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Eriksson, O.

Publications and source records attributed to Eriksson, O..

8 recordsLinked to original sources

CombiCTx: Screening diffusion gradients of anti-cancer drug combinations

The reduced effectiveness of chemotherapy in many patients highlights the need for novel drug combinations and optimal ratios that target multiple survival mechanisms, which tumors may engage to confer drug resistance. Dynamic conditions within the tumor microenvironment shape cell behavior and influence the response to anti-cancer drugs, varying by cell type and local context. Accordingly, assays that identify effective concentrations and drug interactions (additive, synergistic, or antagonistic) in a relevant tumor tissue model are required to discover new combination treatments. To address this need for combinatorial chemotherapeutic (CTx) screening assays, we reconfigured CombiANT, a device for testing antibiotic interactions, and present a new assay called CombiCTx. The assay uses a device with three reservoirs containing gels loaded with chemotherapeutics or other anti-cancer drugs. The drug-loaded device is inverted and placed in a standard culture dish containing cancer cells, and both are then enclosed in gel. As drugs diffuse from the reservoirs, cancer cells are exposed to overlapping dynamic gradients of anti-cancer drugs, which can interact in various ways. We imaged doxorubicin diffusion in the assay using timelapse microscopy and employed the apoptotic agent staurosporine as a model drug, and established an imaging protocol for quantifying MDA-MB-231 breast cancer cell apoptosis along drug diffusion gradients. Finally, we tested navitoclax and gemcitabine to demonstrate the capacity of CombiCTx to evaluate combined cytotoxic effects while accounting for drug diffusion. Evaluating drug combinations with an assay that accounts for drug properties that influence diffusion in a complex tumor matrix may provide clinically relevant information.

cancer biology↗

USP14 regulates pS129 α-synuclein levels and oxidative stress in human SH-SY5Y dopaminergic cells

Ubiquitin specific protease-14 (USP14) is critical for controlling protein homeostasis disturbed in human disorders like Parkinso[n]s disease (PD). Here we investigated the role of USP14 in regulating proteasome and autophagy pathways, and their influence on -synuclein (-syn) degradation. Data showed that -syn and phosphorylated serine129 -syn (pS129 -syn) were elevated in USP14 gene-deleted SH-SY5Y dopaminergic cells with concomitant reduction in proteasome activity. Inhibition of proteasomes using MG132 particularly elevated pS129 -syn in these cells, but the levels were not influenced by inhibiting autophagy using chloroquine. In contrast, autophagy and the CLEAR (Coordinated Lysosomal Expression and Regulation) pathways were elevated in USP14 lacking cells with an upregulation of the transcription factor TFEB. USP14-ablated cells also exhibited increases in reactive oxidative species (ROS) and elongation of mitochondria. The addition of N-Acetylcysteine amide (NACA) to counteract oxidative stress, reduced pS129 -syn and -syn levels in USP14 deficient cells. Phospho-proteomic analyses revealed that USP14 is phosphorylated at S143 affecting its function and structure as shown by molecular modeling, and protein interaction studies. Re-expression of wild-type and the phospho-mimetic S143D-USP14 mutant decreased ROS, pS129 -syn, and -syn in USP14 lacking cells. These results demonstrate that pS129 -syn levels are sensitive to oxidative stress in SH-SY5Y dopaminergic cells. USP14 by stimulating the proteasome activity and reducing oxidative stress is a promising factor for targeting -syn and its pathogenic variants in PD.

neuroscience↗

GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation

Mitochondria contain a multi-copy genome and a distinct set of ribosomes devoted to the exclusive synthesis of proteins that are essential for oxidative phosphorylation. The assembly of mitoribosomes for mitochondrial translation is a poorly understood process. In this study, we identify the uncharacterized GTP-binding protein 8 (GTPBP8) as a mitoribosomal assembly factor that specifically associates with the mitoribosomal large subunit. Genetic depletion of GTPBP8 causes an aberrant accumulation of the large mitoribosomal subunit at a late assembly stage and reduces the level of fully assembled 55S mitoribosomes, resulting in impaired mitochondrial translation and function. Together, our findings uncover an important role for human GTPBP8 in the processes of mitoribosomal assembly and mitochondrial translation. Key pointsO_LIGTPBP8 is a novel GTPase residing in the matrix peripherally bound to the inner mitochondrial membrane C_LIO_LIGTPBP8 specifically associates with the large mitoribosome subunit through interactions with large mitoribosomal proteins assembled at late stages. C_LIO_LIGTPBP is essential for maturation of the mitoribosomal large subunit and monosome formation C_LI

cell biology↗

Heparin-derived theranostic nanoprobes overcome the blood-brain barrier and target glioma in murine model

