Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA.

OBJECTIVES: We analysed whether temporal heterogeneity of ctDNA encodes evolutionary patterns in ovarian cancer. METHODS: Targeted sequencing of 275 cancer-associated genes was performed in a primary tumor biopsy and in ctDNA of six longitudinal plasma samples from 15 patients, using the Illumina platform. RESULTS: While there was low overall concordance between the mutational spectrum of the primary tumor biopsies vs. ctDNA, TP53 variants were the most commonly shared somatic alterations. Up to three variant clusters were detected in each tumor biopsy, likely representing predominant clones of the primary tumor, most of them harbouring a TP53 variant. By tracing these clusters in ctDNA, we propose that liquid biopsy may allow to assess the contribution of ancestral clones of the tumor to relapsed abdominal masses, revealing two evolutionary patterns. In pattern#1, clusters detected in the primary tumor biopsy were likely relapse seeding clones, as they contributed a major share to ctDNA at relapse. In pattern#2, similar clusters were present in tumors and ctDNA; however, they were entirely cleared from liquid biopsy after chemotherapy and were undetectable at relapse. ctDNA private variants were present among both patterns, with some of them mirroring subclonal expansions after chemotherapy. CONCLUSIONS: We demonstrate that tracing the temporal heterogeneity of ctDNA, even below exome scale resolution, deciphers evolutionary trajectories in ovarian cancer. Furthermore, we describe two evolutionary patterns that may help to identify relapse seeding clones for targeted therapy.

Establishment and Molecular Characterization of an In Vitro Model for PARPi-Resistant Ovarian Cancer.

Overcoming PARPi resistance is a high clinical priority. We established and characterized comparative in vitro models of acquired PARPi resistance, derived from either a BRCA1-proficient or BRCA1-deficient isogenic background by long-term exposure to olaparib. While parental cell lines already exhibited a certain level of intrinsic activity of multidrug resistance (MDR) proteins, resulting PARPi-resistant cells from both models further converted toward MDR. In both models, the PARPi-resistant phenotype was shaped by (i) cross-resistance to other PARPis (ii) impaired susceptibility toward the formation of DNA-platinum adducts upon exposure to cisplatin, which could be reverted by the drug efflux inhibitors verapamil or diphenhydramine, and (iii) reduced PARP-trapping activity. However, the signature and activity of ABC-transporter expression and the cross-resistance spectra to other chemotherapeutic drugs considerably diverged between the BRCA1-proficient vs. BRCA1-deficient models. Using dual-fluorescence co-culture experiments, we observed that PARPi-resistant cells had a competitive disadvantage over PARPi-sensitive cells in a drug-free medium. However, they rapidly gained clonal dominance under olaparib selection pressure, which could be mitigated by the MRP1 inhibitor MK-751. Conclusively, we present a well-characterized in vitro model, which could be instrumental in dissecting mechanisms of PARPi resistance from HR-proficient vs. HR-deficient background and in studying clonal dynamics of PARPi-resistant cells in response to experimental drugs, such as novel olaparib-sensitizers.

Performance and characterization of the FinEstBeAMS beamline at the MAX IV Laboratory.

FinEstBeAMS (Finnish-Estonian Beamline for Atmospheric and Materials Sciences) is a multidisciplinary beamline constructed at the 1.5 GeV storage ring of the MAX IV synchrotron facility in Lund, Sweden. The beamline covers an extremely wide photon energy range, 4.5-1300 eV, by utilizing a single elliptically polarizing undulator as a radiation source and a single grazing-incidence plane grating monochromator to disperse the radiation. At photon energies below 70 eV the beamline operation relies on the use of optical and thin-film filters to remove higher-order components from the monochromated radiation. This paper discusses the performance of the beamline, examining such characteristics as the quality of the gratings, photon energy calibration, photon energy resolution, available photon flux, polarization quality and focal spot size.

Optimized highly efficient multilayer-coated blazed gratings for the tender X-ray region.

The optimized design of multilayer-coated blazed gratings (MLBG) for high-flux tender X-ray monochromators was systematically studied by numerical simulations. The resulting correlation between the multilayer d-spacing and grating blaze angle significantly deviated from the one predicted by conventional equations. Three high line density gratings with different blaze angles were fabricated and coated by the same Cr/C multilayer. The MLBG with an optimal blaze angle of 1.0° showed a record efficiency reaching 60% at 3.1 keV and 4.1 keV. The measured efficiencies of all three gratings were consistent with calculated results proving the validity of the numerical simulation and indicating a more rigorous way to design the optimal MLBG structure.

Open biomedical pluralism: formalising knowledge about breast cancer phenotypes.

We demonstrate a heterogeneity of representation types for breast cancer phenotypes and stress that the characterisation of a tumour phenotype often includes parameters that go beyond the representation of a corresponding empirically observed tumour, thus reflecting significant functional features of the phenotypes as well as epistemic interests that drive the modes of representation. Accordingly, the represented features of cancer phenotypes function as epistemic vehicles aiding various classifications, explanations, and predictions. In order to clarify how the plurality of epistemic motivations can be integrated on a formal level, we give a distinction between six categories of human agents as individuals and groups focused around particular epistemic interests. We analyse the corresponding impact of these groups and individuals on representation types, mapping and reasoning scenarios. Respecting the plurality of representations, related formalisms, expressivities and aims, as they are found across diverse scientific communities, we argue for a pluralistic ontology integration. Moreover, we discuss and illustrate to what extent such a pluralistic integration is supported by the distributed ontology language DOL, a meta-language for heterogeneous ontology representation that is currently under standardisation as ISO WD 17347 within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. We particularly illustrate how DOL supports representations of parthood on various levels of logical expressivity, mapping of terms, merging of ontologies, as well as non-monotonic extensions based on circumscription allowing a transparent formal modelling of the normal/abnormal distinction in phenotypes.