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PhD position: Gene Transfer in Human Organoid Cultures for Non-Invasive Imaging of Biological Processes
We are searching for a PhD student to work in this interdisciplinary project. Your tasks would include:
- test efficiency of viral vectors across multiple cellular systems (gut organoids, endometrial organoids,brain spheroids) to deliver expression constructs (e.g. reporter constructs,crispr/sgRNA)
- test efficiency of various matrices to grow variousorganoid like structures and to deliver viral vectors and nanoparticles
Interested?
Check more details here.
Published:
PhD position: Making Cells Feel At Home: Matrix And Culture Medium Optimization For Organoids
We are searching for a PhD student to work in this interdisciplinary project. Your focus would be the optimization of organoid culture conditions for each tissue, by scrutinizing medium and matrix composition. Both top-down and bottom-up approach will be applied in continuous and dynamic interaction with the tested matrix composition.
Interested?
Check more details here.
Published:
publications
Expression-Enhanced Fluorescent Proteins Based on Enhanced Green Fluorescent Protein for Super-resolution Microscopy
Abstract
“Smart fluorophores”, such as reversibly switchable fluorescent proteins, are crucial for advanced fluorescence imaging. However, only a limited number of such labels is available, and many display reduced biological performance compared to more classical variants. We present the development of robustly photoswitchable variants of enhanced green fluorescent protein (EGFP), named rsGreens, that display up to 30-fold higher fluorescence in E. coli colonies grown at 37 °C and more than 4-fold higher fluorescence when expressed in HEK293T cells compared to their ancestor protein rsEGFP. This enhancement is not due to an intrinsic increase in the fluorescence brightness of the probes, but rather due to enhanced expression levels that allow many more probe molecules to be functional at any given time. We developed rsGreens displaying a range of photoswitching kinetics and show how these can be used for multimodal diffraction-unlimited fluorescence imaging such as pcSOFI and RESOLFT, achieving a spatial resolution of ∼70 nm. By determining the first ever crystal structures of a negative reversibly switchable FP derived from Aequorea victoria in both the “on”- and “off”-conformation we were able to confirm the presence of a cis–trans isomerization and provide further insights into the mechanisms underlying the photochromism. Our work demonstrates that genetically encoded “smart fluorophores” can be readily optimized for biological performance and provides a practical strategy for developing maturation- and stability-enhanced photochromic fluorescent proteins.
Published in Nature Methods, 2015
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ArAAV-CFTRΔR Rescues the Cystic Fibrosis Phenotype in Human Intestinal Organoids and Cystic Fibrosis Mice
Abstract
Rationale: Gene therapy holds promise for a curative mutation-independent treatment applicable to all patients with cystic fibrosis (CF). The various viral vector–based clinical trials conducted in the past have demonstrated safety and tolerance of different vectors, but none have led to a clear and persistent clinical benefit. Recent clinical breakthroughs in recombinant adeno-associated viral vector (rAAV)-based gene therapy encouraged us to reexplore an rAAV approach for CF.
Published in American Journal of Respiratory and Critical Care Medicine, 2015
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De novo design of a biologically active amyloid
Abstract
Amyloid aggregation is driven by short sequences within proteins that self-assemble into characteristic amyloid structures. About 30 human proteins are implicated in amyloid-associated diseases, but many more contain short sequences that are potentially amyloidogenic. Gallardo et al. designed a peptide based on an amyloidogenic sequence in the vascular endothelial growth factor receptor VEGFR2. The peptide induced VEGFR2 to form aggregates with features characteristic of amyloids. Amyloids were toxic only in cells that required VEGFR2 activity, suggesting that the toxicity was due to loss of function of VEGFR2, rather than to inherent toxicity of the aggregates. The peptide inhibited VEGFR2-dependent tumor growth in a mouse tumor model.
