P10.21.B Pharmacogenomics profiling of gliomas for precision medicine

Background

Molecular characterization based on genomic, transcriptomic and epigenetic profiling has led to a better delineation of various glioma subtypes and highlighted the individual paths of glioma evolution upon treatment and recurrence. However, due to cellular and molecular diversity of these tumors, the pharmacological treatment of gliomas, in particular of its most malignant subtype Glioblastoma (GBM), remains a major challenge. To address this challenge, we here apply a pharmacogenomics approach, modelling the disease in matched patient-derived preclinical models and profiling the differential drug response among individual patients and glioma subtypes

Material and Methods

We generated a cohort of 45 Patient-Derived Orthotopic Xenografts (PDOX) from a collection of over 400 glioma patients. We used a multi-parametric approach based on genetic, transcriptomic and longitudinal profiling of patients and their matched xenografts for a comprehensive subgrouping of our glioma cohort. Based on PDOX-derived 3D tumor organoids we carried out a targeted drug screen focused on epigenetic regulators. A high throughput drug screening using an unbiased large chemical library containing a unique collection of FDA approved compounds with high pharmacological diversity is currently ongoing.

Results

Our glioma cohort with matched PDOX and 3D tumor organoids represents diverse subgroups of glioma patients, including a unique collection of primary and relapsed tumors from the same patient. Our preliminary drug screen analysis on 3D organoids highlights selective susceptibility to certain epigenetic inhibitors in primary disease but not in the same patient’s relapse. Results of matching genomics and functional data will be presented.

Conclusion

An integrated personalized approach to profile gliomas at multiple genomic and functional levels allows for pharmacogenomic subgrouping of patients for personalized treatment strategies. This analysis will allow to link genotypes to functional phenotypes and hopefully identify therapeutic options for selected glioma sub-populations.

Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2

Lysyl oxidase-like 2 (LOXL2) has emerged as a promising therapeutic target against metastatic/invasive tumors and organ and tissue fibrosis. LOXL2 catalyzes the oxidative deamination of lysine and hydroxylysine residues in extracellular matrix (ECM) proteins to promote crosslinking of these proteins, and thereby plays a major role in ECM remodeling. LOXL2 secretes as 100-kDa full-length protein (fl-LOXL2) and then undergoes proteolytic cleavage of the first two scavenger receptor cysteine-rich (SRCR) domains to yield 60-kDa protein (Δ1-2SRCR-LOXL2). This processing does not affect the amine oxidase activity of LOXL2 in vitro. However, the physiological importance of this cleavage still remains elusive. In this study, we focused on characterization of biophysical properties of fl- and Δ1-2SRCR-LOXL2s (e.g., oligomeric states, molecular weights, and hydrodynamic radii in solution) to gain insight into the structural role of the first two SRCR domains. Our study reveals that fl-LOXL2 exists predominantly as monomer but also dimer to the lesser extent when its concentration is <~1 mM. The hydrodynamic radius (R_h) determined by multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) indicates that fl-LOXL2 is a moderately asymmetric protein. In contrast, Δ1-2SRCR-LOXL2 exists solely as monomer and its R_h is in good agreement with the predicted value. The R_h values calculated from a 3D modeled structure of fl-LOXL2 and the crystal structure of the precursor Δ1-2SRCR-LOXL2 are within a reasonable margin of error of the values determined by SEC-MALS for fl- and Δ1-2SRCR-LOXL2s in mature forms in this study. Based on superimposition of the 3D model and the crystal structure of Δ1-2SRCR-LOXL2 (PDB:5ZE3), we propose a configuration of fl-LOXL2 that explains the difference observed in R_h between fl- and Δ1-2SRCR-LOXL2s in solution.

Combining parallel pattern generation of electrohydrodynamic lithography with serial addressing

Electrohydrodynamic lithography (EHDL) is a parallel patterning process which typically makes use of topographically structured electrodes to guide pattern formation along areas of higher electrical field strength. The main driving force for pattern formation is an electrostatic pressure acting on a thin film polymer surface caused by a voltage applied between a top and bottom electrode. We here demonstrate that the principle can be applied using an addressable electrode composed of interdigitated fingers. Depending on the applied voltages, line patterns with different periodicities were fabricated. Our proof-of-concept experiments pave the way for a parallel pattern replication process where a serially addressed master is used. We complement the experiments by modelling the potentials across the electrodes and electrostatic forces acting on the polymer surface using different addressing schemes. Numerical simulations of the experimental setup pointed to some critical issues we experienced during the design of the experiments.

