June 01, 2020

CeMM study reveals how a master regulator of gene transcription operates

Georg Winter and Martin Jäger (Laura Alvarez/CeMM).

The human Mediator complex is selectively required for cell-type-specifying transcription

Using targeted protein degradation technology, researchers at CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, set out to understand the primary role of a key regulator of transcription, the human Mediator complex. Mediator, a 30 subunit molecular machine, was thus far positioned as a factor that is generally required for the transcription of all protein-coding genes in human cells. In contrast, the recent study by Georg Winter’s group at CeMM discovered that Mediator particularly safeguards the transcription of a small set of cell-type-specifying genes. In collaboration with Patrick Cramer’s lab at the Max Planck Institute for Biophysical Chemistry in Göttingen, the scientists revealed mechanistic details of how Mediator enables cells to robustly exert their dedicated functions. The study “Selective Mediator dependence of cell-type-specifying transcription” was published in Nature Genetics, on 1 June 2020.

Georg Winter’s lab at CeMM uses chemical tools to understand the molecular basis of gene control and aberrations thereof in cancer. To do so, the team combines particularly fast-acting protein ablation systems (“degradation Tag”/ “dTAG”, co-developed by Georg Winter in Jay Bradner’s lab at the Dana Farber Cancer Institute, in Boston) with precise and unbiased measurements of gene activity at high kinetic resolution. Together with Patrick Cramer’s lab and others, the international team of scientists now unveiled how the Mediator molecular machine mechanistically directs gene activation, which had long remained poorly understood owing to challenges in experimental manipulation.

Mediator was identified over 30 years ago as a molecular bridge that allows DNA-binding proteins, called transcription factors, to communicate with the cellular gene-copying machine, called RNA polymerase II (Pol II), to activate target genes. Understanding the direct role of Mediator in this process requires technologies that rapidly block Mediator function and measure changes in Pol II activity within the subsequent minutes. Using targeted protein degradation, scientists in the Winter lab now managed to rapidly remove individual parts of the Mediator complex to ask the question, whether the copying of all human genes depends to the same extent on Mediator integrity. In contrast to the existing paradigm, the study first-authored by CeMM PhD student Martin Jäger suggests that Mediator is not generally required for transcription of all genes. Rather, the data imply that Mediator selectively safeguards the expression of a small set of genes, which form densely connected regulatory circuits to instruct cell-type-specific functions.

By visualizing Pol II enzymes in cells, the scientists observed that Mediator nucleates large clusters of transcription machinery components that are thought to form around regulatory DNA regions, called super-enhancers. These super-enhancers direct the expression of cell-type-specific genes by physically touching their target genes, which are often millions of DNA bases away. When Mediator was degraded, the large Pol II clusters rapidly disappeared, but super-enhancers still seemed to touch their target genes, indicating that Mediator was not required to maintain these DNA contacts.

Together with experts from the Cramer lab in Göttingen, however, the team observed dramatic changes in the dynamics of Pol II turnover at super-enhancer-driven genes after Mediator loss. The data suggested that Mediator clusters drove highly efficient recruitment of Pol II enzymes to these cell-type-specific genes, allowing their copying at remarkable efficiency. At the same time, the majority of other genes seemed to be surprisingly mildly affected by acute Mediator loss, which made the scientists suspect that they undergo some unexpected type of compensatory boost.

The team went on to address this compensatory mechanism, and found that promoter-proximal pausing of Pol II was globally reduced in response to Mediator loss. Pausing is a phenomenon, where Pol II enzymes are held back for several minutes right after they started copying a gene. The waiting Pol II constitutes a roadblock that prevents the passing of other Pol II enzymes behind it, thus limiting the number of RNA copies produced in a given timespan. After Mediator degradation, the scientists observed that the main factor responsible for signaling pause release, called cyclin dependent kinase 9 (CDK9), more efficiently bound to DNA in cells and more actively tagged its protein targets with a phosphate group. Chemically blocking CDK9 activity made the transcriptional defects of Mediator ablation less selective for super-enhancer target genes, which highlights that the uncovered CDK9 activation shapes how cells react to acute Mediator loss. This unexpected finding suggested that pausing may have evolved as a buffering capacity to rapidly react to and partially compensate acute defects in Pol II recruitment.

The study opens up new avenues to understand the composition of Mediator-nucleated Pol II clusters and how CDK9 is so efficiently activated in response to transcriptional stresses. Furthermore, Georg Winter imagines future possibilities to perhaps tackle diseases, where Mediator function went awry: “Very preliminarily, our work might also have revealed some potential for Mediator as a drug target and next steps might be to develop direct degrader molecules against this complex.

The study “Selective Mediator dependence of cell-type-specifying transcription” was published in Nature Genetics on 1 June 2020. DOI: 10.1038/s41588-020-0635-0.

