BackgroundA fusion gene is a hybrid gene consisting of parts from two previously independent genes. Chromosomal rearrangements leading to gene breakage are frequent in high-grade serous ovarian carcinomas and have been reported as a common mechanism for inactivating tumor suppressor genes. However, no fusion genes have been repeatedly reported to be recurrent driver events in ovarian carcinogenesis. We combined genomic and transcriptomic information to identify novel fusion gene candidates and aberrantly expressed genes in ovarian carcinomas.MethodsExamined were 19 previously karyotyped ovarian carcinomas (18 of the serous histotype and one undifferentiated). First, karyotypic aberrations were compared to fusion gene candidates identified by RNA sequencing (RNA-seq). In addition, we used exon-level gene expression microarrays as a screening tool to identify aberrantly expressed genes possibly involved in gene fusion events, and compared the findings to the RNA-seq data.ResultsWe found a DPP9-PPP6R3 fusion transcript in one tumor showing a matching genomic 11;19-translocation. Another tumor had a rearrangement of DPP9 with PLIN3. Both rearrangements were associated with diminished expression of the 3′ end of DPP9 corresponding to the breakpoints identified by RNA-seq. For the exon-level expression analysis, candidate fusion partner genes were ranked according to deviating expression compared to the median of the sample set. The results were collated with data obtained from the RNA-seq analysis. Several fusion candidates were identified, among them TMEM123-MMP27, ZBTB46-WFDC13, and PLXNB1-PRKAR2A, all of which led to stronger expression of the 3′ genes. In view of our previous findings of nonrandom rearrangements of chromosome 19 in this cancer type, particular emphasis was given to changes of this chromosome and a DDA1-FAM129C fusion event was identified.ConclusionsWe have identified novel fusion gene candidates in high-grade serous ovarian carcinoma. DPP9 was involved in two different fusion transcripts that both resulted in deregulated expression of the 3′ end of the transcript and thus possible loss of the active domains in the DPP9 protein. The identified rearrangements might play a role in tumorigenesis or tumor progression.Electronic supplementary materialThe online version of this article (10.1186/s12885-017-3625-6) contains supplementary material, which is available to authorized users.

The optimal hemoglobin level in patients with hypertension or heart failure is not yet defined. The aim of the present investigation was to examine the relation of hemoglobin with cardiovascular outcomes in high-risk patients with isolated systolic hypertension (ISH) and left ventricular hypertrophy (LVH). In 1,326 patients with ISH in the Losartan Intervention For Endpoint Reduction in Hypertension (LIFE) study, hemoglobin and cardiovascular outcomes were examined using Cox proportional hazard models. Baseline hemoglobin was negatively related to rate of cardiovascular death (hazard ratio 0.81 per 1 g/dl, 95% confidence interval [CI] 0.67 to 0.98, p = 0.032) after adjusting for baseline Framingham risk score, LVH, treatment, and estimated glomerular filtration rate. Hemoglobin decreased slightly during the study and the decrease was more pronounced in the losartan group (13.9 +/- 1.3 to 13.6 +/- 1.4 g/dl) than in the atenolol group (13.9 +/- 1.2 to 13.8 +/- 1.4 g/dl). Hemoglobin as a time-varying covariate was negatively associated with rate of cardiovascular death (hazard ratio 0.75, 95% CI 0.63 to 0.90, p <0.001) and stroke (hazard ratio 0.84, 95% CI 0.72 to 0.99, p = 0.040) after adjusting for baseline Framingham risk score, LVH, treatment, and estimated glomerular filtration rate. In conclusion, in this high-risk population with ISH and LVH, lower hemoglobin at baseline was associated with higher probability of cardiovascular death, and decrease in hemoglobin over time was associated with higher probability of cardiovascular death or stroke; this effect was attenuated by treatment with losartan.

Chromosome 19 is frequently rearranged in ovarian carcinomas, but the pathogenetic consequences of this are not clearly understood. We performed microarray gene expression analysis on 12 ovarian carcinomas that carry a rearranged chromosome 19 in their karyotype. These aberrant chromosomes have previously been microdissected and analyzed by array-based CGH. In the current study, we wanted to explore whether the genomic alterations thus detected correlated with changes in gene expression. The microarray gene expression analysis gave information on 407 genes mapping in gained genomic regions on chromosome 19, of which 92 showed association between DNA gain and upregulated expression. Of the genes showing this association, 39 (42%) showed gain in at least two samples. The majority of these 39 genes of interest (n = 24, 62%) encode zinc finger proteins, which otherwise make up only 15% of the approximately 1,400 genes on chromosome 19. The strongest association was found for ZNF223 which was upregulated in samples with genomic gain compared with samples without gain. We suggest that DNA copy number changes brought about by rearrangements of chromosome 19 contribute to ovarian carcinogenesis by leading to upregulation of ZNF223 and other zinc finger genes. © 2014 Wiley Periodicals, Inc.