Via different electrode addressing schemes in electrohydrodynamic lithography, different patterns were generated.

Changes in urine autofluorescence in ovarian cancer patients

Ovarian cancer is the type of cancer with the highest mortality rate among gynaecologic malignancies. Due to lack of screening tools, this disease is mainly diagnosed at a progressed stage, when it is too late to adequate therapy. Despite many attempts, enough sensitive and specific biomarker was not still uncovered. Fluorescence spectroscopy has proven to be a useful diagnostic tool with high efficiency. Fluorescence detection has three major advantages over other light-based investigation methods: high sensitivity, high speed, and reliability. Biological materials consist of a number of intrinsic fluorescent compounds -autofluorophores, which are associated with cardinal metabolic pathways. It is well known, that cancerous tissue metabolism is altered compared to healthy one, what influence also intrinsic fluorophores composition of bodily fluids. Urine is one of the biological fluids that could be obtained most easily and displays a blue - green fluorescence that can change in case of pathological process. Analysis of urine autofluorescence is non invasive and simple technique. Using fluorescent spectroscopy, ovarian cancer patients and healthy control group were discerned with high significance, so we predict that fluorescence analysis of urine could be a potential means of ovarian cancer screening.

Effects of exercise stress on the endocannabinoid system in humans under field conditions

The effects of physical exercise stress on the endocannabinoid system in humans are almost unexplored. In this prospective study, we investigated in a crossover design and under field conditions at different altitudes the effects of physical exercise on the endocannabinoid system (ECS) in 12 trained healthy volunteers. For determination of alterations on the ECS three different protocols were analyzed: Protocol A (physical exercise at lower altitude) involved strenuous hiking below 2,100 m, whereas Protocol B (physical exercise by active ascent to high altitude) involved hiking up to 3,196 m, an accommodation at the cottage and a descent the next day. Protocol C (passive ascent) included a helicopter ascent to 3,196 m, an overnight stay at this altitude and a flight back to the base camp the following day. The cumulative hiked altitude in Protocol A and B was comparable (~1,650 m). The blood EC concentrations of anandamide increased significantly in Protocol A/B from baseline (T0) 0.12 ± 0.01/0.16 ± 0.02 (mean ± SEM) to 0.27 ± 0.02/0.42 ± 0.02 after exercise (T1) (p < 0.05). Anandamide levels in Protocol C remained stable at 0.20 ± 0.02. We conclude that the ECS is activated upon strenuous exercise whereas the combination with hypoxic stress further increases its activity. The reduced partial pressure of oxygen at high altitude alone did not affect this system. In summary, physical exercise activates the endocannabinoid system, whereas the combination with high altitude enhances this activation. This discloses new perspectives to adaptation mechanisms to physical exercise.

Mesencephalic dopamine neuron number and tyrosine hydroxylase content: Genetic control and candidate genes

The mesotelencephalic dopamine system shows substantial genetic variation which fundamentally affects normal and pathological behaviors related to motor function, motivation, and learning. Our earlier radioenzyme assay studies demonstrated significantly higher activity of tyrosine hydroxylase (TH), the first and rate limiting enzyme in the biosynthesis of catecholamine neurotransmitters, in the substantia nigra-ventral tegmental area of BALB/cJ mice in comparison with that of C57BL/6ByJ mice. Here, using quantitative immunoblotting and immunocytochemistry, we tested the hypothesis that mesencephalic TH protein content and number of nigral TH-positive neurons show strain-dependent differences in C57BL/6ByJ and BALB/cJ parallel to those observed in the TH activity studies. Immunoblotting experiments detected significantly higher mesencephalic TH protein content in BALB/cJ in comparison to C57BL/6ByJ (P<0.05). Immunocytochemical studies demonstrated that the number of TH-positive cells in substantia nigra was 31.3% higher in BALB/cJ than that in C57BL/6ByJ (P<0.01), while the average dopamine neuron volume was not significantly different. In a search for candidate genes that modulate TH content and the size of mesencephalic dopamine neuron populations we also studied near-isogenic mouse sublines derived from the C57BL/6ByJ and BALB/cJ progenitor strains. A whole-genome scan with 768 single nucleotide polymorphism markers indicated that two sublines, C4A6/N and C4A6/B, were genetically very similar (98.3%). We found significantly higher mesencephalic TH protein content in C4A6/B in comparison to C4A6/N (P=0.01), and a tendency for higher number of dopamine neurons in the substantia nigra in C4A6/B in comparison to C4A6/N, which, however, did not reach statistical significance. To identify the genetic source of the TH content difference we analyzed the single nucleotide polymorphism (SNP) genotype data of the whole-genome scan, and detected two small differential chromosome segments on chr. 13 and chr. 14. Microarray gene expression studies and bioinformatic analysis of the two differential regions implicated two cis-regulated genes (Spock1 and Cxcl14, chr. 13), and two growth factor genes [bone morphogenetic protein 6 (Bmp6) (chr. 13), and fibroblast growth factor 14 (Fgf14) (chr. 14)]. Taken together, the results suggest that (1) nigral dopamine neuron number and TH protein content may be genetically associated but further studies are needed to establish unequivocally this linkage, and (2) Spock1, Cxcl14, Bmp6, and Fgf14 are novel candidates for modulating the expression and maintenance of TH content in mesencephalic dopamine neurons in vivo.