Published in Science, 2016
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Linking single-cell measurements of mass, growth rate, and gene expression
Abstract
Although p53 protein aggregates have been observed in cancer cell lines and tumour tissue, their impact in cancer remains largely unknown. Here, we extensively screened for p53 aggregation phenotypes in tumour biopsies, and identified nuclear inclusion bodies (nIBs) of transcriptionally inactive mutant or wild‐type p53 as the most frequent aggregation‐like phenotype across six different cancer types. p53‐positive nIBs co‐stained with nuclear aggregation markers, and shared molecular hallmarks of nIBs commonly found in neurodegenerative disorders. In cell culture, tumour‐associated stress was a strong inducer of p53 aggregation and nIB formation. This was most prominent for mutant p53, but could also be observed in wild‐type p53 cell lines, for which nIB formation correlated with the loss of p53's transcriptional activity. Importantly, protein aggregation also fuelled the dysregulation of the proteostasis network in the tumour cell by inducing a hyperactivated, oncogenic heat‐shock response, to which tumours are commonly addicted, and by overloading the proteasomal degradation system, an observation that was most pronounced for structurally destabilized mutant p53. Patients showing tumours with p53‐positive nIBs suffered from a poor clinical outcome, similar to those with loss of p53 expression, and tumour biopsies showed a differential proteostatic expression profile associated with p53‐positive nIBs. p53‐positive nIBs therefore highlight a malignant state of the tumour that results from the interplay between (1) the functional inactivation of p53 through mutation and/or aggregation, and (2) microenvironmental stress, a combination that catalyses proteostatic dysregulation. This study highlights several unexpected clinical, biological and therapeutically unexplored parallels between cancer and neurodegeneration.
Published in Journal of Pathology, 2016
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Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution
Abstract
Compartmentalized biochemical activities are essential to all cellular processes, but there is no generalizable method to visualize dynamic protein activities in living cells at a resolution commensurate with cellular compartmentalization. Here, we introduce a new class of fluorescent biosensors that detect biochemical activities in living cells at a resolution up to threefold better than the diffraction limit. These 'FLINC' biosensors use binding-induced changes in protein fluorescence dynamics to translate kinase activities or protein–protein interactions into changes in fluorescence fluctuations, which are quantifiable through stochastic optical fluctuation imaging. A protein kinase A (PKA) biosensor allowed us to resolve minute PKA activity microdomains on the plasma membranes of living cells and to uncover the role of clustered anchoring proteins in organizing these activity microdomains. Together, these findings suggest that biochemical activities of the cell are spatially organized into an activity architecture whose structural and functional characteristics can be revealed by these new biosensors.
Published in Nature Methods, 2017
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Development of organoids from mouse and human endometrium showing endometrial epithelium physiology and long-term expandability
Abstract
The endometrium, which is of crucial importance for reproduction, undergoes dynamic cyclic tissue remodeling. Knowledge of its molecular and cellular regulation is poor, primarily owing to a lack of study models. Here, we have established a novel and promising organoid model from both mouse and human endometrium. Dissociated endometrial tissue, embedded in Matrigel under WNT-activating conditions, swiftly formed organoid structures that showed long-term expansion capacity, and reproduced the molecular and histological phenotype of the tissue's epithelium. The supplemented WNT level determined the type of mouse endometrial organoids obtained: high WNT yielded cystic organoids displaying a more differentiated phenotype than the dense organoids obtained in low WNT. The organoids phenocopied physiological responses of endometrial epithelium to hormones, including increased cell proliferation under estrogen and maturation upon progesterone. Moreover, the human endometrial organoids replicated the menstrual cycle under hormonal treatment at both the morpho-histological and molecular levels. Together, we established an organoid culture system for endometrium, reproducing tissue epithelium physiology and allowing long-term expansion. This novel model provides a powerful tool for studying mechanisms underlying the biology as well as the pathology of this key reproductive organ.
Published in Development, 2017
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Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI
Abstract
We expand photochromic super-resolution optical fluctuation imaging (pcSOFI) to monochromatic dual-channel sub-diffraction microscopy. Multi-tau (mt-)pcSOFI unmixes spectrally identical reversibly switchable fluorescent proteins (RSFPs) based on their blinking kinetics. We show that mt-pcSOFI can be used to simultaneously image two structures in living cells with existing RSFPs and the newly developed ffDronpa-F.
