Gene expression-based identification of differential expression genes on gastric cancer samples with or without lymph node metastasis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE72305 | GEO | 2017/09/01
SECONDARY ACCESSION(S): PRJNA293699
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundTo investigate the necessity of routine lymph node dissection (LND) in intrahepatic cholangiocarcinoma (ICC) patients without indications of lymph node metastasis (LNM) preoperatively.Methods422 consecutive ICC patients who undergone curative resection from January 2009 to December 2014 were enrolled and categorized as two groups (hepatectomy only or hepatectomy plus LND). Clinicopathologic data was compared between the groups by χ2 or Fisher's exact test. Overall survival (OS) and recurrence-free survival (RFS) were calculated by the Kaplan-Meier method and differences were analyzed using the log-rank test. Cox regression model was adopted for multivariable analysis.ResultsThe median OS time of all 422 patients was 41.4 months. One-, 3-, and 5-year OS was 67%, 47%, and 35%, respectively. A total of 73 patients had undergone curative resection combined with LND, of whom 20.5% (15/73) were confirmed lymph node positive pathologically. The clinicopathologic characteristics between LND and control groups showed no significant differences. Of the 422 patients, 271 patients had recurrence. The recurrence rates were 65.8% for the LND group and 63.9% for the non-LND group. Survival analysis revealed that, neither the OS (LND vs. non-LND: 32.2 months vs. 46.2 months; p = 0.16) nor the RFS (LND vs. non-LND: 23.1 months vs. 17.0 months; p = 0.09) had significant difference. Multivariate analysis revealed that tumor size, tumor number, carbohydrate antigen19-9, carcinoembryonic antigen, and gamma-glutamyl transpeptidase were independent predictive factors for OS and RFS.ConclusionRoutine LND may not improve survival in resectable ICC patients with negative LNM diagnosis before operation.
| S-EPMC5768365 | biostudies-literature
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:The aim of the current study is to identify genes that show differential expression within the gastric lymph node of parasite resistant and susceptible sheep. For this we exploited parasite-naïve Blackface lambs with diversity in their predicted genetic resistance to T. circumcincta, which were trickle-infected with L3 larvae to mimic natural infection. This regime resulted in lambs with a spectrum of resistance as assessed by adult worm counts, faecal egg counts and IgA levels. Gastric lymph node tissue was used for transcription profiling of resistant and susceptible lambs to identify genes and physiological pathways associated with the differential activation of the immune response linked to the different disease outcomes.
2013-05-30 | E-MTAB-1580 | biostudies-arrayexpress
Project description:Emerging evidences demonstrate that metabolic reprogramming is a hallmark of malignancies, including gastric cancer (GC). Abnormal expression of metabolic rate-limiting enzymes, as the executive medium of energy metabolism, drives the occurrence and development of cancer. However, a comprehensive model of metabolic rate-limiting enzymes associated with the development and progression of GC remains unclear. In this research, we identified a rate-limiting enzyme, sterol O-acyltransferase 1 (SOAT1), was highly expressed in cancerous tissues, which was associated with advanced tumor stage and lymph node metastasis, leading to the poor prognosis of GC. It was shown that knockdown of SOAT1 or pharmacological inhibition of SOAT1 by avasimibe could suppress GC cell proliferation, cholesterol ester synthesis, and lymphangiogenesis. However, overexpression of SOAT1 promoted these biological processes. Mechanistically, SOAT1 regulated the expression of cholesterol metabolism genes SREBP1 and SREBP2, which could induce lymphangiogenesis via increasing the expression of VEGF-C. In conclusion, our results indicated that SOAT1 promotes gastric cancer lymph node metastasis through lipid synthesis, which suggested that it may be a promising prognostic biomarker for guiding clinical management and treatment decisions.
| S-EPMC8591064 | biostudies-literature
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:Objective: To develop and evaluate a diffusion-weighted imaging (DWI)-based radiomic nomogram for lymph node metastasis (LNM) prediction in advanced gastric cancer (AGC) patients. Overall Study: This retrospective study was conducted with 146 consecutively included pathologically confirmed AGC patients from two centers. All patients underwent preoperative 3.0 T magnetic resonance imaging (MRI) examination. The dataset was allocated to a training cohort (n = 71) and an internal validation cohort (n = 47) from one center along with an external validation cohort (n = 28) from another. A summary of 1,305 radiomic features were extracted per patient. The least absolute shrinkage and selection operator (LASSO) logistic regression and learning vector quantization (LVQ) methods with cross-validations were adopted to select significant features in a radiomic signature. Combining the radiomic signature and independent clinical factors, a radiomic nomogram was established. The MRI-reported N staging and the MRI-derived model were built for comparison. Model performance was evaluated considering receiver operating characteristic (ROC) analysis, calibration curves, and decision curve analysis (DCA). Results: A two-feature radiomic signature was found significantly associated with LNM (p < 0.01, training and internal validation cohorts). A radiomic nomogram was established by incorporating the clinical minimum apparent diffusion coefficient (ADC) and MRI-reported N staging. The radiomic nomogram showed a favorable classification ability with an area under ROC curve of 0.850 [95% confidence interval (CI), 0.758-0.942] in the training cohort, which was then confirmed with an AUC of 0.857 (95% CI, 0.714-1.000) in internal validation cohort and 0.878 (95% CI, 0.696-1.000) in external validation cohort. Meanwhile, the specificity, sensitivity, and accuracy were 0.846, 0.853, and 0.851 in internal validation cohort, and 0.714, 0.952, and 0.893 in external validation cohort, compensating for the MRI-reported N staging and MRI-derived model. DCA demonstrated good clinical use of radiomic nomogram. Conclusions: This study put forward a DWI-based radiomic nomogram incorporating the radiomic signature, minimum ADC, and MRI-reported N staging for individualized preoperative detection of LNM in patients with AGC.