Oriented immobilisation of engineered single-chain antibodies to develop biosensors for virus detection

Single chain variable fragment (scFv) molecules were selected from a synthetic phage display library then cloned into a generic vector for expression of the scFv fused to the light chain constant domain of human immunoglobulin with a C-terminal cysteine residue (scFvC(L)cys). A heterobifunctional maleimide linker was synthesised and a strategy for functionalization of gold with the scFvC(L)cys fusion proteins elaborated. Successful covalent attachment of functional scFvC(L)cys was demonstrated using a surface plasmon resonance-based sensor. The results showed that the immobilised scFvC(L)cys molecules were functional and specific binding curves (with response relative to the concentration of virus antigen) were obtained over more than 25 cycles of binding and dissociation. ScFv molecules lacking the C-terminal cysteine performed poorly in similar experiments. The work demonstrates the feasibility of using simple scFv selection and cloning procedures combined with oriented immobilisation of scFvC(L)cys fusion proteins for robust antigen sensing surfaces in immunosensor or other biotechnological applications.

In situ derivatisation using pressurized liquid extraction to determine phenols, sterols and carboxylic acids in environmental samples and microbial biomasses

Pressurized liquid extraction was combined with in-situ derivatisation to extract polar analytes such as phenols (including chlorophenols) sterols and carboxylic acids from environmental and microbial samples. This one-step protocol uses acetic anhydride as an acetylation agent, N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) as an silylation agent, and boron trifluoride-methanol, phenyltrimethyl ammoniumhydroxide and trimethyl sulfoniumhydroxide as methylation agents. It results in faster extraction rates and better or comparable extraction efficiencies when compared to classical approaches. The addition of a silylation agent also facilitates the extraction kinetics of analytes not accessible to silylation (e.g. polycyclic aromatic hydrocarbons or alkylbenzenes). This may be attributed to a dissociative action of the agent to weaken analyte-matrix interactions.

Light-induced nuclear import of phytochrome-A:GFP fusion proteins is differentially regulated in transgenic tobacco and Arabidopsis

Phytochromes (phy) are a family of photoreceptors that control various aspects of light-dependent plant development. Phytochrome A (phyA) is responsible for the very low fluence response (VLFR) under inductive light conditions and for the high irradiance response (HIR) under continuous far-red light. We have recently shown that nuclear import of rice phyA:GFP is regulated by VLFR in transgenic tobacco. The import is preceded by very fast, light-induced formation of sequestered areas of phyA:GFP in the cytosol. Here we report that expression of the Arabidopsis phyA:GFP fusion protein in phyA-deficient Arabidopsis plants complements the mutant phenotype. In these transgenic Arabidopsis lines, both light-dependent cytosolic formation of sequestered areas of the phyA:GFP as well as VLFR or HIR-mediated nuclear import of the fusion protein was observed. By contrast, light-dependent nuclear import of the same fusion protein was induced only by continuous far-red light (HIR) but not by pulses of far-red light (VLFR) in transgenic tobacco. These results demonstrate that photoregulation of intracellular partitioning of the Arabidopsis phyA:GFP differs significantly in different genetic backgrounds.