Published in Chemical Communications, 2017
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Linking single-cell measurements of mass, growth rate, and gene expression
Abstract
Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing. We resolve transcriptional signatures associated with single-cell mass and growth rate in L1210 and FL5.12 cell lines and activated CD8+ T cells. Further, we demonstrate a framework using these linked measurements to characterize biophysical heterogeneity in a patient-derived glioblastoma cell line with and without drug treatment. Our results highlight the value of coupled phenotypic metrics in guiding single-cell genomics.
Published in Genome Biology, 2018
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Polymeric Engineering of Nanoparticles for Highly Efficient Multifunctional Drug Delivery Systems
Abstract
Most targeting strategies of anticancer drug delivery systems (DDSs) rely on the surface functionalization of nanocarriers with specific ligands, which trigger the internalization in cancer cells via receptor-mediated endocytosis. The endocytosis implies the entrapment of DDSs in acidic vesicles (endosomes and lysosomes) and their eventual ejection by exocytosis. This process, intrinsic to eukaryotic cells, is one of the main drawbacks of DDSs because it reduces the drug bioavailability in the intracellular environment. The escape of DDSs from the acidic vesicles is, therefore, crucial to enhance the therapeutic performance at low drug dose. To this end, we developed a multifunctionalized DDS that combines high specificity towards cancer cells with endosomal escape capabilities. Doxorubicin-loaded mesoporous silica nanoparticles were functionalized with polyethylenimine, a polymer commonly used to induce endosomal rupture, and hyaluronic acid, which binds to CD44 receptors, overexpressed in cancer cells. We show irrefutable proof that the developed DDS can escape the endosomal pathway upon polymeric functionalization. Interestingly, the combination of the two polymers resulted in higher endosomal escape efficiency than the polyethylenimine coating alone. Hyaluronic acid additionally provides the system with cancer targeting capability and enzymatically controlled drug release. Thanks to this multifunctionality, the engineered DDS had cytotoxicity comparable to the pure drug whilst displaying high specificity towards cancer cells. The polymeric engineering here developed enhances the performance of DDS at low drug dose, holding great potential for anticancer therapeutic applications.
Published in Scientific reports, 2019
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Patient-derived organoids from endometrial disease capture clinical heterogeneity and are amenable to drug screening
Abstract
Endometrial disorders represent a major gynaecological burden. Current research models fail to recapitulate the nature and heterogeneity of these diseases, thereby hampering scientific and clinical progress. Here we developed long-term expandable organoids from a broad spectrum of endometrial pathologies. Organoids from endometriosis show disease-associated traits and cancer-linked mutations. Endometrial cancer-derived organoids accurately capture cancer subtypes, replicate the mutational landscape of the tumours and display patient-specific drug responses. Organoids were also established from precancerous pathologies encompassing endometrial hyperplasia and Lynch syndrome, and inherited gene mutations were maintained. Endometrial disease organoids reproduced the original lesion when transplanted in vivo. In summary, we developed multiple organoid models that capture endometrial disease diversity and will provide powerful research models and drug screening and discovery tools.
Published in Nature Cell Biology, 2019
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Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272–26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272–26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.
