The long term microbiota and metabolic status in patients with colorectal cancer after curative colon surgery
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ABSTRACT:
PROVIDER: PRJEB32249 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3288490_1.fastq.gz | Fastqsanger.gz | |||
| ERR3288490_2.fastq.gz | Fastqsanger.gz | |||
| ERR3288500_1.fastq.gz | Fastqsanger.gz | |||
| ERR3288500_2.fastq.gz | Fastqsanger.gz | |||
| ERR3288510_1.fastq.gz | Fastqsanger.gz |
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Project description:This SuperSeries is composed of the following subset Series: GSE27854: Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery (gene expression analysis) GSE27910: Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery (copy number analysis) Refer to individual Series
2012-10-16 | E-GEOD-27913 | biostudies-arrayexpress
Project description:Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery
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Project description:Whether there are subsequent changes of metabolic profiles and microbiota status after partial colectomy remains unknown. We evaluated and compared long-term effects of microbiota status and metabolic profiles in early colorectal cancer (CRC) patients after curative colectomy to the controls. In this cross-sectional study, we analyzed metabolic syndrome occurrence in 165 patients after curative partial colectomy with right hemicolectomy (RH) or low anterior resection (LAR) and 333 age-sex matched controls. Fecal samples from some of those with RH, LAR, and controls were analyzed by next-generation sequencing method. The occurrences of metabolic syndrome were significantly higher in patients after RH, but not LAR, when compared with the controls over the long term (> 5 years) follow-up (P = 0.020). Compared with control group, RH group showed lower bacterial diversity (P = 0.007), whereas LAR group showed significantly higher bacterial diversity at the genera level (P = 0.016). Compared with the control group, the principal component analysis revealed significant differences in bacterial genera abundance after RH and LAR (P < 0.001). Furthermore, the Firmicutes to Bacteroidetes ratio was significantly lower in the RH group than the control group (22.0% versus 49.4%, P < 0.05). In conclusion, early CRC patients after RH but not LAR were associated with a higher occurrence of metabolic syndrome than the controls during long-term follow-up. In parallel with metabolic change, patients with RH showed dysbiosis with a tendency to decreased richness and a significant decrease in the diversity of gut microbiota.
| S-EPMC6570030 | biostudies-literature
Project description:Purpose: Our study aimed to disclose the specific gene expression profile representing peritoneal relapses inherent in primary gastric cancers and to identify patients at high risk of peritoneal relapse in a prospective study on the basis of the molecular prediction. Experimental Design: RNA samples from 141 primary gastric cancer tissues after curative surgery were profiled using oligonucleotide microarrays covering 30,000 human probes. Firstly we constructed molecular prediction system and validated the robustness and prognostic validity of the analysis by 500 times multiple random sampling in 56 retrospective set consisting of 38 relapse free and 18 peritoneal relapse patients. Secondly we applied this prediction to 85 prospective set to assess the predictive accuracy and prognostic validity. Results: In retrospective phase, 500 times multiple random sampling analysis yielded 68% predictive accuracy in average and 22 gene expression profile associated with peritoneal relapse was identified. This prediction could identify significantly poor prognostic patients. In prospective phase, the molecular prediction yielded 76.9% overall accuracy. Kaplan–Meier analysis with peritoneal relapse free survival showed a significant difference between ‘good signature group’ and ‘poor signature group’ (Log-rank p=0.0017). Multivariate analysis by Cox regression hazards model revealed that the molecular prediction was the only independent peritoneal relapse prognostic factor. Conclusions: Gene expression profile inherent in primary gastric cancer tissues can be useful to predict peritoneal relapse prospectively after curative surgery and individualize postoperative management to improve the prognosis of advanced gastric cancers.
2009-03-04 | GSE15081 | GEO
Project description:We performed whole blood gene expression profiling in 26 patients undergoing laparoscopic surgery for colon cancer stage I-III UICC. Saples were taken the day before surgery (-1), day one postoperatively (+1) and day 10 postoperatively (+10). The aim of the study was to investigate whether gene expression was altered after laparoscopic colon cancer surgery.
2021-11-01 | GSE122626 | GEO
Project description:Purpose: Our study aimed to disclose the specific gene expression profile representing peritoneal relapses inherent in primary gastric cancers and to identify patients at high risk of peritoneal relapse in a prospective study on the basis of the molecular prediction. Experimental Design: RNA samples from 141 primary gastric cancer tissues after curative surgery were profiled using oligonucleotide microarrays covering 30,000 human probes. Firstly we constructed molecular prediction system and validated the robustness and prognostic validity of the analysis by 500 times multiple random sampling in 56 retrospective set consisting of 38 relapse free and 18 peritoneal relapse patients. Secondly we applied this prediction to 85 prospective set to assess the predictive accuracy and prognostic validity. Results: In retrospective phase, 500 times multiple random sampling analysis yielded 68% predictive accuracy in average and 22 gene expression profile associated with peritoneal relapse was identified. This prediction could identify significantly poor prognostic patients. In prospective phase, the molecular prediction yielded 76.9% overall accuracy. KaplanâMeier analysis with peritoneal relapse free survival showed a significant difference between âgood signature groupâ and âpoor signature groupâ (Log-rank p=0.0017). Multivariate analysis by Cox regression hazards model revealed that the molecular prediction was the only independent peritoneal relapse prognostic factor. Conclusions: Gene expression profile inherent in primary gastric cancer tissues can be useful to predict peritoneal relapse prospectively after curative surgery and individualize postoperative management to improve the prognosis of advanced gastric cancers. Of 141 samples, 56 represented the retrospective phase and 85 represented the prospective phase.
