* joint first author # joint corresponding author

Said El Bouhaddani✳︎, Matthias Höllerhage✳︎, Hae-Won Uh, Claudia Moebius, Marc Bickle, Günter U Höglinger, Jeanine Houwing-Duistermaat
Statistical integration of multi-omics and drug screening data from cell lines.
PLoS Comput Biol, 20(1) Art. No. e1011809 (2024)
Open Access DOI
Data integration methods are used to obtain a unified summary of multiple datasets. For multi-modal data, we propose a computational workflow to jointly analyze datasets from cell lines. The workflow comprises a novel probabilistic data integration method, named POPLS-DA, for multi-omics data. The workflow is motivated by a study on synucleinopathies where transcriptomics, proteomics, and drug screening data are measured in affected LUHMES cell lines and controls. The aim is to highlight potentially druggable pathways and genes involved in synucleinopathies. First, POPLS-DA is used to prioritize genes and proteins that best distinguish cases and controls. For these genes, an integrated interaction network is constructed where the drug screen data is incorporated to highlight druggable genes and pathways in the network. Finally, functional enrichment analyses are performed to identify clusters of synaptic and lysosome-related genes and proteins targeted by the protective drugs. POPLS-DA is compared to other single- and multi-omics approaches. We found that HSPA5, a member of the heat shock protein 70 family, was one of the most targeted genes by the validated drugs, in particular by AT1-blockers. HSPA5 and AT1-blockers have been previously linked to α-synuclein pathology and Parkinson's disease, showing the relevance of our findings. Our computational workflow identified new directions for therapeutic targets for synucleinopathies. POPLS-DA provided a larger interpretable gene set than other single- and multi-omic approaches. An implementation based on R and markdown is freely available online.

Ekaterina Osipova, Rico Barsacchi, Tom Brown, Keren Sadanandan, Andrea H Gaede, Amanda Monte, Julia Jarrells, Claudia Moebius, Martin Pippel, Douglas L Altshuler, Sylke Winkler, Marc Bickle, Maude W Baldwin, Michael Hiller
Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds.
Science, 379(6628) 185-190 (2023)
Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.

Prasath Paramasivam, Martin Stöter, Eloina Corradi, Irene Dalla Costa, Andreas Höijer, Stefano Bartesaghi, Alan Sabirsh, Lennart Lindfors, Marianna Yanez Arteta, Peter Nordberg, Shalini Andersson, Marie-Laure Baudet, Marc Bickle, Marino Zerial
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining.
RNA, 28(3) 433-446 (2022)
Open Access DOI
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.

Prasath Paramasivam✳︎, Christian Franke✳︎, Martin Stöter, Andreas Höijer, Stefano Bartesaghi, Alan Sabirsh, Lennart Lindfors, Marianna Yanez Arteta, Anders Dahlén, Annette Bak, Shalini Andersson, Yannis Kalaidzidis, Marc Bickle, Marino Zerial
Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale.
J Cell Biol, 221(2) Art. No. e202110137 (2022)
Open Access PDF DOI
Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal compartments and capture events of mRNA escape from endosomal recycling tubules. Our results change the view of the mechanisms of endosomal escape and define quantitative parameters to guide the development of mRNA formulations toward higher efficacy and lower cytotoxicity.

Elisabeth Kemter✳︎, Andreas Müller✳︎, Martin Neukam, Anna Ivanova, Nikolai Klymiuk, Simone Renner, Kaiyuan Yang, Johannes Broichhagen, Mayuko Kurome, Valeri Zakhartchenko, Barbara Kessler, Klaus-Peter Knoch, Marc Bickle, Barbara Ludwig, Kai Johnsson, Heiko Lickert, Thomas Kurth, Eckhard Wolf✳︎#, Michele Solimena✳︎#
Sequential in vivo labeling of insulin secretory granule pools in INS-SNAP transgenic pigs.
Proc Natl Acad Sci U.S.A., 118(37) Art. No. e2107665118 (2021)
Open Access DOI
β cells produce, store, and secrete insulin upon elevated blood glucose levels. Insulin secretion is a highly regulated process. The probability for insulin secretory granules to undergo fusion with the plasma membrane or being degraded is correlated with their age. However, the molecular features and stimuli connected to this behavior have not yet been fully understood. Furthermore, our understanding of β cell function is mostly derived from studies of ex vivo isolated islets in rodent models. To overcome this translational gap and study insulin secretory granule turnover in vivo, we have generated a transgenic pig model with the SNAP-tag fused to insulin. We demonstrate the correct targeting and processing of the tagged insulin and normal glycemic control of the pig model. Furthermore, we show specific single- and dual-color granular labeling of in vivo-labeled pig pancreas. This model may provide unprecedented insights into the in vivo insulin secretory granule behavior in an animal close to humans.

Sven Schreiter, Katerina Vafia, Rico Barsacchi, Stephen H Tsang, Marc Bickle, Marius Ader, Mike Karl, Elly M. Tanaka, Seba Almedawar
A Human Retinal Pigment Epithelium-Based Screening Platform Reveals Inducers of Photoreceptor Outer Segments Phagocytosis.
Stem Cell Rep, 15(6) 1347-1361 (2020)
Open Access DOI
Phagocytosis is a key function in various cells throughout the body. A deficiency in photoreceptor outer segment (POS) phagocytosis by the retinal pigment epithelium (RPE) causes vision loss in inherited retinal diseases and possibly age-related macular degeneration. To date, there are no effective therapies available aiming at recovering the lost phagocytosis function. Here, we developed a high-throughput screening assay based on RPE derived from human embryonic stem cells (hRPE) to reveal enhancers of POS phagocytosis. One of the hits, ramoplanin (RM), reproducibly enhanced POS phagocytosis and ensheathment in hRPE, and enhanced the expression of proteins known to regulate membrane dynamics and ensheathment in other cell systems. Additionally, RM rescued POS internalization defect in Mer receptor tyrosine kinase (MERTK) mutant hRPE, derived from retinitis pigmentosa patient induced pluripotent stem cells. Our platform, including a primary phenotypic screening phagocytosis assay together with orthogonal assays, establishes a basis for RPE-based therapy discovery aiming at a broad patient spectrum.

Masin Abo-Rady✳︎, Norman Kalmbach✳︎, Arun Pal, Carina Schludi, Antje Janosch, Tanja Richter, Petra Freitag, Marc Bickle, Anne-Karin Kahlert, Susanne Petri, Stefan Stefanov, Hannes Glass, Selma Staege, Walter Just, Rajat Bhatnagar, Dieter Edbauer, Andreas Hermann, Florian Wegner#, Jared Sterneckert#
Knocking out C9ORF72 Exacerbates Axonal Trafficking Defects Associated with Hexanucleotide Repeat Expansion and Reduces Levels of Heat Shock Proteins.
Stem Cell Rep, 14(3) 390-405 (2020)
Open Access DOI
In amyotrophic lateral sclerosis (ALS) motor neurons (MNs) undergo dying-back, where the distal axon degenerates before the soma. The hexanucleotide repeat expansion (HRE) in C9ORF72 is the most common genetic cause of ALS, but the mechanism of pathogenesis is largely unknown with both gain- and loss-of-function mechanisms being proposed. To better understand C9ORF72-ALS pathogenesis, we generated isogenic induced pluripotent stem cells. MNs with HRE in C9ORF72 showed decreased axonal trafficking compared with gene corrected MNs. However, knocking out C9ORF72 did not recapitulate these changes in MNs from healthy controls, suggesting a gain-of-function mechanism. In contrast, knocking out C9ORF72 in MNs with HRE exacerbated axonal trafficking defects and increased apoptosis as well as decreased levels of HSP70 and HSP40, and inhibition of HSPs exacerbated ALS phenotypes in MNs with HRE. Therefore, we propose that the HRE in C9ORF72 induces ALS pathogenesis via a combination of gain- and loss-of-function mechanisms.

Steven W Poser, Oliver Otto, Carina Arps-Forker, Yan Ge, Maik Herbig, Cordula Andree, Konrad Gruetzmann, Melissa F Adasme, Szymon Stodolak, Polyxeni Nikolakopoulou, Deric M Park, Alan Mcintyre, Mathias Lesche, Andreas Dahl, Petra Lennig, Stefan R. Bornstein, Evelin Schroeck, Barbara Klink, Ronen R Leker, Marc Bickle, George P Chrousos, Michael Schroeder, Carlo Vittorio Cannistraci, Jochen Guck, Andreas Androutsellis-Theotokis
Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery.
FASEB J, 33(8) 9235-9249 (2019)
Cancer cells can switch between signaling pathways to regulate growth under different conditions. In the tumor microenvironment, this likely helps them evade therapies that target specific pathways. We must identify all possible states and utilize them in drug screening programs. One such state is characterized by expression of the transcription factor Hairy and Enhancer of Split 3 (HES3) and sensitivity to HES3 knockdown, and it can be modeled in vitro. Here, we cultured 3 primary human brain cancer cell lines under 3 different culture conditions that maintain low, medium, and high HES3 expression and characterized gene regulation and mechanical phenotype in these states. We assessed gene expression regulation following HES3 knockdown in the HES3-high conditions. We then employed a commonly used human brain tumor cell line to screen Food and Drug Administration (FDA)-approved compounds that specifically target the HES3-high state. We report that cells from multiple patients behave similarly when placed under distinct culture conditions. We identified 37 FDA-approved compounds that specifically kill cancer cells in the high-HES3-expression conditions. Our work reveals a novel signaling state in cancer, biomarkers, a strategy to identify treatments against it, and a set of putative drugs for potential repurposing.-Poser, S. W., Otto, O., Arps-Forker, C., Ge, Y., Herbig, M., Andree, C., Gruetzmann, K., Adasme, M. F., Stodolak, S., Nikolakopoulou, P., Park, D. M., Mcintyre, A., Lesche, M., Dahl, A., Lennig, P., Bornstein, S. R., Schroeck, E., Klink, B., Leker, R. R., Bickle, M., Chrousos, G. P., Schroeder, M., Cannistraci, C. V., Guck, J., Androutsellis-Theotokis, A. Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery.

