Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA237332 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray was used to find out the differentially expressed in tumor sites of early-stage oral squamous cell carcinoma compared with Normal parts. Furthermore, we compared cases of early-stage oral squamous cell carcinoma with lymph node metastasis with cases without lymph node metastasis. The miRNAs obtained may not only serve as predictive biomarkers for lymph node metastasis, but may also be used further to understand disease.
2023-08-22 | GSE241289 | GEO
Project description:Gene expression profiling comparing biological mechanisms for lymphatic metastases in lung adenocarcinoma and squamous cell carcinoma Two-condition comparison: primary invasive tumors (TN+), without lymph node metastasis (TN-), matched tumor cells in metastatic lymph nodes (MT) in ADC and SCC separately
2011-08-30 | E-GEOD-29827 | biostudies-arrayexpress
Project description:Objective: The purpose of this study was to investigate the molecular basis of tumorigenesis and regional lymph node metastasis in LSCC, and provide a set of genes that may be useful for the development of novel diagnostic markers and/or more effective therapeutic strategies. Methods: A total number of 10 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for microarray analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by Illumina mRNA microarrays,and LSCC tissues with regional lymph node metastasis and LSCC tissues without regional lymph node metastasis were analyzed in the same manner.The most frequently differently expressed genes screened by microarrays were also validated by qRT-PCR in another 42 patients diagnosed for LSCC . Results: Analysed by Illumina mRNA microarrays,there were 361 genes significantly related to tumorigenesis while 246 genes significantly related to regional lymph node metastasis in LSCC. We found that the six genes (CDK1,CDK2,CDK4,MCM2,MCM3,MCM4) were most frequently differently expressed functional genes related to tumorigenesis while eIF3a and RPN2 were most frequently differently expressed functional genes related to regional lymph node metastasis in LSCC. The expressions of these genes were also validated by qRT-PCR. Conclusions: The research revealed a gene expression signature of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma.Of the total, the deregulation of several genes (CDK1, CDK2, CDK4, MCM2, MCM3, MCM4, EIF3a and RPN2) were potentially associated with disease development and progression. The result will contribute to the understanding of the molecular basis of LSCC and help to improve diagnosis and treatment. A total number of 10 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for microarray analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by Illumina mRNA microarrays,and LSCC tissues with regional lymph node metastasis and LSCC tissues without regional lymph node metastasis were analyzed in the same manner.The most frequently differently expressed genes screened by microarrays were also validated by qRT-PCR in another 42 patients diagnosed for LSCC .
2013-11-02 | E-GEOD-51985 | biostudies-arrayexpress
Project description:Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible.
2007-08-25 | E-GEOD-2280 | biostudies-arrayexpress
Project description:A classifier was build on 82 training samples to differentiate between lymph node negative (N0) and lymph node metastasis (N+) head and neck squamous-cell carcinomas (HNSCC). The 102 predictor genes that resulted from this classifier where then validated against a independent validation set.
2005-01-09 | E-UMCU-11 | biostudies-arrayexpress
Project description:Controlling metastatic lesions is an important part of improving cancer prognosis, in addition to controlling the primary lesion. There have been many histological examinations of primary and metastatic lesions, but little basic research using cell strains from primary and metastatic lesions belonging to the same patient. In this study, we successfully established a cell strain derived from lower gingival carcinoma (WK2) and a strain derived from secondary cervical lymph node metastasis (WK3F) through primary cultures of tissue from a patient with oral squamous cell carcinoma. We then investigated the biological characteristics of the cancer cell strains from these primary and metastatic lesions, and analyzed metastasis-related genes. Comparing the biological characteristics in vitro showed WK3F to have higher cell proliferation ability and shorter cell doubling time than WK2. It also showed increased cell migratory ability, and high invasive and self-replication abilities. Heterotransplantation into nude mice resulted in high tumor formation rates in the tongue and high metastasis rates in the cervical lymph nodes. Changes in WK2 and WK3F gene expression were comprehensively analyzed with the microarray method. Genes with increased expression in WK3F compared to WK2 were extracted when Z-score ≥ 2.0 and ratio ≥ 5.0, while genes with reduced expression in WK3F compared to WK2 were extracted when Z-score ≤ -2.0 and ratio ≤ 0.2. As a result, differences were found in 604 genes. From these, MAGEC1 (88.0 times), MMP-7 (18.6 times), SNAI1 (6.6 times), MACC1 (6.2 times), and HTRA1 (0.012 times) were selected as metastasis-related candidate genes. The results suggest that these molecules could be important to clarifying the mechanism of metastasis, and could become therapeutic targets. We successfully established a cell strain derived from lower gingival carcinoma (WK2) and a strain derived from secondary cervical lymph node metastasis (WK3F) through primary cultures of tissue from a patient with oral squamous cell carcinoma. Changes in WK2 and WK3F gene expression were comprehensively analyzed with the microarray method.
