Distinct gene expression profile between ARID1Ahigh and good prognosis and ARID1Alow and poor prognosis groups
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE110078 | GEO | 2018/02/06
REPOSITORIES: GEO
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Project description:Distinct gene expression profile between ARID1Ahigh and good prognosis and ARID1Alow and poor prognosis groups
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Project description:Lymph node sections from 29 patients with StageIIIB and IIIC melanoma, with divergent clinical outcome including 16 poor and 13 good prognosis patients as defined by time to tumor progression (TTP), were profiled using MWG oligonucleotide arrays,.
2008-10-21 | E-TABM-403 | biostudies-arrayexpress
Project description:Epithelial-mesenchymal transition (EMT) is in the highlights as a significant role in tumor progression and invasion. Snail was known as the one of regulators of EMT in various malignant tumors. The aim of this study was to investigate the effect of Snail on invasiveness/migratory ability of gastric cancer cell lines and clinicopathological and prognostic significance of Snail over-expression using immunohistochemistry in tissue microarray of 314 gastric adenocarcinomas (GC). Differential gene expression in Snail over-expressed GC was investigated using cDNA microarray analysis. Silencing of Snail by ShRNA induced decreased of invasion, migration of gastric cancer cell lines. In contrast, over-expression of Snail induced increased invasiveness and migratory ability of gastric cancer cell lines in accordance increase of VEGF and MMP11. Furthermore, the over-expression of Snail (?75% nuclear staining of Snail) was significantly associated with tumor progression (p<0.0001), lymph node metastases (p=0.002), lymphovascular invasion (p=0.002), and perineural invasion (p=0.002) in 314 GC patient. Snail over-expression was also associated with poor prognosis (shorter survival) in GC patients (p=0.023). cDNA microarray revealed 213 differential expressed genes in Snail over-expressed GC tissues, including genes related to metastasis, invasion. Based on above results, it was suggested that Snail plays a significant role in invasiveness/migratory ability of GCs. In addition, Snail might be used to predictive biomarker for evaluation of prognosis or aggressiveness in GCs. 48 primary gastric adenocarcinoma fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at Pusan National University Hospital (PNUH, Busan, Korea) and Cheonnam University Hospital (CNUH, Cheonnam, Korea). Microarray experiment and data analysis were done at Cancer research institute, PNUH, Busan, Korea.
2012-05-17 | E-GEOD-38024 | biostudies-arrayexpress
Project description:Clinical heterogeneity of gastric cancer reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of gastric cancer. Using microarray technologies, we analyzed gene expression profiling data from patients with advanced gastric cancer and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis. Using microarray technologies, we analyzed gene expression profiling data from patients with advanced gastric cancer and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis.
2012-04-29 | E-GEOD-28541 | biostudies-arrayexpress
Project description:Epithelial-mesenchymal transition (EMT) is in the highlights as a significant role in tumor progression and invasion. Snail was known as the one of regulators of EMT in various malignant tumors. The aim of this study was to investigate the effect of Snail on invasiveness/migratory ability of gastric cancer cell lines and clinicopathological and prognostic significance of Snail over-expression using immunohistochemistry in tissue microarray of 314 gastric adenocarcinomas (GC). Differential gene expression in Snail over-expressed GC was investigated using cDNA microarray analysis. Silencing of Snail by ShRNA induced decreased of invasion, migration of gastric cancer cell lines. In contrast, over-expression of Snail induced increased invasiveness and migratory ability of gastric cancer cell lines in accordance increase of VEGF and MMP11. Furthermore, the over-expression of Snail (≥75% nuclear staining of Snail) was significantly associated with tumor progression (p<0.0001), lymph node metastases (p=0.002), lymphovascular invasion (p=0.002), and perineural invasion (p=0.002) in 314 GC patient. Snail over-expression was also associated with poor prognosis (shorter survival) in GC patients (p=0.023). cDNA microarray revealed 213 differential expressed genes in Snail over-expressed GC tissues, including genes related to metastasis, invasion. Based on above results, it was suggested that Snail plays a significant role in invasiveness/migratory ability of GCs. In addition, Snail might be used to predictive biomarker for evaluation of prognosis or aggressiveness in GCs.
2012-05-18 | GSE38024 | GEO
Project description:TRPS1 is aberrantly expressed in a variety of tumors, including breast, prostate, and gastric cancers, and is strongly associated with tumorigenesis or prognosis. However, the role of TRPS1 in high grade serous ovarian carcinoma (HGSC) is unknown. We investigated the relationship between TRPS1 expression and clinicopathology in HGSC patients. The tumor-related regulatory mechanisms of TRPS1 was explored through in vivo and vitro experiments. The results showed that TRPS1 was highly expressed in HGSC compared to normal tissues. It was also linked to the cell proliferation index Ki67 and poor prognosis. In vivo experiments showed that knockdown of TRPS1 could inhibit tumor growth. In vitro experiments, knockdown of TRPS1 inhibited the proliferation of ovarian cancer cells. TRPS1 exerted its regulatory role as a transcription factor, binding to the PSAT1 promoter and promoting the expression of PSAT1 gene. Meanwhile, PSAT1 was positively correlated with CCND1 expression. These results suggest that TRPS1 affects HGSC proliferation and cell cycle by regulating PSAT1 and thus CCND1 expression.