Ioannis Giannios, Ioannis Serafimidis, Vivian Anastasiou, Daniela Pezzolla, Mathias Lesche, Cordula Andree, Marc Bickle, Anthony Gavalas
Protein Methyltransferase Inhibition Decreases Endocrine Specification Through the Upregulation of Aldh1b1 Expression.
Stem Cells, 37(5) 640-651 (2019)
Open Access DOI
Understanding the mechanisms that promote the specification of pancreas progenitors and regulate their self-renewal and differentiation will help to maintain and expand pancreas progenitor cells derived from human pluripotent stem (hPS) cells. This will improve the efficiency of current differentiation protocols of hPS cells into β-cells and bring such cells closer to clinical applications for the therapy of diabetes. Aldehyde dehydrogenase 1b1 (Aldh1b1) is a mitochondrial enzyme expressed specifically in progenitor cells during mouse pancreas development, and we have shown that its functional inactivation leads to accelerated differentiation and deficient β-cells. In this report, we aimed to identify small molecule inducers of Aldh1b1 expression taking advantage of a mouse embryonic stem (mES) cell Aldh1b1 lacZ reporter line and a pancreas differentiation protocol directing mES cells into pancreatic progenitors. We identified AMI-5, a protein methyltransferase inhibitor, as an Aldh1b1 inducer and showed that it can maintain Aldh1b1 expression in embryonic pancreas explants. This led to a selective reduction in endocrine specification. This effect was due to a downregulation of Ngn3, and it was mediated through Aldh1b1 since the effect was abolished in Aldh1b1 null pancreata. The findings implicated methyltransferase activity in the regulation of endocrine differentiation and showed that methyltransferases can act through specific regulators during pancreas differentiation. Stem Cells 2019;37:640-651.

Lydia Reinhardt, Susanne Kordes, Peter Reinhardt, Michael Glatza, Michael Baumann, Hannes C A Drexler, Sascha Menninger, Gunther Zischinsky, Jan Eickhoff, Claudia Fröb, Prabesh Bhattarai, Guruchandar Arulmozhivarman, Lara Marrone, Antje Janosch, Kenjiro Adachi, Martin Stehling, Eric D Anderson, Masin Abo-Rady, Marc Bickle, Udai Pandey, Michell M Reimer, Caghan Kizil, Hans R Schöler, Peter Nussbaumer, Bert Klebl, Jared Sterneckert
Dual Inhibition of GSK3β and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo.
Stem Cell Rep, 12(3) 502-517 (2019)
Open Access DOI
Neuroinflammation is a hallmark of neurological disorders and is accompanied by the production of neurotoxic agents such as nitric oxide. We used stem cell-based phenotypic screening and identified small molecules that directly protected neurons from neuroinflammation-induced degeneration. We demonstrate that inhibition of CDK5 is involved in, but not sufficient for, neuroprotection. Instead, additional inhibition of GSK3β is required to enhance the neuroprotective effects of CDK5 inhibition, which was confirmed using short hairpin RNA-mediated knockdown of CDK5 and GSK3β. Quantitative phosphoproteomics and high-content imaging demonstrate that neurite degeneration is mediated by aberrant phosphorylation of multiple microtubule-associated proteins. Finally, we show that our hit compound protects neurons in vivo in zebrafish models of motor neuron degeneration and Alzheimer's disease. Thus, we demonstrate an overlap of CDK5 and GSK3β in mediating the regulation of the neuronal cytoskeleton and that our hit compound LDC8 represents a promising starting point for neuroprotective drugs.

Antje Janosch, Carolin Kaffka, Marc Bickle
Unbiased Phenotype Detection Using Negative Controls.
SLAS Discov, 24(3) 234-241 (2019)
Open Access DOI
Phenotypic screens using automated microscopy allow comprehensive measurement of the effects of compounds on cells due to the number of markers that can be scored and the richness of the parameters that can be extracted. The high dimensionality of the data is both a rich source of information and a source of noise that might hide information. Many methods have been proposed to deal with this complex data in order to reduce the complexity and identify interesting phenotypes. Nevertheless, the majority of laboratories still only use one or two parameters in their analysis, likely due to the computational challenges of carrying out a more sophisticated analysis. Here, we present a novel method that allows discovering new, previously unknown phenotypes based on negative controls only. The method is compared with L1-norm regularization, a standard method to obtain a sparse matrix. The analytical pipeline is implemented in the open-source software KNIME, allowing the implementation of the method in many laboratories, even ones without advanced computing knowledge.

Marc Bickle
The Academic Pill: How Academia Contributes to Curing Diseases.
SLAS Discov, 24(3) 203-212 (2019)
Open Access DOI

Matthias Höllerhage, Marc Bickle, Günter U Höglinger
Unbiased Screens for Modifiers of Alpha-Synuclein Toxicity.
Curr Neurol Neurosci Rep, 19(2) Art. No. 8 (2019)
We provide an overview about unbiased screens to identify modifiers of alpha-synuclein (αSyn)-induced toxicity, present the models and the libraries that have been used for screening, and describe how hits from primary screens were selected and validated.

Jessica Bellmann, Anne Monette, Vadreenath Tripathy, Anna Sójka, Masin Abo-Rady, Antje Janosh, Rajat Bhatnagar, Marc Bickle, Andrew J Mouland, Jared Sterneckert
Viral Infections Exacerbate FUS-ALS Phenotypes in iPSC-Derived Spinal Neurons in a Virus Species-Specific Manner.
Front Cell Neurosci, 13 Art. No. 480 (2019)
Open Access DOI
Amyotrophic lateral sclerosis (ALS) arises from an interplay of genetic mutations and environmental factors. ssRNA viruses are possible ALS risk factors, but testing their interaction with mutations such as in FUS, which encodes an RNA-binding protein, has been difficult due to the lack of a human disease model. Here, we use isogenic induced pluripotent stem cell (iPSC)-derived spinal neurons (SNs) to investigate the interaction between ssRNA viruses and mutant FUS. We find that rabies virus (RABV) spreads ALS phenotypes, including the formation of stress granules (SGs) with aberrant composition due to increased levels of FUS protein, as well as neurodegeneration and reduced restriction activity by FUS mutations. Consistent with this, iPSC-derived SNs harboring mutant FUS are more sensitive to human immunodeficiency virus (HIV-1) and Zika viruses (ZIKV). We demonstrate that RABV and HIV-1 exacerbate cytoplasmic mislocalization of FUS. Our results demonstrate that viral infections worsen ALS pathology in SNs with genetic risk factors, suggesting a novel role for viruses in modulating patient phenotypes.

Martin Stöter, Antje Janosch, Rico Barsacchi, Marc Bickle
CellProfiler and KNIME: Open-Source Tools for High-Content Screening.
Methods Mol Biol, 1953 43-60 (2019)
High-content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using open-source software. We present and discuss the open-source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions, which increase flexibility and keep costs low.

Juliana G. Roscito✳︎, Katrin Sameith✳︎, Genis Parra✳︎, Bjoern Langer, Andreas Petzold, Claudia Moebius, Marc Bickle, Miguel Trefaut Rodrigues, Michael Hiller
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.
Nat Commun, 9(1) Art. No. 4737 (2018)
Open Access PDF DOI
Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

Neil O Carragher, Filippo Piccinini, Anna Tesei, O Joseph Trask Jr, Marc Bickle, Peter Horvath
Concerns, challenges and promises of high-content analysis of 3D cellular models.
Nat Rev Drug Discov, 17(8) Art. No. 606 (2018)

Alvin Kuriakose Thomas, Robert Wieduwild, Ralf Zimmermann, Weilin Lin, Jens Friedrichs, Marc Bickle, Karim Fahmy, Carsten Werner, Yixin Zhang
Layer-by-Layer Assembly of Heparin and Peptide-Polyethylene Glycol Conjugates to Form Hybrid Nanothin Films of Biomatrices.
ACS Appl Mater Interfaces, 10(17) 14264-14270 (2018)
We investigated the utility of a heparin/peptide-polyethylene glycol conjugate system to build layer-by-layer (LbL) structures, to assemble tailored multilayer-biomatrices for cell culture. The LbL assembly balances the advantages of polyelectrolyte systems and protein-based systems. Human umbilical vein endothelial cells showed distinct responses to the film thickness and structure; the presence, density, and spatial arrangement of a cell adhesion ligand within the nanothin film; and the pretreatment of the film with morphogens. The LbL technique presents a versatile tool for modifying cell culture substrates with defined and diverse biochemical and structural features, for investigating cell-material interactions.

