Mutational scanning pinpoints distinct binding sites of key ATGL regulators in lipolysis.

ATGL is a key enzyme in intracellular lipolysis and plays an important role in metabolic and cardiovascular diseases. ATGL is tightly regulated by a known set of protein-protein interaction partners with activating or inhibiting functions in the control of lipolysis. Here, we use deep mutational protein interaction perturbation scanning and generate comprehensive profiles of single amino acid variants that affect the interactions of ATGL with its regulatory partners: CGI-58, G0S2, PLIN1, PLIN5 and CIDEC. Twenty-three ATGL amino acid variants yield a specific interaction perturbation pattern when validated in co-immunoprecipitation experiments in mammalian cells. We identify and characterize eleven highly selective ATGL switch mutations which affect the interaction of one of the five partners without affecting the others. Switch mutations thus provide distinct interaction determinants for ATGL's key regulatory proteins at an amino acid resolution. When we test triglyceride hydrolase activity in vitro and lipolysis in cells, the activity patterns of the ATGL switch variants trace to their protein interaction profile. In the context of structural data, the integration of variant binding and activity profiles provides insights into the regulation of lipolysis and the impact of mutations in human disease.

Biomimetic Mineralization of Iron-Fumarate Nanoparticles for Protective Encapsulation and Intracellular Delivery of Proteins.

Biomimetic mineralization of proteins and nucleic acids into hybrid metal-organic nanoparticles allows for protection and cellular delivery of these sensitive and generally membrane-impermeable biomolecules. Although the concept is not necessarily restricted to zeolitic imidazolate frameworks (ZIFs), so far reports about intracellular delivery of functional proteins have focused on ZIF structures. Here, we present a green room-temperature synthesis of amorphous iron-fumarate nanoparticles under mildly acidic conditions in water to encapsulate bovine serum albumin (BSA), horseradish peroxidase (HRP), green fluorescent protein (GFP), and Cas9/sgRNA ribonucleoproteins (RNPs). The synthesis conditions preserve the activity of enzymatic model proteins and the resulting nanoparticles deliver functional HRP and Cas9 RNPs into cells. Incorporation into the iron-fumarate nanoparticles preserves and protects the activity of RNPs composed of the acid-sensitive Cas9 protein and hydrolytically labile RNA even during exposure to pH 3.5 and storage for 2 months at 4 °C, which are conditions that strongly impair the functionality of unprotected RNPs. Thus, the biomimetic mineralization into iron-fumarate nanoparticles presents a versatile platform for the delivery of biomolecules and protects them from degradation during storage under challenging conditions.

Directed invasion of cancer cell spheroids inside 3D collagen matrices oriented by microfluidic flow in experiment and simulation.

Invasion is strongly influenced by the mechanical properties of the extracellular matrix. Here, we use microfluidics to align fibers of a collagen matrix and study the influence of fiber orientation on invasion from a cancer cell spheroid. The microfluidic setup allows for highly oriented collagen fibers of tangential and radial orientation with respect to the spheroid, which can be described by finite element simulations. In invasion experiments, we observe a strong bias of invasion towards radial as compared to tangential fiber orientation. Simulations of the invasive behavior with a Brownian diffusion model suggest complete blockage of migration perpendicularly to fibers allowing for migration exclusively along fibers. This slows invasion toward areas with tangentially oriented fibers down, but does not prevent it.

Mesoporous Biodegradable Magnesium Phosphate-Citrate Nanocarriers Amplify Methotrexate Anticancer Activity in HeLa Cells.

