Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters.

BACKGROUND: Intratumoural heterogeneity (ITH) is well recognised in prostate cancer (PC), but its role in high-risk disease is uncertain. A prospective, single-arm, translational study using targeted multiregion prostate biopsies was carried out to study genomic and T-cell ITH in clinically high-risk PC aiming to identify drivers and potential therapeutic strategies. PATIENTS AND METHODS: Forty-nine men with elevated prostate-specific antigen and multiparametric-magnetic resonance imaging detected PC underwent image-guided multiregion transperineal biopsy. Seventy-nine tumour regions from 25 patients with PC underwent sequencing, analysis of mutations, copy number and neoepitopes combined with tumour infiltrating T-cell subset quantification. RESULTS: We demonstrated extensive somatic nucleotide variation and somatic copy number alteration heterogeneity in high-risk PC. Overall, the mutational burden was low (0.93/Megabase), but two patients had hypermutation, with loss of mismatch repair (MMR) proteins, MSH2 and MSH6. Somatic copy number alteration burden was higher in patients with metastatic hormone-naive PC (mHNPC) than in those with high-risk localised PC (hrlPC), independent of Gleason grade. Mutations were rarely ubiquitous and mutational frequencies were similar for mHNPC and hrlPC patients. Enrichment of focal 3q26.2 and 3q21.3, regions containing putative metastasis drivers, was seen in mHNPC patients. We found evidence of parallel evolution with three separate clones containing activating mutations of ß-catenin in a single patient. We demonstrated extensive intratumoural and intertumoural T-cell heterogeneity and high inflammatory infiltrate in the MMR-deficient (MMRD) patients and the patient with parallel evolution of ß-catenin. Analysis of all patients with activating Wnt/ß-catenin mutations demonstrated a low CD8+/FOXP3+ ratio, a potential surrogate marker of immune evasion. CONCLUSIONS: The PROGENY (PROstate cancer GENomic heterogeneitY) study provides a diagnostic platform suitable for studying tumour ITH. Genetic aberrations in clinically high-risk PC are associated with altered patterns of immune infiltrate in tumours. Activating mutations of Wnt/ß-catenin signalling pathway or MMRD could be considered as potential biomarkers for immunomodulation therapies. CLINICAL TRIALS.GOV IDENTIFIER: NCT02022371.

iDermatoPath - a novel software tool for mitosis detection in H&E-stained tissue sections of malignant melanoma.

BACKGROUND: Malignant Melanoma (MM) is characterized by a growing incidence and a high malignant potential. Besides well-defined prognostic factors such as tumour thickness and ulceration, the Mitotic Rate (MR) was included in the AJCC recommendations for diagnosis and treatment of MM. In daily routine, the identification of a single mitosis can be difficult on haematoxylin and eosin slides alone. Several studies showed a big inter- and intra-individual variability in detecting the MR in MM even by very experienced investigators, thus raising the question for a computer-assisted method. OBJECTIVE: The objective was to develop a software system for mitosis detection in MM on H&E slides based on machine learning for diagnostic support. METHODS: We developed a computer-aided staging support system based on image analysis and machine learning on the basis of 59 MM specimens. Our approach automatically detects tumour regions, identifies mitotic nuclei and classifies them with respect to their diagnostic relevance. A convenient user interface enables the investigator to browse through the proposed mitoses for fast and efficient diagnosing. RESULTS: A quantitative evaluation on manually labelled ground truth data revealed that the tumour region detection yields a medium spatial overlap index (dice coefficient) of 0.72. For the mitosis detection, we obtained high accuracies of above 83%. CONCLUSION: On the technical side, the developed iDermatoPath software tool provides a novel approach for mitosis detection in MM, which can be further improved using more training data such as dermatopathologist annotations. On the practical side, a first evaluation of the clinical utility was positive, albeit this approach provides most benefit for difficult cases in a research setting. Assuming all slides to be digitally processed and reported in the near future, this method could become a helpful additional tool for the pathologist.

Taming microwave plasma to beat thermodynamics in CO2 dissociation.

The strong non-equilibrium conditions provided by the plasma phase offer the opportunity to beat traditional thermal process energy efficiencies via preferential excitation of molecular vibrations. Simple molecular physics considerations are presented to explain potential dissociation pathways in plasma and their effect on energy efficiency. A common microwave reactor approach is evaluated experimentally with Rayleigh scattering and Fourier transform infrared spectroscopy to assess gas temperatures (exceeding 10(4) K) and conversion degrees (up to 30%), respectively. The results are interpreted on a basis of estimates of the plasma dynamics obtained with electron energy distribution functions calculated with a Boltzmann solver. It indicates that the intrinsic electron energies are higher than is favorable for preferential vibrational excitation due to dissociative excitation, which causes thermodynamic equilibrium chemistry to dominate. The highest observed energy efficiencies of 45% indicate that non-equilibrium dynamics had been at play. A novel approach involving additives of low ionization potential to tailor the electron energies to the vibrational excitation regime is proposed.