2014-06-30 | E-GEOD-54672 | biostudies-arrayexpress
Project description:Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible. Keywords = oral carcinoma lymphatic metastasis predict Keywords: repeat sample
2005-02-19 | GSE2280 | GEO
Project description:An experiment was performed to investigate the perservation of gene expression upon metastasis of primary head and neck squamous cell carcinomas to the cervical lymph node.
2006-10-23 | E-TABM-114 | biostudies-arrayexpress
Project description:Tumor-adjacent noncancerous tissues often exhibited abnormalities on molecular levels, which is described as field effect of cancerization. Accumulated evidence demonstrated that filed effect may also play important role in cancer progression. In the present study, we found that the gene expression profile in noncancerous lung tissues adjacent to lung squamous cell carcinoma (SCC) was significantly associated with regional lymph node status of patients. Significance Analysis of Microarrays (SAM) showed that 121 genes were significantly associated with lymph node metastasis (delta=0.75, FDR=0.069). Interestingly, all of the significant genes were up-regulated in the lymph node positive samples. For these genes, the most significant biological GO terms were extracellular structure organization, cell adhesion, regulation of cell motion/migration, and vessel development, etc, which were also involved in EMT process supported by another experiment in vitro. Tumor-adjacent histologically normal lung tissues were collected from 60 primary lung SCC patients, of whom 34 (56.7%) suffered regional lymph node metastasis. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray (G4112F).
2014-10-06 | E-GEOD-40588 | biostudies-arrayexpress
Project description:Background: Cervical lymph node metastasis is a potent prognostic factor in oral squamous cell carcinoma (OSCC). However, lymph nodes resected by sentinel node biopsy or neck dissection are usually diagnosed by examining only one or two sections of the maximal cut surface. Accurate diagnosis of the metastasis in lymph nodes is important but depends on a heavy workload of the pathologist. In this study, we have attempted to identify novel molecular markers to find the harboring cancer cells in the lymph node and establish rapid detection method. Methods: We determined the gene expression profiles of 7 metastatic lymph nodes from patients with OSCC and 1 normal lymph node and 5 salivary glands from non-cancerous patients by microarray analysis. We found the overexpression genes in all metastatic lymph nodes. Subsequently, we examined the expression of these genes in newly 23 metastatic lymph nodes and 9 normal lymph nodes by real-time quantitative RT-PCR (qRT-PCR) assay. Moreover, the rapid detection of lymph node metastasis by these genes was examined using the reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Result: Among the 4 genes identified by microarray analysis, annexin A8 (ANXA8) and desmoglein 3 (DSG3) were detected in all metastatic lymph nodes at a much higher level but not in normal lymph nodes at all by qRT-PCR. Furthermore, RT-LAMP method targeting ANXA8 rapidly detected almost lymph nodes with metastasis. Conclusions: ANXA8 could be a useful marker for detecting lymph node metastasis in OSCC. Using AB1700 system, we determined the gene expression profiles of lymph nodes with metastasis of OSCC. Normal lymph node and salivary gland tissues were used as control samples.
2015-12-21 | E-GEOD-70604 | biostudies-arrayexpress