We present the synthesis of amorphous, mesoporous, colloidal magnesium phosphate-citrate nanoparticles (MPCs) from biogenic precursors, resulting in a biocompatible and biodegradable nanocarrier that amplifies the action of the anticancer drug methotrexate (MTX). Synthesis conditions were gradually tuned to investigate the influence of the chelating agent citric acid on the colloidal stability and the mesoporosity of the obtained nanoparticles. With optimized synthesis conditions, a large BET surface area of 560 m2/g was achieved. We demonstrate the potential of these biocompatible and biodegradable mesoporous MPCs as a drug delivery system. Lipid-coated MPCs were used to load the fluorescent dye calcein and the chemotherapeutic agent MTX into the mesopores. In vitro experiments show very low premature release of the cargo but efficient stimuli-responsive release in an environment of pH 5.5, in which MPCs degrade. Lipid-coated MPCs are taken up by cancer cells and are nontoxic up to concentrations of 100 µg/mL. When loaded with MTX serving as a representative model drug for in vitro studies, MPCs induced efficient cell death with an IC50 value of 1.1 µg/mL. Compared to free MTX, its delivery with MPCs enhances its efficiency by an order of magnitude. In summary, we have developed a biodegradable nanomaterial synthesized from biocompatible precursors that are neither toxic by themselves nor in the form of nanoparticles. With these features, MPCs may be applied as drug delivery systems and have the potential to reduce the side effects of current chemotherapies.

Volumetric measurements of target lesions: does it improve inter-reader variability for oncological response assessment according to RECIST 1.1 guidelines compared to standard unidimensional measurements?

PURPOSE: Target lesion selection is known to be a major factor for inter-reader discordance in RECIST 1.1. The purpose of this study was to assess whether volumetric measurements of target lesions result in different response categorization, as opposed to standard unidimensional measurements, and to evaluate the impact on inter-reader agreement for response categorization when different readers select different sets of target lesions. MATERIAL AND METHODS: Fifty patients with measurable disease from solid tumours, in which 3 readers had blindly and independently selected different sets of target lesions and subsequently reached clinically significant discordant response categorizations (progressive disease [PD] vs. non-progressive disease [non-PD]) based on RECIST 1.1 analyses were included in this study. Additional volumetric measurements of all target lesions were performed by the same readers in a second read. Intra-reader agreement between standard unidimensional measurements (uRECIST) and volumetric measurements (vRECIST) was assessed using Cohen's k statistics. Fleiss k statistics was used to analyse the inter-reader agreement for uRECIST and vRECIST results. RESULTS: The 3 readers assigned the same response classifications based on uRECIST and vRECIST in 33/50 (66%), 42/50 patients (84%), and 44/50 patients (88%), respectively. Inter-reader agreement improved from 0% when using uRECIST to 36% when using vRECIST. CONCLUSIONS: Volumetric measurement of target lesions may improve inter-reader variability for response assessment as opposed to standard unidimensional measurements. However, in about two-thirds of patients, readers disagreed regardless of the measurement method, indicating that a limited set of target lesions may not be sufficiently representative of the whole-body tumour burden.

Liquid-liquid phase separation underpins the formation of replication factories in rotaviruses.

RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liquid phase separation of the viroplasm-forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus-infected cells. Early infection stage condensates could be reversibly dissolved by 1,6-hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate-forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA-rich condensates that support replication of multi-segmented genomes represent an attractive target for developing novel therapeutic approaches.

Protocol for photoactivation of YAP in cancer cell spheroids embedded in collagen gels.

This protocol describes the necessary preparations and procedures to photo-activate Yes-associated protein (YAP) with optoYAP in cancer cell spheroids in 3D collagen matrices. We detail steps for immunofluorescent staining of the resulting YAP-activated HeLa spheroids. In addition, we describe handling of optoYAP on 2D substrates. While this protocol focuses on the use of optoYAP in 3D HeLa cell culture, it can be modified for other cell types. For complete details on the use and execution of this protocol, please refer to Illes et al. (2021).

Mesoporous Silica Nanoparticles as pH-Responsive Carrier for the Immune-Activating Drug Resiquimod Enhance the Local Immune Response in Mice.

