Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA127177 | ENA |
REPOSITORIES: ENA
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Project description:In this study, we have analyzed the transcriptional patterns of breast cancer cell lines and tumors of NAC resistant patients evaluated by GGI, and screened potential genes associated with chemoresistance. Furthermore, we have constructed a neoadjuvant chemotherapy response risk model and examined the evaluation accuracy of the risk score for NAC response. We conducted molecular bioinformatics analysis of the genes that constitute the chemotherapy resistance risk score, and explored potential drugs to reverse breast cancer chemotherapy resistance. Finally, we have examined the the risk score for predicting prognosis in breast cancer. In all, we have reported a novel signature to evaluate neoadjuvant chemotherapy response and predicts prognosis in breast cancer, and screened out potential drugs to reverse chemotherapy resistance in breast cancer.
2022-10-11 | GSE197931 | GEO
Project description:GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer
| PRJNA146953 | ENA
Project description:Abstract Motivation Breast cancer is a heterogeneous disease with distinct subtypes. Even within these subtypes differences at the molecular level are present which are reflected in variable responses to chemotherapy. We set out to identify genes associated with chemotherapy resistance by analyzing a set of HER2-positive breast cancers. Methods We collected, gene expression profiled and analyzed 60 HER2-positive breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy. In addition to conventional supervised approaches for the detection of reporters of resistance, we report on a novel approach specifically tailored to the detection of small groups of resistant samples that show aberrant gene expression patterns. Results We propose a novel analytical approach that takes heterogeneity in response into account. We show that this approach is more powerful than classical approaches for detecting small subgroups of samples showing aberrant expression in a controlled setting. We applied this approach to our 60 breast cancer samples prior to neoadjuvant chemotherapy, and generated candidate response reporter lists for each subtype. Discussion Using a novel analytical approach we report on the mRNA gene expression analysis of a cohort of breast cancers prior to neoadjuvant chemotherapy. An important characteristic of this approach is that it takes heterogeneity in neoadjuvant treatment response into account. Such approaches are needed to identify biomarkers for predicting treatment response. We collected, gene expression profiled and analyzed 60 breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy.
2013-10-22 | E-GEOD-41656 | biostudies-arrayexpress
Project description:An expression profile that predicts the therapeutic response of the basal-like breast cancer to neoadjuvant chemotherapy
| PRJNA121873 | ENA
Project description:These data can be used for evaluation of the clinical utility of the research-based PAM50 subtype predictor in predicting pathological complete response (pCR) and event-free survival (EFS) in women enrolled in the NeOAdjuvant Herceptin (NOAH) trial. The NeOAdjuvant Herceptin [NOAH] trial demonstrated that trastuzumab significantly improves pCR rates and 3-year event-free survival (EFS) in combination with neoadjuvant chemotherapy compared with neoadjuvant chemotherapy alone in patients with HER2+ breast cancer.
2014-01-21 | GSE50948 | GEO
Project description:Neoadjuvant chemotherapy (NAC) is the major pre-treatment for breast cancer before surgery. Patients who achieve pathologic complete response (pCR) have a higher chance to receive lumpectomy and a better quality of life after neoadjuvant treatment. Luminal subtype breast cancer has poor NAC response compared with triple-negative breast cancer (TNBC) subtype. The molecular and cellular mechanisms underlying this chemoresistance are not fully understood. Here we report that the 17 featured transcriptional factors (TFs) in luminal and TNBC were identified. The association between 17 TFs and NAC pCR were analysis and exogenous luminal featured TF GATA3 overexpression promotes chemotherapy resistance in TNBC cell lines whereas its knockdown promotes sensitivity. In mechanism, we found that anthracycline based chemotherapy induces robust cellular ROS and Fe2+ overload in sensitivity cells; GATA3 mediates cell survival through repress CYB5R2 expression and Fenton reducing in DOX recycle which reduce cellular ROS and Fe2+ level during chemotherapy procedure. These founding altogether indicate that luminal featured transcription factor GATA3 enhance NAC resistance thorough repress ROS production and Fenton reducing. Breast cancer patient with GATA3 high expression might not suit for anthracycline based NAC regimen.
2023-01-01 | GSE216413 | GEO
Project description:Purpose: Identified the expression profile of lncRNA associated to neoadjuvant chemotherapy response in 11 tumor of locally advanced breast cancer patients Methods: We implemented the transcriptomic analysis from 11 breast cancer samples by paired-end RNA-Seq, as a case-control study (responders vs nonresponders group). Differential expression analysis for lncRNA and mRNA were made to identify lncRNA as predictive biomarkers. Results: We identified the over-expressed lncRNA GATA3-AS1 in nonresponders group. Additionally, we identified the pathways were differentially expressed lncRNA and mRNA are associated in neoadjuvant chemotherapy response. Conclusion: we propose lncRNA GATA3-AS1 as a potential predictive biomarker for patients with LABC luminal B-like subtype that will not respond to neoadjuvant chemotherapy
2021-07-12 | GSE159448 | GEO
Project description:PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared. Neoadjuvant validation cohort of 198 HER2-negative breast cancer cases treated with taxane-anthracycline chemotherapy pre-operatively and endocrine therapy if ER-positive. Response was assessed at the end of neoadjuvant treatment and distant-relapse-free survival was followed for at least 3 years post-surgery.
2011-05-11 | E-GEOD-25065 | biostudies-arrayexpress
Project description:PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared. Neoadjuvant study of 310 HER2-negative breast cancer cases treated with taxane-anthracycline chemotherapy pre-operatively and endocrine therapy if ER-positive. Response was assessed at the end of neoadjuvant treatment and distant-relapse-free survival was followed for at least 3 years post-surgery.
2011-05-11 | E-GEOD-25055 | biostudies-arrayexpress
Project description:A stroma-related gene signature predicts sensitivity to epirubicin-containing neoadjuvant chemotherapy in breast cancer.
| PRJNA95553 | ENA