Monosomy of chromosome 10 associated with dysregulation of epidermal growth factor signaling in glioblastomas

Abstract

Context: Glioblastomas--uniformly fatal brain tumors--often have both monosomy of chromosome 10 and gains of the epidermal growth factor receptor (EGFR) gene locus on chromosome 7, an association for which the mechanism is poorly understood.

Objectives: To assess whether coselection of EGFR gains on 7p12 and monosomy 10 in glioblastomas promotes tumorigenic epidermal growth factor (EGF) signaling through loss of the annexin A7 (ANXA7) gene on 10q21.1-q21.2 and whether ANXA7 acts as a tumor suppressor gene by regulating EGFR in glioblastomas.

Design, setting, and patients: Multidimensional analysis of gene, coding sequence, promoter methylation, messenger RNA (mRNA) transcript, protein data for ANXA7 (and EGFR), and clinical patient data profiles of 543 high-grade gliomas from US medical centers and The Cancer Genome Atlas pilot project (made public 2006-2008; and unpublished, tumors collected 2001-2008). Functional analyses using LN229 and U87 glioblastoma cells.

Main outcome measures: Associations among ANXA7 gene dosage, coding sequence, promoter methylation, mRNA transcript, and protein expression. Effect of ANXA7 haploinsufficiency on EGFR signaling and patient survival. Joint effects of loss of ANXA7 and gain of EGFR expression on tumorigenesis.

Results: Heterozygous ANXA7 gene deletion is associated with significant loss of ANXA7 mRNA transcript expression (P = 1 x 10(-15); linear regression) and a reduction (mean [SEM]) of 91.5% (2.3%) of ANXA7 protein expression compared with ANXA7 wild-type glioblastomas (P = .004; unpaired t test). ANXA7 loss of function stabilizes the EGFR protein (72%-744% increase in EGFR protein abundance) and augments EGFR transforming signaling in glioblastoma cells. ANXA7 haploinsufficiency doubles tumorigenic potential of glioblastoma cells, and combined ANXA7 knockdown and EGFR overexpression promotes tumorigenicity synergistically. The heterozygous loss of ANXA7 in approximately 75% of glioblastomas in the The Cancer Genome Atlas plus infrequency of ANXA7 mutation (approximately 6% of tumors) indicates its role as a haploinsufficiency gene. ANXA7 mRNA transcript expression, dichotomized at the median, associates with patient survival in 191 glioblastomas (log-rank P = .008; hazard ratio [HR], 0.667; 95% confidence interval [CI], 0.493-0.902; 46.9 vs 74.8 deaths/100 person-years for high vs low ANXA7 mRNA expression) and with a separate group of 180 high-grade gliomas (log-rank P = .00003; HR, 0.476; 95% CI, 0.333-0.680; 21.8 vs 50.0 deaths/100 person-years for high vs low ANXA7 mRNA expression). Deletion of the ANXA7 gene associates with poor patient survival in 189 glioblastomas (log-rank P = .042; HR, 0.686; 95% CI, 0.476-0.989; 54.0 vs 80.1 deaths/100 person-years for wild-type ANXA7 vs ANXA7 deletion).

Conclusion: Haploinsufficiency of the tumor suppressor ANXA7 due to monosomy of chromosome 10 provides a clinically relevant mechanism to augment EGFR signaling in glioblastomas beyond that resulting from amplification of the EGFR gene.

Figure 1. Relationship Between the ANXA7 and EGFR Genes (193 Tumors)

A, Gene dosage relationship for annexin A7 (ANXA7) and epidermal growth factor receptor (EGFR) in glioblastomas from The Cancer Genome Atlas (TCGA) pilot project. Analysis included 193 of 219 TCGA samples for which all EGFR probes on the Agilent aCGH array yielded consistent amplification or wild-type (wt) calls. Scatterplot shows the relationship between EGFR and ANXA7 gene dosage along the Cartesian coordinates for each of the 193 tumors. Gene dosage values indicate the log₂ ratio of red-to-green fluorescence dye intensity (log₂R/G) estimated by the circular binary segmentation algorithm. Negative gene dosage indicates lower gene dosage compared with that observed for the majority of the samples, ie, lower gene dosage compared with a normal diploid state. Boxplots depict the first quartile minus 1.5 × interquartile range (IQR) (left whiskers) and the third quartile plus 1.5 × IQR (right whiskers), IQR (box), and median (vertical line); 1 observation outside the whiskers indicates an outlier. Wilcoxon rank-sum testing for the difference in ANXA7 gene dosage in EGFR-amplified (ampl) vs wild-type tumors discloses a significantly diminished ANXA7 gene dosage in the EGFR-amplified tumors (P=.000000001). B, Representative fluorescence in situ hybridization analysis of EGFR gene dosage in 1 ANXA7–wild-type and 1 ANXA7-deleted (del) glioblastoma, from the Stanford set of tumors, on paraffin. Red dots (Spectrum Orange dye) are specific for the EGFR gene locus probe and green dots (Spectrum Green dye) arise from a probe specific for the centromeric region of chromosome 7. The ANXA7–wild-type tumor is nonamplified for EGFR gene dosage with most cells showing normal diploid levels of 2 red and 2 green signals per cell, while the ANXA7-deleted tumor is amplified for EGFR gene dosage as the cells show a robust increase in the number of EGFR red dots. Additionally, the ANXA7-deleted tumor is polyploidic for chromosome 7 as there are more than 2 green dots (centromere of chromosome 7) in most cells (original magnification ×40).