Nanoparticle-based delivery systems for cancer immunotherapies aim to improve the safety and efficacy of these treatments through local delivery to specialized antigen-presenting cells (APCs). Multifunctional mesoporous silica nanoparticles (MSNs), with their large surface areas, their tunable particle and pore sizes, and their spatially controlled functionalization, represent a safe and versatile carrier system. In this study, we demonstrate the potential of MSNs as a pH-responsive drug carrier system for the anticancer immune-stimulant R848 (resiquimod), a synthetic Toll-like receptor 7 and 8 agonist. Equipped with a biotin-avidin cap, the tailor-made nanoparticles showed efficient stimuli-responsive release of their R848 cargo in an environmental pH of 5.5 or below. We showed that the MSNs loaded with R848 were rapidly taken up by APCs into the acidic environment of the lysosome and that they potently activated the immune cells. Upon subcutaneous injection into mice, the particles accumulated in migratory dendritic cells (DCs) in the draining lymph nodes, where they strongly enhanced the activation of the DCs. Furthermore, simultaneous delivery of the model antigen OVA and the adjuvant R848 by MSNs resulted in an augmented antigen-specific T-cell response. The MSNs significantly improved the pharmacokinetic profile of R848 in mice, as the half-life of the drug was increased 6-fold, and at the same time, the systemic exposure was reduced. In summary, we demonstrate that MSNs represent a promising tool for targeted delivery of the immune modulator R848 to APCs and hold considerable potential as a carrier for cancer vaccines.

Spatio-selective activation of nuclear translocation of YAP with light directs invasion of cancer cell spheroids.

The mechanical properties of the extracellular matrix strongly influence tumor progression and invasion. Yes-associated protein (YAP) has been shown to be a key regulator of this process translating mechanical cues from the extracellular matrix into intracellular signals. Despite its apparent role in tumor progression and metastasis, it is not clear yet, whether YAP activation can actively trigger the onset of invasion. To address this question, we designed a photo-activatable YAP (optoYAP), which allows for spatiotemporal control of its activation. The activation mechanism of optoYAP is based on optically triggered nuclear translocation of the protein. Activation of optoYAP induces downstream signaling for several hours and leads to increased proliferation in two- and three-dimensional cultures. Applied to cancer spheroids, optoYAP activation induces invasion. Site-selective activation of optoYAP in cancer spheroids strikingly directs invasion into the activated direction. Thus, nuclear translocation of YAP may be enough to trigger the onset of invasion.

CT-based whole-body tumor volumetry versus RECIST 1.1: Feasibility and implications for inter-reader variability.

PURPOSE: To investigate whether volumetric measurements of the whole-body tumor volume (WBTV) are feasible and whether they improve inter-reader variability in patients in whom conventional RECIST 1.1 assessment yielded discordant results. METHODS: 50 patients (29 male, 21 female, mean age 60.9 ±â€¯12.3 years) with metastases of solid tumors in whom three readers had selected different sets of target lesions and subsequently reached different results for response assessment (progressive vs. non-progressive disease) when using RECIST 1.1 were included. In a second read, all readers performed volumetric measurements of the WBTV on neck/chest/abdomen/pelvis CTs and measured the time needed for these measurements. Cohen's kappa and Fleiss kappa statistics were used to compare the intra- and inter-reader agreement for response assessment. RESULTS: In 8/50 patients (16 %), the WBTV was too extensive for volumetric measurements and these patients were therefore excluded. In the remaining 42 patients, WBTV measurements required a mean time of 18 min and 9 s. Readers assigned the same response categorizations based on unidimensional RECIST measurements and WBTV measurements in 15/42 patients (33 %), 24/42 patients (57 %) and 30/42 patients (71 %) for reader 1,2 and 3 respectively. When performing response assessment based on WBTV measurements, the three readers agreed in 40/42 patients (95 %) regarding the distinction progressive vs. non-progressive disease, resulting in a near-perfect agreement on a patient-based level (Fleiss' κ = 0.921, 0.95-CI:0.746-1.095). CONCLUSIONS: WBTV measurements yielded an almost perfect inter-reader agreement in a cohort of patients, in which three readers reached discordant response assessment results when following conventional RECIST 1.1 guidelines. This supports the hypothesis, that a limited subset of metastases may not be sufficient to accurately assess response-to-treatment.

Factors That Drive Heterogeneity of Response-to-Treatment of Different Metastatic Deposits Within the Same Patients as Measured by RECIST 1.1 Analyses.

