Gene Expression Indicates Altered Immune Modulation and Signaling Pathway Activation in Ovarian Cancer Patients Resistant to Topotecan

Abstract

Epithelial ovarian cancer (EOC) is one of the deadliest gynecological malignancies. Topotecan remains an essential tool in second-line therapy; even so, most patients develop resistance within a short period of time. We aimed to identify biomarkers of topotecan resistance by using gene expression signatures derived from patient specimens at surgery and available subsequent responses to therapy. Gene expression was collected for 1436 patients and 10,103 genes. Based on disease progression, patients were categorized as responders/nonresponders depending on their progression free survival (PFS) state at 9, 12, 15 and 18 months after surgery. For each gene, the median expression was compared between responders and nonresponders for two treatment regimens (chemotherapy including/excluding topotecan) with Mann-Whitney U test at each of the four different PFS cutoffs. Statistical significance was accepted in the case of p < 0.05 with a fold change (FC) ≥ 1.44. Four genes (EPB41L2, HLA-DQB1, LTF and SFRP1) were consistently overexpressed across multiple PFS cutoff times in initial tumor samples of patients with disease progression following topotecan treatment. A common theme linked to topotecan resistance was altered immune modulation. Genes associated with disease progression after systemic chemotherapy emphasize the role of the initial organization of the tumor microenvironment in therapy resistance. Our results uncover biomarkers with potential utility for patient stratification.

Keywords: biomarker; gene arrays; gene expression; ovarian carcinoma; resistance; survival; tumor microenvironment.

Figure 1

Patient characteristics including stage, grade and histological subtype across the entire epithelian ovarian cancer dataset and in the sub-cohort treated with systemic therapy including topotecan. (A) Proportion of responders (grey)/nonresponders (blue) to systemic chemotherapy including/excluding topotecan at the four progression free survival (PFS) cutoff times in topotecan-untreated (B) and -treated (C) patients.

Figure 2

Analysis workflow for the database setup and the number of systemic chemotherapy-treated (including/excluding topotecan) patients at each PFS-cutoff.

Figure 3

List of genes with higher expression in specimens of nonresponders who received systemic chemotherapy excluding topotecan. The figure is color-coded for expression (high-red), fold change (high-red) and p-values (low-red).

Figure 4

Significantly upregulated genes at the four different progression free survival (PFS) cutoff points in the topotecan-treated patient cohort (A). Combined expression of significant upregulated genes at 12, 15 and 18-month PFS cutoffs associated with disease progression in the group of topotecan-treated patients (B). Combined receiver operator characteristic (ROC) curve for EPB41L2, HLA-DQB1 and SFRP1, consistently overexpressed in initial tumor samples of subsequent nonresponders to topotecan, which were also significant at the 12-month PFS cutoff (C).

Figure 5

Consistently upregulated genes in EOC tumor specimens associated with subsequent resistance to topotecan-containing systemic chemotherapy. The high expression of the identified genes is associated with worse progression-free survival among topotecan-treated patients.