Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression data of locally advanced rectal cancer patients by KRAS status

ABSTRACT: Stromal and extracellular matrix related genes are downregulated in KRAS mutant rectal adenocarcinoma We used Affymetrix U133 platform to profile the differences in the transcriptome of KRAS-wild-type and KRAS-mutant rectal cancer specimens

ORGANISM(S): Homo sapiens

PROVIDER: GSE170999 | GEO | 2021/03/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Gene expression data of locally advanced rectal cancer patients by KRAS status

Project description:Gene expression data of locally advanced rectal cancer patients by KRAS status

| PRJNA718067 | ENA

Kinase activity profiling of human locally advanced rectal cancer samples

Project description:Locally advanced rectal cancer characterized by multiplex kinase activity profiling

2010-08-05 | E-TABM-913 | biostudies-arrayexpress

Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas

Project description:Mutations of the KRAS oncogene are predictive for resistance to treatment with antibodies against the epithelial growth factor receptor in patients with colorectal cancer. Overcoming this therapeutic dilemma could potentially be achieved by the introduction of drugs that inhibit signaling pathways that are activated by KRAS mutations. To comprehensively identify such signaling pathways we profiled pretreatment biopsies from 65 patients with locally advanced rectal cancer – 30 of which carried mutated KRAS - using global gene expression microarrays. By comparing all tumor tissues exclusively to matched normal mucosa, we could improve assay sensitivity, and identified a total of 22,297 features that were differentially expressed (adjusted p-value p<0.05) between normal mucosa and cancer, including several novel potential rectal cancer genes. We then used this comprehensive description of the rectal cancer transcriptome as the baseline for identifying KRAS-dependent alterations. The presence of activating KRAS mutations resulted in significant upregulation of 13 genes (adjusted p-value < 0.05), among them DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase. Inhibition of the expression of both genes has been achieved therapeutically with the MEK1-inhibitor PD98059 and the antibacterial compound Novobiocin, respectively, suggesting a potential approach to overcome resistance to treatment with antibodies against the epithelial growth factor receptor in patients with KRAS-mutant rectal carcinomas. Paired samples of tumor and mucosa from a total of 65 patients, i.e. 130 arrays

2011-03-11 | E-GEOD-20842 | biostudies-arrayexpress

Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas

2011-03-11 | GSE20842 | GEO

Transcriptional analysis of locally advanced rectal cancer pre-therapeutic biopsies and post-therapeutic resections

Project description:Understanding transcriptional changes in locally advanced rectal cancer which are therapy-related and dependent upon tumour regression will drive stratified medicine in the rectal cancer paradigm

2018-11-01 | GSE94104 | GEO

Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Project description:locally advanced rectal cancer (LARC) patients were sorted according to their radio-responsiveness. Patients were categorized into two groups—complete response (n = 3) and poor response (n = 3)—based on the tumor regression grade. Expression profiles for each group were obtained using RNA-seq on a HiSeq 4000 system (Illumina).

2023-03-01 | GSE226034 | GEO

Locally Advanced Rectal Cancer - Radiation Response Prediction Study - Serum Proteins

Project description:The study objective was to find new biomarkers of treatment response and adverse events in patients receiving neoadjuvant therapy for locally advanced rectal cancer. Patients received neoadjuvant chemotherapy (NACT) followed by chemoradiotherapy (CRT) and underwent treatment evaluation four weeks after CRT completion. Radical pelvic surgery was planned 2-4 weeks later. Patients were scored for treatment adverse events, according to Common Terminology Criteria for Adverse Events (CTCAE) version 3.0, throughout the neoadjuvant treatment course, including at NACT and CRT completion. Treatment response was assessed by histologic ypTN staging and tumor regression grade (TRG) scoring, as well as progression-free survival (time from Inclusion date to Date of local relapse or Date of metastatic disease, whichever came first) recorded for five years after surgery.

2016-04-21 | GSE65622 | GEO

Locally advanced rectal cancer transcriptomic-based secretome analysis according to neoadjuvant chemoradiotherapy response

Project description:Most patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. Here, we performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies carefully selected and collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between cases with complete (pCR) and incomplete response to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome Database and Plasma and Proteome Database). Seventeen potentially secreted candidates (pCR=1, pIR=13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC. The potential secreted biomarkers were also confirmed as associated with the nCRT response (GSE68204). These putative proteins are candidates to be assessed in liquid biopsies aiming a personalized treatment in LARC patients.

2019-07-01 | GSE123390 | GEO

Prediction of sensitivity of rectal cancer cells in response to preoperative chemoradiotherapy by DNA microarray analysis of gene expression profiles.

Project description:Samples were prospectively collected during colonoscopic examination from 46 rectal cancer patients before starting preoperative chemoradiotherapy. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for prediction of the response to radiotherapy in rectal cancer. Specimens from 46 rectal cancer patients who approved to receive preoperative chemoradiotherapy were studied. We prospectively collected biopsy specimens during colonoscopic examination from rectal cancer before starting preoperative chemoradiotherapy. Specimens from tumors were snap-frozen in liquid nitrogen and stored at -80 C until use. Paralleled tumor specimens were formalin fixed and paraffin embedded for histologic examination and other specimens were used for RNA extraction. RNA was extracted from tumor tissue using frozen samples. The patients provided written, informed consent to the collection of specimens, and the local Ethics Committee approved the study protocol. All patients received a total dose of 50.4 Gy of radiation, UFT(300-500mg/day) and LV (75mg/day) and underwent standardized curative resection, following an interval of 4 weeks after chemoradiotherapy.

2013-01-29 | E-GEOD-35452 | biostudies-arrayexpress

Gene expression in rectal epithelia of cystic fibrosis patients

Project description:Gene expression profiles were recorded from rectal suction specimens of Cystic Fibrosis (CF) patients, carrying the CF-specific D508 mutated CFTR-allele. These profiles were compared with gene expression profiles from rectal suction specimens of non-CF subjects (control).

2013-11-28 | GSE15568 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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