RATIONALE AND OBJECTIVE: This study uses the rate of between-reader variability under Response Evaluation Criteria for Solid Tumors (RECIST) 1.1 as a metric to estimate the prevalence of biologic heterogeneity of individual metastases, and to determine whether this prevalence is modulated by the type of primary tumor, or type of treatment administered. MATERIALS AND METHODS: Three radiologists independently used dedicated oncologic response-assessment software (MintLesion) to prospectively determine RECIST1.1 treatment response in contrast-enhanced computed tomography studies of 355 patients with metastatic disease of different primaries between 07/2015 and 12/2017. In 200 patients, readers had chosen different sets of target lesions; these cases were used for further analysis. Clinically significant heterogeneity of response was considered to be present when RECIST1.1 results differed regarding the distinction of progressive versus non-progressive disease. Rates of response heterogeneity were compared for different types of primary cancers, and different types of systemic treatment. RESULTS: Heterogeneous treatment response was observed in 67 of 200 (34%) patients. Breast cancer was the only primary tumor associated with statistically significantly increased odds for heterogeneity of treatment response (Odds Ratio: 3.972, 0.95 Confidence Interval: 1.275-12.376, p = 0.017). No association was found between type of systemic treatment and rate of biologic heterogeneity. CONCLUSION: Clinically significant heterogeneity of response-to-treatment is a frequent phenomenon, observed in about one-third of patients undergoing contemporary systemic therapies. Patients with breast cancer are more likely to exhibit such heterogeneity. Type of systemic treatment did not modulate the likelihood of exhibiting metastases with diverging treatment response.

Particle-Size-Dependent Delivery of Antitumoral miRNA Using Targeted Mesoporous Silica Nanoparticles.

Multifunctional core-shell mesoporous silica nanoparticles (MSN) were tailored in size ranging from 60 to 160 nm as delivery agents for antitumoral microRNA (miRNA). The positively charged particle core with a pore diameter of about 5 nm and a stellate pore morphology allowed for an internal, protective adsorption of the fragile miRNA cargo. A negatively charged particle surface enabled the association of a deliberately designed block copolymer with the MSN shell by charge-matching, simultaneously acting as a capping as well as endosomal release agent. Furthermore, the copolymer was functionalized with the peptide ligand GE11 targeting the epidermal growth factor receptor, EGFR. These multifunctional nanoparticles showed an enhanced uptake into EGFR-overexpressing T24 bladder cancer cells through receptor-mediated cellular internalization. A luciferase gene knock-down of up to 65% and additional antitumoral effects such as a decreased cell migration as well as changes in cell cycle were observed. We demonstrate that nanoparticles with a diameter of 160 nm show the fastest cellular internalization after a very short incubation time of 45 min and produce the highest level of gene knock-down.

Metal-Organic Framework Nanoparticles Induce Pyroptosis in Cells Controlled by the Extracellular pH.

Ion homeostasis is essential for cellular survival, and elevated concentrations of specific ions are used to start distinct forms of programmed cell death. However, investigating the influence of certain ions on cells in a controlled way has been hampered due to the tight regulation of ion import by cells. Here, it is shown that lipid-coated iron-based metal-organic framework nanoparticles are able to deliver and release high amounts of iron ions into cells. While high concentrations of iron often trigger ferroptosis, here, the released iron induces pyroptosis, a form of cell death involving the immune system. The iron release occurs only in slightly acidic extracellular environments restricting cell death to cells in acidic microenvironments and allowing for external control. The release mechanism is based on endocytosis facilitated by the lipid-coating followed by degradation of the nanoparticle in the lysosome via cysteine-mediated reduction, which is enhanced in slightly acidic extracellular environment. Thus, a new functionality of hybrid nanoparticles is demonstrated, which uses their nanoarchitecture to facilitate controlled ion delivery into cells. Based on the selectivity for acidic microenvironments, the described nanoparticles may also be used for immunotherapy: the nanoparticles may directly affect the primary tumor and the induced pyroptosis activates the immune system.

Supersensitive Multifluorophore RNA-FISH for Early Virus Detection and Flow-FISH by Using Click Chemistry.

