Addressing Modern Diagnostic Pathology for Patient-Derived Soft Tissue Sarcosphere Models in the Era of Functional Precision Oncology.

Responses to therapy often cannot be exclusively predicted by molecular markers, thus evidencing a critical need to develop tools for better patient selection based on relations between tumor phenotype and genotype. Patient-derived cell models could help to better refine patient stratification procedures and lead to improved clinical management. So far, such ex vivo cell models have been used for addressing basic research questions and in preclinical studies. As they now enter the era of functional precision oncology, it is of utmost importance that they meet quality standards to fully represent the molecular and phenotypical architecture of patients' tumors. Well-characterized ex vivo models are imperative for rare cancer types with high patient heterogeneity and unknown driver mutations. Soft tissue sarcomas account for a very rare, heterogeneous group of malignancies that are challenging from a diagnostic standpoint and difficult to treat in a metastatic setting because of chemotherapy resistance and a lack of targeted treatment options. Functional drug screening in patient-derived cancer cell models is a more recent approach for discovering novel therapeutic candidate drugs. However, because of the rarity and heterogeneity of soft tissue sarcomas, the number of well-established and characterized sarcoma cell models is extremely limited. Within our hospital-based platform we establish high-fidelity patient-derived ex vivo cancer models from solid tumors for enabling functional precision oncology and addressing research questions to overcome this problem. We here present 5 novel, well-characterized, complex-karyotype ex vivo soft tissue sarcosphere models, which are effective tools to study molecular pathogenesis and identify the novel drug sensitivities of these genetically complex diseases. We addressed the quality standards that should be generally considered for the characterization of such ex vivo models. More broadly, we suggest a scalable platform to provide high-fidelity ex vivo models to the scientific community and enable functional precision oncology.

Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma.

Defects in homologous recombination repair (HRR) in tumors correlate with poor prognosis and metastases development. Determining HRR deficiency (HRD) is of major clinical relevance as it is associated with therapeutic vulnerabilities and remains poorly investigated in sarcoma. Here, we show that specific sarcoma entities exhibit high levels of genomic instability signatures and molecular alterations in HRR genes, while harboring a complex pattern of chromosomal instability. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signature that predicts PARP inhibitor sensitivity in patient-derived sarcoma cells. Concomitantly, HRDhigh sarcoma cells lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HRR. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness and demonstrate the clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways ex vivo and in the clinic. In summary, we provide a personalized oncological approach to treat sarcoma patients successfully.

Structural responses of model biomembranes to Mars-relevant salts.

Lipid membranes are a key component of contemporary living systems and are thought to have been essential to the origin of life. Most research on membranes has focused on situations restricted to ambient physiological or benchtop conditions. However, the influence of more extreme conditions, such as the deep subsurface on Earth or extraterrestrial environments are less well understood. The deep subsurface environments of Mars, for instance, may harbor high concentrations of chaotropic salts in brines, yet we know little about how these conditions would influence the habitability of such environments for cellular life. Here, we investigated the combined effects of high concentrations of salts, including sodium and magnesium perchlorate and sulfate, and high hydrostatic pressure on the stability and structure of model biomembranes of varying complexity. To this end, a variety of biophysical techniques have been applied, which include calorimetry, fluorescence spectroscopies, small-angle X-ray scattering, dynamic light scattering, and microscopy techniques. We show that the structure and phase behavior of lipid membranes is sensitively dictated by the nature of the salt, in particular its anion and its concentration. We demonstrate that, with the exception of magnesium perchlorate, which can also induce cubic lipid arrangements, long-chain saturated lipid bilayer structures can still persist at high salt concentrations across a range of pressures. The lateral organization of complex heterogeneous raft-like membranes is affected by all salts. For simple, in particular bacterial membrane-type bilayer systems with unsaturated chains, vesicular structures are still stable at Martian brine conditions, also up to the kbar pressure range, demonstrating the potential compatibility of environments containing such ionic and pressure extremes to lipid-encapsulated life.

Liquid droplets of protein LAF1 provide a vehicle to regulate storage of the signaling protein K-Ras4B and its transport to the lipid membrane.

