More than one-fifth of all human cancers harbor mutations in one of the members of the BAF chromatin remodeling complex. Deep biochemical and epigenomic characterization of a cell line panel comprehensively representing all these mutations enabled researchers at the CeMM Research Center for Molecule Medicine of the Austrian Academy of Sciences to identify new approaches to target BAF mutant cancers. The study describing these findings has now been published in the journal Nature Genetics.
Chromatin organizes the approximately two meters of DNA present in the nucleus of every human cell so that, dependent on the cell type and state, certain genes can be activated, others repressed. The fundamental organizing unit of chromatin is the nucleosome, consisting of 146 base pairs of DNA wrapped around a histone octamer. Whenever a cell needs to adapt – for example, to respond to developmental or environmental signals or to DNA damage –, it needs to alter the accessibility of its DNA. Doing exactly this is the function of chromatin remodelers, enzymes that use the energy of ATP to move or evict nucleosomes. Chromatin remodeling complexes come in multiple flavors in human cells; a particularly interesting complex is the BAF complex. In fact, it is not only one complex, but many different ones. Up to 15 complex positions can be occupied by proteins encoded from 29 different genes, the combinatorics adding up to more than 10,000 theoretically possible different complexes.
What makes the BAF complex so relevant for human disease are the mutations that are found in the BAF complex genes in approximately every fifth human cancer. Currently, we have only a limited understanding how these mutations contribute to cancer development. Even more problematic, we do not have therapies to specifically cure BAF mutant cancers. Finding such therapies is challenging, because typically the genetic aberrations are so called loss of function mutations. These result in cancer cells lacking a specific BAF subunit protein, and it is hard to develop a drug against something that is not there.
To find ways to nevertheless target BAF mutant cells, Sandra Schick, postdoctoral fellow in the laboratory of Stefan Kubicek of the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, first needed to generate a relevant cellular model. She therefore established a panel of 22 isogenic cell lines that differed only in each lacking a single different BAF subunit. In these cells, she first characterized the consequences of loss of a single subunit on complex composition, chromatin accessibility and transcription. “We identified preferential BAF complex configurations, which can be altered when single subunits are lost” said Schick. “Furthermore, there is an intense cross-talk between these subunits, so that, depending on the lost gene, other BAF subunits are incorporated with higher or lower frequency”. These data indicate that although the original mutation results in the loss of one BAF subunit, the cancer promoting properties might be conferred by aberrant functions of the remaining BAF complexes. And such aberrant functions might again be druggable.
To test whether it is indeed the case that BAF mutant cancers become addicted to the function of the remaining complexes, the team went on to systematically deplete a second member of the BAF complexes in these cells that had already lost one subunit. From this large dataset they focused on three novel intra-complex synthetic lethalities, SMARCA4-ARID2, SMARCA4-ACTB, and SMARCC1-SMARCC2. The extensive systematic data on interaction proteomics, chromatin accessibility and transcription changes helped explain the molecular mechanism for these synthetic interactions. “But even more important to us was to prove that these novel targets hold up in relevant cancer cell lines beyond our cellular model system” explains Stefan Kubicek. And this is exactly what the researchers could prove, in a panel of 22 different cancer cell lines. “The SMARCC1-SMARCC2 pair was particularly strong and conserved, and we could show that cell lines with low SMARCC1 levels are extremely sensitive to loss of SMARCC2.”
The project, conducted in the context of the Christian Doppler Laboratory for Chemical Epigenetics in collaboration with Boehringer Ingelheim, provided not only a deep molecular insight in the biochemical and epigenetic alterations after the loss of a BAF subunit, but also identified novel targets towards the goal of developing targeted treatments for BAF-mutated cancers.
The study “Systematic characterization of BAF mutations explains intra-complex synthetic lethalities in human cancers” was published in Nature Genetics on 19 August 2019. DOI: 10.1038/s41588-019-0477-9.
Sandra Schick, André F. Rendeiro, Kathrin Runggatscher, Anna Ringler, Bernd Boidol, Melanie Hinkel, Peter Májek, Loan Vulliard, Thomas Penz, Katja Parapatics, Christian Schmidl, Jörg Menche, Guido Boehmelt, Mark Petronczki, André C. Mueller, Christoph Bock, Stefan Kubicek
The study was funded by the Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology, and Development, the Austrian Science Fund (FWF), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme.