Shovamayee Maharana, Jie Wang, Dimitrios Papadopoulos, Doris Richter, Andrei I. Pozniakovsky, Ina Poser, Marc Bickle, Sandra Rizk, Jordina Guillén-Boixet, Titus Franzmann, Marcus Jahnel, Lara Marrone, Young-Tae Chang, Jared Sterneckert, Pavel Tomancak, Anthony Hyman#, Simon Alberti#
RNA buffers the phase separation behavior of prion-like RNA binding proteins.
Science, 360(6391) 918-921 (2018)
Prion-like RNA binding proteins (RBPs) such as TDP43 and FUS are largely soluble in the nucleus but form solid pathological aggregates when mislocalized to the cytoplasm. What keeps these proteins soluble in the nucleus and promotes aggregation in the cytoplasm is still unknown. We report here that RNA critically regulates the phase behavior of prion-like RBPs. Low RNA/protein ratios promote phase separation into liquid droplets, whereas high ratios prevent droplet formation in vitro. Reduction of nuclear RNA levels or genetic ablation of RNA binding causes excessive phase separation and the formation of cytotoxic solid-like assemblies in cells. We propose that the nucleus is a buffered system in which high RNA concentrations keep RBPs soluble. Changes in RNA levels or RNA binding abilities of RBPs cause aberrant phase transitions.

Lara Marrone, Ina Poser, Ian Casci, Julia Japtok, Peter Reinhardt, Antje Janosch, Cordula Andree, Hyun-Ok Kate Lee, Claudia Moebius, Ellen Koerner, Lydia Reinhardt, Maria Elena Cicardi, Karl Hackmann, Barbara Klink, Angelo Poletti, Simon Alberti, Marc Bickle, Andreas Hermann, Udai Pandey, Anthony Hyman, Jared Sterneckert
Isogenic FUS-eGFP iPSC Reporter Lines Enable Quantification of FUS Stress Granule Pathology that Is Rescued by Drugs Inducing Autophagy.
Stem Cell Rep, 10(2) 375-389 (2018)
Open Access DOI
Perturbations in stress granule (SG) dynamics may be at the core of amyotrophic lateral sclerosis (ALS). Since SGs are membraneless compartments, modeling their dynamics in human motor neurons has been challenging, thus hindering the identification of effective therapeutics. Here, we report the generation of isogenic induced pluripotent stem cells carrying wild-type and P525L FUS-eGFP. We demonstrate that FUS-eGFP is recruited into SGs and that P525L profoundly alters their dynamics. With a screening campaign, we demonstrate that PI3K/AKT/mTOR pathway inhibition increases autophagy and ameliorates SG phenotypes linked to P525L FUS by reducing FUS-eGFP recruitment into SGs. Using a Drosophila model of FUS-ALS, we corroborate that induction of autophagy significantly increases survival. Finally, by screening clinically approved drugs for their ability to ameliorate FUS SG phenotypes, we identify a number of brain-penetrant anti-depressants and anti-psychotics that also induce autophagy. These drugs could be repurposed as potential ALS treatments.

Milan Esner, Felix Meyenhofer, Marc Bickle
Live-Cell High Content Screening in Drug Development.
Methods Mol Biol, 1683 149-164 (2018)
In the past decade, automated microscopy has become an important tool for the drug discovery and development process. The establishment of imaging modalities as screening tools depended on technological breakthroughs in the domain of automated microscopy and automated image analysis. These types of assays are often referred to as high content screening or high content analysis (HCS/HCA). The driving force to adopt imaging for drug development is the quantity and quality of cellular information that can be collected and the enhanced physiological relevance of cellular screening compared to biochemical screening. Most imaging in drug development is performed on fixed cells as this allows uncoupling the preparation of the cells from the acquisition of the images. Live-cell imaging is technically challenging, but is very useful for many aspects of the drug development pipeline such as kinetic studies of compound mode of action or to analyze the motion of cellular components. Most vendors of HCS microscopy systems offer the option of environmental chambers and onboard pipetting on their platforms. This reflects the wish and desire of many customers to have the ability to perform live-cell assays on their HCS automated microscopes. This book chapter summarizes the challenges and advantages of live-cell imaging in drug discovery. Examples of applications are presented and the motivation to perform these assays in kinetic mode is discussed.

Guruchandar Arulmozhivarman, Martin Kräter, Manja Wobus, Jens Friedrichs, Elham Pishali Bejestani, Katrin Müller, Katrin Lambert, Dimitra Alexopoulou, Andreas Dahl, Martin Stöter, Marc Bickle, Nona Shayegi, Jochen Hampe, Friedrich Stölzel, Michael Brand#, Malte von Bonin, Martin Bornhäuser#
Zebrafish In-Vivo Screening for Compounds Amplifying Hematopoietic Stem and Progenitor Cells: - Preclinical Validation in Human CD34+ Stem and Progenitor Cells.
Sci Rep, 7(1) Art. No. 12084 (2017)
Open Access DOI
The identification of small molecules that either increase the number and/or enhance the activity of human hematopoietic stem and progenitor cells (hHSPCs) during ex vivo expansion remains challenging. We used an unbiased in vivo chemical screen in a transgenic (c-myb:EGFP) zebrafish embryo model and identified histone deacetylase inhibitors (HDACIs), particularly valproic acid (VPA), as significant enhancers of the number of phenotypic HSPCs, both in vivo and during ex vivo expansion. The long-term functionality of these expanded hHSPCs was verified in a xenotransplantation model with NSG mice. Interestingly, VPA increased CD34(+) cell adhesion to primary mesenchymal stromal cells and reduced their in vitro chemokine-mediated migration capacity. In line with this, VPA-treated human CD34(+) cells showed reduced homing and early engraftment in a xenograft transplant model, but retained their long-term engraftment potential in vivo, and maintained their differentiation ability both in vitro and in vivo. In summary, our data demonstrate that certain HDACIs lead to a net expansion of hHSPCs with retained long-term engraftment potential and could be further explored as candidate compounds to amplify ex-vivo engineered peripheral blood stem cells.

Matthias Höllerhage, Claudia Moebius, Johannes Melms, Wei-Hua Chiu, Joachim N Goebel, Tasnim Chakroun, Thomas Koeglsperger, Wolfgang H Oertel, Thomas W Rösler, Marc Bickle, Günter U Höglinger
Protective efficacy of phosphodiesterase-1 inhibition against alpha-synuclein toxicity revealed by compound screening in LUHMES cells.
Sci Rep, 7(1) Art. No. 11469 (2017)
Open Access DOI
α-synuclein-induced neurotoxicity is a core pathogenic event in neurodegenerative synucleinopathies such as Parkinson's disease, dementia with Lewy bodies, or multiple system atrophy. There is currently no disease-modifying therapy available for these diseases. We screened 1,600 FDA-approved drugs for their efficacy to protect LUHMES cells from degeneration induced by wild-type α-synuclein and identified dipyridamole, a non-selective phosphodiesterase inhibitor, as top hit. Systematic analysis of other phosphodiesterase inhibitors identified a specific phosphodiesterase 1 inhibitor as most potent to rescue from α-synuclein toxicity. Protection was mediated by an increase of cGMP and associated with the reduction of a specific α-synuclein oligomeric species. RNA interference experiments confirmed PDE1A and to a smaller extent PDE1C as molecular targets accounting for the protective efficacy. PDE1 inhibition also rescued dopaminergic neurons from wild-type α-synuclein induced degeneration in the substantia nigra of mice. In conclusion, this work identifies inhibition of PDE1A in particular as promising target for neuroprotective treatment of synucleinopathies.

J Gray Camp✳︎, Keisuke Sekine✳︎, Tobias Gerber, Henry Loeffler-Wirth, Hans Binder, Malgorzata Gac, Sabina Kanton, Jorge Kageyama, Georg Damm, Daniel Seehofer, Lenka Belicova, Marc Bickle, Rico Barsacchi, Ryo Okuda, Emi Yoshizawa, Masashi Kimura, Hiroaki Ayabe, Hideki Taniguchi, Takanori Takebe#, Barbara Treutlein#
Multilineage communication regulates human liver bud development from pluripotency.
Nature, 546(7659) 533-538 (2017)
Conventional two-dimensional differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. Three-dimensional organoids generate complex organ-like tissues; however, it is unclear how heterotypic interactions affect lineage identity. Here we use single-cell RNA sequencing to reconstruct hepatocyte-like lineage progression from pluripotency in two-dimensional culture. We then derive three-dimensional liver bud organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during liver bud development. We find that liver bud hepatoblasts diverge from the two-dimensional lineage, and express epithelial migration signatures characteristic of organ budding. We benchmark three-dimensional liver buds against fetal and adult human liver single-cell RNA sequencing data, and find a striking correspondence between the three-dimensional liver bud and fetal liver cells. We use a receptor-ligand pairing analysis and a high-throughput inhibitor assay to interrogate signalling in liver buds, and show that vascular endothelial growth factor (VEGF) crosstalk potentiates endothelial network formation and hepatoblast differentiation. Our molecular dissection reveals interlineage communication regulating organoid development, and illuminates previously inaccessible aspects of human liver development.