Liquid-liquid phase separation has been shown to promote the formation of functional membraneless organelles involved in various cellular processes, including metabolism, stress response and signal transduction. Protein LAF1 found in P-granules phase separates into liquid-like droplets by patterned electrostatic interactions between acidic and basic tracts in LAF1 and has been used as model system in this study. We show that signaling proteins, such as K-Ras4B, a small GTPase that acts as a molecular switch and regulates many cellular processes including proliferation, apoptosis and cell growth, can colocalize in LAF1 droplets. Colocalization is facilitated by electrostatic interactions between the positively charged polybasic domain of K-Ras4B and the negatively charged motifs of LAF1. The interaction partners B- and C-Raf of K-Ras4B can also be recruited to the liquid droplets. Upon contact with an anionic lipid bilayer membrane, the liquid droplets dissolve and K-Ras4B is released, forming nanoclusters in the lipid membrane. Considering the high tuneability of liquid-liquid phase separation in the cell, the colocalization of signaling proteins and their effector molecules in liquid droplets may provide an additional vehicle for regulating storage and transport of membrane-associated signaling proteins such as K-Ras4B and offer an alternative strategy for high-fidelity signal output.

Impact of the number of rhamnose moieties of rhamnolipids on the structure, lateral organization and morphology of model biomembranes.

Various studies have described remarkable biological activities and surface-active properties of rhamnolipids, leading to their proposed use in a wide range of industrial applications. Here, we report on a study of the effects of monorhamnolipid RhaC10C10 and dirhamnolipid RhaRhaC10C10 incorporation into model membranes of varying complexity, including bacterial and heterogeneous model biomembranes. For comparison, we studied the effect of HAA (C10C10, lacking a sugar headgroup) partitioning into these membrane systems. AFM, confocal fluorescence microscopy, DSC, and Laurdan fluorescence spectroscopy were employed to yield insights into the rhamnolipid-induced morphological changes of lipid vesicles as well as modifications of the lipid order and lateral membrane organization of the model biomembranes upon partitioning of the different rhamnolipids. The partitioning of the three rhamnolipids into phospholipid bilayers changes the phase behavior, fluidity, lateral lipid organization and morphology of the phospholipid membranes dramatically, to what extent, depends on the headgroup structure of the rhamnolipid, which affects its packing and hydrogen bonding capacity. The incorporation into giant unilamellar vesicles (GUVs) of a heterogeneous anionic raft membrane system revealed budding of domains and fission of daughter vesicles and small aggregates for all three rhamnolipids, with major destabilization of the lipid vesicles upon insertion of RhaC10C10, and also formation of huge GUVs upon the incorporation of RhaRhaC10C10. Finally, we discuss the results with regard to the role these biosurfactants play in biology and their possible impact on applications, ranging from agricultural to pharmaceutical industries.

Interaction of rhamnolipids with model biomembranes of varying complexity.

Rhamnolipids represent a large class of biologically produced surface-active compounds, which participate in various essential cellular functions. While many studies have reported on the antibacterial and antifungal effects of rhamnolipids, only a few tried to describe the molecular mechanisms underlying these effects. Here, we first review the literature on rhamnolipid-phospholipid interactions and then add own results on a prominent monorhamnolipid congener, RhaC10C10. By focusing on the interactions between the rhamnolipid and lipid model membranes of different complexity, up to heterogeneous raft-like model biomembranes, we gained new insights into changes of the lateral membrane organization and morphological changes of membrane vesicles induced by partitioning of the rhamnolipid. To this end, AFM, confocal fluorescence microscopy, and Laurdan fluorescence spectroscopy analyses were employed. In summary, we provide a concise description of the physio-chemical effects rhamnolipids impose on lipid membranes, which help us to understand their physiological role.

An Imidazolium-Based Lipid Analogue as a Gene Transfer Agent.

A dicationic imidazolium salt is described and investigated towards its application for gene transfer. The polar head group and the long alkyl chains in the backbone contribute to a lipid-like behavior, while an alkyl ammonium group provides the ability for crucial electrostatic interaction for the transfection process. Detailed biophysical studies regarding its impact on biological membrane models and the propensity of vesicle fusion are presented. Fluorescence spectroscopy, atomic force microscopy and confocal fluorescence microscopy show that the imidazolium salt leads to negligible changes in lipid packing, while displaying distinct vesicle fusion properties. Cell culture experiments reveal that mixed liposomes containing the novel imidazolium salt can serve as plasmid DNA delivery vehicles. In contrast, a structurally similar imidazolium salt without a second positive charge showed no ability to support DNA transfection into cultured cells. Thus, we introduce a novel and variable structural motif for cationic lipids, expanding the field of lipofection agents.

