Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xmal-RRBS on breast carcinoma samples taken before and after neoadjuvant chemotherapy

ABSTRACT: Determination of genes demonstrating differential methylation of CpG islands in tumor samples before and after treatment for revealing main metabolic, regulatory and biological processes

ORGANISM(S): Homo sapiens

PROVIDER: GSE202402 | GEO | 2023/05/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

XmaI-RRBS on Luminal B breast carcinoma samples taken prior to chemotherapy

Project description:Luminal B breast carcinoma samples were taken prior to chemotherapy in order to identify epigenomic profiles predictive of neoadjuvant chemotherapy efficacy

2020-12-12 | GSE123828 | GEO

XmaI-RRBS on triple negative breast carcinoma samples taken prior to chemotherapy

Project description:Triple negative breast carcinoma samples were taken prior to chemotherapy in order to identify epigenomic profiles predictive of neoadjuvant chemotherapy efficacy

2020-12-12 | GSE123712 | GEO

Alterations of biomarker profiles after neoadjuvant chemotherapy in breast cancer: tumor heterogeneity should be taken into consideration.

Project description:Tumor biomarkers including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and Ki-67 are routinely tested in breast cancer patients and their status guides clinical management and predicts prognosis. A few retrospective studies have suggested that neoadjuvant chemotherapy (NAC) in breast cancer may change the status of biomarker expression, which in turn will affect further management of these patients. In this study we take advantage of a relatively large cohort and aim to study the effect of NAC on biomarker expression and explore the impact of tumor size and lymph node involvement on biomarker status changes. We collected 107 patients with invasive breast cancer who received at least three cycles of NAC. We retrospectively performed and scored the immunohistochemistry (IHC) of ER, PR, HER2 and Ki-67 using both the diagnostic core biopsies before NAC and excisional specimens following NAC. HER2 gene status was assessed by fluorescence in situ hybridization for cases with IHC result of 2+. We demonstrated that there was a significant decrease in expression of PR (P = 0.013) and Ki-67 (P = 0.000) in post-NAC specimens compared to pre-NAC core biopsies. In addition, cases with large tumor size (? 2 cm) and cases with lymph node metastasis were more frequently to have biomarker changes. Finally we studied cases with HER2 status changes after NAC treatments in detail and emphasized the nature of tumor heterogeneity.

| S-EPMC4742218 | biostudies-literature

XmaI-RRBS on triple negative breast carcinoma samples taken prior to chemotherapy

Project description:XmaI-RRBS on triple negative breast carcinoma samples taken prior to chemotherapy

| PRJNA509628 | ENA

XmaI-RRBS on Luminal B breast carcinoma samples taken prior to chemotherapy

Project description:XmaI-RRBS on Luminal B breast carcinoma samples taken prior to chemotherapy

| PRJNA509934 | ENA

Neoadjuvant chemotherapy before surgery versus surgery followed by chemotherapy for initial treatment in advanced ovarian epithelial cancer.

Project description: Not available

| S-EPMC8406953 | biostudies-literature

Tumors with neoadjuvant chemotherapy

Project description:Using whole genome mRNA expression profiling of primary human tumors and unsupervised hierarchical cluster analyses, 3 novel molecular subsets (basal, luminal and p53-like subsets) of muscle-invasive bladder cancer (MIBC) were identified. 23 MVAC treated samples were used for the validation of three MIBC subsets MVAC cohort consisted of 23 FFPE pretreatment tumors (TURs) from a Phase III clinical trial were used to validate 3 molecular subsets including basal, luminal and p53-like subsets We used Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) assay that is specifically designed for the gene expression of RNA that is extracted from FFPE.

2014-02-10 | E-GEOD-52219 | biostudies-arrayexpress

Epigenome analysis of pre- and post-neoadjuvant chemotherapy breast tumor samples

Project description:Methylome-wide DNA methylation profiling of spatially separated breast tumor samples pre- and post-neoadjuvant chemotherapy (NAC) to characterize methylation heterogeneity alteration by NAC. The Illumina Infinium HumanMethylation450K Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs in the 47 samples derived from 8 breast cancer patients.

2019-01-31 | GSE106360 | GEO

Blood samples from COPD subjects and Healthy Volunteers taken before and after LPS challenge

Project description:There is a need for non-invasive imaging protocols to support early phase clinical studies for drugs targeting neutrophilic inflammation. The aim of the study was to quantify whole lung neutrophil accumulation in (i) healthy volunteers (HV) following inhaled lipopolysaccharide (LPS) or saline and (ii) stable COPD patients, using radiolabelled autologous neutrophils and single-photon-emission/computed-tomography (SPECT/CT).

2018-12-31 | GSE112811 | GEO

Targeted-Gene Sequencing to Catch Triple Negative Breast Cancer Heterogeneity before and after Neoadjuvant Chemotherapy.

Project description:Triple negative breast cancer (TNBC) patients not attaining pathological Complete Response (pCR) after neo-adjuvant chemotherapy (NAC) have poor prognosis. We characterized 19 patients for somatic mutations in primary tumor biopsy and residual disease (RD) at surgery by 409 cancer-related gene sequencing (IonAmpliSeqTM Comprehensive Cancer Panel). A median of four (range 1-66) genes was mutated in each primary tumor biopsy, and the most common mutated gene was TP53 followed by a long tail of low frequency mutations. There were no recurrent mutations significantly associated with pCR. However, half of patients with RD had primary tumor biopsy with mutations in genes related to the immune system compared with none of those achieving pCR. Overall, the number of mutations showed a downward trend in post- as compared to pre-NAC samples. PIK3CA was the most common altered gene after NAC. The mutational profile of TNBC during treatment as inferred from patterns of mutant allele frequencies in matched pre-and post-NAC samples showed that RD harbored alterations of cell cycle progression, PI3K/Akt/mTOR, and EGFR tyrosine kinase inhibitor-resistance pathways. Our findings support the use of targeted-gene sequencing for TNBC therapeutic development, as patients without pCR may present mutations of immune-related pathways in their primary tumor biopsy, or actionable targets in the RD.

| S-EPMC6895966 | biostudies-literature

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