Diverse LEF/TCF Expression in Human Colorectal Cancer Correlates with Altered Wnt-Regulated Transcriptome in a Meta-Analysis of Patient Biopsies

Abstract

Aberrantly activated Wnt signaling causes cellular transformation that can lead to human colorectal cancer. Wnt signaling is mediated by Lymphoid Enhancer Factor/T-Cell Factor (LEF/TCF) DNA-binding factors. Here we investigate whether altered LEF/TCF expression is conserved in human colorectal tumor sample and may potentially be correlated with indicators of cancer progression. We carried out a meta-analysis of carefully selected publicly available gene expression data sets with paired tumor biopsy and adjacent matched normal tissues from colorectal cancer patients. Our meta-analysis confirms that among the four human LEF/TCF genes, LEF1 and TCF7 are preferentially expressed in tumor biopsies, while TCF7L2 and TCF7L1 in normal control tissue. We also confirm positive correlation of LEF1 and TCF7 expression with hallmarks of active Wnt signaling (i.e., AXIN2 and LGR5). We are able to correlate differential LEF/TCF gene expression with distinct transcriptomes associated with cell adhesion, extracellular matrix organization, and Wnt receptor feedback regulation. We demonstrate here in human colorectal tumor sample correlation of altered LEF/TCF gene expression with quantitatively and qualitatively different transcriptomes, suggesting LEF/TCF-specific transcriptional regulation of Wnt target genes relevant for cancer progression and survival. This bioinformatics analysis provides a foundation for future more detailed, functional, and molecular analyses aimed at dissecting such functional differences.

Keywords: LEF; TCF; Wnt; colorectal cancer; transcriptome.

Figure 1

Forest plots of gene expression of all four LEF/TCF genes (A): TCF7, (B): LEF1, (C): TCF7L1, (D): TCF7L2, and (E): AXIN2, (F): DICKKOPF-1 (DKK1), (G): FZD7, and (H): LGR5, from six selected studies. Columns from left to right indicate: accession no. of study (with GSE20842 [27] separated between kras-positive and kras-mutant samples); number of patients in individual studies; horizontal segments indicate the standardized mean difference between tumor and normal, and their confidence interval, with the size of the square dot being proportional with the weight of the study in the meta-analysis using a ‘random effects’ model. The corresponding values are written in the column on the right: weight of the individual study in percent as part of the meta-analysis; standardized mean difference; and in square brackets confidence interval. The red polygon in the bottom of each plot shows the summary estimate based on the random-effect model. Values to the left of the midline indicated higher expression in the control relative to the tumor sample, e.g., see AXIN2 and LGR5. Individual studies with small sample size (i.e., few patients) as expected often have larger confidence intervals (therefore less reliability, e.g., see TCF7 and LEF1 data for GSE46622 study), but in the meta-analysis (in red) much tighter confidence intervals (therefore higher reliability). Note that, among the four LEF/TCF genes, TCF7, LEF1, are expressed higher, while TCF7L1, TCF7L2 lower in tumor tissue.

Figure 2

Correlation plot matrix of relative gene expression between eight selected genes in six selected studies (A–N), with normal control (A, C, E, G, I, K, M) separated from tumor sample (B, D, F, H, J, L, N), and additionally for the GSE20842 [27] between kras-mutant (“mut”) samples (C, D) and kras-positive (“wild” as in wildtype) samples (E, F). Blue dots indicate positive and red dots negative correlation. The size of the circle and the intensity of the color is proportional to the correlation coefficient; therefore, as an internal control, expected diagonal series of large blue dots where expression of genes is compared to the expression of the same gene). Missing values in GSE46622 [30] is due to low value data for LEF1 in this study. Note positive correlation between AXIN2 expression and LGR5, TCF7 and LEF1 expression, yet negative correlation with TCF7L1 expression, while TCF7L1 and FZD7 expression are positively correlated, though clearly much more so in normal control tissue than in tumor. In contrast, the correlation between AXIN2 and TCF7 expression is clearly more robust in tumor compared to normal tissue. Interestingly, the unearthed correlation between TCF7L1 and FZD7 expression appears to be dependent on wild-type kRAS in the tumor (compare D with F, yet not in normal control C).

Figure 3

Correlation of transcript expression between eight selected genes (TCF7, LEF1, TCF7L1, TCF7L2, AXIN2, DKK1, FZD7 and LGR5) in normal control tissue (A), in tumor tissue (B), and when analyzed combined in normal and tumor tissue (C) (negative numbers and graded red highlighting indicates negative correlation; positive numbers and graded green highlighting positive correlation). (D) Mean difference between normal and tumor tissue of correlation of transcript expression between eight selected genes (red highlighting with positive numbers indicates reduced negative correlation in tumor tissue; green highlighting with negative numbers indicates reduced, with positive numbers increased, positive correlation in tumor tissue; yellow highlighting with positive numbers indicates a switch from negative to positive, and with negative numbers to negative, correlation in tumor tissue. Note generally reduced correlations in tumor tissue; particularly note, reduced positive correlation between TCF7 and LEF1, between TCF7 and LGR5, and between TCF7L1 and FZD7 expression; and reduced negative correlation between AXIN2 and TCF7L1 expression. However, also note exceptional increased positive correlation between AXIN2 and TCF7 in tumor tissue.