Vesicular–arbuscular mycorrhizal colonization in Zea mays affected by breeding for resistance to fungal pathogens

Inbred lines of Zea mays L. (maize) selected for a range of resistances to a variety of fungal pathogens were assayed for percentage colonization by vesicular–arbuscular mycorrhizal fungi. Inbreds that were generally resistant to a number of fungal pathogens had significantly lower levels of vesicular–arbuscular mycorrhizae, matured more slowly, and had larger root systems. Disease-susceptible inbreds had significantly higher levels of mycorrhizal colonization, matured more rapidly, and had smaller root systems. It is uncertain if a general resistance to fungal pathogens or rate of root development, separately or in combination, may have influenced mycorrhizal colonization levels. Irrespective of cause, present breeding programs for disease resistance in maize do influence the plants ability to form mycorrhizae.

Dynamics of arbuscule development and degeneration in onion, bean, and tomato with reference to vesicular–arbuscular mycorrhizae in grasses

A quantitative light and electron microscopic study of developing and degenerating arbuscules of the vesicular–arbuscular mycorrhizal fungus Glomus fasciculatum in onion, bean, and tomato was carried out to estimate three parameters during the colonization cycle and to compare these parameters with those in maize, oats, and wheat. The parameters are (i) Vv(a,c) the fraction of the host cell volume (c) occupied by the arbuscule (a); (ii) VV(cy,c) the fraction of the host cell volume occupied by host cytoplasm (cy); and (iii) SV(p,c) the ratio of the surface area of the host protoplast (p) to the volume of the whole host cell. Uninfected cortical cells contained 3.4% cytoplasm in onion, 3.1% in bean, and 3.5% in tomato. In cells with mature arbuscules, cytoplasm increased to 9.9% in onion, 14.2% in bean, and 13.6% in tomato. Cells with mature arbuscules contained 11.4% fungus in onion, 20.3% in bean, and 20.5% in tomato. The initial SV(p,c) in onion was 0.10 μm2/μm3 and in bean and tomato 0.11 μm2/μm3. This increased to 0.37 μm2/μm3 in onion, 0.82 μm2/μm3 in bean, and 0.54 μm2/μm3 in tomato by the time arbuscules were mature. Development of the arbuscule was estimated to take 2.5 days and occupied 33% of the total cycle time. The variation seen across host species can be used as an indicator of fungal and (or) host control for each parameter. Arbuscular parameters of onion were compared with those obtained by other authors.

Detection of acquired immunodeficiency syndrome (AIDS) retrovirus antibody by lymphadenopathy-associated virus (LAV) enzyme immunoassay in low- and high-risk populations

Antibody to the acquired immunodeficiency syndrome (AIDS) retrovirus was evaluated by an lymphadenopathy-associated (LAV) enzyme immunosorbent assay (EIA) and compared with the standard human T-cell lymphotropic virus, Type III (HTLV-III) screening test in two groups of people. The first group consisted of those at low risk for AIDS, including 1352 random volunteer donors, 1140 of whom were prospective donors and 212 of whom were retrospective donors, repeatedly reactive by HTLV-III EIA. The second group was composed of those at high risk for AIDS, including 54 hemophiliacs, one of whom had AIDS, seven AIDS-related complex (ARC), and one immune thrombocytopenia (ITP). Of the 1140 prospective donors, one was repeatedly reactive by LAV EIA and four by HTLV-III EIA; none was positive by Western blot. Of the 212 retrospective donors, six were repeatedly reactive by LAV EIA and 212 by HTLV-III EIA; only six (the six LAV EIA positive) were positive by Western blot. Of the 54 hemophiliacs, 46 were repeatedly reactive by both LAV EIA and HTLV-III EIA, and all 46 were positive by Western blot. Both LAV EIA and HTLV-III EIA were positive in all hemophiliacs with AIDS, ARC, and ITP. The marked reduction in HTLV-III EIA repeatedly reactive, Western blot nonreactive samples by the LAV EIA system suggests that this assay may be as sensitive but more specific than the standard HTLV-III EIA in low-risk populations. The strong correlation between the LAV EIA and the Western blot assay further suggests that this assay may provide an efficient screening test for AIDS antibody in the donor population.

Total and free plasma neuroleptic levels in schizophrenic patients

Nineteen male patients, under 35 years of age, newly admitted with a diagnosis of schizophrenia, were treated with either chlorpromazine or haloperidol at a fixed dosage for 25 days. Both total and free plasma neuroleptic levels were measured using a radioreceptor assay. Clinical response was measured by the Brief Psychiatric Rating Scale (BPRS). On day 25, nonresponders (those with a decrease of less than 8 points on the BPRS) had both total and free plasma neuroleptic levels within the range observed in responders. It is therefore concluded that lack of therapeutic response is generally not due to inadequate plasma drug levels.

