Identification of low intratumoral gene expression heterogeneity in neuroblastic tumors by genome‐wide expression analysis and game theory

Abstract

BACKGROUND.Neuroblastic tumors (NTs) are largely comprised of neuroblastic (Nb) cells with various quantities of Schwannian stromal (SS) cells. NTs show a variable genetic heterogeneity. NT gene expression profiles reported so far have not taken into account the cellular components. The authors reported the genome‐wide expression analysis of whole tumors and microdissected Nb and SS cells.METHODS.The authors analyzed gene expression profiles of 10 stroma‐poor NTs (NTs‐SP) and 9 stroma‐rich NTs (NTs‐SR) by microarray technology. Nb and SS cells were isolated by laser microdissection from NTs‐SP and NTs‐SR and probed with microarrays. Gene expression data were analyzed by the Significance Analysis of Microarrays (SAM) and Game Theory (GT) methods, the latter applied for the first time to microarray data evaluation.RESULTS.SAM identified 84 genes differentially expressed between NTs‐SP and NTs‐SR, whereas 50 were found by GT. NTs‐SP mainly express genes associated with cell replication, nervous system development, and antiapoptotic pathways, whereas NTs‐SR express genes of cell‐cell communication and apoptosis. Combining SAM and GT, the authors found 16 common genes driving the separation between NTs‐SP and NTs‐SR. Five genes overexpressed in NTs‐SP encode for nuclear proteins (CENPF, EYA1, PBK, TOP2A, TFAP2B), whereas only 1 of 11 highly expressed genes in NTs‐SR encodes for a nuclear receptor (NR4A2).CONCLUSIONS.The results showed that NT‐SP and NT‐SR gene signatures differ for a set of genes involved in distinct pathways, and the authors demonstrated a low intratumoral heterogeneity at the mRNA level in both NTs‐SP and NTs‐SR. The combination of SAM and GT methods may help to better identify gene expression profiling in NTs. Cancer 2008. © 2008 American Cancer Society.

Enhanced expression of centromere protein F predicts clinical progression and prognosis in patients with prostate cancer

“…Silencing CENPF can decrease the ability of HCC cells to proliferate, form colonies and induce tumor formation in nude mice (18). In the present study, using clinical samples, we also found that the expression of CENPF in PCa tissues was significantly higher than that in non-cancerous prostate tissues, which was consistent with the results of previous studies on other tumor types (17)(18)(19)(20)(21)(22)(23). However, we failed to find any correlation of CENPF with the clinicopathological characteristics of the patients with PCa with limited information.…”

“…The results of previous studies have demonstrated that CENPF may play a role in the regulation of cell division and may be used as proliferation marker of malignant cell growth in clinical practice due its localizations in the cell cycle (13)(14)(15)(16). Accumulating evidence has demonstrated the involvement of CENPF in various types of human cancer, such as breast cancer (17), hepatocellular carcinoma (18), colorectal gastrointestinal stromal tumors (19), nasopharyngeal carcinoma (20), non-Hodgkin's lymphoma (21), salivary gland tumors (22) and neuroblastic tumors (23). The overexpression of CENPF has also been reported to be associated with a poor prognosis in hepatocellular carcinoma, breast cancer, colorectal gastrointestinal stromal tumors and nasopharyngeal carcinoma (17)(18)(19)(20).…”

Role of CXCL13-CXCR5 Crosstalk Between Malignant Neuroblastoma Cells and Schwannian Stromal Cells in Neuroblastic Tumors

“…Recently, we studied a series of neuroblastic tumors by gene-expression profiling analysis and we observed different levels of CXCL13 transcripts in microdissected neuroblastic cells with respect to Schwannian stromal cells (5,8). Our results showed that this chemokine was more expressed in stromal cells than in malignant neuroblasts, suggesting a functional role of CXCL13 in the interaction between stroma and neuroblastic cells.…”

“…Isolation of neuroblastic and Schwannian stromal cells by laser capture microdissection and total RNA isolation About 800 cells were laser microdissected from 3 SP and 3 SR frozen tumors to obtain pure cell populations of neuroblastic cells and Schwannian stromal cells, as previously described (8). Total RNA from laser capture microdissection-derived material was extracted by PicoPure RNA isolation kit (Arcturus Engineering), including a DNase treatment, RNA quality control and quantification whereas conducted by RNA 6000 Pico LabChip kit and the 2100 BioAnalyzer instrument (Agilent Technologies).…”

Age‐dependent accumulation of genomic aberrations and deregulation of cell cycle and telomerase genes in metastatic neuroblastoma

“…Total proteins were extracted from four available samples belonging to each group (G1; G2; G3/MYCNþ; G3/MYCNÀ) and subjected to SDS-PAGE and Western blot analysis as previously described 30 using the following antibodies: mouse monoclonal anti-GRB2 (clone 372), anti-RAD18, anti-TERT (clone 2C4; Millipore, Billerica, MA); rabbit polyclonal anti-CDC42 (Sigma Aldrich, St. Louis, MO) and alpha-tubulin (Cell Signaling Technologies, Boston, MA) as control.…”