Browsing by Subject "TNBC"

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Open Access
BRCA:Cohort-vs-TCGA: a webtool for comprehensive exploration and comparison of mutational landscape of breast cancer cohorts with TCGA-BRCA
(2022-08) Ahadli, Farid
Comparisons of mutational landscapes between independent breast cancer (BRCA) cohorts in a comprehensive and statistical manner using online tools are likely to help advance our understanding of the diversity of somatic interactions and mutational signatures. In this thesis I have developed a webtool called BRCA:Cohort-vs-TCGA, which makes the mutational landscape comparison between a breast cancer cohort and TCGA-BRCA cohort accessible to the general public. BRCA:Cohort-vs-TCGA app contains modules to conduct mutational signature identification and comparison, differentially mutated gene and pathway identification and comparison, driver gene identification, and somatic interaction identification and comparison. Among the applications generated for similar purposes in literature, BRCA:Cohort-vs-TCGA provides advantages because of its comparative, statistical, and signature related features. When BRCA:Cohort-vs-TCGA was applied to compare the Gustave Roussy Institute (IGR) metastatic breast cancer cohort with the TCGA-BRCA cohort, a unique to IGR mutational signature related to SBS17b, a reactive oxygen species associated signature, which was missed by the original analysis of the authors, was identified. Interestingly, contribution of SBS17b was significantly higher in TNBC samples when compared to HER+ and HR+ samples. Differentially mutated gene analysis identified four genes, namely, ESR1, FSIP2, ARMCX4 and MALRD4, of which the latter two were unique to re-analysis by BRCA:Cohort-vs-TCGA. Differentially mutated pathway analysis on the other hand pointed to the differential mutation of DNA damage related pathways, NRF2 pathway and WNT pathway. The influence of the hypermutator samples in Fisher's exact test based analyses is well documented, as a result of many spurious mutations these samples contain. Re-analysis of the IGR cohort after removal of the hypermutator samples showed ARMCX4 was no longer differentially mutated anymore. Re-analysis of the differentially mutated pathways resulted in identification of three pathways, namely Mismatch Repair - Core, LIN37 independent P53 Targets, and U5, all of which had an odds ratio of less than one. These results, however, could be biased by the presence of hypermutators in the TCGA-BRCA cohort. In the second case study, I have demonstrated how the extracted somatic interactions for a user selected gene, i.e., CHRNA5 and TP53, can be used to prioritize and filter genes. This was done by merging the somatic interactions with the differential expression profiles of MCF7 cells treated with siRNA against CHRNA5 and TP53. Accordingly, BRCA:Cohort-vs-TCGA can help annotate/enrich other high throughput data with somatic interactions of custom genes.
Open Access
miRNA-mRNA interaction network regulating chemotherapy resistance in triple negative breast cancer
(2019-06) Assidicky, Ridho
Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype, lacking the expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2). Compared to other subtypes, which can be treated with targeted therapies, chemotherapy is the major regimen used to treat TNBCs. Moreover, TNBC patients have better response rate to chemotherapy compared to other breast cancer (BC) subtypes. However, patients develop resistance rapidly, which in turn significantly increases the mortality rate. Therefore, there is urgent unmet need for elucidating the mechanisms of chemotherapy resistance in TNBC and identifying novel targets that can overcome resistance or potentiate the efficacy of chemotherapy. In this line, we developed an in vivo chemoresistant TNBC xenograft model, performed whole transcriptome sequencing of these tumors, and built a miRNA-mRNA interaction network regulating TNBC chemoresistance. We identified an ECM glycoprotein (“EG”) as the central chemoresistance driver gene, and a candidate potential tumor suppressor miRNA (“TSM”) sensitizing cells to EG-induced chemoresistance. Mechanistically, TSM was downregulated by hypoxia in chemoresistant tumor microenvironment that, in turn, led to upregulation of an integrin family protein (“IFP”), which encodes a subunit of receptor recognizing EG. We further showed that TSM directly binds the 3’-UTR of IFP, represses its expression, and inhibits FAK/Src signaling, PI3K signaling and MAPK signaling pathways, which constitute the major pathways in cell survival. Importantly, overexpression of TSM or inhibition of the IFP overcame EG-driven chemotherapy resistance in vitro and potentiated the efficacy of chemotherapy in vivo. Overall, we built the first miRNA-mRNA interaction network of TNBC chemoresistance and identified a hypoxia-regulated novel tumor suppressor miRNA, TSM, or its target IFP as potential targets overcoming chemoresistance or potentiating the efficacy of chemotherapy in TNBCs.
Open Access
Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer
(Springer New York LLC, 2022-03-25) Tokat, Unal Metin; Tarman, Ibrahim Oguzhan; Ersan, Pelin Gulizar; Raza, Umar; Saatci, O.; Sahin, O.; Ogul, H.; Riazalhosseini, Y.; Can, T.; Assidicky, Ridho
Purpose Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer that is frequently treated with chemotherapy. However, many patients exhibit either de novo chemoresistance or ultimately develop resistance to chemotherapy, leading to significantly high mortality rates. Therefore, increasing the efficacy of chemotherapy has potential to improve patient outcomes. Methods Here, we performed whole transcriptome sequencing (both RNA and small RNA-sequencing), coupled with network simulations and patient survival data analyses to build a novel miRNA-mRNA interaction network governing chemoresistance in TNBC. We performed cell proliferation assay, Western blotting, RNAi/miRNA mimic experiments, FN coating, 3D cultures, and ChIP assays to validate the interactions in the network, and their functional roles in chemoresistance. We developed xenograft models to test the therapeutic potential of the identified key miRNA/proteins in potentiating chemoresponse in vivo. We also analyzed several patient datasets to evaluate the clinical relevance of our findings. Results We identified fibronectin (FN1) as a central chemoresistance driver gene. Overexpressing miR-326 reversed FN1-driven chemoresistance by targeting FN1 receptor, ITGA5. miR-326 was downregulated by increased hypoxia/HIF1A and ECM stiffness in chemoresistant tumors, leading to upregulation of ITGA5 and activation of the downstream FAK/Src signaling pathways. Overexpression of miR-326 or inhibition of ITGA5 overcame FN1-driven chemotherapy resistance in vitro by inhibiting FAK/Src pathway and potentiated the efficacy of chemotherapy in vivo. Importantly, lower expression of miR-326 or higher levels of predicted miR-326 target genes was significantly associated with worse overall survival in chemotherapy-treated TNBC patients. Conclusion FN1 is central in chemoresistance. In chemoresistant tumors, hypoxia and resulting ECM stiffness repress the expression of the tumor suppressor miRNA, miR-326. Hence, re-expression of miR-326 or inhibition of its target ITGA5 reverses FN1-driven chemoresistance making them attractive therapeutic approaches to enhance chemotherapy response in TNBCs.