Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: Association of FOXP1 expression levels with prognostic markers and patient outcome in 476 neuroblastomas as determined by microarray analysis. Association of (a) tumor stage, (b) age at diagnosis, (c) MYCN amplification status and (d) gene expression-based classification (PAM classifier) with FOXP1 transcript levels. Boxes, median expression values (horizontal line) and 25th and 75th percentiles; whiskers, distances from the end of the box to the largest and smallest observed values that are less than 1.5 box lengths from either end of the box; open circles, outlying values. Survival curves of neuroblastoma patients for (e) EFS and (f) OS according to FOXP1 expression as determined by microarray analysis. N, patient numbers; amp, amplified; fav, favorable; unfav, unfavorable.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing, Microarray, Biomarker Discovery, Amplification, Gene Expression

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: Multivariate Cox regression models based on EFS and OS, considering single prognostic markers and FOXP1 expression

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing, Amplification

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: Hierarchical clustering of FOXP1 DNA methylation ratios. A total of 45 CpG units of FOXP1 were analyzed in 47 tumor samples and the neuroblastoma cell line IMR-32 (indicated in red). FOXP1 expression levels of the tumors (blue, low; green, high; as defined by the expression cutoff value for dichotomizing patient EFS) are indicated aside. DNA methylation values are indicated by colors ranging from dark red (non-methylated) to bright yellow (65% methylated). Poor quality data are indicated in grey. A histogram is given in the inset that indicates the frequency of each color in the hierarchical clustering.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: DNA Methylation Assay, Expressing, Methylation

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 mRNA expression intensities of 159 tumors for which array-CGH data were available. Green and blue represent high and low FOXP1 expression as defined by the expression cutoff value for dichotomizing patient EFS. Tumors showing loss of the FOXP1 locus at 3p14.1 are indicated in red.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: Inducible expression of FoxP1 in neuroblastoma cell lines and physiological FoxP1 levels in primary neuroblastomas. (a) Inducible FoxP1 protein expression in FOXP1 - versus GFP -expressing neuroblastoma cell lines 48 h after induction of transgene expression. (b) Physiological FoxP1 protein levels in primary tumors; FOXP1 transcript levels are indicated as log intensities (microarray data).

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing, Microarray

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 re-expression inhibits growth of neuroblastoma cells. FoxP1-induced changes in (a) cell viability (Trypan Blue dye exclusion analysis 6 days after induction of transgene expression), (b) cell proliferation (Alamar Blue assay 6 days after induction of transgene expression), (c) the proportion of cells showing apoptotic nuclei (72 h after induction of transgene expression), (d) the proportion of Annexin-V-positive cells (fluorescence-activated cell sorting (FACS)) and (e) cell cycle distribution (FACS). Each value represents the mean of triplicate experiments; error bars indicate S.D.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing, Alamar Blue Assay, Fluorescence, FACS

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 attenuates the malignant phenotype of neuroblastoma cells. (a) Soft agar colony formation assay of FOXP1 - versus GFP -expressing control cells. Cells were cultured in soft agar for 15 days. (b) Boyden chamber migration assay of FOXP1 - versus GFP -expressing control cells. Cells were seeded in Boyden chambers and incubated for 6 days. (c) Gap closure assay of FOXP1 - versus GFP -expressing control cells. Images were captured at the indicated time points. Each value represents the mean of triplicate experiments; error bars indicate S.D. d, days; no., number.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Soft Agar Assay, Expressing, Control, Cell Culture, Migration, Incubation

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 induces genes involved in apoptosis. Gene set enrichment analysis (GSEA) of time-resolved gene expression measurements in FoxP1-induced neuroblastoma cells. Cells were analyzed 0, 12, 24 and 72 hours after transgene induction. The enrichment score (ES) plotted as a function of the position within the ranked list of array probes is shown as a green line. The ranked list metric shown in gray illustrates the correlation of the gene expression values across the time series. Right, individual expression profiles for time leading edge probe sets contributing to the normalized enrichment score are shown. Signal intensities are illustrated by varying shades of red (up-regulation) and blue (down-regulation). FoxP1 up-regulates pro-apoptotic genes in (a) IMR-32 and (b) CHP-212 cells as compared to GFP -expressing controls. (c) Recombinant FOXP1 fails to induce pro-apoptotic genes in the p53 mutant cell line SK-N-BE(2).

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Gene Expression, Expressing, Recombinant, Mutagenesis

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 down-regulates genes involved in migration. Gene set enrichment analysis (GSEA) of time-resolved gene expression measurements in FoxP1-induced neuroblastoma cells. Cells were analyzed 0, 12, 24 and 72 hours after transgene induction. The enrichment score (ES) plotted as a function of the position within the ranked list of array probes is shown as a green line. The ranked list metric shown in gray illustrates the correlation of the gene expression values across the time series. Right, individual expression profiles for time leading edge probe sets contributing to the normalized enrichment score are shown. Signal intensities are illustrated by varying shades of red (up-regulation) and blue (down-regulation). FoxP1 decreases the expression of genes involved in migration processes in (a) IMR-32, (b) CHP-212 and (c) SK-N-BE (2) cells as compared to GFP -expressing controls.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Migration, Gene Expression, Expressing

Journal: BMC Cancer

Article Title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

doi: 10.1186/1471-2407-14-840

Figure Lengend Snippet: FOXP1 induces genes involved in neuronal differentiation. FOXP1 expression up-regulates neuron-related markers in (a) IMR-32 and (b) CHP-212 cells as determined by microarray gene expression analysis. Error bars indicate S.D.

Article Snippet: FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [ , ].

Techniques: Expressing, Microarray, Gene Expression