Martin G. Jaeger, Björn Schwalb, Sebastian D. Mackowiak, Taras Velychko, Alexander Hanzl, Hana Imrichova, Matthias Brand, Benedikt Agerer, Someth Chorn, Behnam Nabet, Fleur M. Ferguson, André C. Müller, Andreas Bergthaler, Nathanael S. Gray,  James E. Bradner, Christoph Bock, Denes Hnisz, Patrick Cramer,* Georg E. Winter*
*co-senior authors

The study was supported by the Austrian Academy of Sciences, the Austrian Science Fund (FWF), the German Research Foundation (DFG), the International Max Planck Research School for Genome Science, and the European Research Council ERC. Martin Jäger was supported by a Boehringer Ingelheim Fonds PhD fellowship.

May 26, 2020

Release of over 200 new SARS-CoV-2 genomes provides unprecedented insights into transmission clusters in Austria

SARS-CoV-2 virion, phylogeny and structural effects of the D614G mutation in the S protein (Bobby Rajesh Malhotra / CeMM)

216 SARS-CoV-2 genome sequences have now been completed and released in the framework of the “Mutational Dynamics of SARS-CoV-2 in Austria” project from CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, in close collaboration with the Medical University of Vienna, the Medical University of Innsbruck and the Austrian Agency for Health and Food Safety (AGES). This data represents another milestone in the project and will help to understand the mutational landscape and evolution of the Austrian SARS-CoV-2 strains. Together with this release, CeMM researchers have published a dedicated website that offers background information as well as interactive access to the data for scientists and laypeople alike. The virus genomes can be explored interactively and intuitively via advanced visualization tools provided by CeMM and the open source project Nextstrain.

The spread of the pandemic SARS-CoV-2 virus in the human population is met with unprecedented collaborative scientific efforts around the world to unravel its virological, immunological and disease-causing properties. Genome sequences of SARS-CoV-2 viruses circulating worldwide are being published and made openly available to the international scientific community. A better understanding of the viral evolution will be instrumental to comprehend the underlying mutational dynamics and support the development of effective antiviral treatment and vaccine strategies to halt the COVID-19 pandemic.

In Austria, CeMM researchers with collaboration partners from the Medical University of Vienna were pioneers in sequencing the first genomes obtained from Austrian patient-derived samples. Within the scope of the “Mutational Dynamics of SARS-CoV-2 in Austria” project, the first samples were made available to the public and the international research community already at the beginning of April 2020. This highly collaborative initiative, led by CeMM Principal Investigators Andreas Bergthaler and Christoph Bock, aims at elucidating 1,000 SARS-CoV-2 genomes in Austrian patients using cutting-edge next-generation sequencing techniques and sophisticated computational analyses. The project includes a wide national collaboration network with partners from the Medical University of Vienna (Judith Aberle, Stephan Aberle, Elisabeth Puchhammer-Stöckl), the Medical University of Innsbruck (Wegene Borena, Dorothee von Laer; Manfred Nairz, Günter Weiss) and the Austrian Agency for Health and Food Safety (Daniela Schmid, Peter Hufnagl) as well as several hospitals and diagnostic laboratories.

Building on their first 21 genome sequences published on 3 April 2020, this second release with 216 new SARS-CoV-2 genomes from across Austria provides a more detailed picture about the circulating viruses and the early phase of the COVID-19 pandemic. The genetic differences of the genomes indicate that the pool of circulating viruses in the early phase of the pandemic was already highly diverse, with some viruses leading to bigger transmission clusters than others. Importantly, Austria has benefited from painstaking contact tracing by the Austrian Agency for Health and Food Safety, which defined more than 250 clusters of COVID-19 cases. “Our integrative analysis of the new SARS-CoV-2 genome information with epidemiological data provides valuable new insights into how the virus has been spreading through the country. The virus sequence data provides independent support for many of the epidemiological findings resulting from contact tracing. At the same time, we observed both heterogeneity within clusters and obtained evidence for multiple viruses circulating at the same time,” says Andreas Bergthaler, project co-coordinator and CeMM Principal Investigator (see illustration 1).

The molecular sequence analysis revealed on average 6.9 mutations per viral genome, of which more than 4 resulted in changed amino acids. A particular focus of interest worldwide rests on mutations in the viral S or spike protein, which decorates the surface of the virion and lends the coronavirus its eponymous crown-like appearance (see illustration 2). This viral S protein is essential for binding to the cellular receptor ACE2 as well as the presumed primary target for neutralizing antibodies. As such, mutations in this region will be important for the development of serological tests and antibody-mediated protection by vaccines. Within all Austrian SARS-CoV-2 genomes, we identified a total number of 12 mutated residues in the 1,273 amino acid long S protein. One particular mutation in the S protein, D614G, represents an early branching point that is dominant in the European infection clusters and parts of North America (see illustrations 2 and 3). This mutation is also found in many of the Austrian samples. The potential functional consequences of the D614G mutation are currently being investigated by several international laboratories. CeMM’s ongoing in-depth viral mutation analyses with an interdisciplinary team from the fields of genomics, biomathematical modeling, evolution biology and virology will yield new insights into how the S protein and other viral proteins evolve as well as how these mutations are transmitted between individuals.