Stefan Kubicek is Principal Investigator at CeMM and Head of the Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives. He also leads the Chemical Screening and PLACEBO (Platform Austria for Chemical Biology) program and the Proteomics and Metabolomics Facility at CeMM.
Picture from the award ceremony at the EMBL Advanced Training Centre in Heidelberg in June 2019. Axel Jahns, Wilhelm Plüster, Laura Machesky, Georg Winter, Maria Leptin, Reinhard Jahn. Photo credit: EMBL Photolab
Listen to a Nature podcast with CeMM PI Georg Winter, this year’s Eppendorf Young European Investigators Award Winner: https://www.nature.com/articles/d42473-019-00212-6
On 27 June 2019, the ceremony for the Eppendorf Award took place at the EMBL Advanced Training Centre in Heidelberg. The laudation honoring Georg’s achievements was held by Award Jury Chairman Reinhard Jahn, Director of the Max Planck Institute for Biophysical Chemistry, Göttingen. Georg received the € 20.000 prize for his pioneering work developing a method for targeting specific proteins for degradation using heterobifunctional chemical compounds to specifically recruit ubiquitin E3 ligases to the intended protein target for destruction.
Statement of the Jury: “This powerful system enables targeting of previously undruggable targets and shows promise both in cells and in vivo in model systems as an emerging therapy. Georg Winter’s work has led to a fury of excitement across pharmaceutical companies and has resulted in several patents; it holds promise to yield novel therapies for cancer and other diseases of unmet need.”
The Eppendorf Award for Young European Investigators was first established in 1995. It acknowledges outstanding contributions to biomedical research in Europe based on methods of molecular biology, including novel analytical concepts. The Award is presented in partnership with the scientific journal Nature.
Langerhans cell histiocytosis (LCH) is a rare disease affecting primarily young children. While LCH may heal by itself without treatment in some patients, others require intensive chemotherapy and suffer from long-term consequences, or may even succumb to the disease. The reasons for these differences in disease severity are poorly understood. In a new study published in Cancer Discovery, researchers from the St. Anna Children’s Cancer Research Institute (CCRI) and the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences revealed important insights into the cellular heterogeneity and molecular mechanisms underlying LCH.
Langerhans cell histiocytosis (LCH) is a very unusual disease: Often classified as a cancer because of uncontrolled cell growth in different parts of the body, it also has features of an autoimmune disease, as LCH lesions attract immune cells and show characteristic tissue inflammation. LCH is clinically variable and often difficult to diagnose. Skin involvement in babies with LCH can look like a nappy rash, whereas bone involvement can be mistaken as sarcoma in an X-ray picture. In its most aggressive form, LCH can present as leukaemia-like disease and lead to organ failure. These diverse manifestations and the enormous clinical heterogeneity of LCH continue to puzzle medical doctors and scientists around the world.
Studying LCH lesions under the microscope, Caroline Hutter – a paediatric oncologist at St. Anna Children’s Hospital, principal investigator at CCRI and co-lead investigator of this study – observed striking heterogeneity among LCH cells. To investigate this diversity in full molecular detail, she assembled an interdisciplinary team including experimental and computational researchers from CCRI and CeMM, as well as medical doctors from St. Anna Children’s Hospital and Vienna General Hospital. Her aim was to answer two fundamental questions: What are the mechanisms behind LCH, and how can we improve treatment of children affected by this disease?
Utilizing state-of-the-art technology in the laboratory of co-lead investigator Christoph Bock (CeMM), LCH lesions were analysed for their molecular composition at single-cell resolution. Spearheaded by one computational postdoc, Florian Halbritter (now at CCRI), and one wet-lab postdoc, Matthias Farlik (now at Medical University of Vienna), the team analysed the molecular profiles of LCH lesions and developed a comprehensive map of cellular heterogeneity in LCH.
In this molecular map of LCH, the team identified multiple LCH cell subtypes. One of these subtypes comprised actively dividing cells, which appear to give rise to the other LCH cell subtypes. In further experiments, the team unravelled the molecular pathways that are active in different branches of this unexpected developmental hierarchy, which corroborated an interplay of developmental, immunological, and oncogenic mechanisms in LCH.