The reliable detection of transcription events through the quantification of the corresponding mRNA is of paramount importance for the diagnostics of infections and diseases. The quantification and localization analysis of the transcripts of a particular gene allows disease states to be characterized more directly compared to an analysis on the transcriptome wide level. This is particularly needed for the early detection of virus infections as now required for emergent viral diseases, e. g. Covid-19. In situ mRNA analysis, however, is a formidable challenge and currently performed with sets of single-fluorophore-containing oligonucleotide probes that hybridize to the mRNA in question. Often a large number of probe strands (>30) are required to get a reliable signal. The more oligonucleotide probes are used, however, the higher the potential off-target binding effects that create background noise. Here, we used click chemistry and alkyne-modified DNA oligonucleotides to prepare multiple-fluorophore-containing probes. We found that these multiple-dye probes allow reliable detection and direct visualization of mRNA with only a very small number (5-10) of probe strands. The new method enabled the in situ detection of viral transcripts as early as 4 hours after infection.

Fiber stiffness, pore size and adhesion control migratory phenotype of MDA-MB-231 cells in collagen gels.

Cancer cell migration is influenced by cellular phenotype and behavior as well as by the mechanical and chemical properties of the environment. Furthermore, many cancer cells show plasticity of their phenotype and adapt it to the properties of the environment. Here, we study the influence of fiber stiffness, confinement, and adhesion properties on cancer cell migration in porous collagen gels. Collagen gels with soft fibers abrogate migration and promote a round, non-invasive phenotype. Stiffer collagen fibers are inherently more adhesive and lead to the existence of an adhesive phenotype and in general confined migration due to adhesion. Addition of TGF-ß lowers adhesion, eliminates the adhesive phenotype and increases the amount of highly motile amoeboid phenotypes. Highest migration speeds and longest displacements are achieved in stiff collagen fibers in pores of about cell size by amoeboid phenotypes. This elucidates the influence of the mechanical properties of collagen gels on phenotype and subsequently migration and shows that stiff fibers, cell sized pores, and low adhesion, are optimal conditions for an amoeboid phenotype and efficient migration.

Coordinative Binding of Polymers to Metal-Organic Framework Nanoparticles for Control of Interactions at the Biointerface.

Metal-organic framework nanoparticles (MOF NPs) are of growing interest in diagnostic and therapeutic applications, and due to their hybrid nature, they display enhanced properties compared to more established nanomaterials. The effective application of MOF NPs, however, is often hampered by limited control of their surface chemistry and understanding of their interactions at the biointerface. Using a surface coating approach, we found that coordinative polymer binding to Zr- fum NPs is a convenient way for peripheral surface functionalization. Different polymers with biomedical relevance were assessed for the ability to bind to the MOF surface. Carboxylic acid and amine containing polymers turned out to be potent surface coatings and a modulator replacement reaction was identified as the underlying mechanism. The strong binding of polycarboxylates was then used to shield the MOF surface with a double amphiphilic polyglutamate-polysarcosine block copolymer, which resulted in an exceptional high colloidal stability of the nanoparticles. The effect of polymer coating on interactions at the biointerface was tested with regard to cellular association and protein binding, which has, to the best of our knowledge, never been discussed in literature for functionalized MOF NPs. We conclude that the applied approach enables a high degree of chemical surface confinement, which could be used as a universal strategy for MOF NP functionalization. In this way, the physicochemical properties of MOF NPs could be tuned, which allows for control over their behavior in biological systems.

A Chemiluminescent Metal-Organic Framework.

The synthesis and characterization of a chemiluminescent metal-organic framework with high porosity is reported. It consists of Zr6 O6 (OH)4 nodes connected by 4,4'-(anthracene-9,10-diyl)dibenzoate as the linker and luminophore. It shows the topology known for UiO-66 and is therefore denoted PAP-UiO. The MOF was not only obtained as bulk material but also as a thin film. Exposure of PAP-UiO as bulk or film to a mixture of bis-(2,4,6-trichlorophenyl) oxalate, hydrogen peroxide, and sodium salicylate in a mixture of dimethyl and dibutyl phthalate evoked strong and long lasting chemiluminescence of the PAP-UiO crystals. Time dependent fluorescence spectroscopy on bulk PAP-UiO and, for comparison, on dimethyl 4,4'-(anthracene-9,10-diyl)dibenzoate provided evidence that the chemiluminescence originates from luminophores being part of the PAP-UiO, including the luminophores inside the crystals.

