Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma

Abstract

While high-grade serous ovarian carcinoma (HGSOC) is the most common histologic subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants [by DNA next-generation sequencing (NGS) using a 50 gene Ion Torrent panel] and gene expression (using the NanoString PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT). NGS was performed on plasma cell free DNA (cfDNA) on a select group of patients (n = 14) to assess the utility of using cfDNA to monitor these changes. A total of 86 genes had significant changes in RNA expression after NACT. Thirty-eight genetic variants (including SNPs) from 6 genes were identified in tumors pre-NACT, while 59 variants from 19 genes were detected in the cfDNA. The number of DNA variants were similar after NACT. Of the 59 variants in the plasma pre-NACT, only 6 persisted, whereas 33 of 38 specific variants in the tumor DNA remained unchanged. Pathway analysis showed the most significant alterations in the cell cycle and DNA damage pathways.Implications: Gene expression profiles at the time of interval debulking provide additional genetic information that could help impact treatment decisions after NACT; although, continued collection and analysis of matched tumor and cfDNA from multiple time points are needed to determine the role of cfDNA in the management of HGSOC. Mol Cancer Res; 16(5); 813-24. ©2018 AACR.

Figure 1.

Genes pre- and post-NACT. A, Histologic comparison of pre and post NACT samples. 1) Pre-NACT sample biopsy. 2) Post-NACT samples had significant reduction of adenocarcinoma in omentum. B, Heirarchical cluster analysis of all 770 genes. C, Heirarchical clustered analysis of 86 significantly changed genes. Cluster 1 (green) was enriched for pre-NACT; cluster 2 (red) was enriched with post-NACT. D, Volcano plot showing genes expression changes post-NACT by Log2 fold change (x-axis) and minuslog₁₀ p-value (y-axis). The top 10 genes with increased and decreased expression, fold change (post vs. pre) and p-value are shown on the right.

Figure 2.

Pathway changes pre-and post-NACT. Pathway scores condense each sample’s gene expression profile using the first principal component analysis. A, Individual pathway scores pre- and post-NACT. B, Box plots for individual pathway scores. Cell cycle, DNA damage, and transcriptional misregulation pathways were statistically different in pre- vs post-NACT (p <0.05). P-values are calculated using paired T-test. C, Individual patient DNA damage pathway scores pre- and post-NACT. D, Individual pathway and gene changes involved in Hereditary Ovarian Cancer Signaling: BRCA1, BRCA2, p53, PTEN, DNA repair, DNA damage response and checkpoint control, protein ubiquitination, transcriptional control and chromatin remodeling.

Figure 3.

Platinum sensitivity gene expression analysis. A, Box plot of NTF3 expression in platinum vs resistant patients pre-NACT. B, Box plots of individual gene expression in chemosensitive (orange) vs chemoresistant (red) pre- and post-NACT samples.

Figure 4.

Arend Variants Compared to AOCS Ovarian Cancer Database. Number of protein-coding mutations found in AOCS 93 patients compared to our 14 patients samples in the Pre-NACT setting.

Figure 5.. Tumor mutations

A, Pie-charts of specific tumor variants in pre- and post-NACT. Variants in red are found in both pre- and post-NACT samples. B, Tumors with KIT mutations showed increased (≥ 2 fold) expression in LEFTY2, FZD2, and FGF19; although not statistically significant, because overall levels of expression were low.

Figure 6.. Tumor and cfDNA mutations.

A, Pie-charts of specific variants in plasma pre- and post-NACT. Variants in red are found in both pre- and post-NACT samples. B, Comparison of genes mutations identified in tumor (green), plasma (red), or both (blue) in pre- and post-NACT samples. Variants that were likely germline are indicated by a star.