indicate downregulation

Fig. 3

Sequence coverage of ARID1A and predominant phosphosite peptide detection from global phosphoproteomics data.The 3D-predicted ARID1A model represents peptides found in 7832 human cellular phosphoproteomic profiling datasets. Sequence coverage is shown in red, while Ser/Thr/Tyr phosphorylation is in blue and all the reported phosphosites in green

Fig. 4

Top 25 high confidence proteins which positively and negatively co-phosphorylated with ARID1A (S1184) and ARID1A (S363). Co-regulation patterns are indicated by letter codes: U = Upregulated; D = Downregulated. For example, UUDD indicates Upregulated, UDDU indicates Downregulated

Fig. 5

Network of selected kinases, phosphatases among the positively and negatively co-differentially regulated ARID1A phosphosites

Fig. 6

Selected binary interactors of ARID1A phosphosite-(S696) (S1184) (S363) which are reported as oncogenic, tumor suppressor and both

Fig. 7

Violin plot illustrating the log2 fold change (Log2FC) distribution of co-differentially regulated proteins associated with ARID1A pS363 across various cancer types, including breast cancer, colon cancer, head and neck cancer, kidney cancer, liver cancer, lung squamous cell carcinoma, ovarian cancer, pancreatic ductal adenocarcinoma, and uterine cancer. Each violin represents the density of Log2FC values for a specific cancer type, with the mean ± standard error of the mean (SEM) indicated by black markers within each distribution. The plot highlights the variability in protein regulation across cancer types, with breast cancer showing the widest range of Log2FC values

Fig. 8

High correlated proteins which have similar motifs as that of upstream kinases