Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ColXα1 and Tumor Infiltrating Lymphocytes: a Marker of Response to Neoadjuvant Therapy in Estrogen Receptor and Human Epidermal Growth Factor Receptor 2 Positive Breast Cancer

ABSTRACT: This study focused on patients with estrogen receptor positive/human epidermal growth factor receptor 2 positive (ER+/HER2+) breast cancer treated with neoadjuvant chemotherapy and HER2-targeted therapy (NAC+H), and was designed to identify novel biomarkers by correlating gene expression, histology and immunohistochemistry with pathologic response. We performed gene expression profiling on 11 pre-treatment tumors samples: 5 who had no or minimal residual disease residual cancer burden (RCB) score of 0 or 1 and 6 who had significant residual disease (RCB score of 2 or 3). ER2/HER2 postive breast tumors biopsied before neoadjuvant chemotherapy were selected to identify potential biomarkers of pathological complete response (pCR)

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Brodsky

PROVIDER: E-GEOD-67982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ColXα1 and Tumor Infiltrating Lymphocytes: a Marker of Response to Neoadjuvant Therapy in Estrogen Receptor and Human Epidermal Growth Factor Receptor 2 Positive Breast Cancer

Project description:This study focused on patients with estrogen receptor positive/human epidermal growth factor receptor 2 positive (ER+/HER2+) breast cancer treated with neoadjuvant chemotherapy and HER2-targeted therapy (NAC+H), and was designed to identify novel biomarkers by correlating gene expression, histology and immunohistochemistry with pathologic response. We performed gene expression profiling on 11 pre-treatment tumors samples: 5 who had no or minimal residual disease residual cancer burden (RCB) score of 0 or 1 and 6 who had significant residual disease (RCB score of 2 or 3).

2015-09-08 | GSE67982 | GEO

Proteomic Alterations Associated with Residual Disease in Neoadjuvant Chemotherapy Treated Ovarian Cancer Tissues

Project description:Optimal cytoreduction to no residual disease (R0) correlates with improved disease outcome in the management of high-grade serous ovarian cancer (HGSOC) patients. Neoadjuvant chemotherapy (NACT) followed by interval debulking surgery (IDS) offers an alternate approach to management of HGSOC patients to achieve complete resection. This study assessed proteomic alterations in matched, chemotherapy naïve and NACT-treated patients tumors obtained from HGSOC patients with suboptimal (R1) versus optimal (R0) debulking at IDS. We describe distinct proteome profiles in pre- and post-NACT HGSOC tumors correlating with residual disease status providing prognostic biomarkers for residual disease at IDS as well as candidate proteins associated with NACT resistance warranting further pre-clinical investigation.

2022-10-05 | PXD031929 | Pride

Gene expression analysis of a series of HER2+ of breast tumors

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

Implementing whole genome array for clinical use in academic centers: A randomized trial comparing neoadjuvant standard chemotherapy to genomic-driven chemotherapy in operable breast cancer (REMAGUS04 trial)

2016-07-01 | GSE63471 | GEO

Project description:REMAUS04 is a phase III trial comparing DNA array-based chemotherapy (by DLD30 score and TOP2A expression) to standard neoadjuvant chemotherapy, in patients with HER2-negative breast carcinoma not eligible for conserving surgery. We evaluated whether whole genome array approach is feasible in daily practice, and if the use of a genomic score (DLD30/TOP2A) improves chemotherapy efficacy. DNA arrays were performed within 15 days after tumor biopsy. Only samples with >30% cancer cells, a RIN>6 and good cDNA quality were eligible for hybridization on arrays U133Av2.

2016-07-01 | E-GEOD-63471 | biostudies-arrayexpress

Neoadjuvant Trastuzumab Response in Breast Cancer

Project description:HER2 (ERBB2) gene amplification and overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents such as trastuzumab are effective treatments, therapeutic resistance remains a concern in HER2-positive breast cancer with 40-50% of patients having residual disease after neoadjuvant treatment with chemotherapy and trastuzumab. To investigate features that may make it possible to predict at diagnosis which cancers will be responsive to trastuzumab and chemotherapy, 48 tumor/normal DNA pairs extracted from pretreatment tumor biopsies and blood of HER2-positive breast cancer cases treated with neoadjuvant chemotherapy and trastuzumab were sequenced. Whole genome and exome sequence from tumor (average depth 49x and 71x) and normal (average depth 33x and 69x) DNA are included here as well as RNAseq data for 42 of the tumors. The study cohort was equally divided between patients who experienced pathological complete response and those with residual disease. Samples were obtained from the American College of Surgeons Oncology Group Z1041 trial (NCT00513292) and a local single-institution study (NCT00353483).

| phs001291 | dbGaP

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

Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer

Project description:Triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy generally have worse outcome; however, some patients with residual tumor after neoadjuvant chemotherapy do not relapse. We hypothesize that there are subgroups of chemoresistant TNBC patients with different prognosis. In this study, 25 chemoresistant samples from 47 neoadjuvant chemotherapy-treated TNBC (The Methodist Hospital) are chosen for study We used gene expression data of TNBC patients with residual disease and different prognosis to molecularly define the clinically relevant subgroups, and developed a 7-gene prognostic signature for chemoresistant TNBCs

2013-01-15 | E-GEOD-43502 | biostudies-arrayexpress

Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer

2013-01-15 | GSE43502 | GEO

In-depth proteomic analysis for discovery of response prediction markers in breast cancer chemotherpy using needle biopsy FFPE tissue

Project description:Breast cancer is the most frequently diagnosed female cancer accounting for 23 % of the total cases and the second leading cause of cancer mortality in the world, particularly in western countries. Since GEPARDUO trial reported the therapeutic benefit of combined doxorubicin and cyclophosphamide regimen in sequential administration with docetaxel, the combination regimen has become a standard therapeutic strategy in neoadjuvant systemic therapy for patients with operable breast cancers regardless of an intrinsic subtype. Although approximately 70% of entire patients are currently receiving the chemotherapy regimen, pathologic complete response (pCR) rate is still low, ranging from 23% to 32.7% due to the high heterogeneity of breast cancers. Therefore, the need for a marker predictive of response to a particular cytotoxic regimen, especially before neoadjuvant chemotherapy, is becoming all the more necessary to optimize therapeutic efficacy and to avoid unnecessary complications caused by systemic therapy. In the study, here we generated the first high-coverage proteomic data for needle biopsy FFPE sample being characterized with identical clinical conditions including chemotherapeutic regimens and the stage classification.

2021-09-08 | PXD013431 | Pride

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