2010-05-23 | E-GEOD-15081 | biostudies-arrayexpress
Project description:We obtained snap-frozen tissue samples from 20 colorectal cancer (CRC) patients with stage III disease who had undergone curative resection. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. We used microarrays to identify potential gene deregulation correlated with the outcomes of colon cancer patients. mRNA from 20 primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. The NexusExp3 procedure was used to make calls of expression. Of the 20 patients, 7 had disease relapse within 3 years after surgery.
2014-08-26 | E-GEOD-60697 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study is to identify a novel biomarker related with distant metastases of colorectal cancer (CRC). Experimental Design: We investigated mRNA expression profiles in 115 patients with CRC using an Affymetrix Gene Chip, and copy number profiles in 122 patients with CRC using an Affymetrix DNA Sty array. Genes in common between copy number and expression data were extracted as candidate genes. We analyzed the mRNA expression of candidate gene by quantitative reverse transcription polymerase chain reaction (RT-PCR) in 86 patients as a validation study. Furthermore, we analyzed the protein expression of candidate gene by immunohistochemical study in 269 patients, and investigated the relationship between protein expression and clinicopathologic features. Results: By the combination of copy number analysis and gene expression analysis, We extracted 2 candidate genes related with distant metastases of CRC. Several reports show that NUCKS1, one of candidate genes, is overexpressed in several cancer tissues. But a study about the relationship between NUCKS1 and CRC is none. The mRNA expression of NUCKS1 in cancer tissues was significantly higher than those in normal tissues. Overexpression of NUCKS1 protein was associated with significantly worse relapse-free survival of CRC. Overexpression of NUCKS1 protein was an independent risk factor for recurrence of CRC. Conclusion: The overexpression of NUCKS1 would be a new biomarker predicting recurrence after colorectal surgery.
2012-10-16 | GSE27854 | GEO
Project description:Purpose: The purpose of this study is to identify a novel biomarker related with distant metastases of colorectal cancer (CRC). Experimental Design: We investigated mRNA expression profiles in 115 patients with CRC using an Affymetrix Gene Chip, and copy number profiles in 122 patients with CRC using an Affymetrix DNA Sty array. Genes in common between copy number and expression data were extracted as candidate genes. We analyzed the mRNA expression of candidate gene by quantitative reverse transcription polymerase chain reaction (RT-PCR) in 86 patients as a validation study. Furthermore, we analyzed the protein expression of candidate gene by immunohistochemical study in 269 patients, and investigated the relationship between protein expression and clinicopathologic features. Results: By the combination of copy number analysis and gene expression analysis, We extracted 2 candidate genes related with distant metastases of CRC. Several reports show that NUCKS1, one of candidate genes, is overexpressed in several cancer tissues. But a study about the relationship between NUCKS1 and CRC is none. The mRNA expression of NUCKS1 in cancer tissues was significantly higher than those in normal tissues. Overexpression of NUCKS1 protein was associated with significantly worse relapse-free survival of CRC. Overexpression of NUCKS1 protein was an independent risk factor for recurrence of CRC. Conclusion: The overexpression of NUCKS1 would be a new biomarker predicting recurrence after colorectal surgery.
2012-10-16 | GSE27910 | GEO
Project description:Colorectal cancer (CRC), among the major cancer types in western world is responsible for 10% of cancer related deaths, often due to late detection when the tumor has already spread out of the colon. Surgery is the mainstay curative treatment for CRC. Nevertheless, between 15-30% of stage II and III patients develop hepatic metastasis within 5 years. Paradoxically, tumor surgery can contribute to the metastatic process, due to inflammatory mediator release in response to surgery, which promotes the metastatic ability of cancer cells. During surgery, bacterial products, such as LPS, from commensal bacteria translocate across the bowel wall, reach systemic circulation and induce an inflammatory response through to the activation of the Nuclear Factor-ĸB (NF-ĸB) pathway. Inflammation promotes malignant transformation by inducing chromosomal and microsatellite instability or CpG island methylation [14], but its direct effect on cancer cells and contribution to metastasis development remains to be elucidated. In this experiment we mimic the perioperative microenvironment where bacterial products get in contact with CRC cancer cells. We assessed the identity of the secreted proteins, including those released through extracellular vesicles (EV), of six CRC cell lines once exposed to lipopolysaccharide (LPS).
2022-02-28 | PXD011611 | Pride