Impact of Tumour Genomics on Response to standard Neo-adjuvant Chemotherapy in Triple Negative Breast Cancer, Integrative co-expression network analysis of mRNA and miRNA profile identifies miRNA 664 as an inhibitor of key genes in Triple negative breast cancer.

Abstract

Abstract - Paper 1 Background The genomic delineation of breast cancer is a novel approach to evaluating the disease. The opportunities arising from this genomic data analysis help in identifying specific cell line models and subtypes that are key for preclinical studies, developing predictive biomarkers, new target agents, and informing therapy selection. There is a wealth of information in previously collected datasets from breast cancer patients, but this has been under-studied and information on clinical association from these datasets has been limited. Triple-Negative Breast Cancer (TNBC) has been especially notorious since a large number of young premenopausal women diagnosed with the disease have suffered a worse outcome than the other known breast cancer types and there is no targeted and effective therapy for the treatment of the disease. This approach of taking a closer look at the genomics of TNBC will help in moving toward the often-cited dream of personalized medicine in difficult to treat areas of breast cancer, more specifically in our case, Triple Negative Breast Disease. However, the adaptation of genomic data into treatment regimens customized or tailor-made for each individual patient has been restricted in part, due to uncertainties in diverging from guideline-based clinical protocols. We report the Genomic Approach to TNBC in the context of predicting favorable outcomes to treatment responses and briefly describe recurrence-related data.

Patients and Methods We studied data derived from three different gene expression profiling platforms. We identified 486 samples associated with disease response to therapy and selected them for in-depth analyses. Hence 3 independent sets of analyses were carried out for each different platform due to the fact that each of these platforms had gene expression profiles that were populated with the TNBC cases with specific neo-adjuvant therapies namely, Platinum-based cohort [referring to HGU133plus2 platform related samples], taxane cohort [referring HGU133A platform samples] and anthracyclines with or without taxane cohort [HTA2.0 array] respectively.

We aimed to analyze recurrence data, however, it was sparse amounting to 50 samples in total across the various publicly available datasets and we could analyze the same only but could not make definitive conclusions owing to the small sample size.

Results In the platinum-based cohort, pathway enrichment analysis using ClusterProfiler revealed the enrichment of key terms like Platinum drug resistance, chemical carcinogenesis, glutathione metabolism-related terms in no response category. In the Taxane-based cohort, pathway enrichment analysis revealed a defined enrichment of oncogenic signaling pathways like Pi3K-AKT, ECM, Focal adhesion in the no response category and the Anthracycline with or without taxane cohort showed that While enrichment of Wnt and TGF beta signaling were observed in no response category the response group was seen populated with immune response-related pathways.

Conclusions Chemotherapy is an important treatment option and is currently the mainstay in cases of Triple-Negative Breast Cancer. It was shown to reduce one-third of the annual death rate regardless of tumour characteristics. Chemotherapy is used as the mainstay in cases of triple-negative disease, HER2-positive tumours and high-risk oestrogen positive tumors. Significant toxicity associated with the therapy aside, not every patient benefits compulsorily from it and there is a sheer dearth of both practically validated and theoretically proven predictive markers to allow the tailoring of chemotherapy regimens to each individual patients needs or tumour type. Achieving pathological complete response (pCR) is associated with favorable outcomes, however, its predictive power in being used as a surrogate endpoint for improved overall survival (OS) has been debated. TNBC and breast cancer in general, need to be viewed in the context of underlying genomic phenotypes. Based on this notion, treatment decisions should be less influenced by guidelines based on set clinical protocols and rather be more driven by tumour biology if we are to improve the response to chemotherapy.

Abstract - Paper 2 Background Triple-negative breast cancer (TNBC) is a specific subtype of breast carcinomas that does not express the oestrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (HER-2), has clinical features that include high invasiveness, high metastatic potential, proneness to relapse, and poor prognosis. The lack of expression of molecular targets, lack of susceptibility to endocrine therapy or targeted treatment modalities make standardized TNBC treatment regimens lacking with respect to effectiveness. The disease afflicts younger women in larger numbers compared to other breast cancer sub-types and the cancers are more aggressive causing earlier morbidity and decrease survival. Therefore, development of new TNBC treatment strategies has become an urgent clinical need.

Materials & Methods The data was obtained from the public gene expression databases. The probe ID is matched with the corresponding gene names from its respective platform file. Co-expression network of GSE76275, GSE103091, and TCGA was done by applying Weighted Gene Co-expression Network Analysis (WGCNA) package. The survival plots were plotted using the MedCalc tool. miRNA regulators of the module genes were identified by investigating the genes in analysis tool miRDB. The module genes were screened during target mining to know the miRNAs of the gene targets.

Result Co-expression based network screening of messenger RNA (mRNA) profile data of Triple negative breast cancer identifies modules of genes consistently co-expressed. Among the different types of modules, the genes of three module TNBC6, TTNBC2, BCNT16 is enriched with gene ontology of immune response, adrenal lymphoid cells, Natural Killer (NK) cells and shows association with survival of TNBC patients. Also, these genes have a high binding score for the micro RNA (miRNA) regulators such as has-miR-664b-3p, has-miR-186-5p, has-miR-miR-548t-3p. These miRNAs are harbingers of disease aggressiveness in Triple negative breast cancer.

Conclusion The study reveals the concept of regulation of immune response genes by miRNA, in particular, has-miR-664b-3p which is also involved in better survival of TNBC patients. In vivo validation of the concept obtained might either discover a novel gene target involved in immune response of TNBC aiding improved survival of patients and can help in identifying specific cell models and subtypes which are key for preclinical studies, developing new targeted agents and can inform therapy selection ushering in the often cited dream of personalized treatment regimens in TNBC with improved efficacy and treatment response.