Peter Horvath, Nathalie Aulner, Marc Bickle, Anthony M Davies, Elaine Del Nery, Daniel Ebner, Maria Montoya, Päivi Östling, Vilja Pietiäinen, Leo S Price, Spencer L Shorte, Gerardo Turcatti, Carina von Schantz, Neil O Carragher
Screening out irrelevant cell-based models of disease.
Nat Rev Drug Discov, 15(11) 751-769 (2016)
The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell- and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates.

Maria Montoya, Thierry Dorval, Marc Bickle
SLAS Europe High-Content Screening Conference in Dresden: A Glimpse of the Future?
J Biomol Screen, 21(9) 883-886 (2016)

Guruchandar Arulmozhivarman, Martin Stöter, Marc Bickle, Martin Kräter, Manja Wobus, Gerhard Ehninger, Friedrich Stölzel, Michael Brand, Martin Bornhäuser, Nona Shayegi
In Vivo Chemical Screen in Zebrafish Embryos Identifies Regulators of Hematopoiesis Using a Semiautomated Imaging Assay.
J Biomol Screen, 21(9) 956-964 (2016)
Hematopoietic stem and progenitor cells (HSPCs) generate all cell types of the blood and are crucial for homeostasis of all blood lineages in vertebrates. Hematopoietic stem cell transplantation (HSCT) is a rapidly evolving technique that offers potential cure for hematologic cancers, such as leukemia or lymphoma. HSCT may be autologous or allogenic. Successful HSCT depends critically on the abundance of engraftment-competent HSPCs, which are currently difficult to obtain in large numbers. Therefore, finding compounds that enhance either the number or the activity of HSPCs could improve prognosis for patients undergoing HSCT and is of great clinical interest. We developed a semiautomated screening method for whole zebrafish larvae using conventional liquid handling equipment and confocal microscopy. Applying this pipeline, we screened 550 compounds in triplicate for proliferation of HSPCs in vivo and identified several modulators of hematopoietic stem cell activity. One identified hit was valproic acid (VPA), which was further validated as a compound that expands and maintains the population of HSPCs isolated from human peripheral blood ex vivo. In summary, our in vivo zebrafish imaging screen identified several potential drug candidates with clinical relevance and could easily be further expanded to screen more compounds.

Susanne Sales, Juergen Graessler, Sara Ciucci, Rania Al-Atrib, Terhi Vihervaara, Kai Schuhmann, Dimple Kauhanen, Marko Sysi-Aho, Stefan Bornstein, Marc Bickle, Carlo Vittorio Cannistraci, Kim Ekroos, Andrej Shevchenko
Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome.
Sci Rep, 6 Art. No. 27710 (2016)
Open Access PDF DOI
Lipidomics of human blood plasma is an emerging biomarker discovery approach that compares lipid profiles under pathological and physiologically normal conditions, but how a healthy lipidome varies within the population is poorly understood. By quantifying 281 molecular species from 27 major lipid classes in the plasma of 71 healthy young Caucasians whose 35 clinical blood test and anthropometric indices matched the medical norm, we provided a comprehensive, expandable and clinically relevant resource of reference molar concentrations of individual lipids. We established that gender is a major lipidomic factor, whose impact is strongly enhanced by hormonal contraceptives and mediated by sex hormone-binding globulin. In lipidomics epidemiological studies should avoid mixed-gender cohorts and females taking hormonal contraceptives should be considered as a separate sub-cohort. Within a gender-restricted cohort lipidomics revealed a compositional signature that indicates the predisposition towards an early development of metabolic syndrome in ca. 25% of healthy male individuals suggesting a healthy plasma lipidome as resource for early biomarker discovery.

Jon M Carthy, Martin Stöter, Claudia Bellomo, Michael Vanlandewijck, Angelos Heldin, Anita Morén, Dimitris Kardassis, Timothy C Gahman, Andrew K Shiau, Marc Bickle, Marino Zerial, Carl-Henrik Heldin, Aristidis Moustakas
Chemical regulators of epithelial plasticity reveal a nuclear receptor pathway controlling myofibroblast differentiation.
Sci Rep, 6 Art. No. 29868 (2016)
Open Access PDF DOI
Plasticity in epithelial tissues relates to processes of embryonic development, tissue fibrosis and cancer progression. Pharmacological modulation of epithelial transitions during disease progression may thus be clinically useful. Using human keratinocytes and a robotic high-content imaging platform, we screened for chemical compounds that reverse transforming growth factor β (TGF-β)-induced epithelial-mesenchymal transition. In addition to TGF-β receptor kinase inhibitors, we identified small molecule epithelial plasticity modulators including a naturally occurring hydroxysterol agonist of the liver X receptors (LXRs), members of the nuclear receptor transcription factor family. Endogenous and synthetic LXR agonists tested in diverse cell models blocked α-smooth muscle actin expression, myofibroblast differentiation and function. Agonist-dependent LXR activity or LXR overexpression in the absence of ligand counteracted TGF-β-mediated myofibroblast terminal differentiation and collagen contraction. The protective effect of LXR agonists against TGF-β-induced pro-fibrotic activity raises the possibility that anti-lipidogenic therapy may be relevant in fibrotic disorders and advanced cancer.

Jerome Gilleron, Prasath Paramasivam, Anja Zeigerer, William Querbes, Giovanni Marsico, Cordula Andree, Sarah Seifert, Pablo Amaya, Martin Stöter, Victor Koteliansky, Herbert Waldmann, Kevin Fitzgerald, Yannis Kalaidzidis, Akin Akinc, Martin A Maier, Muthiah Manoharan, Marc Bickle, Marino Zerial
Identification of siRNA delivery enhancers by a chemical library screen.
Nucleic Acids Res, 43(16) 7984-8001 (2015)
Open Access PDF DOI
Most delivery systems for small interfering RNA therapeutics depend on endocytosis and release from endo-lysosomal compartments. One approach to improve delivery is to identify small molecules enhancing these steps. It is unclear to what extent such enhancers can be universally applied to different delivery systems and cell types. Here, we performed a compound library screen on two well-established siRNA delivery systems, lipid nanoparticles and cholesterol conjugated-siRNAs. We identified fifty-one enhancers improving gene silencing 2-5 fold. Strikingly, most enhancers displayed specificity for one delivery system only. By a combination of quantitative fluorescence and electron microscopy we found that the enhancers substantially differed in their mechanism of action, increasing either endocytic uptake or release of siRNAs from endosomes. Furthermore, they acted either on the delivery system itself or the cell, by modulating the endocytic system via distinct mechanisms. Interestingly, several compounds displayed activity on different cell types. As proof of principle, we showed that one compound enhanced siRNA delivery in primary endothelial cells in vitro and in the endocardium in the mouse heart. This study suggests that a pharmacological approach can improve the delivery of siRNAs in a system-specific fashion, by exploiting distinct mechanisms and acting upon multiple cell types.

Marc Bickle, Hakim Djaballah, Lorenz Martin Mayr
The King Is Dead, Long Live the King! JBS Special Issue on Screening by RNAi and Precise Genome Editing Technologies.
J Biomol Screen, 20(8) 929-931 (2015)

Marisa P. McShane, Tim Friedrichson, Angelika Giner, Felix Meyenhofer, Rico Barsacchi, Marc Bickle, Marino Zerial
A Combination of Screening and Computational Approaches for the Identification of Novel Compounds That Decrease Mast Cell Degranulation.
J Biomol Screen, 20(6) 720-728 (2015)
High-content screening of compound libraries poses various challenges in the early steps in drug discovery such as gaining insights into the mode of action of the selected compounds. Here, we addressed these challenges by integrating two biological screens through bioinformatics and computational analysis. We screened a small-molecule library enriched in amphiphilic compounds in a degranulation assay in rat basophilic leukemia 2H3 (RBL-2H3) cells. The same library was rescreened in a high-content image-based endocytosis assay in HeLa cells. This assay was previously applied to a genome-wide RNAi screen that produced quantitative multiparametric phenotypic profiles for genes that directly or indirectly affect endocytosis. By correlating the endocytic profiles of the compounds with the genome-wide siRNA profiles, we identified candidate pathways that may be inhibited by the compounds. Among these, we focused on the Akt pathway and validated its inhibition in HeLa and RBL-2H3 cells. We further showed that the compounds inhibited the translocation of the Akt-PH domain to the plasma membrane. The approach performed here can be used to integrate chemical and functional genomics screens for investigating the mechanism of action of compounds.

