Gene Expression Profiling of Colorectal Tumors and Normal Mucosa by Microarrays Meta-Analysis Using Prediction Analysis of Microarray, Artificial Neural Network, Classification, and Regression Trees

Chu, Chi‐Ming; Yao, Chung-Tay; Chang, Yu-Tien; Chou, Hsiu‐Ling; Chou, Yu‐Ching; Chen, Kanghua; Terng, Harn-Jing; Huang, Cheng-Yang; Lee, Chia-Cheng; Su, Sui-Lung; Liu, Yao–Chi; Lin, Fu‐Gong; Wetter, Thomas C.; Chang, Chi‐Wen

doi:10.1155/2014/634123

Cited by 48 publications

(57 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, TCN1 rather than vitamin B12 was found to be better correlated with progression in patients with gastric cancer 20. Chu et al recently identified TCN1 as a significantly expressed gene that is associated with advanced CRC by microarray meta-analysis 25. Our results of the present study provide additional evidence that expression status of TCN1 was more produced in tumor cells in parallel to previous research works, suggesting TCN1 as a marker of disease progression in CRC.…”

Section: Discussionsupporting

confidence: 85%

Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy

Lee¹,

Wei²,

Tian³

et al. 2017

J. Cancer

View full text Add to dashboard Cite

Objective: Neoadjuvant concurrent chemoradiotherapy (CCRT) is an increasingly common therapeutic strategy for locally advanced rectal cancer, but stratification of risk and final outcomes remain a major challenge. Transcobalamin 1 (TCN1), a vitamin B12 (cobalamin)-binding protein, regulates cobalamin homeostasis. High expression of TCN1 have been reported in neoplasms such as breast cancer and hepatocellular carcinoma. However, little is known about the relevance of TCN1 to rectal cancer receiving CCRT. This study examined the predictive and prognostic impact of TCN1 expression in patients with rectal cancer following neoadjuvant CCRT.Methods: Through data mining from a published transcriptome of rectal cancers (GSE35452), we identified upregulation of TCN1 gene as the most significantly predicted poor response to CCRT among ion transport-related genes (GO:0006811). We evaluated TCN1 immunohistochemistry and performed an H-score analysis on endoscopic biopsy specimens from 172 rectal cancer patients receiving neoadjuvant CCRT followed by curative surgery. Expression levels of TCN1 were further correlated with clinicopathologic features, therapeutic response, tumor regression grade (TRG) and survivals including metastasis-free survival (MeFS), disease-specific survival (DSS) and recurrent-free survival (LRFS).Results: TCN1 overexpression was significantly related to advanced post-treatment tumor (T3, T4; p<0.001) and nodal status (N1, N2; p<0.001), vascular invasion (p=0.003) and inferior tumor regression grade (p < 0.001). In survival analyses, TCN1 overexpression was significantly associated with shorter DSS (p<0.0001), MeFS (p=0.0002) and LRFS (p=0.0001). Furthermore, it remained an independent prognosticator of worse DSS (p=0.002, hazard ratio=3.344), MeFS (p=0.021, hazard ratio=3.015) and LRFS (p=0.037, hazard ratio=3.037) in the multivariate comparison.Conclusion: Overexpression of TCN1 is associated with poor therapeutic response and adverse outcomes in rectal cancer patients receiving CCRT, justifying the potential prognostic value of TCN1 in rectal cancer receiving CCRT.

show abstract

Section: Discussionsupporting

confidence: 85%

Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy

Lee¹,

Wei²,

Tian³

et al. 2017

J. Cancer

View full text Add to dashboard Cite

show abstract

“…Interestingly, besides PVT1 , only 5 other genes showed a strong misregulation consistently linked with clinical outcome and tumor features in KIRC (phenotype permutation p -value < 0.001, Figure 2E and Table S2). Most of these genes have been previously associated with worst survival or more aggressive state of tumors: MYBL2 [9]; IL20RB [10]; MFSD4 [11]; CRHBP [12] and CWH43 [13]. These results indicate PVT1 as a novel prognostic biomarker in KIRC.…”

Section: Resultsmentioning

confidence: 83%

A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma

et al. 2016

View full text Add to dashboard Cite

The PVT1 lncRNA has recently been involved in tumorigenesis by affecting the protein stability of the MYC proto-oncogene. Both MYC and PVT1 reside in a well-known cancer-risk locus and enhanced levels of their products have been reported in different human cancers. Nonetheless, the extension and relevance of the MYC-PVT1 deregulation in tumorigenesis has not yet been systematically addressed.Here we performed a pan-cancer analysis of matched copy number, transcriptomic, methylation, proteomic and clinicopathological profiles for almost 7000 patients from 17 different cancers represented in the TCGA cohorts. Among all cancers types, kidney renal clear cell carcinoma (KIRC) showed the strongest upregulation of PVT1 and increased levels of both MYC and PVT1 correlated with the clinical outcome. PVT1 misregulation in KIRC is mostly associated to promoter hypomethylation rather than locus amplification. Furthermore, we found an association between MYC levels and PVT1 expression, which impacted on MYC-target genes.Collectively, our study discloses the role of PVT1 as a novel prognostic factor and as a molecular target for novel therapeutic interventions in renal carcinoma.

show abstract

“…REG expression is higher in CRC, and REG therefore may be a potential marker. The expression of TCN1, MMP7, and MAGE‐A3 was increased in CRC tissues. High CST1 expression enhances tumor metastasis and invasiveness in CRC .…”

Section: Discussionmentioning

confidence: 96%

Differentially expressed lncRNAs and mRNAs identified by NGS analysis in colorectal cancer patients

Zhao

et al. 2018

Cancer Medicine

View full text Add to dashboard Cite

Long noncoding RNAs (lncRNAs) play an important role in gene regulation, but their impact on the pathogenesis of colorectal cancer and the biological function of cancer cells is unclear. In this study, we used next‐generation sequencing to study the differences in the expression profiles of lncRNAs and mRNAs in colorectal cancer tissues. We analyzed the differentially expressed genes by Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment and predicted new lncRNA functions. Our results revealed that compared with lncRNAs and mRNAs in nontumor colorectal tissues, 1019 lncRNAs (512 upregulated, 507 downregulated) and 3221 mRNAs (1606 upregulated, 1615 downregulated) were differentially expressed in tumor colorectal tissues (fold change >2 and P < 0.05). We validated some of these genes by qPCR. Furthermore, we identified some new lncRNAs differently expressed in colorectal cancer samples from patients in northern China. We confirmed the function of lncRNA‐FIRRE‐201 and SLCO4A1‐AS1‐202 in colorectal cancer cells to provide an experimental basis for studies on their roles in the occurrence and development of colorectal cancer and in the regulation of networks.

show abstract

Gene Expression Profiling of Colorectal Tumors and Normal Mucosa by Microarrays Meta-Analysis Using Prediction Analysis of Microarray, Artificial Neural Network, Classification, and Regression Trees

Cited by 48 publications

References 30 publications

Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy

Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy

A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma

Differentially expressed lncRNAs and mRNAs identified by NGS analysis in colorectal cancer patients

Contact Info

Product

Resources

About