The study is a significant step forward in the understanding of this enigmatic disease. In future, these finding may help devise better ways of distinguishing severe from less severe disease cases, and they may even open up new treatment possibilities.
The study "Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis" is published ahead of print in Cancer Discovery on 25 July 2019. DOI: 10.1158/2159-8290.CD-19-0138.
Authors: Halbritter F*, Farlik M*, Schwentner R, Jug G, Fortelny N, Schnöller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer W, Simonitsch-Klupp I, Bock C#, Hutter C#. * These authors contributed equally to this work; # CB and CH jointly directed the research.
Funding: The study was partly funded by the Austrian Science Fund, the German Research Foundation, the European Research Council, the Austrian Academy of Sciences, and the Histiocytosis Association.
The St. Anna Children's Cancer Research Institute (CCRI), founded in 1988, develops and optimizes diagnostic, prognostic, and therapeutic strategies for the treatment of children and adolescents with cancer by combining basic research with translational and clinical research. The focus is on the specific characteristics of childhood tumour diseases in order to provide young patients with the best possible and most innovative therapies. Around 120 scientists and students are involved in ongoing research projects at CCRI. Dedicated research groups in the fields of tumour genomics and epigenomics, immunology, molecular biology, cell biology, bioinformatics and clinical research are working together to harmonize scientific experimental findings with the clinical needs of physicians. Every year, about 250 children and adolescents in Austria are diagnosed with cancer. Thanks to interdisciplinary research work on an international level, 70 to 80 % of the children affected can already be cured.
One year after the European Court of Justice (ECJ) ruling on genome editing: Scientists call on EU politicians to amend legislation to secure our food supply and promote sustainable agriculture.
On Thursday, July 25th, 2019, numerous renowned European scientists appealed to the EU to simplify the use of new precision breeding methods to improve crops. This should enable the sustainable development of agriculture and food production in the face of climate change and population growth, according to a public statement to the newly elected EU Parliament and EU Commission. In Austria, the statement was signed by the Austrian Institute of Technology (AIT), The Institute of Science and Technology Austria (IST), the University of Natural Resources and Applied Life Sciences (BOKU), the Gregor Mendel Institute for Molecular Plant Biology (GMI) and the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM).
The appeal comes exactly one year after a controversial ruling by the ECJ, which ruled that plants produced with precision methods such as CRISPR/Cas9 should also be classified as genetically modified organisms. Thus, plants that contain even the smallest CRISPR-mediated alteration, which can also arise spontaneously in nature, fall under the GMO legislation of 2001 and are subject to a complex and expensive approval procedure that only large multinational companies can afford. Researchers fear that investment in EU research will decline and breeding efforts by smaller companies will be prevented.
At the same time, plants produced with far less precise conventional methods of gene modification - for example by chemicals or radiation - are exempt from regulation. These methods produce hundreds to thousands of random mutations in plant genomes and have long been used in breeding. However, they subsequently require time-consuming and costly selection and backcrossing in order to remove the hundreds of unwanted mutations. "The new methods, such as CRISPR/Cas9, allow precision breeding in which the same positive genomic changes can be achieved without the accompanying genomic damage," said Ortrun Mittelsten Scheid, group leader at the GMI.
Furthermore, the minimal genetic changes made through new precision methods cannot be distinguished from the same mutations which occurred naturally or were induced by chemicals or radiation. This implies that the current EU GMO legislation cannot be enforced on such imported products, in spite of the fact that approval of such cultivars developed within the EU is hampered by the GMO approval process.
The world population is growing and many plant species are threatened by longer periods of drought due to climate change. The signatories therefore urgently call for an adaptation of the outdated GMO legislation and harmonisation with other countries in order to facilitate plant breeding by research institutes and smaller producers in the EU.
Human DEF6 deficiency underlies a novel immunodeficiency syndrome with systemic autoimmunity and aberrant CTLA-4 homeostasis
A single gene affected in a young girl resulted in serious autoimmune diseases. By deciphering the underlying mechanism, an international research team led by LBI-RUD Director Kaan Boztug was able to shed some light on the mechanism of autoimmunity in the human body. Based on these findings, an already approved drug has been used to successfully treat the young patient. The researchers uncovered an inborn error of immunity caused by biallelic mutations in DEF6 and characterized by early-onset systemic autoimmunity. They found impaired CTLA-4 availability and trafficking, due to decreased interaction of mutated DEF6 with the small GTPase RAB11, as the mechanistic basis for the autoimmune manifestations. The results of the study were published in the scientific journal Nature Communications.