Anne Eugster, Aaron Lindner, Mara Catani, Anne-Kristin Heninger, Andreas Dahl, Sylvia Klemroth, Denise Kühn, Susanne M Dietz, Marc Bickle, Anette-Gabrielle Ziegler, Enzio Bonifacio
High Diversity in the TCR Repertoire of GAD65 Autoantigen-Specific Human CD4+ T Cells.
J Immunol, 194(6) 2531-2538 (2015)
Autoreactive CD4(+) T cells are an essential feature of type 1 diabetes mellitus. We applied single-cell TCR α- and β-chain sequencing to peripheral blood GAD65-specific CD4(+) T cells, and TCR α-chain next-generation sequencing to bulk memory CD4(+) T cells to provide insight into TCR diversity in autoimmune diabetes mellitus. TCRs obtained for 1650 GAD65-specific CD4(+) T cells isolated from GAD65 proliferation assays and/or GAD65 557I tetramer staining in 6 patients and 10 islet autoantibody-positive children showed large diversity with 1003 different TCRs identified. TRAV and TRBV gene usage was broad, and the TRBV5.1 gene was most prominent within the GAD65 557I tetramer(+) cells. Limited overlap (<5%) was observed between TCRs of GAD65-proliferating and GAD65 557I tetramer(+) CD4(+) T cells. Few TCRs were repeatedly found in GAD65-specific cells at different time points from individual patients, and none was seen in more than one subject. However, single chains were often shared between patients and used in combination with different second chains. Next-generation sequencing revealed a wide frequency range (<0.00001-1.62%) of TCR α-chains corresponding to GAD65-specific T cells. The findings support minor selection of genes and TCRs for GAD65-specific T cells, but fail to provide strong support for TCR-targeted therapies.

Mihaela Anitei, Ramu Chenna, Cornelia Czupalla, Milan Esner, Sara Christ, Steffi Lenhard, Kerstin Korn, Felix Meyenhofer, Marc Bickle, Marino Zerial, Bernard Hoflack
A high-throughput siRNA screen identifies genes that regulate mannose 6-phosphate receptor trafficking.
J Cell Sci, 127(23) 5079-5092 (2014)
The delivery of newly synthesized soluble lysosomal hydrolases to the endosomal system is essential for lysosome function and cell homeostasis. This process relies on the proper trafficking of the mannose 6-phosphate receptors (MPRs) between the trans-Golgi network (TGN), endosomes and the plasma membrane. Many transmembrane proteins regulating diverse biological processes ranging from virus production to the development of multicellular organisms also use these pathways. To explore how cell signaling modulates MPR trafficking, we used high-throughput RNA interference (RNAi) to target the human kinome and phosphatome. Using high-content image analysis, we identified 127 kinases and phosphatases belonging to different signaling networks that regulate MPR trafficking and/or the dynamic states of the subcellular compartments encountered by the MPRs. Our analysis maps the MPR trafficking pathways based on enzymes regulating phosphatidylinositol phosphate metabolism. Furthermore, it reveals how cell signaling controls the biogenesis of post-Golgi tubular carriers destined to enter the endosomal system through a SRC-dependent pathway regulating ARF1 and RAC1 signaling and myosin II activity.

Marc Bickle
The Technology Development Studio of the MPI-CBG: An Open Access Cell-Based Screening Facility.
Comb Chem High Throughput Screen, 17(4) 322-327 (2014)
In the past decade, academic screening centers have been created in many universities worldwide. Most of these screening centers are organized as core facilities that accept projects from both within their organization and from external users in order to maximize staff and instrument usage. The Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, also created such a screening facility named the Technology Development Studio (TDS). The mission of the facility is to provide cell based screening services focused on high resolution confocal imaging. The acquisition of high resolution images allows the mathematical description of cells with image analysis to a high degree of precision. This precision in turn allows classifying phenotypes accurately and compare different cellular treatments to discover underlying mechanisms.

Carsten Wenzel, Björn Riefke, Stephan Gründemann, Alice Krebs, Sven Christian, Florian Prinz, Marc Osterland, Sven Golfier, Sebastian Räse, Nariman Ansari, Milan Esner, Marc Bickle, Francesco Pampaloni, Christian Mattheyer, Ernst H K Stelzer, Karsten Parczyk, Stefan Prechtl, Patrick Steigemann
3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions.
Exp Cell Res, 323(1) 131-143 (2014)
Cancer cells in poorly vascularized tumor regions need to adapt to an unfavorable metabolic microenvironment. As distance from supplying blood vessels increases, oxygen and nutrient concentrations decrease and cancer cells react by stopping cell cycle progression and becoming dormant. As cytostatic drugs mainly target proliferating cells, cancer cell dormancy is considered as a major resistance mechanism to this class of anti-cancer drugs. Therefore, substances that target cancer cells in poorly vascularized tumor regions have the potential to enhance cytostatic-based chemotherapy of solid tumors. With three-dimensional growth conditions, multicellular tumor spheroids (MCTS) reproduce several parameters of the tumor microenvironment, including oxygen and nutrient gradients as well as the development of dormant tumor regions. We here report the setup of a 3D cell culture compatible high-content screening system and the identification of nine substances from two commercially available drug libraries that specifically target cells in inner MCTS core regions, while cells in outer MCTS regions or in 2D cell culture remain unaffected. We elucidated the mode of action of the identified compounds as inhibitors of the respiratory chain and show that induction of cell death in inner MCTS core regions critically depends on extracellular glucose concentrations. Finally, combinational treatment with cytostatics showed increased induction of cell death in MCTS. The data presented here shows for the first time a high-content based screening setup on 3D tumor spheroids for the identification of substances that specifically induce cell death in inner tumor spheroid core regions. This validates the approach to use 3D cell culture screening systems to identify substances that would not be detectable by 2D based screening in otherwise similar culture conditions.

Danielle Borg, Marc Weigelt, Carmen Wilhelm, Michael Gerlach, Marc Bickle, Stephan Speier, Enzio Bonifacio, Angela Hommel
Mesenchymal stromal cells improve transplanted islet survival and islet function in a syngeneic mouse model.
Diabetologia, 57(3) 522-531 (2014)
Islet transplantation is used therapeutically in a minority of patients with type 1 diabetes. Successful outcomes are hampered by early islet beta cell loss. The adjuvant co-transplantation of mesenchymal stromal cells (MSCs) has the promise to improve islet transplant outcome.

Milan Esner, Felix Meyenhofer, Michael Kuhn, Melissa Thomas, Yannis Kalaidzidis, Marc Bickle
Development of a Kinetic Assay for Late Endosome Movement.
J Biomol Screen, 19(7) 1070-1078 (2014)
Automated imaging screens are performed mostly on fixed and stained samples to simplify the workflow and increase throughput. Some processes, such as the movement of cells and organelles or measuring membrane integrity and potential, can be measured only in living cells. Developing such assays to screen large compound or RNAi collections is challenging in many respects. Here, we develop a live-cell high-content assay for tracking endocytic organelles in medium throughput. We evaluate the added value of measuring kinetic parameters compared with measuring static parameters solely. We screened 2000 compounds in U-2 OS cells expressing Lamp1-GFP to label late endosomes. All hits have phenotypes in both static and kinetic parameters. However, we show that the kinetic parameters enable better discrimination of the mechanisms of action. Most of the compounds cause a decrease of motility of endosomes, but we identify several compounds that increase endosomal motility. In summary, we show that kinetic data help to better discriminate phenotypes and thereby obtain more subtle phenotypic clustering.

Varadharajan Sundaramurthy, Rico Barsacchi, Mikhail Chernykh, Martin Stöter, Nadine Tomschke, Marc Bickle, Yannis Kalaidzidis, Marino Zerial
Deducing the mechanism of action of compounds identified in phenotypic screens by integrating their multiparametric profiles with a reference genetic screen.
Nat Protoc, 9(2) 474-490 (2014)
Cell-based high-content screens are increasingly used to discover bioactive small molecules. However, identifying the mechanism of action of the selected compounds is a major bottleneck. Here we describe a protocol consisting of experimental and computational steps to identify the cellular pathways modulated by chemicals, and their mechanism of action. The multiparametric profiles from a 'query' chemical screen are used as constraints to select genes with similar profiles from a 'reference' genetic screen. In our case, the query screen is the intracellular survival of mycobacteria and the reference is a genome-wide RNAi screen of endocytosis. The two disparate screens are bridged by an 'intermediate' chemical screen of endocytosis, so that the similarity in the multiparametric profiles between the chemical and the genetic perturbations can generate a testable hypothesis of the cellular pathways modulated by the chemicals. This approach is not assay specific, but it can be broadly applied to various quantitative, multiparametric data sets. Generation of the query system takes 3-6 weeks, and data analysis and integration with the reference data set takes an 3 additional weeks.

