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. 2019 May 3:3:PO.18.00343.
doi: 10.1200/PO.18.00343. eCollection 2019.

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Jaana Oikkonen  1 , Kaiyang Zhang  1 , Liina Salminen  2 , Ingrid Schulman  1 , Kari Lavikka  1 , Noora Andersson  1 , Erika Ojanperä  1 , Sakari Hietanen  2 , Seija Grénman  2 , Rainer Lehtonen  1 , Kaisa Huhtinen  3 , Olli Carpén  1   3   4 , Johanna Hynninen  2 , Anniina Färkkilä  1   4   5 , Sampsa Hautaniemi  1
Affiliations

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Jaana Oikkonen et al. JCO Precis Oncol. .

Abstract

Purpose: Circulating tumor DNA (ctDNA) detection is a minimally invasive technique that offers dynamic molecular snapshots of genomic alterations in cancer. Although ctDNA markers can be used for early detection of cancers or for monitoring treatment efficacy, the value of ctDNA in guiding treatment decisions in solid cancers is controversial. Here, we monitored ctDNA to detect clinically actionable alterations during treatment of high-grade serous ovarian cancer, the most common and aggressive form of epithelial ovarian cancer with a 5-year survival rate of 43%.

Patients and methods: We implemented a clinical ctDNA workflow to detect clinically actionable alterations in more than 500 cancer-related genes. We applied the workflow to a prospective cohort consisting of 78 ctDNA samples from 12 patients with high-grade serous ovarian cancer before, during, and after treatment. These longitudinal data sets were analyzed using our open-access ctDNA-tailored bioinformatics analysis pipeline and in-house Translational Oncology Knowledgebase to detect clinically actionable genomic alterations. The alterations were ranked according to the European Society for Medical Oncology scale for clinical actionability of molecular targets.

Results: Our results show good concordance of mutations and copy number alterations in ctDNA and tumor samples, and alterations associated with clinically available drugs were detected in seven patients (58%). Treatment of one chemoresistant patient was changed on the basis of detection of ERBB2 amplification, and this ctDNA-guided decision was followed by significant tumor shrinkage and complete normalization of the cancer antigen 125 tumor marker.

Conclusion: Our results demonstrate a proof of concept for using ctDNA to guide clinical decisions. Furthermore, our results show that longitudinal ctDNA samples can be used to identify poor-responding patients after first cycles of chemotherapy. We provide what we believe to be the first comprehensive, open-source ctDNA workflow for detecting clinically actionable alterations in solid cancers.

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Conflict of interest statement

The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. For a detailed description of the disclosure categories, or for more information about ASCO’s conflict of interest policy, please refer to www.asco.org/rwc or po.ascopubs.org/site/ifcSakari HietanenConsulting or Advisory Role: Tesaro, AstraZeneca Travel, Accommodations, Expenses: Roche Pharma AGOlli CarpénStock and Other Ownership Interests: Orion Corporation Honoraria: Merck KGaA, Roche Pharma AGSampsa HautaniemiStock and Other Ownership Interests: NanoString Technologies No other potential conflicts of interest were reported.

Figures

FIG 1.
FIG 1.
Comprehensive circulating tumor DNA (ctDNA) analysis approach identifies mutations and copy number alterations (CNAs) in high-grade serous ovarian cancer (HGSOC). (A) Analysis pipeline to detect genomic alterations from longitudinal ctDNA sampling of patients with HGSOC. After data analysis, the alterations are used to monitor patient responses and are prioritized on the basis of evidence for alterations and existing therapies. (B) Concordance between mutations detected from plasma samples and tumor tissue samples from the same patient. (C) During the treatment, a lower ratio of mutations with decreasing variant allele frequencies (VAFs) and larger mutation counts were detected in the poor-responding patients compared with the good-responding patients (P = .008). Good-responding patients showed either a small number of mutations or a large proportion of decreasing mutations during treatment. PFI, platinum-free interval.
FIG 2.
FIG 2.
Tumor burden measured by circulating tumor DNA (ctDNA), TP53, and cancer antigen 125 (CA-125) during therapy and follow-up. Tumor burden was estimated from ctDNA through TP53 variant allele frequency (VAF) (orange lines) and median VAF (blue lines). Correlation between tumor content and CA-125 was 0.67. The start of the trastuzumab treatment during progression (Prog) in patient EOC736 has been marked with a star. More detailed figures, including all treatments administered to each patient, are given in the Data Supplement. IDS, interval debulking surgery; PDS, primary debulking surgery; PTE, primary treatment end.
FIG 3.
FIG 3.
Pathogenic mutation in NF1 was detected in circulating tumor DNA (ctDNA), leading to functionally overactive mammalian target of rapamycin (mTOR) signaling in the tumor tissue. (A) Mutational frequencies in a good-responding patient (EOC429) during primary treatment and follow-up. Variant allele frequency (VAF) values are normalized for the frequency level to show relative changes in the levels. Mutational profile shows a low mutation rate because only eight mutations were detected. After the last chemotherapy cycle, TP53 VAF declined to 0.4% from the pretreatment value of 34.6%. No novel mutations were detected during or after the treatment. The NF1 mutation (Q1775) was detected in samples before and after primary debulking surgery (PDS) with high VAF (34% and 5.4%, respectively). The samples taken during therapy had too low a tumor burden for reliable mutation detection, and NF1 was not detected in these subsequent samples. (B) mTOR pathway activation was detected in primary tumor tissue with higher staining for phosphorylated mTOR (pmTOR) and E4-BP1 compared with normal ovarian tissue. Scale bar, 100 µm. (C) In addition to having a complete response on the basis of RECIST 1.1, the response to primary therapy was good, as indicated by cancer antigen 125 (CA-125) values that stayed low during treatment and follow-up. A similar pattern was detected for TP53 VAF. Median VAF shows the prolonged effect of chemotherapy. CADD, Combined Annotation Dependent Depletion; HGSOC, high-grade serous ovarian cancer; PTE, primary treatment end; 4E-BP, 4E-binding protein.
FIG 4.
FIG 4.
ERBB2 amplification and the effect of combination treatment with trastuzumab, platinum, and paclitaxel for patient EOC736. (A) ERBB2 amplification was detected from a primary plasma sample and adnexal cancer tissue removed at primary debulking surgery. The amplified region was verified from primary omental metastatic tissue using SNP-array data (orange lines). Amplified region contains multiple genes, of which CDK12 and ERBB2 were included in the targeted panel. RARA was within the amplified region in plasma but not in primary omentum. (B) ERBB2 protein was overexpressed in cancer tissue (arrowheads) in immunohistochemistry (IHC) and the ERBB2 gene was amplified in DNA in situ hybridization (ISH) analysis (scale bars, 20 µm). (C) Treatments and responses measured by circulating tumor DNA (ctDNA) and cancer antigen 125 (CA-125). Trastuzumab and reduced-dose platinum-paclitaxel treatment led to normalization of CA-125 values, from 800 to 19, after only three treatment cycles. (D) The pretreatment computed tomography scan (upper part) shows the largest diameters of the relapsed tumor. After 14 weeks (four cycles) of combination chemotherapy, there was an average 52% reduction in the diameters of the lesion (lower part). The patient had multiple apparently benign cysts in the liver and the right kidney that were unrelated to ovarian cancer. CNV, copy-number variation; HER2, human epidermal growth factor receptor 2; IDS, interval debulking surgery; Prog, progression; PTE, primary treatment end; SNP, single-nucleotide polymorphism; VAF, variant allele frequency.
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References

    1. Merker JD, Oxnard GR, Compton C, et al. Circulating tumor DNA analysis in patients with cancer: American Society of Clinical Oncology and College of American Pathologists joint review. J Clin Oncol. 2018;36:1631–1641. - PubMed
    1. Khan KH, Cunningham D, Werner B, et al. Longitudinal liquid biopsy and mathematical modeling of clonal evolution forecast time to treatment failure in the PROSPECT-C phase II colorectal cancer clinical trial. Cancer Discov. 2018;8:1270–1285. - PMC - PubMed
    1. Cohen JD, Li L, Wang Y, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018;359:926–930. - PMC - PubMed
    1. Parkinson CA, Gale D, Piskorz AM, et al. Exploratory analysis of TP53 mutations in circulating tumour DNA as biomarkers of treatment response for patients with relapsed high-grade serous ovarian carcinoma: A retrospective study. PLoS Med. 2016;13:e1002198. - PMC - PubMed
    1. Giannopoulou L, Kasimir-Bauer S, Lianidou ES. Liquid biopsy in ovarian cancer: Recent advances on circulating tumor cells and circulating tumor DNA. Clin Chem Lab Med. 2018;56:186–197. - PubMed