Today’s release marks yet another crucial milestone as CeMM intensifies its efforts to communicate science and to reach out to the general public. Based on the tools of the open source project Nextstrain.org, CeMM researchers released a Nextstrain Austria version that allows users to compare and visualize all sequenced Austrian virus genomes with more than 8,000 virus genomes from all over the world. The Nextstrain Austria Blog will provide concise up-to-date and data-driven stories to share interesting insights about what the virus genomes tell us about the SARS-CoV-2 pandemic. These narratives will explore the actual genome data generated by CeMM and its partners, and allow users to explore the content interactively with an intuitive design. Users are guided through different dashboards where they encounter interactive graphics with a short explanatory text on different topics related to the SARS-CoV-2 virus. The visualization tool is available in both English and German and can be accessed at https://cemm.at/sars-cov-2/. The blog will be continuously updated and give first-hand insights into ongoing intense research about the SARS-CoV-2 virus.

The project team will continue their efforts to sequence 1,000 SARS-CoV-2 viral genomes, which will provide a detailed picture of emerging viral mutations and virus transmissions. This will offer further valuable scientific insights to epidemiologists, health care professionals and public health experts to assess transmission routes of the virus as well as its potential to subvert vaccine-induced immune responses and to acquire resistance against antiviral drugs.

Access SARS-CoV-2 sequencing data:
The sequences, related information and the blog are accessible at cemm.at/sars-cov-2/

May 18, 2020

Proxygen GmbH – a new CeMM spin-off company


From left to right: Stefan Kubicek, Matthias Brand, Georg Winter, Giulio Superti-Furga, Anita Ender

On 18 May 2020, Proxygen GmbH, a startup company by CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, Georg Winter, Giulio Superti-Furga, Stefan Kubicek and Matthias Brand has been founded.

Proxygen GmbH will develop therapies against cancer and other life-threatening diseases by reprogramming the cellular protein quality control system. Proxygen is focused on particular small molecules called “molecular glue degraders” which induce proximity between a disease-causing protein and an ubiquitin ligase. Consequently, the target protein is ubiquitinated and directed to the proteasome for degradation. Instead of merely blocking the function of harmful proteins, molecular glue degraders enable their complete, targeted and selective elimination. This outlines a clear avenue towards targeting otherwise undruggable proteins and is therefore seen as one of the most promising therapeutic innovations of the last decades.

Proxygen will be located in the VBC 6 Startup Labs, a new co-working space for biotech companies embedded in the Vienna Biocenter campus, and will be supported by funds of the Austrian Business Agency (AWS), as well as by private investors and industry cooperations.

Proxygen is the fifth startup company, after Haplogen, MyeloPro, Allcyte, and Aelian, which has been created based on intellectual property and know-how of CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences. CeMM’s mandate is to do world-class research in biomedicine, train researchers and medical doctors in molecular medicine and accelerate the precise, personalized, participatory and preventative medicine of the future. Integral component of CeMM’s strategy is to identify and support translational initiatives that promise to have an impact on medicine. CeMM, therefore, considers that safeguarding and valorizing its research output is an integral part of its societal responsibility, and that the efficient commercialization of CeMM’s proprietary and ideas will lead to the improvement of healthcare.


Proxygen GmbH – ein neues Spin-Off Unternehmen des CeMM

Heute wurde die Proxygen GmbH gegründet, ein Startup-Unternehmen des CeMM Forschungszentrums für Molekulare Medizin der Österreichischen Akademie der Wissenschaften, Georg Winter, Giulio Superti-Furga, Stefan Kubicek und Matthias Brand.

Proxygen wird Therapien gegen Krebs und andere lebensbedrohliche Krankheiten entwickeln, indem sie das zelluläre Proteinqualitätskontrollsystem neu programmiert. Proxygen konzentriert sich auf bestimmte kleine Moleküle, die als “molecular glue degraders” bezeichnet werden. Die Moleküle bringen ihr Zielprotein in die Nähe einer sogenannten Ubiquitin Ligase, welche das schadhafte Protein für den Abbau markiert. Neu in dieser Behandlungsstrategie ist, dass man nunmehr das Wirkspektrum mittels eines Medikamentes mit hoher Genauigkeit beeinflussen kann. Die Methode wird daher als eine der vielversprechendsten Innovationen der letzten Jahrzehnte angesehen.

Proxygen wird in den VBC 6 Startup Labs angesiedelt sein, einem neuen Kooperationsraum für Biotech-Unternehmen am Vienna Biocenter, und mit Mitteln der Austria Wirtschaftsservice Gesellschaft mbH (AWS) sowie durch private Investoren und Industriekooperationen finanziert.

Proxygen ist nach Haplogen, MyeloPro, Allcyte und Aelian das fünfte Startup-Unternehmen, das auf der Grundlage von geistigem Eigentum und Know-how des CeMM, Forschungszentrums für Molekulare Medizin der Österreichischen Akademie der Wissenschaften, gegründet wurde. Das Mandat von CeMM besteht darin, Spitzenforschung in der Biomedizin zu betreiben, ForscherInnen und ÄrztInnen in der molekularen Medizin auszubilden und die präzise, personalisierte, partizipative und präventive Medizin der Zukunft zu beschleunigen. Ein wesentlicher Bestandteil der CeMM-Strategie ist die Identifizierung und Unterstützung von Verwertungs- und Kommerzialisierungsvorhaben, die eine Weiterentwicklung in der Medizin und einen Nutzen für PatientInnen versprechen. CeMM ist daher der Ansicht, dass die Sicherung seiner Forschungsergebnisse ein wesentlicher Bestandteil der gesellschaftlichen Verantwortung des ÖAW-Instituts ist, und dass die effiziente Verwertung zu einer Verbesserung der Gesundheitsversorgung führen wird.