Anna Ivanova, Yannis Kalaidzidis, Ronald Dirkx, Mihail Sarov, Michael Gerlach, Britta Schroth-Diez, Andreas Müller, Yanmei Liu, Cordula Andree, Bernard Mulligan, Carla Münster, Thomas Kurth, Marc Bickle, Stephan Speier, Konstantinos Anastassiadis, Michele Solimena
Age-dependent labeling and imaging of insulin secretory granules.
Diabetes, 62(11) 3687-3696 (2013)
Insulin is stored within the secretory granules of pancreatic β-cells, and impairment of its release is the hallmark of type 2 diabetes. Preferential exocytosis of newly synthesized insulin suggests that granule aging is a key factor influencing insulin secretion. Here, we illustrate a technology that enables the study of granule aging in insulinoma cells and β-cells of knock-in mice through the conditional and unequivocal labeling of insulin fused to the SNAP tag. This approach, which overcomes the limits encountered with previous strategies based on radiolabeling or fluorescence timer proteins, allowed us to formally demonstrate the preferential release of newly synthesized insulin and reveal that the motility of cortical granules significantly changes over time. Exploitation of this approach may enable the identification of molecular signatures associated with granule aging and unravel possible alterations of granule turnover in diabetic β-cells. Furthermore, the method is of general interest for the study of membrane traffic and aging.

Esther Zanin, Arshad Desai, Ina Poser, Yusuke Toyoda, Cordula Andree, Claudia Moebius, Marc Bickle, Barbara Conradt, Alisa Piekny, Karen Oegema
A conserved RhoGAP limits M phase contractility and coordinates with microtubule asters to confine RhoA during cytokinesis.
Dev Cell, 26(5) 496-510 (2013)
During animal cell cytokinesis, the spindle directs contractile ring assembly by activating RhoA in a narrow equatorial zone. Rapid GTPase activating protein (GAP)-mediated inactivation (RhoA flux) is proposed to limit RhoA zone dimensions. Testing the significance of RhoA flux has been hampered by the fact that the GAP targeting RhoA is not known. Here, we identify M phase GAP (MP-GAP) as the primary GAP targeting RhoA during mitosis and cytokinesis. MP-GAP inhibition caused excessive RhoA activation in M phase, leading to the uncontrolled formation of large cortical protrusions and late cytokinesis failure. RhoA zone width was broadened by attenuation of the centrosomal asters but was not affected by MP-GAP inhibition alone. Simultaneous aster attenuation and MP-GAP inhibition led to RhoA accumulation around the entire cell periphery. These results identify the major GAP restraining RhoA during cell division and delineate the relative contributions of RhoA flux and centrosomal asters in controlling RhoA zone dimensions.

Jerome Gilleron, William Querbes, Anja Zeigerer, Anna Borodovsky, Giovanni Marsico, Undine Schubert, Kevin Manygoats, Sarah Seifert, Cordula Andree, Martin Stöter, Hila Epstein-Barash, Ligang Zhang, Victor Koteliansky, Kevin Fitzgerald, Eugenio Fava, Marc Bickle, Yannis Kalaidzidis, Akin Akinc, Martin A Maier, Marino Zerial
Image-based analysis of lipid nanoparticle-mediated siRNA delivery, intracellular trafficking and endosomal escape.
Nat Biotechnol, 31(7) 638-646 (2013)
Delivery of short interfering RNAs (siRNAs) remains a key challenge in the development of RNA interference (RNAi) therapeutics. A better understanding of the mechanisms of siRNA cellular uptake, intracellular transport and endosomal release could critically contribute to the improvement of delivery methods. Here we monitored the uptake of lipid nanoparticles (LNPs) loaded with traceable siRNAs in different cell types in vitro and in mouse liver by quantitative fluorescence imaging and electron microscopy. We found that LNPs enter cells by both constitutive and inducible pathways in a cell type-specific manner using clathrin-mediated endocytosis as well as macropinocytosis. By directly detecting colloidal-gold particles conjugated to siRNAs, we estimated that escape of siRNAs from endosomes into the cytosol occurs at low efficiency (1-2%) and only during a limited window of time when the LNPs reside in a specific compartment sharing early and late endosomal characteristics. Our results provide insights into LNP-mediated siRNA delivery that can guide development of the next generation of delivery systems for RNAi therapeutics.

Varadharajan Sundaramurthy, Rico Barsacchi, Nikolay Samusik, Giovanni Marsico, Jerome Gilleron, Inna Kalaidzidis, Felix Meyenhofer, Marc Bickle, Yannis Kalaidzidis, Marino Zerial
Integration of chemical and RNAi multiparametric profiles identifies triggers of intracellular mycobacterial killing.
Cell Host Microbe, 13(2) 129-142 (2013)
Pharmacological modulators of host-microbial interactions can in principle be identified using high-content screens. However, a severe limitation of this approach is the lack of insights into the mode of action of compounds selected during the primary screen. To overcome this problem, we developed a combined experimental and computational approach. We designed a quantitative multiparametric image-based assay to measure intracellular mycobacteria in primary human macrophages, screened a chemical library containing FDA-approved drugs, and validated three compounds for intracellular killing of M. tuberculosis. By integrating the multiparametric profiles of the chemicals with those of siRNAs from a genome-wide survey on endocytosis, we predicted and experimentally verified that two compounds modulate autophagy, whereas the third accelerates endosomal progression. Our findings demonstrate the value of integrating small molecules and genetic screens for identifying cellular mechanisms modulated by chemicals. Furthermore, selective pharmacological modulation of host trafficking pathways can be applied to intracellular pathogens beyond mycobacteria.

Martin Stöter, Antje Niederlein, Rico Barsacchi, Felix Meyenhofer, Holger Brandl, Marc Bickle
CellProfiler and KNIME: open source tools for high content screening.
Methods Mol Biol, 986 105-122 (2013)
High content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using Open Source software. We present and discuss the Open Source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions which increase flexibility and keep costs low.

Marc Bickle
Systems drug discovery: a quantitative, objective approach for safer drug development.
Expert Opin Drug Discov, 7(9) 757-759 (2012)
We are currently witnessing a dramatic change in the pharmaceutical industry as many companies are downscaling their efforts to discover new drug candidates and are instead turning toward collaboration with academic partners. This trend has been dubbed open innovation. The reason for this change of policy stems from the realization that, in spite of massive investments in their drug development programs in the past 30 years, the number of new drugs reaching the market has remained stable over the same period. We review past and present drug discovery strategies and present a novel more holistic approach that we term Systems Drug Discovery. This approach aims at quantifying the physiological state of organ slice cultures using high content imaging and metabolomics. The characterization in a quantitative manner of healthy, diseased, and drug-treated tissues will allow defining a multiparametric space, within which tissues are healthy. This in turn will allow an objective assessment of the impact of candidate drugs on cells. This quantitative approach should help guide the development of new drugs reducing failure rates in clinical phase.

Julia Franziska Winter✳︎, Sebastian Höpfner✳︎, Kerstin Korn, Benjamin Farnung, Charles R. Bradshaw, Giovanni Marsico, Michael Volkmer, Bianca Habermann, Marino Zerial
Caenorhabditis elegans screen reveals role of PAR-5 in RAB-11-recycling endosome positioning and apicobasal cell polarity.
Nat Cell Biol, 14(7) 666-676 (2012)
Apically enriched Rab11-positive recycling endosomes (Rab11-REs) are important for establishing and maintaining epithelial polarity. Yet, little is known about the molecules controlling trafficking of Rab11-REs in an epithelium in vivo. Here, we report a genome-wide, image-based RNA interference screen for regulators of Rab11-RE positioning and transport of an apical membrane protein (PEPT-1) in C. elegans intestine. Among the 356 screen hits was the 14-3-3 and partitioning defective protein PAR-5, which we found to be specifically required for Rab11-RE positioning and apicobasal polarity maintenance. Depletion of PAR-5 induced abnormal clustering of Rab11-REs to ectopic sites at the basolateral cortex containing F-actin and other apical domain components. This phenotype required key regulators of F-actin dynamics and polarity, such as Rho GTPases (RHO-1 and the Rac1 orthologue CED-10) and apical PAR proteins. Our data suggest that PAR-5 acts as a regulatory hub for a polarity-maintaining network required for apicobasal asymmetry of F-actin and proper Rab11-RE positioning.

Eugenio Fava✳︎, J Dehghany✳︎, Joke Ouwendijk, A Müller, Antje Niederlein, Paul Verkade, M Meyer-Hermann, Michele Solimena
Novel standards in the measurement of rat insulin granules combining electron microscopy, high-content image analysis and in silico modelling.
Diabetologia, 55(4) 1013-1023 (2012)
Knowledge of number, size and content of insulin secretory granules is pivotal for understanding the physiology of pancreatic beta cells. Here we re-evaluated key structural features of rat beta cells, including insulin granule size, number and distribution as well as cell size.

Andreas Ettinger, Michaela Wilsch-Bräuninger, Anne-Marie Marzesco, Marc Bickle, Annett Lohmann, Zoltan Maliga, Jana Karbanová, Denis Corbeil, Anthony A. Hyman, Wieland B. Huttner
Proliferating versus differentiating stem and cancer cells exhibit distinct midbody-release behaviour.
Nat Commun, 2 Art. No. 503 (2011)
The central portion of the midbody, a cytoplasmic bridge between nascent daughter cells at the end of cell division, has generally been thought to be retained by one of the daughter cells, but has, recently, also been shown to be released into the extracellular space. The significance of midbody-retention versus -release is unknown. Here we show, by quantitatively analysing midbody-fate in various cell lines under different growth conditions, that the extent of midbody-release is significantly greater in stem cells than cancer-derived cells. Induction of cell differentiation is accompanied by an increase in midbody-release. Knockdown of the endosomal sorting complex required for transport family members, Alix and tumour-suppressor gene 101, or of their interaction partner, centrosomal protein 55, impairs midbody-release, suggesting mechanistic similarities to abscission. Cells with such impaired midbody-release exhibit enhanced responsiveness to a differentiation stimulus. Taken together, midbody-release emerges as a characteristic feature of cells capable of differentiation.

