Gene expression profiles of tumor and paired normal lung tissues from primary non-small cell lung cancer (NSCLC) patients in Taiwan.
ABSTRACT: Genome-wide expression profiling of NSCLC patients were done using Phalanx Human OneArray chip. The surgically resected tumor tissue and corresponding normal tissue were collected from 21 patients diagnosed with primary NSCLC admitted to Taipei Veterans General Hospital, Taiwan. Overall design: In this study, we used cDNA microarray to detect gene expression profiling in tumor and corresponding normal samples from 21 NSCLC patients. There were 11 AD patients and 10 SQ patients. The patients consisted of 10 early stage patients (stages I and II) and 11 late stage patients (stages III and IV). Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1082 experimental control probes).
Project description:Genome-wide expression profiling of NSCLC patients were done using Phalanx Human OneArray chip. The surgically resected tumor tissue and corresponding normal tissue were collected from 21 patients diagnosed with primary NSCLC admitted to Taipei Veterans General Hospital, Taiwan. In this study, we used cDNA microarray to detect gene expression profiling in tumor and corresponding normal samples from 21 NSCLC patients. There were 11 AD patients and 10 SQ patients. The patients consisted of 10 early stage patients (stages I and II) and 11 late stage patients (stages III and IV). Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1082 experimental control probes).
Project description:In the present study, we used expression microarray to establish a transcriptome on epileptogenic zone versus irritative zone from removed brain tissues of patients affected with intractable neocortical epilepsies. Our results showed that expression profiling of a total of 30,968 human genes in 10 patients brain samples. Overall design: A total of 10 patients were recruited in this study. Mean age and period of intractable neocortical epilepsy were 19.8±2.5 and 13.7±2.3 years, respectively. After clinical evaluatng by EEG, SPEC, MRI, and v-EEG, patients were performed with surgical removal of epileptogenic zone and irritative zone. Removed surgical samples were obtained snap-frozen on dry ice for total RNA extraction commissined to Phalanx Biotech Group, Taiwan. RNA samples were evaluated using Human OneArray TM with 30,968 human genome probes.
Project description:Background: α-catulin may functions as an oncoprotein, sustaining proliferation by preventing cellular senescence and promoting cancer cell migration. In this study, we investigated the mechanism of α-catulin in cancer cell migration and metastasis in lung cancer. Method: α-catulin mRNA expression was isolated from A549/AS2neo (control) and A549/AS2neo-α-catulin stable cells. The Phalanx Human OneArray microarray analysis was performed to identify α-catulin downstream genes. Results: Overexpression of α-catulin increased cancer cell migration and metastasis. By using Phalanx Human OneArray microarray we have identified panel of genes altered by α-catulin overexpression, consisting of CDC42, intergrins and genes related to cytoskeleton remodeling. Conclusion: α-catulin is an oncoprotein and promotes lung cancer cell migration and metastasis. Two-condition experiment, Vector vs. alpha-catulin overexpression cells.The cDNAs encoding full-length human alpha-catulin were amplified and subcloned into lentiviral pLKO_AS2.neo which generated full-length alpha-catulin. Vector control or alpha-catulin lentivirus were transduced into A549 cells and G418 was used to select stable cells.
Project description:Detection, treatment, and prediction of outcome for lung cancer patients increasingly depend on a molecular understanding of tumor development and sensitivity of lung cancer to therapeutic drugs. The application of genomic technologies, such as microarray, is widely used to monitor global gene expression and has built up invaluable information and knowledge, which is essential to the discovery of new insights into the mechanisms common to cancer cells, resulting in the identification of unique, identifiable signatures and specific characteristics. It is likely that application of microarray may revolutionize many aspects of lung cancer being diagnosed, classified, and treated in the near future. We used microarrays to detail the global gene expression patterns of lung cancer. Keywords: Disease state analysis Overall design: Adjacent normal-tumor matched lung cancer samples were selected at early and late stages for RNA extraction and hybridization on Affymetrix microarrays. A total of 66 samples were used for microarray analysis, including pairwise samples from 27 patients, who underwent surgery for lung cancer at the Taipei Veterans General Hospital, two tissue mixtures from the Taichung Veterans General Hospital (one was adjacent normal lung mixtures and the other was lung adenocarcinoma mixtures), two commercial human normal lung tissues (Clontech (Catalog No. 636524) and Stratagene (Catalog No. 735020)), one immortalized, nontumorigenic human bronchial epithelial cell line (NL-20 (ATCC® No. CRL-2503)), and 7 lung cancer cell lines (A-549 (ATCC® No. CCL-185), NCI-H1299 (ATCC® No. CRL-5803), NCI-H661 (ATCC® No. HTB-183), CL1-0, CL1-1, CL1-5 and CL1-5-F4.