Cardiac muscle development in mice exposed to ethanol in utero

The purpose of the present research was to determine the effect of in utero ethanol exposure on cardiac muscle development. Pregnant albino mice (Swiss strain) at 8 days of gestation were divided into three groups: a normal group fed Purina lab chow for rodents and water ad libitum; an ethanol group fed the liquid diet ENSURE with 20% of the calories derived from ethanol (12.6 +/- 1.2 gm/kg body weight per day); and an isocaloric group pairfed ENSURE with 20% of the calories derived from sucrose. These diets were continued until birth, at which time the litter size, crown to rump length, and weight were recorded. Randomly selected neonatal pups from each litter were decapitated and their hearts immediately processed for transmission electron microscopy. Litter size, crown to rump length, and body weight of the ethanol-treated mice at birth were significantly less than normal but not less than pairfed controls. Ultrastructural evaluation of cardiac muscle from mice treated in utero with ethanol in comparison to that from both normal and pair-fed control animals revealed various degrees of morphological alterations. The most pronounced alterations were in mitochondrial structure and included an increase in mitochondrial volume per cytoplasmic volume and a marked decrease in the amount of inner mitochondrial membrane. Myofibrillar abnormalities were also evident in the ethanol group but not in either control group. These abnormalities included a decrease in the myofibril volume per cytoplasmic volume and a disruption in myofibril organization particularly the Z-bands. The ultrastructural alterations in the cardiac muscle from the ethanol treated group were not a result of malnutrition or dehydration as the pairfed group did not exhibit these changes. It is apparent from this study that exposure of mice in utero to ethanol can cause ultrastructural abnormalities in cardiac muscle cells. Whether these changes result in heart pathophysiology and persist to adulthood are not known.

Cytochemical localization of acid phosphatase in endophyte cells of the semiparasitic angiosperm Comandra umbellata (Santalaceae)

Acid phosphatase (orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2) has been localized in cells at the growing tips of the endophyte in the semiparasitic angiosperm Comandra umbellata. Lysosomes in tip cells release their contents into the apoplast at the host–parasite interface before any possible release of enzyme from disrupted host lysosomes. However, a large-scale digestion of host cells does not occur. Parasite cells release acid phosphatase and probably other lysosomal enzymes which appear to disrupt host cell membranes causing a loss in turgor pressure followed by the eventual crushing of host cells by the invading endophyte.

Anatomy and ultrastructure of the haustorium in Comandra (Santalaceae)

The endophyte of the haustorium in Comandra and the tissues of the upper haustorium have a complex developmental and structural relationship with each other. Glands may be found near the tip of a young endophyte, providing evidence that the gland and surrounding tissues have been moved into the host as a unit. A distinct interrupted zone is present, traversed by a small number of unbranched vessels. Additionally, some apparently blind vessels in the more central portion of this zone are occluded with fibrous material which seems to be secreted by vesicles in the adjacent parenchyma. Advance into the host seems to involve crushing host cells and subsequent absorption of cell contents. It is suggested that superficial digitate cells are also crushed and that the lytic enzymes thus liberated play a role in the attack on host cells. The dark-staining non-cellular layer delimiting many parts of the endophyte seems to be made up of crushed cell walls from both partners. No cytoplasmic connections between host and parasite have been observed. Mature xylem contacts may be abutments in pit areas of host vessels or actual invasions of the latter, often with cell divisions within such invaded tracheary members. The function of the gland remains obscure.

Anatomy and ultrastructure of the young haustorial gland in Comandra (Santalaceae)

The haustorial gland of Comandra (Santalaceae) originates from an internal meristem-like area in the young haustorium and involves the differentiation of a double layer of palisade-like parenchyma cells in the median region. These cells secrete substances (positive with periodic acid – Schiff s reagent (PAS)) which seem to be deposited by vesicles that migrate to the median plane to deposit their products between the cell membrane and cell wall. Cell walls in the median area become extremely thin and finally disappear, leaving a cavity filled with secretory products. The lower portion of the gland shows a distinct duct region lined with a single layer of cells secreting a fibrous, layered substance apparently by means of endoplasmic reticulum (ER) vesicles; this substance appears to be neither cellulose nor starch and cannot be called wall-like. The duct in Comandra has not been observed to reach the haustorial surface, but events at the time of penetration of host tissues remain undescribed. Despite past speculations as to the digestive function of the gland, convincing evidence supporting this or any other function is still lacking.