Marc Bickle
The beautiful cell: high-content screening in drug discovery.
Anal Bioanal Chem, 398(1) 219-226 (2010)
The term "high-content screening" has become synonymous with imaging screens using automated microscopes and automated image analysis. The term was coined a little over 10 years ago. Since then the technology has evolved considerably and has established itself firmly in the drug discovery and development industry. Both the instruments and the software controlling the instruments and analyzing the data have come to maturity, so the full benefits of high-content screening can now be realized. Those benefits are the capability of carrying out phenotypic multiparametric cellular assays in an unbiased, fully automated, and quantitative fashion. Automated microscopes and automated image analysis are being applied at all stages of the drug discovery and development pipeline. All major pharmaceutical companies have adopted the technology and it is in the process of being embraced broadly by the academic community. This review aims at describing the current capabilities and limits of the technology as well as highlighting necessary developments that are required to exploit fully the potential of high-content screening and analysis.

Akin Akinc, William Querbes, Soma De, June Qin, Maria Frank-Kamenetsky, K Narayanannair Jayaprakash, Muthusamy Jayaraman, Kallanthottathil G Rajeev, William L Cantley, J Robert Dorkin, James S Butler, Liuliang Qin, Timothy Racie, Andrew Sprague, Eugenio Fava, Anja Zeigerer, Michael J Hope, Marino Zerial, Dinah W Y Sah, Kevin Fitzgerald, Mark A Tracy, Muthiah Manoharan, Victor Koteliansky, Antonin de Fougerolles, Martin A Maier
Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms.
Mol Ther, 18(7) 1357-1364 (2010)
Lipid nanoparticles (LNPs) have proven to be highly efficient carriers of short-interfering RNAs (siRNAs) to hepatocytes in vivo; however, the precise mechanism by which this efficient delivery occurs has yet to be elucidated. We found that apolipoprotein E (apoE), which plays a major role in the clearance and hepatocellular uptake of physiological lipoproteins, also acts as an endogenous targeting ligand for ionizable LNPs (iLNPs), but not cationic LNPs (cLNPs). The role of apoE was investigated using both in vitro studies employing recombinant apoE and in vivo studies in wild-type and apoE(-/-) mice. Receptor dependence was explored in vitro and in vivo using low-density lipoprotein receptor (LDLR(-/-))-deficient mice. As an alternative to endogenous apoE-based targeting, we developed a targeting approach using an exogenous ligand containing a multivalent N-acetylgalactosamine (GalNAc)-cluster, which binds with high affinity to the asialoglycoprotein receptor (ASGPR) expressed on hepatocytes. Both apoE-based endogenous and GalNAc-based exogenous targeting appear to be highly effective strategies for the delivery of iLNPs to liver.

Hesso Farhan, Markus W Wendeler, Sandra Mitrovic, Eugenio Fava, Yael Silberberg, Roded Sharan, Marino Zerial, Hans-Peter Hauri
MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening.
J Cell Biol, 189(6) 997-1011 (2010)
To what extent the secretory pathway is regulated by cellular signaling is unknown. In this study, we used RNA interference to explore the function of human kinases and phosphatases in controlling the organization of and trafficking within the secretory pathway. We identified 122 kinases/phosphatases that affect endoplasmic reticulum (ER) export, ER exit sites (ERESs), and/or the Golgi apparatus. Numerous kinases/phosphatases regulate the number of ERESs and ER to Golgi protein trafficking. Among the pathways identified, the Raf-MEK (MAPK/ERK [extracellular signal-regulated kinase] kinase)-ERK cascade, including its regulatory proteins CNK1 (connector enhancer of the kinase suppressor of Ras-1) and neurofibromin, controls the number of ERESs via ERK2, which targets Sec16, a key regulator of ERESs and COPII (coat protein II) vesicle biogenesis. Our analysis reveals an unanticipated complexity of kinase/phosphatase-mediated regulation of the secretory pathway, uncovering a link between growth factor signaling and ER export.

Claudio Collinet, Martin Stöter, Charles R. Bradshaw, Nikolay Samusik, Jochen Rink, Denise Kenski, Bianca Habermann, Frank Buchholz, Robert Henschel, Matthias S Mueller, Wolfgang E Nagel, Eugenio Fava, Yannis Kalaidzidis, Marino Zerial
Systems survey of endocytosis by multiparametric image analysis.
Nature, 464(7286) 243-249 (2010)
Endocytosis is a complex process fulfilling many cellular and developmental functions. Understanding how it is regulated and integrated with other cellular processes requires a comprehensive analysis of its molecular constituents and general design principles. Here, we developed a new strategy to phenotypically profile the human genome with respect to transferrin (TF) and epidermal growth factor (EGF) endocytosis by combining RNA interference, automated high-resolution confocal microscopy, quantitative multiparametric image analysis and high-performance computing. We identified several novel components of endocytic trafficking, including genes implicated in human diseases. We found that signalling pathways such as Wnt, integrin/cell adhesion, transforming growth factor (TGF)-beta and Notch regulate the endocytic system, and identified new genes involved in cargo sorting to a subset of signalling endosomes. A systems analysis by Bayesian networks further showed that the number, size, concentration of cargo and intracellular position of endosomes are not determined randomly but are subject to specific regulation, thus uncovering novel properties of the endocytic system.

Antje Niederlein, Felix Meyenhofer, Dan White, Marc Bickle
Image Analysis in High-Content Screening.
Comb Chem High Throughput Screen, 12(9) 899-907 (2009)
The field of High Content Screening (HCS) has evolved from a technology used exclusively by the pharmaceutical industry for secondary drug screening, to a technology used for primary drug screening and basic research in academia. The size and the complexity of the screens have been steadily increasing. This is reflected in the fact that the major challenges facing the field at the present are data mining and data storage due to the large amount of data generated during HCS. On the one hand, technological progress of fully automated image acquisition platforms, and on the other hand advances in the field of automated image analysis have made this technology more powerful and more accessible to less specialized users. Image analysis solutions for many biological problems exist and more are being developed to increase both the quality and the quantity of data extracted from the images acquired during the screens. We highlight in this review some of the major challenges facing automatic high throughput image analysis and present some of the software solutions available on the market or from academic open source solutions.

Jesper B Bramsen, Maria B Laursen, Anne F Nielsen, Thomas B Hansen, Claus Bus, Niels Langkjaer, B Ravindra Babu, Torben Højland, Mikhail Abramov, Arthur Van Aerschot, Dalibor Odadzic, Romualdas Smicius, Jens Haas, Cordula Andree, Jharna Barman, Malgorzata Wenska, Puneet Srivastava, Chuanzheng Zhou, Dmytro Honcharenko, Simone Hess, Elke Müller, Georgii V Bobkov, Sergey N Mikhailov, Eugenio Fava, Thomas F Meyer, Jyoti Chattopadhyaya, Marino Zerial, Joachim W Engels, Piet Herdewijn, Jesper Wengel, Jørgen Kjems
A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity.
Nucleic Acids Res, 37(9) 2867-2881 (2009)
The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

Vinciane Grimard, Julia Massier, Doris Richter, Dominik Schwudke, Yannis Kalaidzidis, Eugenio Fava, Albin Hermetter, Christoph Thiele
siRNA screening reveals JNK2 as an evolutionary conserved regulator of triglyceride homeostasis.
J Lipid Res, 49(11) 2427-2440 (2008)
Lipid homeostasis is essential for proper function of cells and organisms. To unravel new regulators of this system, we developed a screening procedure, combining RNA interference in HeLa cells and TLC, which enabled us to monitor modifications of lipid composition resulting from short, interfering RNA knock-downs. We applied this technique to the analysis of 600 human kinases. Despite the occurrence of off-target effects, we identified JNK2 as a new player in triglyceride (TG) homeostasis and lipid droplet metabolism and, more specifically, in the regulation of lipolysis. Similar control of the level of TGs and lipid droplets was observed for its Schizosaccharomyces pombe homolog, Sty1, suggesting an evolutionary conserved function of mitogen-activated protein kinases in the regulation of lipid storage in eukaryotic cells.

Marc Bickle
High-content screening: a new primary screening tool?
IDrugs, 11(11) 822-826 (2008)
Given a pharmaceutical landscape in which fewer drugs are succeeding in reaching the market, pharmaceutical and biotechnological companies are seeking alternative screening methodologies that will be compatible with the large scale of current combinatorial chemical libraries. In this context, HCS has received considerable attention. Imaging technologies are playing an increasing role in the drug discovery and development process, and this role is projected to increase further in the future. Currently, these technologies are rarely applied in primary screening campaigns but, rather, are used in the processes that precede and follow primary screening. Imaging technologies are employed for target identification and validation, secondary screening, ADMET studies, and pharmacokinetic studies. Various labeling technologies are deployed for such imaging, including fluorescence, luminescence, PET and computer tomography (CT). This feature review discusses high-content analysis (HCA), including the HCS technology and methodology involved, and the future potential of HCA in the drug discovery process.

