Tumor evolution and intratumor heterogeneity of an epithelial ovarian cancer investigated using next-generation sequencing

Jung-Yun Lee, Jung-Ki Yoon, Boyun Kim, Soochi Kim, Min A Kim, Hyeonseob Lim, Duhee Bang, Yong-Sang Song, Jung-Yun Lee, Jung-Ki Yoon, Boyun Kim, Soochi Kim, Min A Kim, Hyeonseob Lim, Duhee Bang, Yong-Sang Song

Abstract

Background: The extent to which metastatic tumors further evolve by accumulating additional mutations is unclear and has yet to be addressed extensively using next-generation sequencing of high-grade serous ovarian cancer.

Methods: Eleven spatially separated tumor samples from the primary tumor and associated metastatic sites and two normal samples were obtained from a Stage IIIC ovarian cancer patient during cytoreductive surgery prior to chemotherapy. Whole exome sequencing and copy number analysis were performed. Omental exomes were sequenced with a high depth of coverage to thoroughly explore the variants in metastatic lesions. Somatic mutations were further validated by ultra-deep targeted sequencing to sort out false positives and false negatives. Based on the somatic mutations and copy number variation profiles, a phylogenetic tree was generated to explore the evolutionary relationship among tumor samples.

Results: Only 6% of the somatic mutations were present in every sample of a given case with TP53 as the only known mutant gene consistently present in all samples. Two non-spatial clusters of primary tumors (cluster P1 and P2), and a cluster of metastatic regions (cluster M) were identified. The patterns of mutations indicate that cluster P1 and P2 diverged in the early phase of tumorigenesis, and that metastatic cluster M originated from the common ancestral clone of cluster P1 with few somatic mutations and copy number variations.

Conclusions: Although a high level of intratumor heterogeneity was evident in high-grade serous ovarian cancer, our results suggest that transcoelomic metastasis arises with little accumulation of somatic mutations and copy number alterations in this patient.

Figures

Figure 1
Figure 1
Intra-tumoral mutational profiles of HGSC. (A) Sampling sites of tumor and normal control tissues. (B) Phylogenetic tree of somatic mutations. (C) Phylogenetic tree of somatic copy number variations. (D) Patterns of somatic mutations across samples. HGSC: high grade serous ovarian cancer, RO: right ovary, RF: right fimbriae, LO: left ovary, LF: left fimbriae, BP: bladder peritoneum, OM: omentum.
Figure 2
Figure 2
Genomic profiles of somatic copy number alterations (SCNA). (a) Common segments (green) and Shared segments (grey). (b, c, d) Cluster P1 samples, RO1, RF, and LO4. (e, f) Cluster M samples, OM1, and OM2. (g) Cluster P2 sample, LO3. Overall the pattern of SCNA in cluster M was similar to the pattern in cluster P1 except for a large deletion on chromosome X. Cluster P2 showed distinct SCNA patterns compared to other clusters. red: amplification, blue: deletion.
Figure 3
Figure 3
Evolutionary model of non-spatial clustered metastatic ovarian cancer. (CCR: cytokine-cytokine receptor pathway, SCNA: somatic copy number alteration).

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