Elsevier

Gynecologic Oncology

Volume 156, Issue 2, February 2020, Pages 415-422
Gynecologic Oncology

Intratumor heterogeneity and homologous recombination deficiency of high-grade serous ovarian cancer are associated with prognosis and molecular subtype and change in treatment course

https://doi.org/10.1016/j.ygyno.2019.11.013Get rights and content

Highlights

  • High intratumor heterogeneity in high-grade serous ovarian cancer associated with a shorter first recurrent interval.

  • High loss of heterozygosity score in high-grade serous ovarian cancer associated with a good prognosis.

  • The number of the tumor clone decreased after chemotherapy and then increased at recurrence.

  • Chemosensitivity are not always consistent with homologous recombination deficiency.

Abstract

Objective

High-grade serous ovarian cancers (HGSOC) are genomically characterized by homologous recombination deficiency (HRD) and TP53 mutations, which lead to intratumor heterogeneity (ITH). This study aimed to reveal the relationship between HRD, ITH and prognosis and analyze their changes during treatment.

Methods

We obtained 573 SNP array and gene expression array data from The Cancer Genome Atlas. SNP array data were processed to calculate the Clonality Index (CI) and loss of heterozygosity (LOH) scores. Gene expression array data were used for classifying molecular subtypes. Additionally, we obtained 33 samples from 20 HGSOC patients, including 4 samples from interval debulking surgery (IDS) and 9 samples from recurrent surgery.

Results

We divided HGSOC samples into 2 groups. The high CI group showed a high recurrent risk, and the high LOH group showed a statistically good prognosis. Combining the two factors, the high LOH/low CI group showed a statistically good prognosis. In terms of molecular subtypes, the mesenchymal subtype, which had a poor prognosis, showed a high CI with statisitically significant difference and the immunoreactive subtype, which had a good prognosis, showed a tendency to have a high LOH score. Throughout treatment, the CI decreased to one at the IDS (n = 4) and then increased at recurrence (n = 3). LOH scores greatly decreased in two cases at the IDS.

Conclusions

ITH and HRD were associated with prognosis in HGSOC. ITH decreased after neoadjuvant chemotherapy, suggesting that the chemo-resistant cancer clone remains after chemotherapy.

Introduction

Ovarian cancer has a poor prognosis among gynecologic malignancies [1]. High-grade serous ovarian cancer (HGSOC), which is the most frequent epithelial ovarian cancer, is commonly diagnosed as an advanced cancer [2]. HGSOC is mainly treated by chemotherapy; however, most HGSOCs recur as a chemo-resistant tumor even though the first chemotherapy is usually effective and results in lethal treatment.

The Cancer Genome Atlas (TCGA) has revealed some characteristics of the cancer genome of HGSOC. One of the characteristics is homologous recombination repair deficiency (HRD) [3]. Almost half of HGSOCs have HRD due to BRCA1/2 mutation or other homologous recombination repair pathway-related gene alterations [4]. HRD is associated with sensitivity to platinum agents [5] and poly- (ADP ribose) polymerase (PARP) inhibitors [[6], [7], [8]], and quantifying the genomic loss of heterozygosity (LOH) provides the possibility of measuring HRD as a biomarker [9]. In the ARIEL2 study, the LOH score was used as a treatment biomarker for the PARP inhibitor, and it was shown that the PARP inhibitor was effective in cases with a high LOH score [10].

The TP53 mutation can be detected at a high frequency in HGSOC [3]. TP53 mutations give rise to chromosomal instability due to disruption of the control of the cell cycle and apoptosis [11]. Chromosomal instability causes subclonal evolution, which shows different genomic characteristics in tumorigenesis and tumor progression and results in high intratumor heterogeneity [12,13], which is associated with resistance to treatment and poor prognosis [[14], [15], [16]]. We have already reported that a single nucleotide polymorphism (SNP) array with formalin-fixed paraffin-embedded specimens can be used to analyze intratumor heterogeneity [17]. With this method, we can evaluate intratumor heterogeneity from various clinical specimens and apply the findings to clinical features, such as prediction of prognosis.

Although each of these main characteristics of HGSOC was investigated in several studies, no reports have examined the association between HRD and intratumor heterogeneity and how these factors changed before and after chemotherapy. In the current study, we first investigated the association between prognosis and HRD or intratumor heterogeneity with the use of TCGA data, and second, we analyzed the changes in these factors throughout treatment of HGSOC with samples from our institution.

Section snippets

Data sources

We obtained TCGA CEL-formatted SNP array data from Affymetrix Genome-Wide Human SNP Array 6.0 via the Genomic Data Commons (GDC) Data Portal (https://portal.gdc.cancer.gov) and extracted 573 HGSOC cases with matched tumor-normal data. We obtained TCGA CEL-formatted gene expression array data from the GeneChip HT Human Genome U133A data via the GDC Data Portal and extracted cases having the same samples as the SNP array data. Additionally, we obtained TCGA XML-formatted clinical data for each

Results

CI and LOH scores could be estimated in 536 and 542 samples out of 573 samples, respectively. Both CI and LOH scores could be calculated in 502 samples, so 502 samples were subjected to analysis. The background data for patients in each sample set are shown in Supplementary Table 1. The averages and standard deviations of the CI and LOH scores were 3.53 ± 1.95 and 17.90 ± 9.41, respectively (Fig. 1A and B). The correlation coefficient between the CI and LOH scores was −0.176, which indicated a

Discussion

We analyzed intratumor heterogeneity and HRD in HGSOC with SNP array data in the current study. Some methods to analyze the intratumor heterogeneity of malignant tumors, including ovarian cancer, have previously been reported, such as multi-region sequencing [28], deep sequencing [29], and single-cell sequencing [30]. We could analyze intratumor heterogeneity from a single sampling of a tumor by applying a previous method [17], which we reported in the current study. The merit of this method is

Conclusion

We have shown that both the CI and LOH in HGSOC is related to prognosis using SNP array data from a single sample. Furthermore, we have shown that the intratumor heterogeneity of chemo-resistant tumors that remained at IDS after NAC decreased compared with that of primary tumors. This study indicated that for analysis of tumors that remain after chemotherapy, investigation of the mechanism underlying the development of chemoresistance is important; thus, further studies are needed.

Declaration of competing interest

All authors declare no conflicts of interest.

Acknowledgements

This work was supported by JSPS Grant-in-Aid for Young Scientists (B) Grant Number JP17K16873.

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