Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

Abstract

Background: Patients diagnosed with high-grade serous ovarian cancer (HGSOC) who received initial debulking surgery followed by platinum-based chemotherapy can experience highly variable clinical responses. A small percentage of women experience exceptional long-term survival (long term (LT), 10+ years), while others develop primary resistance to therapy and succumb to disease in less than 2 years (short term (ST)). To improve clinical management of HGSOC, there is a need to better characterize clinical and molecular profiles to identify factors that underpin these disparate survival responses.

Methods: To identify clinical and tumor molecular biomarkers associated with exceptional clinical response or resistance, we conducted an integrated clinical, exome, and transcriptome analysis of 41 primary tumors from LT (n = 20) and ST (n = 21) HGSOC patients.

Results: Younger age at diagnosis, no residual disease post debulking surgery and low CA125 levels following surgery and chemotherapy were clinical characteristics of LT. Tumors from LT survivors had increased somatic mutation burden (median 1.62 vs. 1.22 non-synonymous mutations/Mbp), frequent BRCA1/2 biallelic inactivation through mutation and loss of heterozygosity, and enrichment of activated CD4+, CD8+ T cells, and effector memory CD4+ T cells. Characteristics of ST survival included focal copy number gain of CCNE1, lack of BRCA mutation signature, low homologous recombination deficiency scores, and the presence of ESR1-CCDC170 gene fusion.

Conclusions: Our findings suggest that exceptional long- or short-term survival is determined by a concert of clinical, molecular, and microenvironment factors.

Keywords: Immuno-genomics; Ovarian cancer; Tumor microenvironment.

Fig. 1

Somatic mutation burden of high-grade serous ovarian cancer exceptional short and long survivors. a Comparison of non-synonymous somatic mutation burden between exceptional short-term (n = 19) and long-term (n = 20) HGSOC survivor cohorts in this study. b Comparison of somatic mutation burden between exceptional short-term (n = 40) and long-term (n = 8) HGSOC survivor cohorts selected from the TCGA ovarian serous cystadenocarcinoma study. Non-synonymous mutation burden for each individual in each group is shown in increasing order. Data points are colored by group, short-term in orange, long-term in purple, and others in black. Boxplot for each group shows the group summary statistics for each survival group. Statistical significance is tested by non-parametric 2-sided Wilcoxon rank test for non-paired data and raw p value is reported. For TCGA, only difference between short- and long-term survivors is assessed

Fig. 2

Landscape of genomic alterations in exceptional long- and short-term survivors of HGSOC. Summary of selected clinical and measured molecular characteristics by whole exome sequencing is shown for each primary tumor in the research cohort ordered by survival cohort and increasing somatic mutation burden. Mutations in genes found to be significantly recurrently mutated in HGSOC from the TCGA study are shown, with color for each alteration type illustrated in the legend

Fig. 3

Mutation burden in BRCA1- and BRCA2-mutated HGSOC. a Comparison of somatic mutation burden between wild-type (no mutations detected, n = 27), BRCA1 (n = 7), and BRCA2 (n = 7)-mutated (germline and somatic) HGSOC in our study. b Comparison of somatic mutation burden between wild type (n = 40), BRCA1 (n = 5) and BRCA2 (n = 3) mutated (germline and somatic) in short- and long-term exceptional surviving HGSOC from the TCGA ovarian serous cystadenocarcinoma study. Mutation burden for each individual in each group is shown in increasing order. The patient with the highest mutation burden in the BRCA1-mutated group also has biallelic MLH1 loss. Data points are colored by group, wild-type in black, BRCA1-mutated in dark-blue, and BRCA2-mutated in light-blue. Groups are sorted by increasing median mutation burden. Boxplot for each group shows the group summary statistics for each survival group. Statistical significance is tested by non-parametric 2-sided Wilcoxon rank test for non-paired data and raw p value is reported. n.s. p > 0.05

Fig. 4

Homologous recombination deficiency in exceptional short- and long-term HGSOC survivors. a Comparison of estimated tumor cell cellularity in the sequenced tumor tissue between long- (n = 20) and short- (n = 19) term HGSOC in this study. b Comparison of whole exome sequencing data derived HRD-LOH scores from tumors with greater than 50% tumor cellularity between exceptional survivor groups (long-term = 14, short-term 13). Individual data points in each group is shown in increasing order. Data points are colored by group, short-term in orange and long-term in purple. Boxplot for each group shows the group summary statistics for each survival group. Statistical significance is tested by non-parametric 2-sided Wilcoxon rank test for non-paired data and raw p values are reported. n.s. p > 0.05

Fig. 5

Inference of tumor microenvironment in exceptional short- and long-term survivors of HGSOC. a Heat-map of TCGA/Verhaak HGSOC gene-expression subtype scores for 29 fresh-frozen preserved primary tumor tissues in our study group (long-term survival = 13, short-term survival = 16). The display order of tumors is determined by unsupervised hierarchical clustering the z-score normalized HGSOC gene-expression subtype score profiles. Mutations in DNA damage repair genes (BRCA1, BRCA2, and MLH1) and survival groups are annotated in color tracks above the heatmap. Annotation colors are shown in the legend. b Comparison of enrichment of cellular components within the tumor immune microenvironment between long-term and short-term survivors with or without mutations in BRCA1 and BRCA2. Enrichment of selected immune cellular components is inferred from available RNA-seq gene-expression profiles and publicly available cell-type-specific gene sets by ssGSEA. Boxplots for each group, long-term with BRCA1/2 mutation (n = 8, dark-grey), long-term without BRCA1/2 mutation (n = 5, medium-grey), and short-term without BRCA1/2 mutation (n = 16, light-grey), show the summary statics. Statistical significance is tested by non-parametric 2-sided Wilcoxon rank test for non-paired data between long-term surviving BRCA1/2 mutated group (n = 8) to all BRCA1/2 not-mutated group (n = 21), and between long- (n = 13) to short- (n = 16) term survivors. p values are multiple-testing corrected (false discovery rate) and q values are presented. q values ≤ 0.1 are high-lighted in red

Fig. 6

Recurrent ESR1-CCDC170 gene fusion in exceptional short-term surviving HGSOC. a Schematic diagram of the exons from ESR1 and CCDC170 included within the detected gene-fusion mRNA by RNA-seq in the two HGSOC primary tumor tissues from exceptionally short-term surviving patients. Diagram of protein domains encoded by the retained exons is shown for each fusion. b RNA-seq reads supporting the ESR1-CCDC170 fusion mRNA in patient LTS-034. c RNA-seq reads supporting the ESR1-CCDC170 fusion mRNA in patient LTS-002. Portions of the junction-spanning reads that align to the reference sequence of ESR1 and CCDC170 are colored in grey and the mismatched bases are shown in color