Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Surface proteoglycans expressions in oral squamous cell carcinoma

ABSTRACT: In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2, were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells In situ distributional analysis of these PGs on a total of 149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs. A total of 166 surgical specimens of primary SCCOC were collected after informed consent from individuals who underwent surgical removal of the tumor lesions and RNA from 119 surgical specimens were extracted; a pool of RNAs extracted from 5 normal epithelia tissues was adopted as a sample calibrator (HEALTHY sample). cDNA from each samples and from pool of normal epithelial were loaded on TLDA and amplified. HEALTHY sample were amplified 20 times in two replicates (in each TLDA card); each patient sample were amplified 1 time in two replicates and 7 samples of them were loaded two times in a separate TLDA card (for a total of 4 replicates).

ORGANISM(S): Homo sapiens

SUBMITTER: Silvia Rossi

PROVIDER: E-GEOD-33788 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A comprehensive expression analysis of Wnt signaling genes was performed in a panel of prostate cancer cell lines and tissue specimens using TaqMan low density arrays. The effect of DNA methylation on gene expression was investigated using DNMT inhibitor 5-Aza-CdR. Tissue specimens from a range of disease states were used to represent the stepwise progression of prostate cancer, including benign prostatic hyperplasia (BPH), histologically benign epithelium adjacent to tumor (HB), pre-invasive high-grade prostatic intraepithelial neoplasia (HGPIN) and primary localized tumors categorized into low- and high-grade disease. Fifteen Wnt signaling related genes were idenified with significantly altered expression in prostate cancer; the majority of which were upregulated in tumors. Notably, histologically benign tissue from men with prostate cancer appeared more similar to tumour (r=0.76) than to BPH (r=0.57) (P<0.001). Overall, the expression profile was highly similar between tumors of high (M-bM-^IM-%7) and low (M-bM-^IM-$6) Gleason scores. Pharmacological demethylation of PC-3 cells reactivated 38 genes (M-bM-^IM-%2-fold); 40% of which inhibit Wnt signaling. qPCR gene expression profiling using TLDA Human Wnt Gene set v1.0 microfluidic card (Applied Biosystems, Foster City, CA).The TLDA consisted of 4 identical 96-gene sets preconfigured in a 384-well format. Three different malignant cell lines were profiled LNCaP, 22Rv1 and PC3 (+/- 5-Aza-2M-bM-^@M-^YDeoxycytidine). One benign cell line was included for comparative puposes: PWR1E. Patient samples were obtained from FFPE tissue sections from men who underwent radical prostatectomy or transrectal resection of the prostate. To overcome the limited amount of RNA obtained from FFPE tissues, RNA samples were pooled. Five different pools were generated: high grade prostate cancer (Gleason score M-bM-^IM-%7), low grade prostate cancer (Gleason score M-bM-^IM-$6), HGPIN, HB and BPH. Each pool consisted of DNase-treated total RNA (100ng), isolated from microdissected tissue from 4 individual cases, selected on the basis of similar histological and clinical features and previous epigenetic characterization in our laboratory. Two Biological replicates for each pool were prepared. The high capacity cDNA Archive Kit (Applied Biosystems) was used to reverse transcribe pooled RNA (400ng). TaqManM-BM-. reactions were performed in duplicate on a 7900HT Sequence Detection System. RQ data from TLDAs were analyzed using Real Time StatMinerM-BM-. v3.1 (Integromics, Granada, Spain).

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Surface proteoglycans expressions in oral squamous cell carcinoma

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