2023-12-11 | GSE249935 | GEO
Project description:Purpose: To improve clinical outcome of gastric cancer patients, most emphasis is on improving therapeutic regimens, including more extensive surgery as well as (neo)adjuvant chemotherapy. The present study set out to identify, based on DNA copy number profiling, subgroups of patients with different clinical outcomes who thus would qualify for different therapy intensities. Experimental Design: DNA of 206 gastric cancer patients was isolated and analyzed by genome wide array comparative genomic hybridization. DNA copy number profiles were evaluated and correlated to lymph node status and survival. In addition, HSP90 protein expression was analyzed and correlated to survival in 290 gastric cancer patients. Results: Frequent (>20%) DNA copy number gains were observed on chromosomes 1p, 6p, 7p, 7q, 8q, 11q, 12q, 13q, 16p, 16q, 17q, 19p, 19q, 20p, 20q, 21q and 22q, and losses on chromosomes 4p, 4q, 6p, 6q, 9p, 13q and 21q. Lymph node negative gastric cancers showed significantly more losses on chromosomes 5q11.2-q35.1, 10q11.23-21.3 and 14q32.11-q32.33. In addition, losses on 5q11.2-q31.3 and 14q32.11-q32.33 were highly correlated to good clinical outcome, in both lymph node negative and positive gastric cancer patients. Loss of expression of HSP90, located on chromosome 14q32.2, correlated to good survival time. Conclusion: Genome wide DNA copy number profiling allows to identify a subgroup of gastric cancers, marked by losses on chromosomes 5q11.2-q31.3 and 14q32.11-q32.33 that have an excellent clinical outcome after surgery alone, and patients with these tumors are unlikely to benefit from additional intensified therapies. Possible biological mechanisms could involve loss of heat shock proteins, of which the coding genes are located at these chromosomal regions. 183 gastric adenocarcinomas
2012-05-09 | E-GEOD-26389 | biostudies-arrayexpress
Project description:Gastric cancer (GC) is associated with high mortality rates and an unfavorable prognosis at advanced stages. In addition, there are no effective methods for diagnosing gastric cancer at an early stage or for predicting the outcome for the purpose of selecting patient-specific treatment options. Therefore, it is important to investigate new methods for GC diagnosis. We designed a custom microarray of gastric cancer. The customized microarray contained 1042 canceration and prognosis related genes identical to the probes on the Agilent microarray. DNA microarray profilling analysis was performed on gastric cancer tissues and premalignant tissues (20 samples per group).
2014-03-01 | E-MTAB-1881 | biostudies-arrayexpress
Project description:Background Neuroendcrine carcinoma (NEC) of lung consists of small-cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC). Although long-term outcomes of SCLC patients are usually poor, a few patients achieve long-term survivals. Prognostic factors in SCLC have not been fully elucidated. microRNAs (miRNAs) are known to negatively regulate gene expression and to be relevant to tumorigenesis, tumor classification and prognosis. Methods 63 samples (46 neuroendocrine carcinoma including 35 SCLC and 11 LCNEC, 4 adenocarcinoma, 5 squamous cell carcinoma and 8 normal lung) were obtained through surgical resection. miRNA expression in each sample was comprehensively investigated using miRNA microarray. Results Unsupervised hierarchial clustering classified the all NEC into two subgroups, group 1 and 2. Group 1 was felt into an independent branch that consisted of only NEC, whereas group 2 was included in a branch that contained both NEC and non-NEC. Compared with SCLC of group 1 (SCLC 1), SCLC of group 2 (SCLC 2) was a distinct subgroup with surprisingly good prognosis (0% v 79% survived for 5 years; p=0.007). Serum proGRP level was significantly lower in SCLC 2 than in SCLC 1 despite of similar tumor stages between the two groups. Among 12 cases treated by presurgical chemotherapy, PR:NC ratio was 6:3 in SCLC 1 and 2:1 in SCLC 2, suggesting no apparent difference of chemosensitivity. Histologically, distinction between both groups was difficult. Cox regression analysis demonstrated that three miRNA signature was correlated with survival of SCLC patients. These prognostic miRNAs were differentially expressed between SCLC 1 and 2, which were validated by quantitative real time RT-PCR. Bioinformatics analysis predicted that these miRNAs targeted not only genes involving with tumorigenesis but also genes associated with neuroendocrine function. Conclusion miRNA expression profiling identified a distinct subgroup of SCLC with favorable prognosis. This subgroup might have less neuroendocrine character than usual SCLC. All samples were tissue samples obtained by surgical resection. 35 samples of small-cell lung cancer were investigated. 11 samples of larege cell neuroendocrine cancer, 4 samples of adenocarcinoma, 5 samples of squamous cell carcinoma and 8 samples of normal lung were also included as reference.
2013-01-31 | E-GEOD-19945 | biostudies-arrayexpress
Project description:MicroRNAs are important cellular components and their dysfunctions are associated with various disease.Small-cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, but little is know about the underlying machinery that leads to rapid tumor growth and early metastases.In this study, clinical outcome prediction miRNAs were successfully found through expression profiling of a total of 924 miRNA genes in 42 SCLC cases. 42 patients with respectable very limited disease (training set) were enrolled. All the patients underwent surgical resection followed by adjuvant chemotherapy according to the standard of care. Total RNA was extracted from formalin-fixed paraffin-embedded （FFPE）specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3 biochip representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.
2011-02-22 | E-GEOD-27435 | biostudies-arrayexpress