OS12.2 Targeting epigenetic pathways in the treatment of recurrent high-grade glioma

BACKGROUND

High grade glioma (HGG) patients develop resistance to standard treatment leading to disease progression and limited life expectancy. Advances in the molecular characterisation of treatment-naïve HGGs based on next-generation sequencing and DNA methylation analyses have led to a better delineation of HGG subtypes and the identification of distinct genomic abnormalities. Furthermore, using large patient cohorts of longitudinal tumor samples, comprehensive genomic profiling studies emerged to investigate therapy-associated evolution of gliomas. All together, those studies point out the need for personalised treatment strategies, where applied drugs will be adapted to the unique patient-specific genetic abnormalities.

MATERIAL AND METHODS

We collected fresh samples of more than 800 brain tumors containing almost 300 glioma specimen with approximately 100 longitudinal samples of initial and recurrent tumors from 43 matched patients. By now, we have successfully established 34 patient-derived orthotopic xenografts (PDOXs) in mice. We performed comprehensive molecular profiling using array comparative genomic hybridisation, DNA methylation analysis and targeted DNA sequencing on patient specimen and their derivatives such as 3D tumor organoids and PDOXs. The custom-design sequencing panel comprises 234 genes that reflect both established genetic identifiers for individual glioma subtype classification and novel genes encoding mainly epigenetic effector genes. Based on patient-derived material we carried out drug response screening on 3D tumor organoids using a compound library matching the majority of genes that were assessed by targeted sequencing.

RESULTS

We succeeded in generating a live biobank of HGG patient-derived xenografts and 3D organoids that neatly recapitulates the mutational spectrum including structural DNA variation and methylation-based subtypes of gliomas. A highlight is the generation of 19 PDOXs of paired initial and relapse HGGs from a total of 9 glioma patients. A detailed analysis of the paired longitudinal samples indicated that PDOX models closely recapitulate the evolutionary trajectory of the parental tumors. Targeted sequencing of longitudinal HGG PDOXs suggests that relapse tumors accumulate somatic mutations in epigenetic effectors compared with the Initial. Differential drug responses between initial and relapse tumors were observed after screening of in vitro 3D tumor organoids.

CONCLUSION

Response assessment of naïve initial gliomas and recurrences provides crucial information on the differential sensitivity between initial and relapsed HGGs and offers novel personalised therapeutic options in the relapse setting. Furthermore, in depth correlation of the profiled somatic molecular landscape with drug response will enable pharmacogenomic predictions of potential inhibitors in the clinical setting.

Diagnosing eosinophilic asthma using a multivariate prediction model based on blood granulocyte responsiveness

BACKGROUND

The identification of inflammatory asthma phenotypes, using sputum analysis, has proven its value in diagnosis and disease monitoring. However due to technical limitations of sputum analysis, there is a strong need for fast and noninvasive diagnostics. This study included the activation state of eosinophils and neutrophils in peripheral blood to phenotype and monitor asthma.

OBJECTIVES

To (i) construct a multivariable model using the activation state of blood granulocytes, (ii) compare its diagnostic value with sputum eosinophilia as gold standard and (iii) validate the model in an independent patient cohort.

METHODS

Clinical parameters, activation of blood granulocytes and sputum characteristics were assessed in 115 adult patients with asthma (training cohort/Utrecht) and 34 patients (validation cohort/Oxford).

RESULTS

The combination of blood eosinophil count, fractional exhaled nitric oxide, Asthma Control Questionnaire, medication use, nasal polyposis, aspirin sensitivity and neutrophil/eosinophil responsiveness upon stimulation with formyl-methionyl-leucyl phenylalanine was found to identify sputum eosinophilia with 90.5% sensitivity and 91.5% specificity in the training cohort and with 77% sensitivity and 71% specificity in the validation cohort (relatively high percentage on oral corticosteroids [OCS]).

CONCLUSIONS

The proposed prediction model identifies eosinophilic asthma without the need for sputum induction. The model forms a noninvasive and externally validated test to assess eosinophilic asthma in patients not on OCS.

Controlled covalent binding of antiferromagnetic tetramanganese complexes to carbon nanotubes

Tetramanganese complexes are covalently attached to carbon nanotubes such, that the magnetic properties of the antiferromagnetic molecules are preserved.

Understanding the formation mechanism and the 3D structure of Mo(SxSe1−x)2 nanoflowers

Colloidal synthesis of MoS₂, MoSe₂ and their alloys produces fine nanoflowers with tunable composition. Their reaction mechanism produces homogeneous solid solutions, beneficial for designing specific properties.

Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy

We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti-L2,3 and O-K edges for a specimen of SrTiO3 oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti-L2,3 and O-K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations.