Interaction of imidazolium-based lipids with phospholipid bilayer membranes of different complexity.

In recent years, alkylated imidazolium salts have been shown to affect lipid membranes and exhibit general cytotoxicity as well as significant anti-tumor activity. Here, we examined the interactions of a sterically demanding, biophysically unexplored imidazolium salt, 1,3-bis(2,6-diisopropylphenyl)-4,5-diundecylimidazolium bromide (C11IPr), on the physico-chemical properties of various model biomembrane systems. The results are compared with those for the smaller headgroup variant 1,3-dimethyl-4,5-diundecylimidazolium iodide (C11IMe). We studied the influence of these two lipid-based imidazolium salts at concentrations from 1 to about 10 mol% on model biomembrane systems of different complexity, including anionic heterogeneous raft membranes which are closer to natural membranes. Fluorescence spectroscopic, DSC, surface potential and FTIR measurements were carried out to reveal changes in membrane thermotropic phase behavior, lipid conformational order, fluidity and headgroup charge. Complementary AFM and confocal fluorescence microscopy measurements allowed us to detect changes in the lateral organization and membrane morphology. Both lipidated imidazolium salts increase the membrane fluidity and lead to a deterioration of the lateral domain structure of the membrane, in particular for C11IPr owing to its bulkier headgroup. Moreover, partitioning of the lipidated imidazolium salts into the lipid vesicles leads to marked changes in lateral organization, curvature and morphology of the lipid vesicles at high concentrations, with C11IPr having a more pronounced effect than C11IMe. Hence, these compounds seem to be vastly suitable for biochemical and biotechnological engineering, with high potentials for antimicrobial activity, drug delivery and gene transfer.

Effect of ectoine, hydroxyectoine and ß-hydroxybutyrate on the temperature and pressure stability of phospholipid bilayer membranes of different complexity.

Previous research has shown that ectoines fluidize lipid monolayers by increasing the liquid expanded region in DPPC monolayers and also decreasing the line tension responsible for the phase morphology. Here, we explored possible effects of the compatible osmolytes ectoine, hydroxyectoine and ß-hydroxybutyrate on lipid bilayer membranes, including effects of temperature and pressure. The effect of the protective osmolytes on the phase transition of DPPC bilayers was investigated by fluorescence spectroscopy, differential scanning calorimetry and pressure perturbation calorimetry. A slight change of the phase behavior was observed, which resulted in a stabilization of the gel phase, which may be caused by an alteration of the hydration properties at the lipid interface and H-bond and electrostatic interactions in the headgroup region. We then explored the cosolvents' effects on giant unilamellar vesicles (GUVs) formed by lipid mixtures exhibiting phase separation into liquid-ordered (lo) and liquid-disordered (ld) domains using BODIPY-PC and the DiI18 dye as labels. The presence of both, ectoine and hydroxyectoine showed significant effects on the lateral organization increasing the fluid domains. Moreover, we observed a considerable increase in the adhesion behavior of small vesicles onto GUV surfaces. Diffusion studies by fluorescence recovery after photobleaching experiments on POPC giant vesicles quantitatively showed a hydroxyectoine-induced increase of the diffusion coefficient values, clearly demonstrating an increase in the lateral mobility of lipid within the bilayer membrane. This study provides clear evidence for the fluidizing effect of the compatible solutes on bilayer lipid membranes. A marked effect, however, was only detected if phase separated domains exist.

Impact of Y3+-ions on the structure and phase behavior of phospholipid model membranes.

Trivalent yttrium cations are able to mimic the behavior of Ca2+ in many important biochemical processes, and their application in medicinal chemistry has increased in recent years. While the effect of mono- and divalent salts on lipid membranes has been studied extensively, the effect of trivalent cations, such as Y3+, on the structure and phase behavior of lipid bilayers is largely unknown. Here, we studied the effect of YCl3 on the structure, phase behavior and thermodynamic parameters of zwitterionic DPPC, 20% anionic DPPC/DPPG (80/20) and 10% anionic DOPC/DOPG/DPPC/DPPG/cholesterol (20/5/45/5/25) model biomembrane systems using Fourier-transform infrared spectroscopy, differential scanning calorimetry, Laurdan fluorescence spectroscopy, confocal fluorescence microscopy, zeta potential measurements and atomic force microscopy, covering a wide range of salt concentrations, temperature and pressure. Y3+ ions penetrate deep into the lipid headgroup region and are coordinated to the phosphate groups, resulting in a stronger lipid packing and partial dehydration of the headgroup region. Increasing Y3+ concentration leads to a pronounced increase of the gel-to-fluid phase transition temperature of the phospholipid bilayers, owing to an increased lateral compression pressure, particularly for anionic lipid membranes. Increased lipid chain order and phase segregation of anionic membranes is fostered at high salt concentrations owing to lipid sorting. The fluid-to-gel phase transition pressure decreases significantly with the concentration of the trivalent ion, most pronounced for the negatively charged lipid vesicles. Remarkably, the Y3+-induced ordering effect is much stronger than a hydrostatic pressure-induced ordering of the lipid chains.

