Time dependent changes of gene expression in surgical specimen of colorectal cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE50746 | GEO | 2013/09/11
SECONDARY ACCESSION(S): PRJNA218630
REPOSITORIES: GEO
Similar Datasets
Project description:To investigate time-dependent changes the comprehensive gene expressions in colorectal normal and tumor surgical specimen within two hours. Both normal and tumor tissues were extracted at 0, 30, 60, 120 min after surgical removal in seven patients with locally advanced colorectal cancer and stabilized. RNA was extracted and calculated, time dependent changes of gene expression were examined by microarray data.
2013-09-11 | E-GEOD-50746 | biostudies-arrayexpress
Project description:Enterobacter cloacae strain:clinical specimen | isolate:clinical specimen Genome sequencing
| PRJNA341281 | ENA
Project description:Surgical resection is the major clinical intervention for Stage III colorectal cancer (CRC) currently. However, as much as 30.8% of the patients who had ever taken curative resection came out of recurrence eventually. Therefore, to facilitate formulating effective treatment plans, there is an intense demand for Stage III CRC post-surgical prognostic biomarkers. In this study, we identified total 146 differentially expressed proteins (DEPs) associated with poor prognosis in Stage III CRC patients with TMT-based quantitative mass spectrometry (MS). In these DEPs, the protein expression level of R-Ras and Transgelin were tested with immunohistochemistry (IHC) of 192 individual specimens. Further Kaplan-Meier analysis revealed that the level of R-Ras and Transgelin is associated with patients’ 5-year overall survival (OS) and disease-free survival (DFS) significantly, and multivariate Cox-regression analyses revealed that R-Ras and Transgelin are independent prognostic factors for OS and DFS respectively. In conclusion, our study presents that R-Ras and Transgelin are potential post-surgical prognostic biomarkers of Stage III CRC.
2016-06-20 | PXD002903 | Pride
Project description:We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. We identified 277 probes, in common between the three types of fibroblasts, whose expression level is sequentially deregulated according to cancer progression (NCF→CAF-PT→CAF-LM; fold change Log2 normalized expression>1.5 in each step). Prediction Analysis of Microarrays was applied to obtain a 25-gene signature that better characterizes each fibroblast class. The signature is able to classify patients carrying primary tumors according to prognosis. This fact was exploited to obtain a 19-gene signature (from the 277 deregulated probes) predicting recurrence with high accuracy in stage II/III colorectal cancer patients. Signature validation has been carried out in two independent datasets and in a meta-cohort of 336 stage II/III patients. Since the 25-gene signature was obtained regardless of gene expression data of tumor specimens or patient’s clinical data, the prognostic power of this signature provides strong evidence of the link between the tumor stroma and cancer progression. Furthermore, the 19-gene signature was able to identify low-risk patients with very high accuracy, especially relevant for those high-risk stage-II patients. We hybridised fibroblast RNA in Affymetrix GeneChip 1.0 st arrays
2013-05-10 | E-GEOD-46824 | biostudies-arrayexpress
Project description:Gene expression profiling is a promising diagnostic and prognostic tool. Expression profiles are snap-shots of mRNA levels at time of extraction and they have been shown to be affected by tissue handling during sample collection. The effect of cold (room temperature) ischemia in the time interval between surgical removal of the specimen and freezing has been described in a number of studies. However, not much is known about the effect of warm (body temperature) ischemia during surgery.
2018-11-21 | GSE71053 | GEO
Project description:We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. We identified 277 probes, in common between the three types of fibroblasts, whose expression level is sequentially deregulated according to cancer progression (NCF→CAF-PT→CAF-LM; fold change Log2 normalized expression>1.5 in each step). Prediction Analysis of Microarrays was applied to obtain a 25-gene signature that better characterizes each fibroblast class. The signature is able to classify patients carrying primary tumors according to prognosis. This fact was exploited to obtain a 19-gene signature (from the 277 deregulated probes) predicting recurrence with high accuracy in stage II/III colorectal cancer patients. Signature validation has been carried out in two independent datasets and in a meta-cohort of 336 stage II/III patients. Since the 25-gene signature was obtained regardless of gene expression data of tumor specimens or patient’s clinical data, the prognostic power of this signature provides strong evidence of the link between the tumor stroma and cancer progression. Furthermore, the 19-gene signature was able to identify low-risk patients with very high accuracy, especially relevant for those high-risk stage-II patients.
2013-05-10 | GSE46824 | GEO
Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study is to compare gene expressions in colorectal tumor versus adjacent normal colorectal tissue.
2022-12-16 | GSE142279 | GEO
Project description:Time dependent changes of gene expression in surgical specimen of colorectal cancer
| PRJNA218630 | ENA
Project description:In this study 40 urine samples were analyzed in 5 batches. There are 3 labels: control group volunteers (8 pcs., CG), colorectal cancer patients before surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post).
2019-10-29 | ST001271 | MetabolomicsWorkbench
Project description:Lymph node (LN) retrieval is a critical procedure to determine the pathological stage and adjuvant therapy for colorectal cancer. The present study aimed to recommend a novel method by using sodium hypochlorite to improve colorectal surgical specimen LN harvest. Dissolving time of mesenteric LNs and fat tissue was firstly investigated in different concentrations of sodium hypochlorite. In the sodium hypochlorite group, 65 patients with colorectal cancer who underwent curative surgery were included. After standard manual gross dissection, the mesenteric tissue was subsequently immersed in 1% sodium hypochlorite for ~30 min, and then manual dissection was again applied for additional LN harvest. In the manual method group, 68 patients with colorectal cancer were selected and only manual dissection method was applied for LN harvest. The number of LNs in both groups were recorded for each case. Sodium hypochlorite could dissolve fat tissue significantly faster than LNs and the low concentration sodium hypochlorite had the maximum dissolving time difference between fat tissue and LNs (P<0.001). After sodium hypochlorite treatment, more LNs were identified when compared with the manual dissection method (28.2±12.1 vs. 16.5±8.7; P=0.010), whereas the number of positive LNs had no significant statistical difference between the two groups (P=0.181). After sodium hypochlorite immersion, 818 additional LNs (12.5±4.8 per case) were identi?ed and LNs ?2 mm were 58.4% (478/818). Moreover, 16 additional metastatic LNs were found in 10 patients. A total of 7 of them were upstaged, including 2 initially N0 cases. Using sodium hypochlorite at low concentrations may be the most simple, rapid, cost-saving, nontoxic and effective technique to improve LN harvest in colorectal carcinoma specimens so far. This method should be used routinely regardless of whether the number of LNs is <12 or not.
| S-EPMC7179393 | biostudies-literature