Project description:Genome-Wide Screening of Genomic Alterations and Transcriptional Modulation in Non-Smoking Female Lung Cancer in Taiwan Sixty-one pairs of cancer and normal lung tissue specimens from non-smoking females were collected at National Taiwan University Hospital and Taichung Veterans General Hospital. The selection criteria of clinical specimens depend on pathology report, physical examination and cigarette-smoking history. Surgical lung tissue specimens were immediately snap-frozen in liquid N2 and stored at -80 °C. Surgical specimens would be further processed for RNA and DNA extraction. Only those samples passed quality controls were processed for gene expression profiling analysis and single nucleotide polymorphism (SNP) analysis respectively.
Project description:Background: Current histopathological methods are inadequate for predicting outcome and recurrence in patients with non-small cell lung carcinoma (NSCLC) after surgery. In this study, we investigated the use of gene expression signatures to predict outcome and metastasis in lung cancer patients. Methods: Gene expression was studied by microarray and the real-time reverse transcriptase polymerase chain reaction (RT-PCR) in normal and lung tumor tissue of 188 NSCLC patients who underwent surgical resection. The 5 cancer-related genes and 1 reference gene expression levels measureed by real-time RT-PCR were used in a prospectively defined algorithm to determine the risk for each patient. Finally, we used an independent cohort to verify the 5 gene-based predictive model derived from decision tree analysis. Results: The 5 gene-based decision tree model was able to predict the prognosis. The recurrence rate at 36 months was 53% in the low-risk group versus 83% in the high-risk group (P=0.002). The 5 gene-based model could also predict overall survival (P<0.001). In multivariate analysis, the decision tree model predicted that high-low dichotomy and stage were both significant for recurrence. In addition, it could also predict metastasis and survival of NSCLC patients within the stage I-II subgroups. A similar result was found using an independent cohort of NSCLC patients. The high-risk patients had a significantly poorer overall survival than the low-risk patients (P=0.005). We also found distinct gene signatures which could distinguish between NSCLC, and normal tissue and histology subtypes. Conclusions: A gene expression signature can predict metastasis and survival of NSCLC patients. Keywords: Survival and metastasis analysis Overall design: In this study, we investigated the use of gene expression signatures to predict outcome and metastasis in lung cancer patients. Lung cancer tissue specimens from 125 patients who underwent surgical resection of their primary NSCLC at the Taichung Veterans General Hospital in Taiwan between December 1999 and December 2003 were included in this study. Specimens were stored frozen. Of these patients, 60 had adenocarcinoma, 52 squamous cell carcinoma, and 13 other types, all histologically defined.
Project description:The underlying mechanisms of miR-330-3p in the progresion of NSCLC have not been well investigated. Thus we design this expirment tying to find out the pathways and target genes involved in NSCLC metastasis. Overall design: Total RNA was extracted from A549 cells transfected with lentivirus knocking down miR-330-3p and vector, respectively. Isolations and microarray analyses were performed using the Human OneArray.
Project description:We compared gene expression profile between healthy-donor peripheral monocytes and glioblastoma-patient peripheral monocytes as well as glioblastoma-patient peripheral monocytes with matched tumor-infiltrating myeloid cells. Overall design: In the study presented here, 12 samples, including peripheral monocyte samples from 4 healthy donors, peripheral monocytes from 4 GBM patients and matched tumor-infiltrating macrophages extracted from the glioblastoma microenvironment, were used to acquire the mRNA expression (30,275 human genes) via the Phalanx Human Whole Genome OneArray Microarray v5.1 Platform.
Project description:Gene expression profiling of betulinic acid and fluorinated betulinic acid-treated MCF-7 human breast cancer cells. We used Phalanx Biotech Human Whole Genome OneArray HOA6.2 Array to determine differential gene expression. Overall design: Samples were collected from betulinic acid and fluorinated betulinic acid-treated MCF-7 cells.
Project description:Ets2-null ES cells are defective in differentiating into cardiac myocytes, evidenced by the lack of spontaneous beating, cardiac transcription factors and structural proteins. With the Phalanx mouse Onearray v2, we compared the gene expression profiles of cells derived from Ets2-null and wildtype ES cells. Standard embryoid body culture protocol was used to induce differentiation of murine ES cells. On the 10th day, replicates of either Ets2-null or control wildtype EB culture were collected in Trizol for total RNA extraction. Microarray was preformed by Phalanx.