| S-EPMC6883384 | biostudies-literature
Project description:Computed tomography is the most commonly used imaging modality for preoperative assessment of lymph node status, but the reported accuracy is unsatisfactory. To evaluate and verify the predictive performance of computed tomography deep learning on the presurgical evaluation of lymph node metastasis in patients with gastric cancer. 347 patients were retrospectively selected (training cohort: 242, test cohort: 105). The enhanced computed tomography arterial phase images of gastric cancer were used for lesion segmentation, radiomics and deep learning feature extraction. Three methods were used for feature selection. Support vector machine (SVM) or random forest (RF) was used to build models. The classification performance of the models was evaluated using the area under the receiver operating characteristic curve (AUC). We also established a nomogram that included clinical predictors. The model based on ResNet50-RF showed favorable classification performance and was verified in the test cohort (AUC = 0.9803). The nomogram based on deep learning feature scores and the lymph node status reported by computed tomography showed excellent discrimination. AUC of 0.9978 was achieved in the training cohort and verified in the test cohort (AUC = 0.9914). Decision analysis curve showed the value of nomogram in clinical application. The computed tomography-based deep learning nomogram can accurately and effectively evaluate lymph node metastasis in patients with gastric cancer before surgery.
| S-EPMC10102043 | biostudies-literature
Project description:Background and aimEndoscopic submucosal dissection (ESD) for undifferentiated type early gastric cancer is regarded as an investigational treatment. Few studies have tried to identify the risk factors that predict lymph-node metastasis (LNM) in intramucosal poorly differentiated adenocarcinomas (PDC). This study was designed to develop a risk scoring system (RSS) for predicting LNM in intramucosal PDC.MethodsFrom January 2002 to July 2015, patients diagnosed with mucosa-confined PDC, among those who underwent curative gastrectomy with lymph node dissection were reviewed. A risk model based on independent predicting factors of LNM was developed, and its performance was internally validated using a split sample approach.ResultsOverall, LNM was observed in 5.2% (61) of 1169 patients. Four risk factors [Female sex, tumor size ≥ 3.2 cm, muscularis mucosa (M3) invasion, and lymphatic-vascular involvement] were significantly associated with LNM, which were incorporated into the RSS. The area under the receiver operating characteristic curve for predicting LNM after internal validation was 0.69 [95% confidence interval (CI), 0.59-0.79]. A total score of 2 points corresponded to the optimal RSS threshold with a discrimination of 0.75 (95% CI 0.69-0.81). The LNM rates were 1.6% for low risk (<2 points) and 8.9% for high-risk (≥2 points) patients, with a negative predictive value of 98.6% (95% CI 0.98-1.00).ConclusionsA RSS could be useful in clinical practice to determine which patients with intramucosal PDC have low risk of LNM.
| S-EPMC4881979 | biostudies-literature
Project description:Lymph nodes are important peripheral immune organs in which numerous important immune responses occur. During the process of lymphatic metastasis, lymph nodes are also sites through which tumor cells must pass. Therefore, it is essential to develop a drug delivery system that can specifically transfer immunostimulatory medicine into lymph nodes to block lymphatic metastasis. Here, we developed a nucleic acid drug delivery system containing cationic agarose (C-agarose) and CpG oligodeoxynucleotides. C-agarose has a high affinity for Siglec-1 on the surface of lymph node sinus macrophages, which have a high specificity for targeting lymph nodes. Subcutaneous implantation of C-agarose+CpG gel caused the accumulation of CpG in the lymph node sinus macrophages and generated antitumor immune responses in the lymph node. C-agarose+CpG gel treatment decreased the metastasis size in the tumor-draining lymph node (TDLN) and lung metastatic nodules and suppressed tumor growth in both a mouse 4T1 breast cancer model and a B16F10 melanoma model. On this basis, this study proposes a nonsurgical invasive lymph node targeting immunotherapy concept that may provide a new approach for antitumor metastasis.
| S-EPMC6529739 | biostudies-literature
Project description:The consensus of endoscopic therapy for early gastric cancer (EGC) mainly depends on its clinicopathological features. However, the roles of tumor-associated neutrophils (TANs) in EGC remain uncertain. Here, we explored its predictive role for lymph node metastasis (LNM) in EGC. Three hundred twenty-two patients who underwent radical gastrectomy for EGC were enrolled. Preoperative peripheral blood was used to analyze the neutrophil-to-lymphocyte ratio (NLR), and the different status of TANs was determined by hematoxylin-and-eosin staining (H&E) and immunohistochemistry (IHC). TANs, rather than NLR, were positively associated with tumor size, Lauren classification, lymphovascular invasion (LVI), and LNM. Univariate analysis revealed that TANs were associated with LNM as well as tumor size, depth of invasion, Lauren classification, histological classification, LVI, and perineural invasion. In addition to histological classification and LVI, TANs were found to be an independent risk factor for LNM in EGC (P = 0.013). Stratification analysis by depth of invasion showed LVI in SM1 tumor, and both LVI and TANs (P = 0.042) in SM2 tumor were independent risk factors for LNM. In conclusion, TANs in EGC can predict LNM, and TANs may help to estimate LNM precisely in addition to the current criteria.
| S-EPMC7537418 | biostudies-literature