Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stranded bulk Illumina RNASeq of human mammary tumors before and after neoadjuvant chemotherapy treatment

ABSTRACT: This study is designed to find a reliable marker enabling to predict the response to treatment in patients with early breast cancers treated by neoadjuvant chemotherapy. This marker would allow on one hand to select more homogeneous patient cohorts requiring treatment escalation strategies, and on the other hand reduce the burden of toxicity (both treatment-related and financial) for the patients that will already derive high benefit from the conventional treatments. In this study, gene expression profiles were measured and correlated with the clinical response to neoadjuvant chemotherapy and other features like the epithelial to mesenchymal transition and the tumor immune cell infiltration.

ORGANISM(S): Homo sapiens

PROVIDER: GSE240671 | GEO | 2024/02/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

TMT-based Quantitative Proteomics Identifies Protein Markers of Resistance to Neoadjuvant Chemotherapy in Ovarian Cancer

Project description:The high rate of recurrence and chemoresistance necessitates in ovarian cancer warrants further research into tumor markers characterizing the resistant population. The proportion of drug-resistant tissue cells in residual lesions after neoadjuvant chemotherapy increases, and drug-resistant markers are enriched. However, there is a lack of comprehensive understanding of tumor marker predoninance pre- and post- neoadjuvant chemotherapy. Here we performed quantitative proteomic analysis of TMT in three patients with matched pretreatment biopsies and post-NACT ovarian cancer tissues. This study highlights a dominant molecular subpopulation that persists in the ovary after neoadjuvant chemotherapy exposure in order to elucidate how it is involved in mediating chemotherapy response, which will lay the foundation for the development.

2023-08-01 | PXD044243 | iProX

HER2-enriched tumor initiating cell (HTIC) genomic predictor of response following neoadjuvant trastuzumab-based chemotherapy in HER2+ breast cancer

Project description:We identified a 17-gene Her2-enriched tumor initiating cell (HTIC) signature in MMTV-Her2/Neu mouse mammary TICs. Here, we show that patients with HTICS+ HER2+:ERα− tumors are more likely to achieve a pathologic complete response to trastuzumab-based neoadjuvant chemotherapy compared with HER2+:ER+ tumors. Neoadjuvant study of 50 HER2-positive breast cancer cases treated with trastuzumab-based chemotherapy pre-operatively. Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to Affymetrix microarrays according to manufacturer protocol. Pathologic response was assessed at the end of neoadjuvant treatment.

2012-05-11 | E-GEOD-37946 | biostudies-arrayexpress

Differential neoadjuvant chemotherapy response in urothelial carcinoma molecular subtypes

Project description:For patients with muscle-invasive bladder cancer, there are no biomarkers in clinical use that can identify patients that are sensitive or resistant to neoadjuvant chemotherapy. This study investigates how molecular subtypes impact pathological response and survival in 149 patients receiving preoperative cis-platin based chemotherapy by tumor classification using transcriptomic profiling and a 13-marker immunostaining panel. Furthermore, we explored to what extent gene expression signatures can predict chemotherapy response beyond molecular subtypes. We observed improved pathological response rates and survival outcomes for patients presenting with genomically unstable (GU) and urothelial-like (Uro) subtypes compared to the basal-squamous (BASQ) subtype following neoadjuvant chemotherapy and radical cystectomy. Also, SPP1, coding for osteopontin, displayed a clear subtype-dependent effect on chemotherapy response, confirmed at the protein level. Based on our findings, we hypothesize that urothelial cancer of the luminal-like GU- and Uro-subtypes are more responsive to cisplatin-based chemotherapy which may influence patient selection pending further research.

2021-11-19 | GSE169455 | GEO

Gene expression profiling of primary HER2-positive breast cancers treated with neoadjuvant trastuzumab

Project description:Trastuzumab, a humanized monoclonal antibody directed to the HER2 protein, is the standard-of-care treatment for patients with HER2 positive breast cancer, reducing the risk of relapse and death in patients. Nonetheless, some patients do not benefit from this treatment, underscoring the need to identify patients for whom chemotherapy + trastuzumab is adequate versus patients requiring additional drugs. The series comprised 24 incisional biopsies of breast carcinomas derived from patients that received neoadjuvant trastuzumab based therapy. Gene expression profiling was performed using RNA from frozen core biopsies from 24 patients with primary HER2-positive (HER2+) tumors treated with neoadjuvant chemotherapy and trastuzumab.

2016-03-31 | E-GEOD-62327 | biostudies-arrayexpress

Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

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

Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

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

Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

Project description:This SuperSeries is composed of the following subset Series: GSE25055: Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer GSE25065: Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer Refer to individual Series

2011-05-11 | E-GEOD-25066 | biostudies-arrayexpress

Identification of DNA methylation biomarkers for prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer [EPIC Array]

Project description:Response to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer is linked to long-term patient survival. However, response to NAC is highly variable and cannot reliably be predicted by clinical or other current methods. This study aims to address this problem by utilising the stable, yet dynamic marker known as DNA methylation. By defining the methylation differences at diagnosis in patients that achieve a pathological complete remission against those that do not respond, we can identify a marker that can potentially predict chemotherapy response and help further personalise the chemotherapy decision making in the clinic.

2021-12-17 | GSE184159 | GEO

Proteome characterization of the neoadjuvant clinical trial PROMIX

Project description:Proteome characterization of the neoadjuvant clinical trial PROMIX. https://www.clinicaltrials.gov/ct2/show/NCT00957125 Patients received six rounds of chemotherapy with epirubicin and docetaxel, and if PR or PD after the second course, bevacizumab.

2024-03-19 | PXD039529 | JPOST Repository

Project description:We explore the potential of immune-associated expression profiles in a series of Epithelial Ovarian Cancer (EOC) patients undergoing neoadjuvant chemotherapy (NACT), comparing primary lesions before patients underwent carboplatin/paclitaxel-based NACT (so-called ´biopsy samples´) and interval debulking surgery (IDS) samples from residual lesions after treatment with chemotherapy (so-called ´surgery samples´).

2022-01-27 | GSE181597 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data