Johanna Hynninen

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.

Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer

Abstract Ovarian high-grade serous carcinoma (HGSC) is characterized by pervasive genomic instability and high inter- and intra-tumor heterogeneity. Approximately half of HGSC tumors harbor homologous recombination deficiency (HRD), rendering them vulnerable to PARP inhibitors and platinum-based chemotherapy. In contrast, patients lacking HRD (HR-proficient, HRP) generally respond poorly to current therapies. To overcome heterogeneity and identify relevant HGSC subtypes, we characterized the genomic landscape of 640 tumors from 243 patients using whole-genome sequencing. Our chromosomal instability signature–based analysis characterized the structural variation landscape and revealed five HGSC subtypes, validated in an independent dataset. Two HRD subtypes, associated with BRCA1- or BRCA2-driven alterations, demonstrated favorable treatment responses. Strikingly, three HRP subtypes emerged, marked by unique structural alterations and gene expression patterns, tumor microenvironment interactions, and different chemotherapy responses. Notably, organoid experiments showed subtype-specific sensitivity to CHK1 inhibition, suggesting prexasertib as a potential targeted treatment for most currently untreatable HRP patients. Significance: These findings demonstrate that HGSC tumors can be divided into functionally and clinically distinct subtypes, offering new insights into the underlying biology of HGSC and providing a foundation to develop tailored therapeutic strategies for HRP tumors, which currently lack effective options.

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/.

A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells

Resistance to therapy commonly develops in patients with high-grade serous ovarian carcinoma (HGSC) and triple-negative breast cancer (TNBC), urging the search for improved therapeutic combinations and their predictive biomarkers. Starting from a CRISPR knockout screen, we identified that loss of RB1 in TNBC or HGSC cells generates a synthetic lethal dependency on casein kinase 2 (CK2) for surviving the treatment with replication-perturbing therapeutics such as carboplatin, gemcitabine, or PARP inhibitors. CK2 inhibition in RB1-deficient cells resulted in the degradation of another RB family cell cycle regulator, p130, which led to S phase accumulation, micronuclei formation, and accelerated PARP inhibition–induced aneuploidy and mitotic cell death. CK2 inhibition was also effective in primary patient-derived cells. It selectively prevented the regrowth of RB1-deficient patient HGSC organoids after treatment with carboplatin or niraparib. As about 25% of HGSCs and 40% of TNBCs have lost RB1 expression, CK2 inhibition is a promising approach to overcome resistance to standard therapeutics in large strata of patients.

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.

Association of clinical and laboratory variables with risk of venous thromboembolism in high-grade serous ovarian cancer

This study aimed to assess the incidence and time course of venous thromboembolism and to survey clinical and laboratory features predicting the risk for these complications in patients with high-grade serous ovarian cancer. Patients with high-grade serous ovarian cancer treated in a prospective ovarian cancer study at the Turku University Hospital between 2009 and 2020 were retrospectively analyzed for the incidence of venous thromboembolism. This diagnosis was based on the International Classification of Diseases, 10 Among the 146 patients with high-grade serous ovarian cancer, 24 (16.4%) had a confirmed venous thromboembolism. In 5 patients (3.4%), venous thromboembolism preceded the cancer diagnosis. The median time from cancer diagnosis to the venous thromboembolism event was 12.8 months. Patients with venous thromboembolism had shorter median survival (30.6 versus 41.6 months, p = .014), but age, disease stage at diagnosis, and co-morbidities were similar. In a multivariable analysis, short platinum-free interval (p < .005) and increased leukocyte (p = .004) and neutrophil (p = .013) counts both indicated an increased probability of venous thromboembolism event. Conversely, longer carbohydrate antigen 125 doubling time (p = .036), along with higher hemoglobin (p < .0001) and albumin levels (p = .015), were linked to a reduced risk of venous thromboembolism. The combination of these findings in high-grade serous ovarian cancer patients could be incorporated into their venous thromboembolism risk stratification. Given the reduced overall survival in patients with venous thromboembolism, future studies should prioritize proactively targeted thromboprophylaxis.

Bexmarilimab Activates Human Tumor-Associated Macrophages to Support Adaptive Immune Responses in Interferon-Poor Immune Microenvironments

Abstract Immune checkpoint inhibitors (ICI) show substantially greater efficacy in inflamed tumors characterized by preexisting T-cell infiltration and IFN signaling than in noninflamed “cold” tumors, which often remain immunotherapy resistant. The cancer immunotherapy bexmarilimab, which inhibits the scavenger receptor Clever-1 to release macrophage immunosuppression and activate adaptive immunity, has shown treatment benefit in subsets of patients with advanced solid malignancies. However, the mechanisms that determine bexmarilimab therapy outcome in individual patients are unknown. Here we characterized bexmarilimab response in ovarian cancer ascites macrophages ex vivo using single-cell RNA sequencing and demonstrated increased IFN signaling and CXCL10 secretion following bexmarilimab treatment. We further showed that bexmarilimab was most efficacious in macrophages with low baseline IFN signaling, as chronic IFNγ priming abolished bexmarilimab-induced TNFα release. These results highlight an approach to target immunologically cold tumors and to increase the likelihood of their subsequent response to ICIs.

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