The mechanisms behind bilaterality of ovarian carcinomas are not fully understood, as the two tumors could possibly represent two primary tumors, a primary tumor and a metastasis, or two metastases. The gene expression profiles from bilateral high-grade serous carcinomas (HGSCs) and clear cell carcinomas (CCCs) of the ovary were compared to study the association between the tumors of the two sides. A separate analysis of genes from chromosome 19 was also performed, since this chromosome is frequently rearranged in ovarian carcinomas. Tumors from four patients were included (three pairs of HGSC and one pair of CCC). The gene expression was analyzed at the exon level, and bilateral tumors were compared to identify within-pair differences. Gene expression data were also compared with genomic information on the same tumors. Similarities in gene expression were observed between the tumors within each pair, as expected if the two tumors were clonally related. However, certain genes exhibited differences in expression between the two sides, indicating metastasis involvement. Among the most differently expressed genes, one gene was common to all four pairs: Immunoglobulin J. In all HGSC pairs, serpin peptidase inhibitor, clade B (ovalbumin), member 2, serpin family E member 1 and phospholipase A2, group IIA (platelets, synovial fluid) were also among the differentially expressed genes. The specific analysis of chromosome 19 highlighted expression differences in the zinc finger protein 36 gene. These results indicate that bilateral ovarian tumors represent different stages during progression of a single clonal process. Several of the genes observed to be differently expressed are known to be metastasis-related, and are likely to be also involved in spreading from one side to the other in the bilateral cancer cases examined.

Vi har identifisert gener som er potensielle kliniske biomarkører eller terapeutiske mål i eggstokkreft. Funnene våre gir også økt kunnskap om kreftutviklingen i eggstokkene. Foto: Erik DyrhaugÅrlig rammes rundt 450 norske kvinner av eggstokkreft, og den vanligste typen er karsinom. Det finnes ikke gode diagnostiske biomarkører for å oppdage denne kreftformen tidlig, og få pasienter blir tilbudt målrettet behandling. Tidligere DNA-studier har vist at mange kreftceller har forandringer av kromosom 19. Å identifisere kreftspesifikke genendringer og vite hvilke følger disse har, er grunnleggende for å kunne tilby bedre diagnostikk og terapi.I mitt doktorgradsarbeid har mine kolleger og jeg undersøkt endringer i genuttrykket i eggstokkarsinomer med kjent endring av kromosom 19. Vi analyserte RNA-nivået og sammenlignet resultatene med DNA-funn. Onkogener som er involvert i kreftutviklingen, viser ofte assosiasjon mellom økt kopitall på DNA-nivå og økt genuttrykk. Vi fant den sterkeste assosiasjonen av denne typen for en gruppe gener som koder for transkripsjonsfaktorer.Vi lette også etter fusjonsgener, som er nye gener som dannes når biter av to friske gener kobles sammen. Slike fusjonsgener er ofte kreftspesifikke. Det mest interessante fusjonsgenet vi fant, var DPP9-PPP6R3. Fusjonen fører til et lavere uttrykk av genet DPP9, som har vist seg å kunne beskytte mot kreftutvikling.Genene vi har identifisert, er potensielle diagnostiske biomarkører eller terapeutiske mål i kreftcellene. Denne kunnskapen kan bidra til å utvikle målrettet kreftbehandling og forbedre utsiktene for pasienter med eggstokkarsinom. DisputasMarianne Lislerud Smebye disputerte for ph.d.-graden ved Universitetet i Oslo 17. mars 2017.