Marc Bickle
Live cell high content screening in drug development
European Pharmaceutical Review, 13(4) 54-60 (2008)
Cell-based assays are essential for drug discovery and development as they increase the quality of lead compounds due to their physiological relevance. Toxicological data can be gathered during the early phases of hit selection and verification, reducing costs and attrition rates during clinical trials. Amongst the various cell-based assays that are currently being used, high content screening (HCS) has enjoyed particular interest and is now widely considered as an essential tool for the drug discovery and development industry and is implemented at every step of the process. This powerful technology is used for target validation1,2, primary screening3, secondary screening4, structure-activity relationship studies5,6 and ADMET (adsorption, distribution, metabolism, excretion and toxicity) studies7. Several factors have contributed to the success of HCS. Firstly, it is arguably the cell-based assay that can yield the most data due to the richness of information contained in the images. Thus, not only quantitative information such as intensity or number of structures can be obtained, but also descriptive qualifiers, such as size, morphology and texture of objects. Secondly, it is one of the few technologies that can measure spatial data, allowing the assay of translocations events and distribution of objects in regards to each other or to other objects (i.e. vesicle clustering or vesicle distance to plasma membrane). Thirdly, due to the analytical power of modern image analysis, subpopulations can be analysed, making HCS a very sensitive technique, allowing a person to screen for rare events. Lastly, due to the multiplexing capability of HCS, toxicity can be directly assayed by using appropriate markers, instead of being indirectly inferred by reduced cell numbers. Also, several parameters can be screened in parallel, allowing for screening and counter-screening to be performed in a single assay. All these properties facilitate the decision-making process during hit prioritisation and lead development. In recent years, live cell imaging has emerged as a new trend in HCS and most vendors of HCS readers now offer versions with incubation chambers and environmental control. Live cell imaging adds a further level of complexity to HCS and poses many new technological challenges. This article will review some of the advantages and challenges of kinetic HCS and discuss future directions.

Kerstin Korn, Eberhard Krausz
High-content siRNA screening for target identification and validation
Expert Opin Drug Discov, 3(5) 551-564 (2008)

Kerstin Korn, Eberhard Krausz
Cell-based high-content screening of small-molecule libraries.
Curr Opin Chem Biol, 11(5) 503-510 (2007)
Advanced microscopy and the corresponding image analysis have been developed in recent years into a powerful tool for studying molecular and morphological events in cells and tissues. Cell-based high-content screening (HCS) is an upcoming methodology for the investigation of cellular processes and their alteration by multiple chemical or genetic perturbations. Multiparametric characterization of responses to such changes can be analyzed using intact live cells as reporter. These disturbances are screened for effects on a variety of molecular and cellular targets, including subcellular localization and redistribution of proteins. In contrast to biochemical screening, they detect the responses within the context of the intercellular structural and functional networks of normal and diseased cells, respectively. As cell-based HCS of small-molecule libraries is applied to identify and characterize new therapeutic lead compounds, large pharmaceutical companies are major drivers of the technology and have already shown image-based screens using more than 100,000 compounds.

Torben Lessmann, Michele G Leuenberger, Sascha Menninger, Meritxell Lopez-Canet, Oliver Müller, Stefan Hümmer, Jenny Bormann, Kerstin Korn, Eugenio Fava, Marino Zerial, Thomas U Mayer, Herbert Waldmann
Natural product-derived modulators of cell cycle progression and viral entry by enantioselective oxa Diels-Alder reactions on the solid phase.
Chem Biol, 14(4) 443-451 (2007)
The underlying frameworks of natural product classes with multiple biological activities can be regarded as biologically selected and prevalidated starting points in vast chemical structure space in the development of compound collections for chemical biology and medicinal chemistry research. For the synthesis of natural product-derived and -inspired compound collections, the development of enantioselective transformations in a format amenable to library synthesis, e.g., on the solid support, is a major and largely unexplored goal. We report on the enantioselective solid-phase synthesis of a natural product-inspired alpha,beta-unsaturated delta-lactone collection and its investigation in cell-based screens monitoring cell cycle progression and viral entry into cells. The screens identified modulators of both biological processes at a high hit rate. The screen for inhibition of viral entry opens up avenues of research for the identification of compounds with antiviral activity.

Anne-Kristin Heninger, Karol Kozak, Ralf Kittler, Jan Wagner, Annett Lohmann, Ina Poser, Hannes Grabner, Eberhard Krausz, Frank Buchholz
RNAi libraries for Funtional Genomics: Avoid the Difficulties of Predicting Efficient siRNAs and the Cost of Chemical Synthesis
Genetic Engineering News, 26(19) 22-23 (2006)

Eberhard Krausz
Challenges in High-Content siRNA Screening
European Pharmaceutical Review, 6 13-20 (2006)
Huge progress has been made, both in RNA interference technology applied to mammalian cells and in automated microscopy to analyse gene functions upon silencing in the cellular context. Large-scale siRNA screens have been published recently, mainly applying assays that gain multi-parametric information on biological processes. It is a long way to establish an infrastructure that allows high-content siRNA screening, and in this article the major challenges are summarised.

Ayano Satoh, Jörg Malsam, Graham Warren
Tethering assays for COPI vesicles mediated by golgins
In: GTPases regulating membrane dynamics. (Eds.) William E. Balch Methods in enzymology ; 404.,Amsterdam, Netherlands,Elsevier (2005),125-134 Ch. 13
A method is described that allows the attachment of COPI vesicles and Golgi membranes to glass slides that can then be analyzed using electron microscopy (EM) and immuno-EM methods. Subpopulations of COPI vesicles can be bound selectively using recombinant golgins. Alternatively, COPI vesicles can be attached to prebound Golgi membranes. Marking these vesicles selectively with biotin allows their site of attachment to be identified.

Eberhard Krausz
Linking Multi-parametric Cell-based Assays to HTS
Screening (Darmstadt), 6 22-24 (2005)

Christoph Sachse, Eberhard Krausz, Andrea Krönke, Michael Hannus, Andrew Walsh, Anne Grabner, Dmitriy Ovcharenko, David Dorris, Claude Trudel, Birte Sönnichsen, Christophe J. Echeverri
High throughput RNA interference strategies for target discovery and validation using syntheic short interfering RNAs: functional genomics investigations of biological pathways
In: RNA interference. (Eds.) David R. Engelke, John J. Rossi Methods in enzymology ; 392.,Amsterdam, Netherlands,Elsevier (2005),242-277 Ch. 15
During the past five years, RNA interference (RNAi) has emerged as arguably the best functional genomics tool available to date, providing direct, causal links between individual genes and loss-of-function phenotypes through robust, broadly applicable, and readily upscalable methodologies. Originally applied experimentally in C. elegans and Drosophila, RNAi is now widely used in mammalian cell systems also. The development of commercially available libraries of short interfering RNAs (siRNAs) and other RNAi silencing reagents targeting entire classes of human genes provide the opportunity to carry out genome-scale screens to discover and characterize gene functions directly in human cells. A key challenge of these studies, also faced by earlier genomics or proteomics approaches, resides in reaching an optimal balance between the necessarily high throughput and the desire to achieve the same level of detailed analysis that is routine in conventional small-scale studies. This chapter discusses technical aspects of how to perform such screens, what parameters to monitor, and which readouts to apply. Examples of homogenous assays and multiplexed high-content microscopy-based screens are demonstrated.

Eberhard Krausz, Lucas Pelkmans, Eugenio Fava, Michael Hannus, Claudia Möbius, Kerstin Korn, Francoise Halley, Annett Lohmann, Hannes Grabner, Marino Zerial
Genomweite funktionelle Analyse des Kinoms mittels RNA-Interfernz
BIOspektrum, 11(Sonderausgabe) 518-520 (2005)
In den Laboratorien des „High-Throughput Technology Development Studio“ (TDS) werden in enger Zusammenarbeit mit internen und externen Forschungsgruppen phänotypische Assays (qualitative/ quantitative Untersuchungen) entwickelt und mikroskopiegestützte Durchmusterungen, so genanntes „High-Content Screening“, sowohl in kultivierten Zellen als auch in Modellorganismen durchgeführt. Dabei werden automatisierte Pipettierstationen, Mikroskope und Bildverarbeitungsprogramme zu Hilfe genommen, um neue Genfunktionen oder Wirkungsweisen chemischer Substanzen zu entdecken.

Eberhard Krausz, Anne Grabner, Andrea Kroenke, Christoph Sachse, Christophe J. Echeverri
Optimizing High Throughput RNAi-Based Assays Using Transient Transfection of Synthetic siRNAs in Cultured Mammalian Cells
In: RNA Interference (RNAi) - Nuts & Bolts of RNAi Technology. (Eds.) David R. Engelke,Eagleville, USA,DNA Press (2003),131-168