Figure 2. ANXA7 Gene–mRNA Transcript Expression Relationship (175 Tumors)

Relationship between the annexin A7 (ANXA7) gene and ANXA7 mRNA transcript in 175 glioblastomas from The Cancer Genome Atlas with combined availability of gene dosage and expression data for ANXA7. Gene dosage and mRNA expression values are expressed as ratios of red-to-green fluorescence dye intensity (log₂R/G) estimated by circular binary segmentation and robust multigene average preprocessing algorithms, respectively. Linear regression of gene expression on gene dosage confirms a significant gene dosage effect on transcription for ANXA7 in 174 tumors (1 outlier excluded) (P=1×10⁻¹⁵). Locally weighted least squares (LOWESS) smooth fit confirmed the appropriateness of a linear regression analysis.

Figure 3. ANXA7 Gene-Protein Relationship

A, Annexin A7 (ANXA7) protein abundance by proximity ligation assay on paraffin as percentage of protein abundance relative to the population median (horizontal dotted line). The 2 left boxplots compare the ANXA7 protein profiles of 12 glioblastomas from Stanford University (6 ANXA7–wild-type vs 6 ANXA7-deleted tumors); right boxplot reports the ANXA7 protein profiles of 24 high-grade gliomas with unknown ANXA7 gene status from Northwestern University. Boxplots depict the first quartile minus 1.5 × interquartile range (IQR) (lower whiskers) and the third quartile plus 1.5 × IQR (upper whiskers), IQR (box), and median (horizontal line). B, Images of proximity ligation assay demonstrate the range of ANXA7 protein expression in a set of glioblastomas from Stanford University. Left, tumor with highest ANXA7 abundance has ANXA7–wild-type (wt) status; right, tumor with lowest ANXA7 abundance is ANXA7-deleted (del). Proximity ligation assay signals captured by Texas Red and nuclear counterstaining by Hoechst 33342. Arrowheads indicate single ANXA7 proteins (original magnification ×200).

Figure 4. ANXA7 Promoter Methylation Analysis and ANXA7 Promoter-Gene–mRNA Transcript Relationship

A, Pyrosequencing was used to assess the methylation percentage of 9 CpG sites close to the transcriptional start site within the annexin A7 (ANXA7) promoter in 59 human gliomas from Stanford University and various control cells. Bars indicate the overall promoter methylation profile per sample by averaging the methylation profiles of all 9 CpG sites; error bars indicate SD. Horizontal dotted line denotes the average methylation percentage across all samples. Tumors showing deletion of the ANXA7 gene indicated by arrows. Bar colors denote histological subtypes of gliomas. Dark blue coloration of bars for LN229, U118, and U87 cells indicates their origin from glioblastoma tumors. Green bars denote cells with stem cell–like phenotype; brown bars, normal brain tissue and normal brain cells. B, Linear regression of ANXA7 mRNA expression on ANXA7 promoter methylation in 45 of the 59 Stanford University tumors profiled in panel A; availability of corresponding ANXA7 gene expression data reveals no significant relationship (P=.627). The mRNA transcript expression values indicate the log₂ ratio of red-to-green fluorescence dye intensity (log₂R/G) and are normalized to the median ANXA7 gene expression of all tumors. Locally weighted least squares (LOWESS) smooth fit confirmed the appropriateness of a linear regression analysis. C, Similar linear regression of mRNA transcript expression on gene dosage in the same 45 tumors confirms a significant gene–mRNA transcript relationship for ANXA7 (P=.0005). Gene dosage values are expressed as log₂R/G ratios estimated by the circular binary segmentation algorithm. Negative gene dosage indicates lower gene dosage compared with that observed for the majority of the samples, ie, lower gene dosage compared with a normal diploid state.