May 13, 2020

Missing component of innate immune signaling identified

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From left to right: Manuele Rebsamen, Leonhard Heinz and Giulio Superti-Furga.

How cells recognize pathogens and alert the immune system swiftly is a fundamental process of high importance for the survival of any species, including humans. A key role is ascribed to so-called adapters, that equal little molecular platforms inside cells where signals from pathogen detectors are integrated for safety and accuracy and conveyed to lasting signals leading to the activation of the major “red alarm” genes, like interferons. Researchers from the lab of Giulio Superti-Furga at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in collaboration with Boehringer Ingelheim have identified a new key element of the multi-component machinery that is responsible for sorting out the nature and severity of the pathogen challenge. The new protein, named TASL, is indispensable for the signaling of so-called Toll-like receptors (TLR) in the endosomes leading to activation of the gene-activator IRF5 in certain immune cells. Sensitive “tuning” of the machinery is highly important as too much output causes inflammation also in the absence of the pathogen, as in auto-immune diseases. This particular version of the machinery seems particularly associated with disorders such as systemic lupus erythematosus (SLE). This discovery highlights a potential new target for the development of drugs to treat certain autoimmune diseases and possibly also overreaction to viral and other infections, and has been published in the renowned scientific journal Nature.

The immune system is the body’s natural defense system and is made up of a network of cells, molecules, tissues, and organs working together to protect the body against infectious agents, such as viruses, bacteria or pathogenic fungi. The immune system is equipped with a sophisticated repertoire of sensing mechanisms which detect these pathogens and orchestrate an appropriate immune response. Autoimmune diseases originate when the immune system loses the ability to differentiate between itself and other foreign bodies.
Previous studies revealed that SLC15A4, a member of the body’s biggest family of transporter proteins, was known as an essential component required for the correct function of these TLRs. Based on their strong research interests in pathogen-sensing by the innate immune system and the characterization of solute carriers, researchers in the group of CeMM Scientific Director Giulio Superti-Furga set out to investigate how SLC15A4 influences the ability of TLRs to sense pathogens, and, consequently, gain a better understanding on its implication in autoimmune conditions, and in particular SLE.

In their study, first author Leonhard Heinz and the team, including Boehringer Ingelheim researchers in Ridgefield, undertook a precise investigative work, not taking for granted previous findings on SLC15A4 and the connection to this group of specially located TLRs. They painstakingly determined by biochemistry and mass spectrometry the molecular interactions that involved SLC15A4. This led to the identification of an uncharacterized protein CXorf21, belonging to the functionally orphan genes that are merely numbered and assigned to the chromosome of origin. The gene, like SLC15A4, had been previously loosely associated with SLE.

The team demonstrated that the interaction between TASL and SLC15A4 was crucial for the localization and function of the TASL protein and could pinpoint the precise involved portions of both proteins. A eureka moment for the understanding of the protein came with the observation that TASL harbors a specific motif essential for the recruitment and activation of IRF5. “After STING, MAVS and TRIF, the new protein TASL is the fourth key innate immunity adaptor functioning as a platform for the encounter of a kinase and a gene activator of the IRF family”, says Manuele Rebsamen, CeMM senior postdoctoral fellow and project leader of the study.

These findings raise the possibility that interfering pharmacologically with the SLC15A4/TASL complex could allow the regulation of TLR responses and, consequently, modulate inflammatory responses in the body. “It was clear to us that SLC15A4 plays a key role in endosomal TLR function and is involved in disease, but the underlying mechanism was not understood. These are exactly the exciting scientific questions that we love to address at our institute”, says Giulio Superti-Furga, CeMM Scientific Director and responsible for the study. He adds: ”We are happy that the vision we share with Boehringer Ingelheim regarding Solute Carriers being a group of disease-relevant proteins worthy of investigation was rewarded in this successful and exciting partnership.

This study is the result of a collaboration between CeMM and the Drug Concept Discovery Group led by Charles Whitehurst and JangEun Lee in the Immunology and Respiratory Diseases Department at Boehringer Ingelheim (Ridgefield, CT, USA). Researchers also benefited from the support of the Proteomics and Metabolomics (Pro-Met-) facility and the Biomedical Sequencing Facility (BSF) at CeMM.

The study “TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7–9” was published in Nature on 13 May 2020. DOI: 10.1038/s41586-020-2282-0.