Beamlet scraping and its influence on the beam divergence at the BATMAN Upgrade test facility.

For the ITER fusion experiment, two neutral beam injectors are required for plasma heating and current drive. Each injector supplies a power of about 17 MW, obtained from neutralization of 40 A (46 A), 1 MeV (0.87 MeV) negative deuterium (hydrogen) ions. The full beam is composed of 1280 beamlets, formed in 16 beamlet groups, and strict requirements apply to the beamlet core divergence (<7 mrad). The test facility BATMAN Upgrade uses an ITER-like grid with one beamlet group, which consists of 70 apertures. In a joint campaign performed by IPP and Consorzio RFX to better assess the beam optics, the divergence of a single beamlet was compared to a group of beamlets at BATMAN Upgrade. The single beamlet is measured with a carbon fiber composite tile calorimeter and by beam emission spectroscopy, whereas the divergence of the group of beamlets is measured by beam emission spectroscopy only. When increasing the RF power at low extraction voltages, the divergence of the beamlet and of the group of beamlets is continuously decreasing and no inflection point toward an overperveant beam is found. At the same time, scraping of the extracted ion beam at the second grid (extraction grid) takes place at higher RF power, supported by the absence of the normally seen linear behavior between the measured negative ion density in the plasma close to the extraction system and the measured extracted ion current. Beside its influence on the divergence, beamlet scraping needs to be considered for the determination of the correct perveance and contributes to the measured coextracted electron current.

Targeting mitosis-regulating genes in cisplatin-sensitive and -resistant melanoma cells: A live-cell RNAi screen displays differential nucleus-derived phenotypes.

Chemoresistance in malignant melanoma remains an unresolved clinical issue. In the search for novel molecular targets, a live-cell high-content RNAi screen based on gene expression data was performed in cisplatin-sensitive and cisplatin-resistant MeWo melanoma cells, Mel-28 cells and a melanocyte cell line. Cells were exposed to 91 siRNAs and distinct nucleus-derived phenotypes such as cell division, cell death and migration phenotypes were detected by time-lapse microscopy over 60 h. Using this approach, cisplatin-sensitive and cisplatin-resistant melanoma cells were compared by automated image analysis and visual inspection. In cisplatin-sensitive MeWo melanoma cells, 14 genes were identified that showed distinct phenotype abnormalities after exposure to gene-specific siRNAs. In cisplatin-resistant MeWo cells, five genes were detected. Nine genes were detected whose knock-down led to differential nuclear phenotypes in cisplatin-sensitive and -resistant cells. In Mel-28 cells, nine genes were identified which induced nuclear phenotypes including all eight genes which were identified in cisplatin-resistant MeWo cells. An analogous RNAi screen on melanocytes revealed no detectable phenotype abnormalities after RNAi. Pathway analysis showed in cisplatin-sensitive MeWo cells and Mel-28 cells an enrichment of at least three genes in major mitotic pathways. We hereby show that siRNA screening may help to identify tumor-specific genes leading to phenotype abnormalities. These genes may serve as potential therapeutic targets in the treatment of melanoma.

Automated classification of mitotic phenotypes of human cells using fluorescent proteins.

High-throughput screens of the gene function provide rapidly increasing amounts of data. In particular, the analysis of image data acquired in genome-wide cell phenotype screens constitutes a substantial bottleneck in the evaluation process and motivates the development of automated image analysis tools for large-scale experiments. In this chapter, we present a computational scheme to process multicell time-lapse images as they are produced in high-throughput screens. We describe an approach to automatically segment and classify cell nuclei into different mitotic phenotypes. This enables automated identification of cell cultures that show an abnormal mitotic behavior. Our scheme proves high classification accuracy, suggesting a promising future for automating the evaluation of high-throughput experiments.

New materials for optical thin films.

New materials for optical thin films are presented. Zirconium oxide, titanium oxide, cerie oxide, and hafnium oxide in the form of black tablets or cones of various sizes for the electron beam evaporation technique were developed. These materials are oxygen depleted and give an uniform melt during the evaporation to give reproducible evaporation characteristics. A new mixture consisting of ZrO(2) and ZrTiO(4) for the production of high index layers is described. The evaporation conditions of the substance and the properties of thin layers of the mixture are given. The refractive index is 2.15 at 500 nm. The transmittance range is 0.4-7 microm. The layers are optically homogeneous. The application of layers of this mixture in a three-layer antireflection coating is described.