Figure 5. ANXA7 Knockdown and EGFR Protein Abundance and EGFR Signaling

A, Knockdown of annexin A7 (ANXA7)—mimicking a hemizygous gene loss and thus haploinsufficiency—via ANXA7-targeting short hairpin RNA (shRNA) (shANXA7) using transient plasmid-based transfection (LN229) or stable, retroviral transduction (U87) increases epidermal growth factor receptor (EGFR) protein abundance compared with cells transfected with empty backbone control vector (EV) only, as assessed by immunoblotting. The α-tubulin protein was used as a loading control. Displayed blots are representative of multiple experiments. B, Total and phosphospecific EGFR, AKT, and ERK1/2 protein abundance in U87-shANXA7 vs U87-EV cells based on immunoblotting. Sustained EGFR autophosphorylation at Tyr 1086 (Y1086) and increased and sustained activating phosphorylation of AKT at Ser473 (S473) and ERK1/2 at Thr202/Tyr204 (T202/Y204) in shANXA7 compared with EV cells.

Figure 6. ANXA7 Knockdown and EGFR mRNA Transcript Expression

EGFR (epidermal growth factor receptor) mRNA transcript expression based on quantitative real-time polymerase chain reaction in LN229-EV vs LN229-shANXA7 cells (P=.0015) and in U87-EV vs U87-shANXA7 cells (P=.0002). ANXA7 knockdown results in a moderate though significant increase in EGFR mRNA transcript expression in both cell lines. Error bars denote standard error of the mean. P values according to unpaired t test.

Figure 7. ANXA7 Knockdown and EGFR Gene Dosage

Fluorescent in situ hybridization analysis detecting the EGFR (epidermal growth factor receptor) gene (red dots, Spectrum Orange dye) and the centromere of chromosome 7 (green dots, Spectrum Green dye) in LN229-EV vs LN229-shANXA7 cells and in U87-EV vs U87-shANXA7 cells. Images show representative gene dosage profiles in single cells. LN229 is tetraploid both for EGFR gene dosage and chromosome 7 with 4 red/green pairs in the nucleus (nuclear counterstaining using Hoechst 33342 stain [blue]). U87 is diploid both for EGFR gene dosage and chromosome 7 with 2 red/green pairs. Both cell lines show no change in EGFR gene dosage on ANXA7 knockdown. The equal number of EGFR-specific and centromeric signals indicates the absence of extrachromosomal EGFR gene dosage in double minute chromosomes, small fragments of extrachromosomal DNA, and potential cytogenetic equivalents of EGFR amplification that contain no centromere (original magnification ×100). ANXA7 indicates annexin A7.

Figure 8. ANXA7 Knockdown and Colony-Forming Activity

Significantly increased colony-forming activity of shANXA7 cells compared with EV cells (EV is reference) (LN229-shANXA7 vs LN229-EV: P=.0009; U87-shANXA7 vs U87-EV: P = .0003) and of shANXA7/EGFR+ cells compared with shANXA7 cells (LN229-shANXA7/EGFR+ vs LN229-shANXA7: P = .0002; U87-shANXA7/EGFR+ vs U87-shANXA7: P=.001). Error bars denote standard error of the mean colony number of multiple experiments (colony-forming activity also assessed in EV cells). P values according to unpaired t test. ANXA7 indicates annexin A7; EGFR, epidermal growth factor receptor.

Figure 9. Association of ANXA7 and Survival of Patients With Malignant Glioma

Kaplan-Meier estimates of overall survival in various glioblastoma/high-grade glioma populations according to annexin A7 (ANXA7) mRNA transcript expression or ANXA7 gene dosage. A, Survival estimates in 191 glioblastomas stratified into 2 classes based on median ANXA7 mRNA transcript abundance. Median follow-up for the groups of patients with high and low ANXA7 mRNA transcript expression was 70 weeks (range, 1.4–479) and 51.1 weeks (range, 1.0–310.1), respectively. B, Survival estimates in 180 high-grade gliomas stratified according to median ANXA7 mRNA transcript abundance. Median follow-up for the groups of patients with high and low ANXA7 mRNA transcript expression was 118 weeks (range, 0.1–492) and 57.0 weeks (range, 1.0–467.0), respectively. C, Survival estimates in 189 glioblastomas with available survival data from The Cancer Genome Atlas (TCGA) project analyzed for ANXA7 gene dosage and stratified according to ANXA7–wild-type (wt) vs ANXA7-deleted (del) status based on circular binary segmentation. Median follow-up for the groups of patients with ANXA7–wild-type and ANXA7-deleted status was 53.9 weeks (range, 1.1–503.4) and 50.8 weeks (range, 2.0–307.4), respectively. (D) Survival estimates in the same 189 TCGA glioblastomas grouped into 1 subgroup with ANXA7–wild-type status, and ANXA7-deleted tumors grouped into 2 equally sized subgroups of tumors with low-level (low loss) and high-level (high loss) gene dosage loss based on median gene dosage. Median follow-up was 53.9 weeks (range, 1.1–503.4), 52.9 weeks (range, 2.0–307.4), and 46.7 weeks (range, 2.9–300.6) for the ANXA7–wild-type, low-level and high-level ANXA7 loss groups, respectively.