Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer

Abstract

Context: Attempts to determine the clinical significance of BRCA1/2 mutations in ovarian cancer have produced conflicting results.

Objective: To determine the relationships between BRCA1/2 deficiency (ie, mutation and promoter hypermethylation) and overall survival (OS), progression-free survival (PFS), chemotherapy response, and whole-exome mutation rate in ovarian cancer.

Design, setting, and patients: Observational study of multidimensional genomics and clinical data on 316 high-grade serous ovarian cancer cases that were made public between 2009 and 2010 via The Cancer Genome Atlas project.

Main outcome measures: OS and PFS rates (primary outcomes) and chemotherapy response (secondary outcome).

Results: BRCA2 mutations (29 cases) were associated with significantly better OS (adjusted hazard ratio [HR], 0.33; 95% CI, 0.16-0.69; P = .003 and 5-year OS, 61% for BRCA2-mutated vs 25% for BRCA wild-type cases) and PFS (adjusted HR, 0.40; 95% CI, 0.22-0.74; P = .004 and 3-year PFS, 44% for BRCA2-mutated vs 16% for BRCA wild-type cases), whereas neither BRCA1 mutations (37 cases) nor BRCA1 methylation (33 cases) was associated with prognosis. Moreover, BRCA2 mutations were associated with a significantly higher primary chemotherapy sensitivity rate (100% for BRCA2-mutated vs 82% [P = .02] and 80% [P = .05] for BRCA wild-type and BRCA1-mutated cases, respectively) and longer platinum-free duration (median platinum-free duration, 18.0 months for BRCA2-mutated vs 11.7 [P = .02] and 12.5 [P = .04] months for BRCA wild-type and BRCA1-mutated cases, respectively). BRCA2-mutated, but not BRCA1-mutated cases, exhibited a "mutator phenotype" by containing significantly more mutations than BRCA wild-type cases across the whole exome (median mutation number per sample, 84 for BRCA2-mutated vs 52 for BRCA wild-type cases, false discovery rate <0.1).

Conclusion: Among women with high-grade serous ovarian cancer, BRCA2 mutation, but not BRCA1 deficiency, was associated with improved survival, improved chemotherapy response, and genome instability compared with BRCA wild-type.

Figure 1. BRCA1/2 mutations and their association with age at diagnosis in 316 OvCa cases

A, B. Germ-line and somatic mutations in BRCA1 and BRCA2, respectively. Mutations are mapped to the corresponding exons of BRCA1 and BRCA2. Red: germ-line mutation; green: somatic mutation. Twelve BRCA1 germ-line mutations corresponded to the well-known founder mutations 185/187delAG and 5382/5385insC (indicated by arrowheads in A); five BRCA2 germ-line mutations corresponded to the well-known founder mutation 6174delT (indicated by the arrowhead in B). C. Scatter plot indicates the distribution of age at diagnosis of patients with different BRCA statuses. The P values are calculated by Wilcoxon rank-sum test. Abbreviations: wt, wild-type; mt, mutation.

Figure 2. Association of BRCA1/2 mutations with survival and chemotherapy responses

A, B. Kaplan-Meier survival curves for OS and PFS durations of BRCA1-mutated, BRCA2- mutated, and wt BRCA OvCa cases. The percent probability of survival is plotted versus time since diagnosis in months. C. Bar chart indicates the distribution of primary chemotherapy sensitivity in BRCA1-, BRCA2-mutated, and wt BRCA OvCa cases. The P values are calculated by two-tailed Fisher’s exact test. D. Kaplan-Meier survival curves for platinum-free duration of BRCA1, BRCA2, and wt BRCA OvCa cases. The percent probability of survival is plotted versus time since the end of adjuvant therapy.

Figure 3. Association of BRCA1/2 mutations with genome instability

Enrichment Score (ES) test (detailed in Methods) of hypermutated sample enrichment in BRCA1- and BRCA2-mutated cases. The bottom portion of the plot shows the total numbers of non-synonymous mutations of 316 decreasingly ranked OvCa cases. The height of each blue discrete line indicates the number of non-synonymous mutations in each OvCa case. The middle portion of the plot shows where the samples with BRCA1 (green bar) or BRCA2 (red bar) mutations appear in the ranked list of samples in the bottom portion. The top portion of the plot shows the running ES for the BRCA1- or BRCA2-mutated cases.

Figure 4. Heatmap indicates the mutation landscape of BRCA1-, BRCA2-mutated, and wt BRCA cases

Sixty-one differentially mutated genes between BRCA2-mutated and wt BRCA cases are arranged in rows; samples are in columns. Yellow: mutation. Blue: non-mutation. Each sample is also labeled as described in the top color bar for BRCA mutation status (green: BRCA1 mutation; red: BRCA2 mutation; blue: wt BRCA), tumor grade, clinical stage, and primary chemotherapy response status.

Figure 5. Hypermethylation of BRCA1 promoter in 316 OvCa cases

A. Locations of BRCA1 CpG islands and methylation microarray probes. The GC percentage (top panel), CpG island (blue), and six probes (red bars) annotated to BRCA1 in an Illumina Infinium DNA methylation microarray were visualized using the University of California Santa Cruz (UCSC) genome browser. The GC percentage track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. Three other probes (see Methods) annotated to BRCA1 are not shown here because they were too far away from the BRCA1 transcription start site (TSS). B. Heatmap shows the DNA methylation of BRCA1 promoter across 316 cases. Four probes located in the promoter CpG island of BRCA1 are arranged in columns. Three hundred sixteen OvCa and eight normal samples are arranged in rows. Red: hypermethylation; blue: hypomethylation. The color bar to the right of the heatmap indicates BRCA1 status: red: BRCA1-hypermethylated OvCa; green: BRCA1 somatically mutated OvCa; yellow: BRCA1 germ-line-mutated OvCa; blue: wt BRCA1 OvCa (excluding the hypermethylated cases); black: normal tissue. C. BRCA1 mRNA expression in different status groups. OvCa cases are grouped by BRCA1 deficiency type, as shown along the right side of Figure 5B. Each data point represents the BRCA1 mRNA expression level (x axis) in the tumor of the corresponding group. Red data points: BRCA1 hypermethylated OvCa; green data points: BRCA1 somatically mutated OvCa; yellow data points: BRCA1 germ-line mutated OvCa; blue data points: wt BRCA1 OvCa; black data points: normal tissue. The box plots indicate the minimum, lower quartile, median, upper quartile, and maximum for each group.