Examination of the Biomark assay as an alternative to Oncotype DX for defining chemotherapy benefit

SCUBE2 as a Marker of Resistance to Taxane-based Neoadjuvant Chemotherapy and a Potential Therapeutic Target in Breast Cancer

Objective

Taxane-based neoadjuvant chemotherapy is the most common neoadjuvant approach in breast cancer, especially in human epidermal growth factor receptor 2 (HER2)-positive and triple-negative subtypes. However, chemoresistance is a problem in many patients, and success rates are low in estrogen receptor (ER)-positive breast cancer. The aim of this study was to identify predictive markers for resistance to taxane-based therapy, which may have a potential as therapeutic targets in breast cancer.

Materials and Methods

Three comprehensive breast cancer Gene Expression Omnibus datasets were analyzed to identify differentially expressed genes (DEGs) in breast cancer patients resistant to taxane-based neoadjuvant chemotherapy. Functional annotation clustering and enrichment analysis were performed on the DEGs list. A protein-protein interaction network was established with the upregulated genes. The predictive value and the differential expression of the central genes were validated in the extensive ROC Plotter database.

Results

Seventeen upregulated genes were found which were associated with resistance to taxane-based neoadjuvant therapy and high connectivity in the network analysis. ESR1, CCND1, and SCUBE2 emerged as the top three key genes associated with resistance. SCUBE2 displayed a high predictive power comparable to ESR1, and better than CCND1, the two commonly accepted markers. The predictive ability of SCUBE2 was higher in ER-positive and HER2-positive breast cancers.

Conclusion

These results suggest that SCUBE2 may be used as a predictive marker to guide decisions on neoadjuvant therapy. Emerging evidence about the role of SCUBE2 as a coreceptor involved in tumor progression and angiogenesis also suggests SCUBE2 as a potential therapeutic target. These points should be investigated in further studies.

Identification of CCNB2 as A Potential Non-Invasive Breast Cancer Biomarker in Peripheral Blood Mononuclear Cells Using The Systems Biology Approach

OBJECTIVE

Breast cancer (BC) still remains an imperative clinical issue, despite advances in the diagnosis, prognosis and treatment modalities of this malignancy. Hence, progress has been made to identify non-invasive, high sensitive and specific biomarkers. Since immune system affects development of breast cancer, peripheral blood mononuclear cells (PBMCs) -a subpopulation of immune cells- can be considered as a promising tool in the field of BC biomarker research. In the current study, we initially attempted to use concept of the present shared biomarkers in solid tumors and systemic immune profile and then evaluate correlation of these biomarkers to clinical use in cancer research.

MATERIALS AND METHODS

In this experimental study, available microarray gene expression datasets of BC as well as the related PBMCs were retrieved and downloaded from the Gene Expression Omnibus (GEO) database, followed by analysis using GEO2R along with affylmGUI, a R-based package, to obtain differentially expressed genes (DEGs). Signature genes from 20 types of cancer were also applied to validate DEGs. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was carried out to assess mRNA level of CCNB2 in PBMC of the BC patients and healthy subjects.

RESULTS

DEGs analysis for the transcription profile of BC cells and PBMCs showed two shared targets, CCNB2 and PGK1. Validation with systems biology using reweighted 20 types of cancer signature genes revealed that CCNB2 is the only common target in BC and its related PBMCs, which was further validated by qRT-PCR implying a significant increase in the level of CCNB2 in the BC patients.

CONCLUSION

Results of this study demonstrated that PBMCs are affected by BC cells and CCNB2 may be of value as a diagnostic biomarker for breast cancer. However, verification would require future detailed experimental plans.