The poor permeability of theranostic agents across the blood-brain-barrier (BBB) significantly hampers the development of new treatment modalities for neurological diseases. We have discovered a new biomimetic nanocarrier using heparin (HP) that effectively passes the BBB and targets glioblastoma. Specifically, we designed HP coated gold nanoparticles (HP-AuNPs) that were labeled with three different imaging modalities namely, fluorescein (FITC-HP-AuNP), radioisotope 68Gallium (68Ga-HP-AuNPs), and MRI active gadolinium (Gd-HP-AuNPs). The systemic infusion of FITC-HP-AuNPs in three different mouse strains (C57BL/6JRj, FVB, and NMRI-nude) displayed excellent penetration and revealed uniform distribution of fluorescent particles in the brain parenchyma (69-86%) with some accumulation in neurons (8-18%) and microglia (4-10%). Tail-vein administration of radiolabeled 68Ga-HP-AuNPs in healthy rats also showed 68Ga-HP-AuNP inside the brain parenchyma and in areas containing cerebrospinal fluid, such as the lateral ventricles, the cerebellum, and brain stem. Finally, tail-vein administration of Gd-HP-AuNPs (that display [~]3 fold higher relaxivity than that of commercial Gd-DTPA) in an orthotopic glioblastoma (U87MG xenograft) model in nude mice demonstrated enrichment of T1-contrast at the intracranial tumor with a gradual increase in the contrast in the tumor region between 1h-3h. We believe, our finding offers the untapped potential of HP-derived-NPs to deliver cargo molecules for treating neurological disorders.

bioengineering↗

RNA nucleotide repeats induce mitochondrial dysfunction and the ribosome associated quality control

Nucleotide repeat sequences are prevalent in the genome and expansion of these sequences is associated with more than 40 neuromuscular disorders. To understand the pathogenic mechanisms underlying RNA-repeat toxicity, we performed a genetic screen in a Caenorhabditis elegans model expressing an expanded CUG repeat specifically in the muscle. Here, we show that expression of this RNA repeat impairs motility by mitochondrial dysfunction, disrupting mitochondrial morphology and respiration. The phenotype is dependent on the RNA-binding factor MBL-1 and requires factors from the ribosome-associated protein quality control complex. Furthermore, Coenzyme Q supplementation rescued the motility impairment and all of the mitochondrial phenotypes. Together, our data reveal the importance of mitochondrial dysfunction in the molecular pathogenesis of RNA repeat expansion disorders.

genetics↗

AKAP79 enables calcineurin to directly suppress protein kinase A activity

Interplay between the second messengers cAMP and Ca2+ is a hallmark of dynamic cellular processes. A common motif is the opposition of the Ca2+-sensitive phosphatase calcineurin and the major cAMP receptor, protein kinase A (PKA). Calcineurin dephosphorylates sites primed by PKA to bring about changes including synaptic long-term depression (LTD). AKAP79 supports signaling of this type by anchoring PKA and calcineurin in tandem. In this study, we discovered that AKAP79 increases the rate of calcineurin dephosphorylation of type II PKA regulatory subunits by an order of magnitude. Fluorescent PKA activity reporter assays, supported by kinetic modeling, show how AKAP79-enhanced calcineurin activity enables suppression of PKA without altering cAMP levels by increasing PKA catalytic subunit capture rate. Experiments with hippocampal neurons indicate that this mechanism contributes towards LTD. This non- canonical mode of PKA regulation may underlie many other cellular processes.

biochemistry↗

A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

Neuroscience incorporates knowledge from a range of scales, from molecular dynamics to neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB(R) scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model. Information Sharing StatementBoth the source code and documentation of the Subcellular Workflow are available at https://github.com/jpgsantos/Subcellular_Workflow and licensed under GNU General Public License v3.0. The model is stored in the SBtab format (Lubitz et al. 2016). Model reduction, parameter estimation and global sensitivity analysis tools are written in MATLAB(R) (RRID:SCR_001622) and require the SimBiology(R) toolbox. Conversion script to VFGEN (Weckesser 2008), MOD and SBML (RRID:SCR_007422) is written in R (RRID:SCR_001905). Conversion to SBML requires the use of libSBML (RRID:SCR_014134). Validations are run in COPASI (RRID:SCR_014260; Hoops et al. 2006), NEURON (RRID:SCR_005393; Hines and Carnevale 1997) and with the subcellular simulation setup application (RRID:SCR_018790; available at https://subcellular.humanbrainproject.eu/model/simulations) that uses a spatial solver provided by STEPS (RRID:SCR_008742; Hepburn et al. 2012) and network-free solver NFsim (available at http://michaelsneddon.net/nfsim/). The medium spiny neuron model (Lindroos et al. 2018) used in NEURON simulations is available in ModelDB database (RRID:SCR_007271) with access code 237653. The FindSim use case model is available in https://github.com/BhallaLab/FindSim (Viswan et al. 2018).

systems biology↗

Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models

MotivationDynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as give guidance on parameters that are essential in distinguishing different qualitative output behaviours.\n\nResultsWe used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a global sensitivity analysis was performed on the prediction using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large and complex model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions.This approach is useful both for experimental design as well as model building.

systems biology↗