Leonhard X. Heinz, JangEun Lee, Utkarsh Kapoor, Felix Kartnig, Vitaly Sedlyarov, Konstantinos Papakostas, Adrian César-Razquin, Patrick Essletzbichler, Ulrich Goldmann, Adrijana Stefanovic, Johannes W. Bigenzahn, Stefania Scorzoni, Mattia D. Pizzagalli, Ariel Bensimon, André C. Müller, F. James King, Jun Li, Enrico Girardi, M. Lamine Mbow, Charles E. Whitehurst, Manuele Rebsamen, Giulio Superti-Furga

The study was funded with support by the Austrian Academy of Sciences, the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 695214, awarded to Giulio Superti-Furga), the Austrian Science Fund (FWF SFB F4711) and by Boehringer Ingelheim (Research Collaboration Agreement BI-CeMM 238114).

May 11, 2020

Single-cell RNA seq method developed to accurately quantify cell-specific drug effects in pancreatic islets

Workflow of identification and removal of contaminating reads in single cell sequencing and the islet cell type-specific drug responses of the decontaminated profiles (© Illustration: Brenda Marquina-Sánchez and Nikolaus Fortelny / CeMM)

Researchers from Stefan Kubicek's and Christoph Bock’s groups, at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, have developed a method to accurately assess the effect of specific drugs in isolated pancreatic tissue by using a refined single-cell RNA sequencing method. Their study published in Genome Biology describes the technique that they have developed to overcome the problem of contaminating RNA molecules in single-cell transcriptomics, which allowed for accurate results of dynamic drug responses in pancreatic cells. These findings will support the development of targeted drug therapies for the treatment of Type 1 diabetes in the future.

The pancreas is an abdominal organ that produces digestive enzymes as well as hormones that regulate blood sugar levels. This hormone-producing function is localized to the islets of Langerhans, which constitute clusters of different endocrine cell types. Among those are beta cells, which produce the hormone insulin needed to lower glucose (a type of sugar) levels in our blood, as well as alpha cells, which generate the hormone glucagon in charge of raising glucose levels in the blood.

Type 1 diabetes is a chronic disease in which the body’s immune system mistakenly attacks and destroys the pancreas’ insulin-producing beta cells. Regenerative medicine aims to replenish beta cell mass, and thus support and ultimately substitute the current insulin replacement therapies. Alterations to islet composition, including insufficient beta cell function and beta cell dedifferention, also contribute to type II diabetes. Therefore, a deeper understanding of the identity and crosstalk of the different islet cell types leads to a better characterization of both forms of diabetes and may contribute to the development of novel therapeutic concepts.

Single-cell transcriptomics is a powerful technique to characterize cellular identity. Previously, CeMM researchers from Christoph Bock’s and Stefan Kubicek’s groups at CeMM published the first single cell transcriptomes from primary human pancreatic islet cells (EMBO Rep. 2016 Feb 17;(2):178-87. DOI: 10.15252/embr.201540946). Advances in the technology have since enabled its application to the generation of global human and mouse single cell transcriptome atlases. Despite these advances, single cell approaches remain technologically challenging given that the miniscule RNA amount present is entirely used up in the experiment. Therefore, it is essential to ensure the quality and purity of the resulting single cell transcriptomes.

CeMM researchers in the two contributing laboratories identified unexpectedly high hormone expression in non-endocrine cell types, both in their own dataset as well as other published single cell studies. They set out to elucidate whether this would be the result of contamination by RNA molecules, for example from dying cells, and how it could be removed to obtain a more reliable dataset. Such contamination seems present in single cell RNA-seq data from most tissues but was most visible in pancreatic islets. Islet endocrine cells are exclusively devoted to the production of single hormones, and insulin in beta cells and glucagon in alpha cells are expressed to higher levels than typical “housekeeping” genes. Thus, redistribution of these transcripts to other cell types was highly pronounced. Based on this observation, their goal was to develop, validate and apply a method to experimentally determine and computationally remove such contamination.

In their investigation, CeMM researchers used spiked-in cells from different cell types, both mouse and human samples, that they added to their pancreatic islet samples. Importantly, the transcriptomes of these spike-in cell were fully characterized. This allowed them to control internally and accurately the level of RNA contamination in single cell RNA-seq, giving that the human transcripts detected in the mouse spike-in cells constitute contaminating RNA. In this way, they found that the samples had a contamination level of up to 20%, and were able to define the contamination in each samples. They then developed a novel bioinformatics approach to computationally remove contaminating reads from single cell transcriptomes.

Having now obtained a “decontaminated” transcriptome, from which the spurious signal has been removed, they proceeded to characterize how the cellular identity in the different cell types responded to the treatment with three different drugs. They found that a small molecule inhibitor of the transcription factor FOXO1 induces dedifferentiation of both alpha and beta cells. Furthermore, they studied artemether, which had been found to diminish the function of alpha cells and could induce insulin production in both in vivo and in vitro studies (Cell. 2017 Jan 12;168(1-2):86-100.e15. DOI: 10.1016/j.cell.2016.11.010). The effects of the drug artemether were species-specific and cell-type-specific. In alpha cells, a fraction of cells increase insulin expression and gain aspects of beta cell identity, both in mouse and human samples. Importantly, researchers found that in human beta cells, there is no significant change in insulin expression, whereas in mouse islets, beta cells reduce their insulin expression and overall beta cell identity.