Nanoparticle mediated delivery and small molecule triggered activation of proteins in the nucleus.

Protein transfection is a versatile tool to study or manipulate cellular processes and also shows great therapeutic potential. However, the repertoire of cost effective techniques for efficient and minimally cytotoxic delivery remains limited. Mesoporous silica nanoparticles (MSNs) are multifunctional nanocarriers for cellular delivery of a wide range of molecules, they are simple and economical to synthesize and have shown great promise for protein delivery. In this work we present a general strategy to optimize the delivery of active protein to the nucleus. We generated a bimolecular Venus based optical sensor that exclusively detects active and bioavailable protein for the performance of multi-parameter optimization of protein delivery. In conjunction with cell viability tests we maximized MSN protein delivery and biocompatibility and achieved highly efficient protein transfection rates of 80%. Using the sensor to measure live-cell protein delivery kinetics, we observed heterogeneous timings within cell populations which could have a confounding effect on function studies. To address this problem we fused a split or dimerization dependent protein of interest to chemically induced dimerization (CID) components, permitting control over its activity following cellular delivery. Using the split Venus protein we directly show that addition of a small molecule dimerizer causes synchronous activation of the delivered protein across the entire cell population. This combination of cellular delivery and triggered activation provides a defined starting point for functional studies and could be applied to other protein transfection methods.

Biocompatible crosslinked ß-cyclodextrin nanoparticles as multifunctional carriers for cellular delivery.

Nanoparticle-based biomedicine has received enormous attention for theranostic applications, as these systems are expected to overcome several drawbacks of conventional therapy. Herein, effective and controlled drug delivery systems with on-demand release abilities and biocompatible properties are used as a versatile and powerful class of nanocarriers. We report the synthesis of a novel biocompatible and multifunctional material, entirely consisting of covalently crosslinked organic molecules. Specifically, ß-cyclodextrin (CD) precursors were crosslinked with rigid organic linker molecules to obtain small (∼150 nm), thermally stable and highly water-dispersible nanoparticles with an accessible pore system containing ß-CD rings. The nanoparticles can be covalently labeled with dye molecules to allow effective tracking in in vitro cell experiments. Rapid sugar-mediated cell-uptake kinetics were observed with HeLa cells, revealing exceptional particle uptake within only 30 minutes. Additionally, the particles could be loaded with different cargo molecules showing pH-responsive release behavior. Successful nuclei staining with Hoechst 33342 dye and effective cell killing with doxorubicin cargo molecules were demonstrated in live-cell experiments, respectively. This novel nanocarrier concept provides a promising platform for the development of controllable and highly biocompatible theranostic systems.

Lipid-Coated Zinc Oxide Nanoparticles as Innovative ROS-Generators for Photodynamic Therapy in Cancer Cells.

In the present paper, we use zinc oxide nanoparticles under the excitation of ultraviolet (UV) light for the generation of Reactive Oxygen Species (ROS), with the aim of further using these species for fighting cancer cells in vitro. Owing to the difficulties in obtaining highly dispersed nanoparticles (NPs) in biological media, we propose their coating with a double-lipidic layer and we evaluate their colloidal stability in comparison to the pristine zinc oxide NPs. Then, using Electron Paramagnetic Resonance (EPR) coupled with the spin-trapping technique, we demonstrate and characterize the ability of bare and lipid-coated ZnO NPs to generate ROS in water only when remotely actuated via UV light irradiation. Interestingly, our results reveal that the surface chemistry of the NPs greatly influences the type of photo-generated ROS. Finally, we show that lipid-coated ZnO NPs are effectively internalized inside human epithelial carcinoma cells (HeLa) via a lysosomal pathway and that they can generate ROS inside cancer cells, leading to enhanced cell death. The results are promising for the development of ZnO-based therapeutic systems.