Strain-induce shift of the crystal-field splitting of SrTiO₃ embedded in scandate multilayers

Strained SrTiO₃ layers have become of interest, since the paraelectric-to-ferroelectric transition temperature can be increased to room temperature. A linear relationship between strain and energy splitting of the fundamental transitions in the fine structure of Ti L(₂,₃) and O K edges is observed, that can be exploited to measure strain from electronic transitions, complementary to measuring local strain directly via high-resolution transmission electron microscopy (HRTEM) images. In particular, for both methods, the geometrical phase analysis performed on high-resolution images and the measurement of the energy splitting by energy loss spectroscopy, tensile strain of SrTiO₃ layers was measured when grown on DyScO₃ and GdScO₃ substrates. The effect of strain on the electron loss near edge structure (ELNES) of the Ti L(₂,₃) edge in comparison to unstrained samples is analyzed. Ab initio calculations of the Ti L(₂,₃) and O K edge show a linear variation of the crystal field splitting with strain. Calculated and experimental values of the crystal field splitting show a very good agreement.

Structural Properties of Microcrystalline Si Solar Cells

The structural properties of nip-µc-Si:H solar cells are investigated by transmission electron microscopy, X-ray diffraction and Raman spectroscopy. Different structural compositions are obtained by variation of the gas mixture during preparation by plasma enhanced chemical vapour deposition. Nucleation and growth of the n-layer onto textured TCO substrate was found to be similar to the growth on glass substrates. The growth of the i-layer follows a local epitaxy. This implies that the structure of the n-layer is of special importance regarding the control of the microstructure in microcrystalline Si nip solar cells.

Plastic-deformation mechanism in complex solids

In simple crystalline materials, plastic deformation mostly takes place by the movement of dislocations. Although the underlying mechanisms in these materials are well explored, in complex metallic alloys--crystalline solids containing up to thousands of atoms per unit cell--the defects and deformation mechanisms remain essentially unknown. Owing to the large lattice parameters of these materials, extended dislocation concepts are required. We investigated a typical complex metallic alloy with 156 atoms per unit cell using atomic-resolution aberration-corrected transmission electron microscopy. We found a highly complex deformation mechanism, based on the movement of a dislocation core mediating strain and separate escort defects. On deformation, the escort defects move along with the dislocation core and locally transform the material structure for the latter. This mechanism implies the coordinated movement of hundreds of atoms per elementary glide step, and nevertheless can be described by simple rearrangement of basic structural subunits.

Defects induced on chemical vapour deposition carbon nanotubes during peapod synthesis on substrates

Individual carbon nanotubes are filled with fullerene molecules directly on the substrate. Two different oxidation techniques for opening the tubes prior to the filling, annealing in air, and acid treatment, are compared. High-resolution transmission electron microscopy images indicate that both methods induce defects on the sidewalls of the nanotubes. In the case of acid treatment, the inner walls can be damaged without affecting the outer walls, while the inner walls are opened along with the outer ones by heating in air. The effect of acid treatment on the tubes is much stronger than known from bulk samples. In contrast to previous studies, we find amorphous carbon inside the nanotubes after oxidation, and an additional high-temperature annealing step is needed to remove these plugs in order to open the tubes for filling.

Atomic-precision determination of the reconstruction of a 90 degree tilt boundary in YBa2Cu3O7-delta by aberration corrected HRTEM

Aberration corrected high-resolution transmission electron microscopy is used to determine the reconstruction of atomic bonds of a 90 degree [100] grain boundary in YBa(2)Cu(3)O(7-delta). A precise measurement of atom positions within the grain boundary and the assessment of the oxygen stoichiometry require at the same time a high control of residual lens aberrations of the electron microscope and a good signal-to-noise ratio. This goal is achieved by the combination of spherical-aberration correction in the microscope with the numerical exit-plane wave function reconstruction from focal series. Atomic column positions for individual cations and anions are determined by the regression analysis of peak maxima in the phase image of the retrieved exit-plane wave function. The measurement accuracy is quantitatively assessed, including the statistical error related to residual noise. Changes in bondlengths between copper atoms and the apical oxygen are measured, indicating the distortion of the square pyramidal oxygen coordination of plane copper sites and the square coordination of chain copper sites in the grain boundary.

A clinicopathological study on overexpression of cyclin D1 and of p53 in a series of 248 patients with operable breast cancer

Overexpression of cyclin D1 is frequently found in various types of human tumours and results from clonal rearrangement and/or amplification involving chromosomal region 11q13. In order to evaluate the pathological relevance of cyclin D1 overexpression in human breast cancer, we generated a polyclonal antiserum against the carboxy-terminal part of the cyclin D1 protein. After affinity purification, the antiserum specifically detected overexpression of cyclin D1 in formalin-fixed, paraffin-embedded tumour material also. The intensity of the nuclear stainings was, in general, proportional to the degree of cyclin D1 amplification. We did not encounter significant variability of staining within individual tumours with overexpression of cyclin D1. Overexpression of cyclin D1 appeared to be associated with oestrogen receptor-positive breast tumours, but not with any other clinicopathological parameter tested. Overexpression of cyclin D1 was not prognostic value for recurrence of survival in a consecutive series of 248 operable breast cancer patients (stage I and II). Overexpression of p53 was also not of prognostic significance in this series, but was associated with undifferentiated histology and oestrogen receptor-negative breast tumours, as has been reported previously by others. A high proportion of breast tumours with a low grade of malignancy in this series of operable breast cancer patients may explain discrepancies concerning the prognostic value of amplification and of overexpression of cyclin D1.