This study is the result of a cross-disciplinary collaboration of the laboratories of Stefan Kubicek and Christoph Bock at CeMM with Patrick Collombat at the Institute of Biology Valrose (France). This is the first study to apply single cell sequencing to analyze dynamic drug response in intact isolated tissue, which benefitted from the high quantitative accuracy of the decontamination method. It provides thus not only a novel method for single-cell decontamination and highly quantitative single-cell analysis of drug responses in intact tissues, but also addresses an important current question in islet cell biology and diabetes research. These findings could open up potential therapeutic avenues to treat Type 1 diabetes in the future.

The study “Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets” was published in Genome Biology on 6 May 2020. DOI: 10.1186/s13059-020-02006-2

Brenda Marquina-Sanchez*, Nikolaus Fortelny*, Matthias Farlik*, Andhira Vieira, Patrick Collombat, Christoph Bock, Stefan Kubicek * shared first authorships

The study was funded by the Juvenile Diabetes Research Foundation (JDRF SRA 201304452). Research in the Kubicek lab is also supported by the Austrian Academy of Sciences, the Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology, and Development, the Austrian Science Fund (FWF Special Research Program F4701-614 B20) and the European Research Council (ERC) under the European Union’s Horizon 615 2020 research and innovation programme (ERC-CoG-772437). Brenda Marquina-Sánchez is supported by a Boehringer Ingelheim Fonds PhD fellowship. Christoph Bock and his lab are supported by a New Frontiers Group award of the Austrian Academy of Sciences and by an ERC Starting Grant under the European Union’s Horizon 2020 research and innovation programme (ERC-StG-679146). Nikolas Fortelny is supported by an Innovation Fund of the Austrian Academy of Sciences (IF_2015_36) and the Austrian Science Fund (FWF Special Research Program SFB-F61.02).

May 05, 2020

Chemical modification of oleanolic acid could pave the way to pharmaceutically relevant derivates

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CeMM Adjunct PI Nuno Maulide’s group at the University of Vienna has developed an efficient reaction sequence to increase the oxidation state in oleanolic acid in the lab. In collaboration with the Georg Winter group at CeMM, the researchers also evaluated the antileukemic activity of the prepared compounds, revealing pronounced antiproliferative activity of a synthetic intermediate. The study, published in the renowned journal Chem, illustrates the value of interdisciplinary collaboration in basic research, when synthetic organic chemistry and cancer biology are harnessed to deliver a synergistic outcome.

Terpenes are a large class of natural products made mostly of carbon atoms and show a broad spectrum of biological activity. They can be divided in numerous subclasses, simply based on the shape of their carbon atom skeleton. However, the biological or physicochemical properties of these molecules are strongly influenced by the decoration of each carbon atom. In nature, enzymes play an essential role in the diversification of these carbon skeletons: they achieve so-called oxidations, which add “OH” (hydroxyl) groups to the carbon skeleton of terpenes and thus improve solubility and bioavailability. 

An example for the different biological availability due to the degree of oxidation are so-called oleanane terpenoids. The parent compound, oleanolic acid, is very abundant. Kilos can be extracted from various plants, such as olive trees. Oleanolic acid has a panoply of interesting biological effects in vitro. However, due to its low oxidation state – its skeleton has only one OH group – it is not readily bioavailable and poorly soluble, limiting further pharmacology. 

In contrast, other compounds isolated from similar sources such as uncargenin C or protobassic acid have a much higher oxidation state. They are significantly more soluble and thus have high potential as drugs. However, only very small amounts can be gained from nature. 

The number of OH groups determines the water solubility of a molecule: the more OH groups, the more soluble a molecule will be. Like oil itself, oleanolic acid is very greasy and does not dissolve well in biological systems. Therefore, further applications of the cheap and abundant compound in pharmacology are very difficult.

This limitation makes the laboratory synthesis of such molecules highly important. Besides enabling access to the natural products, chemical synthesis also allows to generate non-naturally occurring analogues, with great potential value and sometimes even exceeding the biological activity of the natural products themselves. Nuno Maulide’s approach was a synthesis based on natural processes: “Research development around natural products is, forgive the pun, only natural: why would we not look at what chemical tools Mother Nature has developed and try to modify them in order to help society, be it with a new drug, a new material or a new cosmetic.”

The Maulide Group has now developed an efficient reaction sequence to increase the oxidation state in oleanolic acid, in the lab. With the aid of a technique called “C−H oxidation”, the group invented a relay strategy where each newly added OH group was responsible for guiding the addition of the next one. Nuno Maulide: “It is just like in 4 × 100 m relay races that we watch during the Olympic Games: each racer does its job and then hands over the baton to the next one!”

In collaboration with the Winter Group, they also evaluated the antileukemic activity of the prepared compounds, revealing pronounced antiproliferative activity of a synthetic intermediate. The researchers are excited about possible new opportunities: “The ability of synthesis to make molecules of nature by different routes means that, in the course of synthesis, new compounds will be prepared that do not exist in nature and which never before have been made. Each and every one of these compounds presents an opportunity for discovery in biology, because they have never been tested before”.

The study “Application of Relay C−H Oxidation Logic to Polyhydroxylated Oleanane Triterpenoids” was published in Chem on 5 May 2020. DOI: 10.1016/j.chempr.2020.04.007

Authors: Martin Berger, Christian Knittl-Frank, Sophie Bauer, Georg Winter, and Nuno Maulide

Funding: Generous support by the University of Vienna is acknowledged. M. B. and C. K.-F. are fellows of the FWF-funded doctoral program MolTag (W1232). CeMM and the Winter Lab are supported by the Austrian Academy of Sciences.

May 05, 2020

Join the CeMM Alumni Network

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Today CeMM is launching the official Alumni LinkedIn group to provide CeMM Alumni for a space where they can come together with their former colleagues and friends and stay connected. In this private platform, former CeMMies can keep up to date with what is happening at CeMM, as well as post news, relevant job openings and announce events.

The CeMM Alumni Network was established back in 2017 with the aim of connecting or re-connecting with former CeMM colleagues. Currently, the Alumni Network has over 170 members living in 22 different countries and distributed across four continents.

The CeMM Alumni Network is represented by the Alumni Board, which together with CeMM's Administrative Director, Anita Ender, is the driving force behind all activities of the Alumni Network. Yesterday they held their annual board meeting in a virtual format, where the board members connected online to discuss further initiatives to increase the exchange and interaction within the community. We are very thankful for all their support and for helping us to bring this project into fruition.

If you worked for CeMM in the past and would like to become part of this community, please sign up now for the CeMM Alumni Network. Once registered, you can join the LinkedIn group directly via this link.

We look forward to welcoming all of our CeMM colleagues and friends to the community!

April 20, 2020

A Soundtrack of Research – CeMM Research Report 2019

Researchers love music and listen to music all the time. The new CeMM Research Report has a musical backbone. Like in science, where people from different countries and with different cultural backgrounds share a common goal to search truth and to advance knowledge, music brings together individuals with different background. Music is a universal language that speaks to our brain, melts our hearts, goes under our skin and so on. As soundtrack to our 2019 Research Report, we have chosen six pop songs, which by lyrics and mood are suitable to connect you to CeMM’s areas of research.

Nuno Maulide, Adjunct Principal Investigator at CeMM and Professor at the University of Vienna, was our perfect ambassador of both worlds, being an excellent chemist and “Researcher of the Year”, as well as a talented musician. He toured through the different laboratories at  CeMM and where the Adjunct Principal Investigators work, playing the CeMM-blue piano, and giving credit to the research topics and individual groups, who contributed with different choreographies and dancing performances.

We acknowledge the important contribution of  Eva Schweng, Stefanie Lichtwitz, Kriso Leinfellner, Christoph Burgstaller, Thomas Hötzeneder, Alexandra Tirendi, Juliett Zuza, Klaus Pichler and the entire creative team, who brought an abstract idea to life, as well as provided us with an exceptional document filled with interesting visuals of what has been a great team-building experience.

We also take the opportunity to thank our mother organization, the Austrian Academy of Sciences, and all our CeMM members and partner institutes, LBI-RUD, CCRI, Medical University of Vienna, Medical University of Innsbruck, University of Vienna, Technical University of Vienna as well as our collaborators and the various funding organizations, for another year of hard and dedicated work to advance research.

Thank you to everyone who active participated in this collaborative Research Report “experiment” and we very much hope you will enjoy the print and video results!

Giulio Superti-Furga, CeMM Scientific Director
Anita Ender, CeMM Administrative Director

Please download the 2019 CeMM Research Report here,
and also watch the corresponding music video.

The photos for the report and the video have been recorded in January and at the beginning of February 2020 before the COVID-19 health crisis reached Europe. As a leading biomedical research institute, CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences is committed to advancing the molecular understanding of the COVID-19 pandemic and the causative pathogen, SARS-CoV-2. We are willing to take up the challenge of assisting the medical world to fight the disease. Biomedical research on the virus and the disease will contribute substantially to informed policy decisions and, ultimately, the development of new treatments. Seldom has the importance of quality research for humanity been more evident.

SARS CoV-2 Sequencing (created in Unity3D & Octane Renderer for Unity). © Bobby Rajesh Malhotra / CeMM

The first 21 SARS-CoV-2 genomes in Austria have now been completed and published within the scope of the “Mutational Dynamics of SARS-CoV-2” project recently launched by CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, in close collaboration with the Medical University of Vienna. The project aims at sequencing 1,000 viral genomes obtained from Austrian patient-derived samples, in order to learn more about the molecular understanding of the COVID-19 pandemic and the causative pathogen. The project results will integrate Austrian viral genome data into a global map of SARS-CoV-2 mutations, which will help decipher the mutational dynamics underlying the COVID-19 pandemic.

The COVID-19 outbreak caused by the coronavirus SARS-CoV-2 was declared a pandemic by the World Health Organization (WHO) on 12 March 2020. It is thought to have been transmitted from wild animals to humans in the Chinese province of Hubei already in November 2019. More than 180 countries have been affected, and the COVID-19 disease already caused tens of thousands of deaths.

In an effort to understand the evolution of the virus in the human population, the international research community has started to make the genome sequences of circulating SARS-CoV-2 viruses openly available. No virus genomes of isolates from Austria were reported so far, which presented a considerable gap in the comparative analyses of global transmission routes and of the evolution of this virus. To overcome this, CeMM Principal Investigators Andreas Bergthaler and Christoph Bock launched a collaborative project to elucidate SARS-CoV-2 genomes in Austrian patients using cutting-edge next-generation sequencing techniques and sophisticated computational analyses. “Together with the Center for Virology of the Medical University of Vienna, we developed a rapid-response strategy to generate SARS-CoV-2 whole genome sequences from patients in a time-effective manner. This addresses pertinent questions of national public health concerns and medical research such as tracking of infection chains or time-resolved viral analyses during the different stages of acute respiratory disease caused by SARS-CoV-2”, says Andreas Bergthaler, project co-coordinator and CeMM Principal Investigator.

Initial sequence analysis of the 29,900 nucleotide-long SARS-CoV-2 genomes from Austria revealed on average 6 mutations different to the reference genome isolated in Wuhan, the capital city of the province of Hubei, China in December 2019. The observed number of mutations is in line with other recently reported SARS-CoV-2 genomes. Most of the observed mutations lead to changes in viral proteins, providing evidence for positive selection pressure and evolution within the human population. Assessing the actual impact of these mutations for the virus life cycle and its interactions with both the host and the immune system will be within the scope of future investigations. Ongoing in-depth genomic analyses focus on mutational hotspots, dissect viral diversity between the Austrian strains and the strains from other countries as well as study the mutational dynamics of pandemic SARS-CoV-2.

The project builds on an adapted viral evolution sequencing pipeline, which CeMM researchers had developed and applied to a different RNA virus previously, and puts CeMM and its partners in a unique position for in-depth investigations of the mutational dynamics of SARS-CoV-2. To support the CeMM initiative, the Vienna Science and Technology Fund (WWTF) has awarded the project with €50,000 sequencing funds, as part of the WWTF COVID-19 Rapid Response Funding 2020.

The first milestone of the project has been achieved by today’s release of the first 21 SARS-CoV-2 genome sequences into the public databases of GISAID and nextstrain.org. Together with numerous national partners including Elisabeth Puchhammer-Stöckl and her team from the Center for Virology of the Medical University of Vienna as primary collaborator, the Austrian Agency for Health and Food Safety (AGES) and several universities across Austria, CeMM researchers will continue these efforts to complete the sequencing of 1,000 viral genomes within the next weeks. “Whole genome sequence information of 1,000 patient-derived virus samples will provide a clearer picture of the mutation dynamics of the Austrian strains and enable the comparative analysis of these locally circulating strains in the global context. Thereby, this project will support the ongoing epidemiological and clinical investigations for better molecular insights into the spread of SARS-CoV-2 and how to fight this ravaging viral pandemic”, says Christoph Bock, Head of the Biomedical Sequencing Facility of CeMM and MedUni Vienna and Principal Investigator at CeMM.

The elucidation of the first genomes of circulating SARS-CoV-2 strains in Austria was the first milestone of this inter-disciplinary project. CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, as the primary medically-oriented research center in the country, is understanding and willing to take up the challenge of assisting the medical world to fight the disease. Together with a growing network of national and international collaboration partners, it will provide valuable scientific data for health care professionals, epidemiologists and public health experts as well as offer the opportunity to molecularly dissect the mutational landscapes and dynamics of this pandemic virus. Such insights will be critical to understand how the virus evolves during human-to-human transmission and to assess its potential to subvert vaccine responses or acquire resistance against future antiviral drugs.

Access SARS-CoV-2 sequencing data:
The sequences and related information are accessible at https://nextstrain.org/ (Real-time tracking of pathogen evolution) and https://www.gisaid.org/ (Global Initiative on Sharing All Influenza Data).

Funding: The project will be co-funded by a COVID19-Rapid Response grant of the Vienna Science and Technology Fund (WWTF), and through in-kind contributions of CeMM, the Austrian Academy of Sciences, the Medical University of Vienna and respective partners.



April 02, 2020

Obituary Michael Wakelam

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Professor Michael Wakelam in the lipidomics facility at the Babraham Institute. Image used courtesy of Keith Heppell and the Cambridge Independent.

The CeMM community was shocked to hear the tragic news of the passing of Michael Wakelam, Director of The Babraham Institute, Cambridge, U.K.

Since the foundation of the EU-Life Alliance, he was committed to building a community of excellence and promoting science. We will remember him from his visits to CeMM and collaborating with him at EU-Life meetings. Those who met him, even briefly, will remember him as friendly and open, always available for a chat or an in-depth discussion.  His dedication to The Babraham, to EU-Life, to science and science education was immense. His loss will be deeply felt across the European science community.

Our thoughts are with his colleagues and most especially his family at this difficult time.

Michael Wakelam 1955 – 2020