Landscape analysis of proteins in the development of breast cancer brain metastasis.

Abstract

1050 Background: Breast cancer brain metastasis(BCBM) is a major cause of mortality in advanced breast cancer patients, and treatment options are limited. In this project, we investigated the proteomic landscape of primary breast cancer and brain metastasis. Methods: We conducted high-throughput proteomic analysis on primary and brain metastatic breast cancer tissues surgically resected from 21 patients. Following screening and sample processing using pressure cycle technology (PCT) for peptide extraction, we used the data-independent acquisition (DIA) mass spectrometry (MS) method to acquire the data. Additionally, we used biological function assays, co-culture experiments, and transcriptome sequencing analysis to further investigate the differentially expressed proteins. Results: Patients were mostly in clinical stage II, with two excluded from analysis due to no surgery. Breast cancer classifications included 47.6% HER2+/HR-, 28.6% HER2+/HR+, 9% HER2-/HR+, and 14.3% TNBC. All patients received chemotherapy, with 57% undergoing neoadjuvant therapy and 12 receiving targeted therapy (all with trastuzumab). A total of 9430 protein groups were identified, with 692 showing differential expression in BCBM. Notably upregulated proteins included CRYAB, GFAP, STXBP1 and significantly downregulated proteins included CACNA1A, AOC3, PMP2, OGN. Most differentially expressed proteins were involved in extracellular matrix (ECM) and cell-cell interactions, with collagen family proteins (e.g., COL14A1, COL22A1) playing key roles in BCBM. HER2+ BCBM was associated with ECM pathways, while TNBC impacted the immune microenvironment. Regardless of the subtype, we identified 11 proteins that collectively contribute to the development of BCBM, including CRYAB, ATP6V0A1, HLA-DQB1, TPM2, SERPINB9, NFATC2, GRAP, ALDH1L2, DHRS4L2, SEPTIN1 and SAMHD1. We found that high ACOX1 and low KRT9/KRT14 expression were linked to poor prognosis in BCBM. Analyzing whether patients had undergone targeted therapy, we found that resistance might be acquired through the oxidative phosphorylation pathway, promoting brain metastasis in HER2+ breast cancer. Interestingly, CRYAB expression was prominent across all subtypes of BCBM and targeted therapy groups, suggesting it may serve as an essential biomarker for BCBM. We have confirmed that CRYAB can promote the proliferation and migration of HER2+BCBM, and preliminarily verified that CRYAB is closely related to immune infiltration through CXCL5, CXCL8 and CCL3 in tumor microenvironment, which may promote the occurrence of HER2+BCBM by affecting the NF-κB pathway. Conclusions: Leveraging high-throughput proteomics, we present a detailed analysis that elucidates the biological processes involved in developing and progressing BCBM from multiple angles. This work offers new directions for early prediction, treatment, and prognosis of BCBM in clinical practice.