Published in Nature Communications, 2019
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Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and Functional Defects
Abstract
The most common CFTR mutation, F508del, presents with multiple cellular defects. However, the possible multiple defects caused by many rarer CFTR mutations are not well studied. We investigated four rare CFTR mutations E60K, G85E, E92K and A455E against well-characterized mutations, F508del and G551D, and their responses to corrector VX-809 and/or potentiator VX-770. Methods. Using complementary assays in HEK293T stable cell lines, we determined maturation by Western blotting, trafficking by flow cytometry using extracellular 3HA-tagged CFTR, and function by halide-sensitive YFP quenching. In the forskolin-induced swelling assay in intestinal organoids, we validated the effect of tagged versus endogenous CFTR. Results. Treatment with VX-809 significantly restored maturation, PM localization and function of both E60K and E92K. Mechanistically, VX-809 not only raised the total amount of CFTR, but significantly increased the traffic efficiency, which was not the case for A455E. G85E was refractory to VX-809 and VX-770 treatment. Conclusions. Since no single model or assay allows deciphering all defects at once, we propose a combination of phenotypic assays to collect rapid and early insights into the multiple defects of CFTR variants
Published in Cells, 2020
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Structural characterization of fibrous synthetic hydrogels using fluorescence microscopy
Abstract
The structural features of the matrix surrounding the cells play a crucial role in regulating their behavior. Here, we used fluorescence microscopy and customized analysis algorithms to characterize the architecture of fibrous hydrogel networks. As a model system, we investigated a new class of synthetic biomimetic material, hydrogels prepared from polyisocyanides. Our results show that these synthetic gels present a highly heterogeneous fibrous network, with pores reaching a few micrometers in diameter. By encapsulating HeLa cells in different hydrogels, we show that a more porous structure is linked to a higher proliferation rate. The approach described here, for the characterization of the network of fibrous hydrogels, can be easily applied to other polymer-based materials and provide new insights into the influence of structural features in cell behavior. This knowledge is crucial to develop the next generation of biomimetic materials for 3D cell models and tissue engineering applications.
Published in Soft Matter, 2020
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Developing Organoids from Ovarian Cancer as Experimental and Preclinical Models
Abstract
Ovarian cancer (OC) represents the most dismal gynecological cancer. Pathobiology is poorly understood, mainly due to lack of appropriate study models. Organoids, defined as self-developing three-dimensional in vitro reconstructions of tissues, provide powerful tools to model human diseases. Here, we established organoid cultures from patient-derived OC, in particular from the most prevalent high-grade serous OC (HGSOC). Testing multiple culture medium components identified neuregulin-1 (NRG1) as key factor in maximizing OC organoid development and growth, although overall derivation efficiency remained moderate (36% for HGSOC patients, 44% for all patients together). Established organoid lines showed patient tumor-dependent morphology and disease characteristics, and recapitulated the parent tumor's marker expression and mutational landscape. Moreover, the organoids displayed tumor-specific sensitivity to clinical HGSOC chemotherapeutic drugs. Patient-derived OC organoids provide powerful tools for the study of the cancer's pathobiology (such as importance of the NRG1/ERBB pathway) as well as advanced preclinical tools for (personalized) drug screening and discovery.
Published in Stem Cell Reports, 2020
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Fast-tracking of single emitters in large volumes with nanometer precision
Abstract
Multifocal plane microscopy allows capturing images at different focal planes simultaneously. Using a proprietary prism which splits the emitted light into paths of different length, images at 8 different focal depths were obtained, covering a volume of 50x50x4 μm3. The position of single emitters was retrieved using a phasor-based approach across the different imaging planes, with better than 10 nm precision in the axial direction. We validated the accuracy of this approach by tracking fluorescent beads in 3D to calculate water viscosity. The fast acquisition rate (>100 fps) also enabled us to follow the capturing of 0.2 μm fluorescent beads into an optical trap.
Published in Optics Express, 2020
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team
Zeger Debyser
Expertise
* Viral vector technology* Assay development for phenotypic drug screens using high content imaging
* Drug discovery and development
Published:
Marianne Carlon
Expertise
* Studying cystic fibrosis pathophysiology and cell molecular defects (processing, trafficking, ion channel activity) in cell lines and organoid models* Assay development for phenotypic drug screens using high content imaging
* Experienced in viral vector technology, including CRISPR-Cas, in organoids, for assay development and as a therapeutic strategy for cystic fibrosis
Published:
Hugo Vankelecom
Expertise
* Developing organoid models* Developing complex organoid models and organoid-based tissue mimics
* Applying organoid models (e.g. tissue biology and pathology; drug and toxicity screening)
Published:
Frederik De Smet
Expertise
* Brain cancer derived models (glioblastoma)* Multiplexed protein analysis
* Crispr/Cas screening
Published:
Susana Rocha
Expertise
* Synthetic hydrogels for 3D cultures* Nanoparticle-mediated delivery
* Fluorescence labelling and microscopy
Published:
Peter Dedecker
Expertise
* Developing advanced imaging and ‘smart’ labels* High-content visualization of complex biological systems
Published: