Kaisa Huhtinen

Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer

Abstract Long interspersed element-1 (L1) retrotransposons are the only protein-coding active transposable elements in the human genome. Although typically silenced in normal cells, they are highly expressed in many human epithelial cancers, including high-grade serous ovarian cancer (HGSC), and can integrate into the genome through retrotransposition. De novo L1 insertions are known to contribute to genomic instability and cancer evolution in epithelial malignancies, including HGSC, suggesting that they might also play a role in intrapatient tumor heterogeneity. In this study, we quantified de novo L1 insertions in clinical HGSC specimens and uncovered high heterogeneity in total L1 insertion events (L1 burden) between patients. HGSC tumors with high L1 burden were highly proliferative, whereas tumors with low or no L1 insertions showed enrichment of immune response and cell death pathways. Although the overall L1 burden was similar across different tumor sites within the same patient, the specific L1 insertions (L1 profiles) diverged significantly more than their single-nucleotide variants profiles. Taken together, these findings demonstrate that L1 activity and retrotransposition are highly dynamic in vivo and can contribute substantially to tumor genome plasticity, especially at late stages of cancer progression. The patient-specific propensity of acquiring L1 insertions (L1 burden) could be driven by molecular properties of the progenitor tumor. Retrotransposition-associated DNA damage and/or replication stress could be a potential molecular vulnerability for precision cancer medicine approaches. Significance: L1 retrotransposition is a dynamic process that continues at late stages of high-grade serous ovarian cancer and can substantially contribute to intrapatient tumor heterogeneity.

CA-125 glycovariant assays enhance diagnostic sensitivity in the detection of epithelial ovarian cancer

Abstract Objectives Ovarian cancer is the deadliest gynaecologic malignancy. Due to the lack of reliable biomarkers for the detection of the early disease, most patients are diagnosed at an advanced stage resulting in poor survival. We therefore aimed at establishing novel CA-125 glycovariant assays to improve the diagnostic sensitivity and specificity of ovarian cancer. Methods Blood samples of 184 patients with epithelial ovarian cancers (EOC), 127 benign ovarian tumors, and 115 healthy controls were measured using GLYVAR™ Ovarian I and II assays (Uniogen) and the conventional CA-125 protein assay (CanAg CA-125 EIA, Fujirebio). Results The two glycovariant assays differentiated benign and malignant ovarian masses with 88.0 % sensitivity at 99 % specificity, whereas CA-125 showed 72.8 % sensitivity. The improved performance was most evident in patients with borderline or moderately elevated CA-125 concentration at diagnosis, which is a challenging group for differential diagnostics. The CA-125 glycovariant assays showed 2.5 times higher sensitivity (33.3 % with CA-125 vs. 83.3 % with the CA-125 glycovariants) at 94 % specificity. CA-125 glycovariants corrected 82.4 % of false positive results given by CA-125 concentrations with the commonly used cutoff 35 U/mL. Importantly, the CA-125 glycovariant assays detected 63.6 % of early-stage serous carcinomas from benign and healthy controls with very high 99 % specificity, while CA-125 had a sensitivity of only 45.5 %, representing a 40 % increase. Conclusions This is the first study describing the clinical performance of GLYVAR Ovarian I and II assays in ovarian cancer diagnostics. The results indicate that the CA-125 glycovariant assays have remarkable potential to improve ovarian cancer diagnostics.

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

Abstract Background Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Yet, current grammar-based solutions fall short in adequately supporting the interactive analysis of large datasets with extensive sample collections, a pivotal task often encountered in cancer research. Findings We present GenomeSpy, a grammar-based toolkit for authoring tailored, interactive visualizations for genomic data analysis. By using combinatorial building blocks and a declarative language, users can implement new visualization designs easily and embed them in web pages or end-user–oriented applications. A distinctive element of GenomeSpy’s architecture is its effective use of the graphics processing unit in all rendering, enabling a high frame rate and smoothly animated interactions, such as navigation within a genome. We demonstrate the utility of GenomeSpy by characterizing the genomic landscape of 753 ovarian cancer samples from patients in the DECIDER clinical trial. Our results expand the understanding of the genomic architecture in ovarian cancer, particularly the diversity of chromosomal instability. Conclusions GenomeSpy is a visualization toolkit applicable to a wide range of tasks pertinent to genome analysis. It offers high flexibility and exceptional performance in interactive analysis. The toolkit is open source with an MIT license, implemented in JavaScript, and available at https://genomespy.app/.

HE4 in the evaluation of tumor load and prognostic stratification of high grade serous ovarian carcinoma

Human epididymis protein 4 (HE4) is a validated, complementary biomarker to cancer antigen 125 (CA125) for high grade serous ovarian carcinoma (HGSC). Currently, there are insufficient data on the utility of longitudinal HE4 measurement during HGSC treatment and follow up. We set to provide a comprehensive analysis on the kinetics and prognostic performance of HE4 with serial measurements during HGSC treatment and follow up. This prospective study included 143 patients with advanced HGSC (ClinicalTrials.gov identifier: NCT01276574). Serum CA125 and HE4 were measured at baseline, before each cycle of chemotherapy and during follow up until first progression. Baseline biomarker values were compared to the tumor load assessed during surgery and to residual disease. Biomarker nadir values and concentrations at progression were correlated to survival. The baseline HE4 concentration distinguished patients with a high tumor load from patients with a low tumor load assessed during surgery ( HE4 is a feasible biomarker in the treatment monitoring and prognostic stratification of patients with HGSC. Specifically, the serum level of HE4 at first relapse was associated with the survival of patients and it may be a useful complementary tool in the selection of second line treatments. This is to the best of our knowledge the first time this finding has been reported.

A longitudinal analysis of CA125 glycoforms in the monitoring and follow up of high grade serous ovarian cancer

Cancer antigen 125 (CA125) is generally considered the gold standard of biomarkers in the diagnosis and monitoring of high grade serous ovarian carcinoma (HGSC). We recently reported, that two CA125 glycoforms (CA125-STn and CA125-MGL) have a high specificity to HGSC and further hypothesized, that these cancer specific glycoforms are feasible candidates as biomarkers in HGSC treatment and follow up. Our cohort consisted of 122 patients diagnosed with HGSC. Serum samples were collected longitudinally at the time of diagnosis, during treatment and follow up. Serum levels of CA125, CA125-STn and CA125-MGL were determined and compared or correlated with different end points (tumor load assessed intraoperatively, residual disease, treatment response, progression free survival). Serum CA125-STn levels at diagnosis differentiated patients with low tumor load and high tumor load (p = 0,030), indicating a favorable detection of tumor volume. Similarly, the CA125-STn levels at diagnosis were significantly lower in patients with subsequent complete cytoreduction than in patients with suboptimal cytoreduction (p = 0,025). Conventional CA125 did not differentiate these patients (p = 0,363 and p = 0,154). The CA125-STn nadir value predicted the progression free survival of patients. The detection of disease relapse was improved with CA125-STn, which presented higher fold increase in 80,0% of patients and earlier increase in 37,0% of patients. CA125-STn showed promise as a useful biomarker in the monitoring and follow up of patients with HGSC utilizing a robust and affordable technique. Our findings are topical as a suitable indicator of tumor load facilitates patient selection in an era of new targeted therapies.

Ovarian Cancers with Low CIP2A Tumor Expression Constitute an APR-246–Sensitive Disease Subtype

Abstract Identification of ovarian cancer patient subpopulations with increased sensitivity to targeted therapies could offer significant clinical benefit. We report that 22% of the high-grade ovarian cancer tumors at diagnosis express CIP2A oncoprotein at low levels. Furthermore, regardless of their significantly lower likelihood of disease relapse after standard chemotherapy, a portion of relapsed tumors retain their CIP2A-deficient phenotype. Through a screen for therapeutics that would preferentially kill CIP2A-deficient ovarian cancer cells, we identified reactive oxygen species inducer APR-246, tested previously in ovarian cancer clinical trials. Consistent with CIP2A-deficient ovarian cancer subtype in humans, CIP2A is dispensable for development of MISIIR-Tag–driven mouse ovarian cancer tumors. Nevertheless, CIP2A-null ovarian cancer tumor cells from MISIIR-Tag mice displayed APR-246 hypersensitivity both in vitro and in vivo. Mechanistically, the lack of CIP2A expression hypersensitizes the ovarian cancer cells to APR-246 by inhibition of NF-κB activity. Accordingly, combination of APR-246 and NF-κB inhibitor compounds strongly synergized in killing of CIP2A-positive ovarian cancer cells. Collectively, the results warrant consideration of clinical testing of APR-246 for CIP2A-deficient ovarian cancer tumor subtype patients. Results also reveal CIP2A as a candidate APR-246 combination therapy target for ovarian cancer.

Epithelial Ovarian Cancer- Staging and Response to Chemotherapy Evaluated by PET/CT

The purpose of this study is to determine, whether there is clinical benefit of using fdg-PET/CT (F-18-fluorodeoxyglucose- positron emission tomography/computed tomography)compared to contrast-enhanced CT in primary treatment of advanced epithelial ovarian cancer (EOC) * Objectives * the impact of preoperative PET/CT compared to CT on EOC stage definition * to compare the value of preoperative PET/CT, CT and laparoscopy in intra-abdominal tumour assessment. Laparotomy findings evaluated by surgeon and histopathologic results serve as the reference standard. * to compare serum markers HE4(human epididymis protein 4) and CA125 (cancer antigen 125) with FDG-PET/CT and CT in treatment response evaluation during neoadjuvant chemotherapy and primary treatment of EOC * to compare FDG PET/CT based treatment response evaluation with RECIST and GCIG criteria * Methods * All the patients will undergo FDG-PET/CT prior surgery, after possible neoadjuvant chemotherapy (NACT) and 4 weeks after completion of primary platinum-based chemotherapy. * CA125 and HE4 levels are measured pre-operatively, with every chemotherapy cycle and regularly during follow-up until 1st disease relapse