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Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Kaoru Mogushi

PROVIDER: E-GEOD-64258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Prognostic significance of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer.

Takahashi Hidenori H Ishikawa Toshiaki T Ishiguro Megumi M Okazaki Satoshi S Mogushi Kaoru K Kobayashi Hirotoshi H Iida Satoru S Mizushima Hiroshi H Tanaka Hiroshi H Uetake Hiroyuki H Sugihara Kenichi K

BMC cancer 20151024

<h4>Background</h4>The potential of expression profiling using microarray analysis as a tool to predict the prognosis for different types of cancer has been realized. This study aimed to identify a novel biomarker for colorectal cancer (CRC).<h4>Methods</h4>The expression profiles of cancer cells in 152 patients with stage I-III CRC were examined using microarray analysis. High expression in CRC cells, especially in patients with distant recurrences, was a prerequisite to select candidate genes. ...[more]

PMID: 26499327

Similar Datasets

Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer [copy number analysis]

Project description:Introduction: The potential of expression profiling using microarray analysis as a tool to predict the prognosis for different types of cancer has been realized. This study aimed to identify a novel biomarker for colorectal cancer (CRC). Experimental design: The expression profiles of cancer cells in 153 patients with CRC were examined using laser microdissection and oligonucleotide microarray analysis. Overexpression in CRC cells, especially in patients with distant metastases, was a prerequisite to select candidate genes. We analyzed the protein expression and localization of the candidate gene by immunohistochemical study and investigated the relationship between protein expression and clinicopathologic features in 271 CRC patients. Results: Using microarray analysis, we identified 11 candidate genes related to distant metastases in CRC patients. Among these genes, Traf2- and Nck- interacting kinase (TNIK) was known to be associated with aggressiveness in CRC through Wnt signaling. Absence of overexpression of TNIK protein was associated with significantly better overall survival (p < 0.001) and relapse-free survival (p < 0.001). Moreover, overexpression of TNIK protein was an independent risk factor for CRC recurrence (p = 0.009). Conclusion: Overexpression of TNIK might be a predictive biomarker of CRC recurrence. Copy number analysis was performed using LCM samples of 125 colorectal cancer patients by GeneChip Human Mapping 250k Sty arrays. Non-tumor tissues obtained from 47 patients were used as unpaired reference samples.

2015-11-21 | E-GEOD-64257 | biostudies-arrayexpress

Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery (copy number analysis)

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. Copy number analysis was performed using LCM samples of 122 colorectal cancer patients by GeneChip Human Mapping 250k Sty arrays. Non-tumor tissues obtained from 74 patients were used as unpaired reference samples.

2012-10-16 | E-GEOD-27910 | biostudies-arrayexpress

Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery

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

Genome-wide copy number analysis for occult lymph node metastasis in oral squamous cell carcinoma

Project description:Using Affymetrix Mapping 250K array, we studied copy number aberrations in oral squamous cell carcinoma (OSCC) to identified biomarkers associated with occult lymph node metastasis. We used frozen specimens from 60 OSCC patients. Copy number analysis was performed using homogenized samples of 60 oral squamous cell carcinoma patients by GeneChip Human Mapping 250k Sty arrays. As a reference, SNP array data set of 50 normal Asians (Japanese & Chinese) from HapMap database was used.

2012-09-01 | E-GEOD-31984 | biostudies-arrayexpress

Affymetrix SNP array data for acute lymphoblastic leukemia and lymphoblastic lymphoma samples

Project description:Childhood T-cell malignancies include T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LBL). T-ALL and T-LBL share common morphologic and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations suggesting that they may represent two different biological entities. In order to investigate the common and unique genetic aberrations of T-LBL and T-ALL, copy number alteration (CNA) analysis was performed on a subset of the samples analyzed by GEP Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from diagnostic bone marrow aspirates or tumor tissue samples. Copy number analysis of Affymetrix 100K SNP arrays was performed for 9 T-ALL and 9 T-LBL pediatric samples. The samples from leukemia/lymphoma remission were used as references for copy number inference.

2012-06-29 | E-GEOD-30319 | biostudies-arrayexpress

DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-07-07 | E-GEOD-39282 | biostudies-arrayexpress

Truncating mutations of STAG2 define a molecular subgroup of aneuploid bladder cancers with poor prognosis.

Project description:Aneuploidy is among the most common hallmarks of cancer, yet the underlying genetic mechanisms are still poorly defined. We have recently identified STAG2 as a gene that is mutated in human cancer and whose inactivation leads directly to chromosomal instability and aneuploidy. However, no single tumor type has yet been identified in which inactivation of a cohesin subunit represents a predominant mutational event. Here we used immunohistochemistry to screen a panel of 2,214 tumors from each of the major human tumor types to identify additional tumor types harboring somatic loss of STAG2. Strikingly, STAG2 expression was completely absent in 18% of urothelial carcinomas, the most common type of bladder cancer and the fifth most common cancer in the United States. DNA sequencing revealed that somatic mutations of STAG2 were present in 21% of urothelial carcinomas, which were found to be a group of highly aneuploid tumors. The acquisition of STAG2 mutations was shown to be an early event in the pathogenesis of urothelial carcinoma. STAG2 loss was significantly associated with lymph node invasion, increased disease recurrence, and reduced cancer-specific survival. These results identify STAG2 as one of the most commonly mutated genes in bladder cancer discovered to date, and demonstrate that STAG2 inactivation defines an aggressive subtype of bladder cancer with particularly poor prognosis. Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from snap-frozen human urothelial carcinoma primary tumors. Copy number analysis using Affymetrix CytoScan HD Arrays was performed for 12 human urothelial carcinomas of the bladder with truncating mutations of the STAG2 gene.

2013-06-30 | E-GEOD-41581 | biostudies-arrayexpress

Copy number profiling via ArrayCGH on high grade serous epithelial ovarian cancer samples from multiple biopsies

Project description:We performed Array CGH on 25 patients with high grade serous epithelial ovarian cancer (HGS-EOC): each of this had multiple biopsies taken at the moment of the surgery in different anatomical sites, and 18 had also temporal biopsies taken after several cycles of chemotherapy. Blood was used as control. The experiment was performed to identify genomic alterations that can be used to classify the disease, going beyond the individual tumor heterogeneity.

2019-12-19 | E-MTAB-6900 | biostudies-arrayexpress

Somatic copy number variation profiling in matched brain and extracranial metastases of melanoma

Project description:An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by mass-array genotyping, molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors. Somatic copy number variation (CNV) in 47 melanoma brain metastases (BM, except for patient 01, who had a spinal cord metastasis) and extracranial metastases (EM) were analyzed by molecular inversion probe (MIP) array (Affymetrix OncoScan FFPE Express 2.0). DNA were extracted from regions with >70% viable tumor cells from formalin-fixed and paraffin-embedded (FFPE) tissues. Of the 47 tumor samples, 22 were matched BM and EM from the same patients. In addition, 24 DNA samples from normal tissues were included as diploid controls.

2014-05-08 | E-GEOD-50495 | biostudies-arrayexpress

DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Agilent]

Project description:Metastatic urothelial carcinoma (UC) of the bladder is associated with multiple somatic copy number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic UC treated with platinum chemotherapy. We obtained overall survival (OS) and DNA copy number data from UC patients in a Spanish discovery cohort and three validation cohorts. GISTIC was used to identify altered regions, and associations between copy number gains/losses and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease The output files of the GISTIC 2.0 software are linked as supplementary files on Series record along with readme.txt file describing the contents of each file/column.

2013-07-07 | E-GEOD-39281 | biostudies-arrayexpress

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