Identification and Validation of Stage-Associated PBMC Biomarkers in Breast Cancer Using MS-Based Proteomics

Abstract

Background: It is well-described that the transcriptome of peripheral blood mononuclear cells (PBMCs) can be altered in the context of many malignancies to allow them avoid the effective immune response, which leads to cancer invasiveness. Here, we used an MS-based strategy to discover biomarkers in the PBMCs of breast cancer (BC) patients and validated them at different stages of BC. Methods: PBMCs were isolated from the breast cancer patients and were cultured alone or co-cultured with breast cancer cell lines. The role of PBMC in the invasion property of breast cancer cells was explored. NF-kB activity was also measured in the co-cultured breast cancer cells. Identification of protein profiles in the secretome and proteome of the co-cultured PBMCs was performed using SWATH mass spectrometry. Pathway enrichment and gene ontology analyses were carried out to look for the molecular pathways correlated with the protein expression profile of PBMCs in the breast cancer patients. Quantitative real-time polymerase chain reaction (qPCR) was performed to validate the candidate genes in the PBMC fraction of the breast cancer patients at the primary and metastatic stages. In silico survival analysis was performed to assess the potential clinical biomarkers in these PBMC subtypes. Results: PBMCs could significantly increase the invasion property of the BC cells concomitant with a decrease in E-cadherin and an increase in both Vimentin and N-cadherin expression. The NF-kB activity in the BC cells significantly increased following co-culturing implying the role of PBMCs in EMT induction. Enrichment analysis showed that the differentially expressed proteins in PBMCs are mainly associated with IL-17, PI3K-Akt, and HIF-1 signaling pathway, in which a set of seven proteins including TMSB4X, HSPA4, S100A9, SRSF6, THBS1, CUL4A, and CANX were frequently expressed. Finally, in silico analysis confirmed that a gene set consisting of S100A9, SRSF6, THBS1, CUL4A, and CANX were found to provide an insight for the identification of metastasis in breast cancer patients. Moradpoor et al. Stage-Associated PBMC Biomarkers, BCs Conclusion: In conclusion, our study revealed that the protein expression profile in PBMCs is a reflection of the proteins expressed in the BC tissue itself; however, the abundance level is different due to the stage of cancer.

Deep learning based on multi-omics integration identifies potential therapeutic targets in breast cancer

“…For example, we found that low gene expression of ACTR2 (Figure 6B Reassuringly, most of the top-ranked targets we identified were previously proved to be involved in breast cancer progression except FAM157 [55][56][57][58][59][60][61][62][63][64][65][66][67][68][69]. For example, it was reported that the actin-related protein ARP2 encoded by ACTR2 is the main component of Arp2/3 protein that promotes breast cancer proliferation and metastasis [55].…”

“…In the somatic mutation signature layer, the top- 5H). To note, a significant portion of these topranked top signatures we identified were already found to be involved in breast cancer signaling in various biological pathways or mechanisms [55][56][57][58][59][60][61][62][63][64][65][66][67][68][69]. For a comprehensive ranking of landmark omics signatures in patient classification, please refer to Supplemental Table S5.…”

New Clues to Prognostic Biomarkers of Four Hematological Malignancies

“…Moreover, Moradpoor et al . 75 used SRSF6 to distinguish between metastatic and non-metastatic breast cancer at the time of diagnosis.…”

Targeting Splicing Factor SRSF6 for Cancer Therapy

“…PBMCs in breast cancer patients contains several immune suppressive cells, such as myeloid-derived suppressor cells (MDSCs). Interestingly, peripheral mononuclear cells (PBMCs) from patients with metastasis showed dramatic increase in SRSF6 RNA than those without metastasis ( Moradpoor et al, 2020 ). So far, little is known about the function of SRSF6 in cancer immunosuppression.…”