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Introduction: A limited number of drugs are available for use in breast cancer patients, and several are not in practical use due to the lack of adequate biomarkers. We have recently demonstrated the feasibility of using machine learning on molecular data from bulk tumor analysis to create a nine-protein signature named VEGF-inhibition Response Predictor (ViRP) for selecting BC patients for treatment with chemotherapy and bevacizumab. The ViRP score is currently being validated in the NAPEER+ clinical trial (EudraCT 2021-005850-27). Increasing evidence suggests that spatial organization of cells within the tumor microenvironment influences survival and response to therapy in numerous cancer types. In methods based on bulk tumor analysis all tumor cells are profiled simultaneously with both colocalized and distant stroma and immune cells. We are thus pursuing information on spatial organization of cellular phenotypes expressing selected cancer related proteins including our nine ViRP proteins. Methods: From the NeoAva (NCT00773695) clinical trial evaluating the effect of bevacizumab in combination with neoadjuvant chemotherapy (n=132 pts), FFPE tissue sections from patients before, during, and after treatment were made. Cyclic immunofluorescence (cyCIF) was used to profile the spatial expression of 32 cancer-signaling and 32 immune-related proteins, comprising our nine ViRP proteins, on FFPE tissue sections from selected patients (n = 20). The Galaxy-ME platform was used for image processing and downstream analysis of spatial protein profiling. Results: Use of cyCIF for spatial analysis enabled for evaluation of malignant cells in the context of surrounding microenvironmental cells, including immune cells. We found that cell type-specific protein abundance and subcellular localization formed a highly heterogenous pattern in the tissue. This was particularly evident for the nine ViRP proteins, and differences in expression between tumor cell populations will be further elucidated. Among the patients selected for cyCIF analysis, 4 were chosen based on misclassification by the ViRP signature. Ongoing studies focus on revealing spatial expression patterns to optimize the ViRP biomarker and explore why misclassification occurs. Furthermore, the observed molecular biology of the evolving tissues under treatment in responding and non-responding patients may reveal new biomarkers indicative of treatment response or resistance. Conclusion: We observe that the expression of proteins in tumor tissues is highly heterogeneous, and thus include numerous features not captured by bulk tumor analysis. Future development of new predictive tools and biomarkers that integrate molecular data which is multiparametric and spatial will set the stage for a new class of biomarkers in cancer diagnostics. Citation Format: Mads Haugland Haugen, David Kilburn, Hongli Ma, Cameron Watson, Allison Creason, Dong Zhang, Maria Aa Dahle, Ole Christian Lingjaerde, Marianne L. Smebye, Oeystein Garred, Mette S. Foersund, Mai T. Nguyen, Gunhild M. Maelandsmo, Gordon Mills, Olav Engebraaten. Spatial protein profiling by cyclic immunofluorescence to interpret and improve bulk tumor-based predictor of response to chemotherapy with bevacizumab in neoadjuvant breast cancer treatment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5627.

Background and Purpose: Neoadjuvant treatment regimens containing the DNA-targeting chemotherapy carboplatin has been shown to increase the pathological complete response (pCR) rate in triple negative (TN) breast cancer. In addition, the response to such therapy among patients with aggressive hormone receptor positive (HR+) cancer should be investigated. Neither the molecular mechanisms leading to good response, nor the criteria for selection of optimal treatment groups are known. Therefore, predictive biomarkers that identify responders to carboplatin in breast cancer are needed. Materials and Methods: In the I-BCT phase II clinical trial (ClinicalTrials.gov identifier: NCT02546232), HER2-negative breast cancer patients (N = 187) were randomized (1:1) to receive neoadjuvant chemotherapy with or without carboplatin. Pre-treatment tumor biopsies (N = 178, N = 89 in each arm) were analyzed by reverse-phase protein array (RPPA) for expression levels of 494 breast cancer relevant (phospho-) proteins. Change in tumor size during treatment was used as continuous response measure. In addition, response was dichotomized with 30 % tumor shrinkage as cutoff. For the patients that received carboplatin, differential expression analysis between responders and non-responders was performed to identify proteins that may predict response to carboplatin. Gene set enrichment analysis on differentially expressed proteins was performed to identify biologically upregulated pathways. Results: We found differentially expressed proteins related to response to carboplatin in treatment naive tumors. Biologically upregulated pathways have been identified in patients with high tumor shrinkage after treatment with carboplatin. The results demonstrate the importance of the pre-treatment protein landscape in prediction of benefit to carboplatin. Studies regarding biological mechanisms related to response in both TN and HR+ breast cancer, and differences among these subtypes, are ongoing. Conclusion: Our study provides new insight into the mechanisms of response and resistance to carboplatin treatment in the neoadjuvant setting for HER2-negative breast cancer patients. The results support further studies on the protein landscape of tumors as a complementary method to gene expression analysis to unravel the molecular mechanisms of sensitivity and resistance to treatment in breast cancer. Citation Format: Maria Aanesland Dahle, Eivind Valen Egeland, Lina Prasmickaite, Ole Christian Lingjærde, Hege Russnes, Øystein Garred, Marianne L. Smebye, Helle Skjerven, Ellen Schlichting, Bjørn Naume, Gunhild Mælandsmo, Olav Engebraaten, Mads H. Haugen. Pre-treatment protein landscape in HER2-negative breast cancer treated with carboplatin in a neoadjuvant chemotherapy setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2170.