Dataset Information

Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling.

ABSTRACT: Basal cell carcinoma (BCC) is the most frequent malignant tumor of the eyelid; it progresses slowly and rarely metastasizes. However, BCC of the eyelid is partially invasive and can extend to the surrounding ocular adnexa even if appropriate treatment is performed. To understand the molecular mechanism underlying its pathogenesis, global gene expression analysis of surgical tissue samples of BCC of the eyelid (n=2) and normal human epidermal keratinocytes was performed using a GeneChip® system. The histopathological examination of surgically removed eyelid tissues showed the tumor nest composed with small basaloid. In the samples from patients 1 and 2, 687 and 713 genes were identified, respectively, demonstrating ?5.0-fold higher expression than that noted in normal human epidermal keratinocytes. For the 640 genes with upregulated expression in both patient samples, Ingenuity® pathway analysis showed that the gene network in BCC of the eyelid included many BCC-associated genes, such as the following: BCL2 apoptosis regulator; Patched-1; and SRY-box 9. In addition, unique gene networks related to cancer cell growth, tumorigenesis, and cell survival were identified. These results of integrating microarray analyses provide further insights into the molecular mechanisms involved in BCC of the eyelid and may provide a therapeutic approach for this disease.

SUBMITTER: Yunoki T

PROVIDER: S-EPMC6202553 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling.

Yunoki Tatsuya T Tabuchi Yoshiaki Y Hirano Tetsushi T Miwa Shigeharu S Imura Johji J Hayashi Atsushi A

Oncology letters 20180921 5

Basal cell carcinoma (BCC) is the most frequent malignant tumor of the eyelid; it progresses slowly and rarely metastasizes. However, BCC of the eyelid is partially invasive and can extend to the surrounding ocular adnexa even if appropriate treatment is performed. To understand the molecular mechanism underlying its pathogenesis, global gene expression analysis of surgical tissue samples of BCC of the eyelid (n=2) and normal human epidermal keratinocytes was performed using a GeneChip<sup>®</su ...[more]

PMID: 30405815

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Project description:Gene expression profiling has been shown to provide prognostic information on patients with solitary sporadic renal cell carcinoma. To our knowledge there is no reliable way to differentiate synchronous renal metastasis from bilateral primary tumors in patients with bilateral renal cell carcinoma. We present data using a custom kidney cancer cDNA array that can predict the outcome in patients with unilateral and bilateral renal cell carcinoma.Fresh frozen tissue from 38 clear cell renal cell carcinomas was analyzed using a cancer cDNA array containing 3,966 genes relevant to cancer or kidney development. Median followup was 5.3 years. Cancer recurred in 12 patients (43%) and 11 (39%) had died by the last followup.Using a training data set of 8 tumors a 44 gene expression profile distinguishing aggressive and indolent clear cell renal cell carcinoma was identified. Of 29 single clear cell renal cell carcinomas 16 and 13 were predicted to be indolent and aggressive, respectively, by the gene expression profile. Recurrence-free survival at 5 years was 68% and 42% in these 2 groups, respectively (p = 0.032). Clear cell renal cell carcinoma classified as indolent or aggressive according to SSIGN (stage, size, grade and necrosis) score showed a 5-year recurrence-free survival rate of 78% and 42%, respectively (p = 0.021). On Cox proportional hazards analysis the gene expression profile was not an independent predictor of recurrence-free survival after accounting for SSIGN score. Gene expression profile classification correlated with cancer specific survival at 5 years in 4 of 4 patients with metachronous clear cell renal cell carcinoma but in only 2 of 4 with bilateral synchronous clear cell renal cell carcinoma.Gene expression profiling using a kidney cancer relevant cDNA array can differentiate between aggressive and indolent clear cell renal cell carcinomas. Gene expression profile results may be most useful for unilateral clear cell renal cell carcinoma when results are discordant with predictions of tumor behavior based on standard clinicopathological features. In addition, gene expression profiling can provide prognostic information that may help characterize tumors of unknown clinical stage, such as bilateral metachronous clear cell renal cell carcinoma.

Project description:Renal cell carcinoma (RCC) is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays.Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC.Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR). Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved.This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most notably, genes involved in cell adhesion were dominantly up-regulated whereas genes involved in transport were dominantly down-regulated. This study reveals significant gene expression alterations in key biological pathways and provides potential insights into understanding the molecular mechanism of renal cell carcinogenesis.

Dataset Information

Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling.

Publications

Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling.

Similar Datasets

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