Effect of hyaluronic acid on phospholipid model membranes.

The role of hyaluronic acid (HA) in supporting low friction and low abrasion during movement in synovial joints is still not fully understood. In this study, we set out to investigate the interaction between HA and representative lipid model membranes, bilayers as well as monolayers, in detail using a variety of calorimetric, spectroscopic, scattering and microscopic techniques, to explore their role in lubrication of articular cartridge. We also cover a wide range of pressures to mimic pressures occurring upon joint movement, aiming at elucidating a possible mechanism for the low friction forces in synovial joints. Effects of HA on lipid bilayer membranes, encompassing significant adsorption at the membrane, penetration of the hydrophobic regions of the HA between lipid head groups, or changes of the temperature- and pressure dependent phase behavior of the membrane or mechanical properties could not be observed. High molecular weight HA at physiological NaCl concentrations might rather operate independently, via an entropy-driven excluded volume effect, to control the hydrodynamics of the synovial fluid. Minor effects are observed only at domain boundaries using lipid monolayers. As lubrication of natural joints is a synergistic effect, other components of the synovial fluid, such as proteoglycans, might play a more active role.

Combined effects of osmotic and hydrostatic pressure on multilamellar lipid membranes in the presence of PEG and trehalose.

We studied the interaction of lipid membranes with the disaccharide trehalose (TRH), which is known to stabilize biomembranes against various environmental stress factors. Generally, stress factors include low/high temperature, shear, osmotic and hydrostatic pressure. Small-angle X-ray-scattering was applied in combination with fluorescence spectroscopy and calorimetric measurements to get insights into the influence of trehalose on the supramolecular structure, hydration level, and elastic and thermodynamic properties as well as phase behavior of the model biomembrane DMPC, covering a large region of the temperature, osmotic and hydrostatic pressure phase space. We observed distinct effects of trehalose on the topology of the lipid's supramolecular structure. Trehalose, unlike osmotic pressure induced by polyethylene glycol, leads to a decrease of lamellar order and a swelling of multilamellar vesicles, which is attributable to direct interactions between the membrane and trehalose. Our results revealed a distinct biphasic concentration dependence of the observed effects of trehalose. While trehalose intercalates between the polar head groups at low concentrations, the effects after saturation are dominated by the exclusion of trehalose from the membrane surface.

On the Origin of Microtubules' High-Pressure Sensitivity.

For over 50 years, it has been known that the mitosis of eukaryotic cells is inhibited already at high hydrostatic pressure conditions of 30 MPa. This effect has been attributed to the disorganization of microtubules, the main component of the spindle apparatus. However, the structural details of the depolymerization and the origin of the pressure sensitivity have remained elusive. It has also been a puzzle how complex organisms could still successfully inhabit extreme high-pressure environments such as those encountered in the depth of oceans. We studied the pressure stability of microtubules at different structural levels and for distinct dynamic states using high-pressure Fourier-transform infrared spectroscopy and Synchrotron small-angle x-ray scattering. We show that microtubules are hardly stable under abyssal conditions, where pressures up to 100 MPa are reached. This high-pressure sensitivity can be mainly attributed to the internal voids and packing defects in the microtubules. In particular, we show that lateral and longitudinal contacts feature different pressure stabilities, and they define also the pressure stability of tubulin bundles. The intactness of both contact types is necessary for the functionality of microtubules in vivo. Despite being known to dynamically stabilize microtubules and prevent their depolymerization, we found that the anti-cancer drug taxol and the accessory protein MAP2c decrease the pressure stability of microtubule protofilaments. Moreover, we demonstrate that the cellular environment itself is a crowded place and accessory proteins can increase the pressure stability of microtubules and accelerate their otherwise highly pressure-sensitive de novo formation.