Immune responses need to be controlled tightly to prevent autoimmune diseases, yet underlying molecular mechanisms remain partially understood. The current work of the Boztug lab underlines the power of identifying genetic causes for immune diseases as a way to uncover immune regulatory pathways. Given the identified role of DEF6 in tuning the immune checkpoint protein CTLA-4, future studies should address whether DEF6 and related proteins are amenable to manipulation for targeted therapeutic intervention in immune-mediated disorders or potentially also anti-cancer immunotherapeutic approaches.
Nina K. Serwas*, Birgit Hoeger*, Rico Chandra Ardy, Sigrun V. Stulz, Zhenhua Sui, Nima Memaran, Marie Meeths, Ana Krolo, Özlem Yüce Petronczki, Laurène Pfajfer, Tie Z. Hou, Neil Halliday, Elisangela Santos-Valente, Artem Kalinichenko, Alan Kennedy, Emily M. Mace, Malini Mukherjee, Bianca Tesi, Anna Schrempf, Winfried F. Pickl , Joanna I. Loizou, Renate Kain, Bettina Bidmon-Fliegenschnee, Jean-Nicolas Schickel, Salomé Glauzy, Jakob Huemer, Wojciech Garncarz, Elisabeth Salzer, Iro Pierides, Ivan Bilic, Jens Thiel, Peter Priftakis, Pinaki P. Banerjee, Elisabeth Förster-Waldl, David Medgyesi, Wolf-Dietrich Huber, Jordan S. Orange, Eric Meffre, David M. Sansom, Yenan T. Bryceson, Amnon Altman, Kaan Boztug. Human DEF6 deficiency underlies a novel immunodeficiency syndrome with systemic autoimmunity and aberrant CTLA-4 homeostasis. Nature Communications, 2019, doi.org/10.1038/s41467-019-10812-x
The study has been supported by the Austrian Science Fund (FWF P24999-B13, P29951-B30, T934-B30), the European Research Council (ERC grant agreement 310857), and the Austrian Academy of Sciences (ÖAW DOC Fellowship 24486).
The Ludwig Boltzmann Institute for Rare and Undiganosed Diseases (LBI-RUD) under the leadership of Kaan Boztug was launched by the Ludwig Boltzmann Gesellschaft in April 2016 together with its partner institutions CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, the Medical University of Vienna, and the Children’s Cancer Research Institute (CCRI) of the St. Anna Children’s Hospital Vienna. http://rud.lbg.ac.at/
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CeMM has been a pioneer in many ways. We started (literally) from scratch in 2005, setting up a scientific institute, which is able to compete with top research institutes worldwide, which is special in its collaborative spirit, and bold and ambitious in its goals. CeMM’s pact with society is to pursue research excellence and to set new standards in science administration, communication and translational efforts. Many dedicated people (scientists, technical personnel, scientific support staff, administration) worked very hard to bring this institute to success, despite a lot of doubter and different challenges. We tried to create an atmosphere where diversity matters, where different cultures, backgrounds and opinions are valued, and an open dialogue is possible. We are fully aware that CeMM is a very competitive place and not an environment for everyone. However, it is our intention to constantly improve as employer, as collaboration partner and as an institute to achieve maximum scientific innovation in molecular medicine. It is up to you to have a positive impact on our institute! Please use our invitation and the opportunity to have a direct and open conversation, talking about your concerns, and things to improve with the Directors, HR, Faculty, Admin Team Leaders and Colleagues, with the aim of solving any kind of conflict when it arises and a friendly solution is still possible.
The human immune system is essential for the prevention of infections and the detection of tumor cells, and severe congenital allergic (atopic) diseases can be the result of a genetic disorder effecting the immune system. An international team of researchers from the USA, UK and Kaan Boztug's research group at the Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD) in Vienna has now discovered a novel genetic defect that leads to infections and severe atopic reactions.
This new study identifies a novel primary immunodeficiency, clarifying the contribution of IL-6 to the phenotype of patients with mutations in IL6ST, STAT3 and ZNF341, genes encoding different components of the IL-6 signalling pathway, and alerts us to the potential toxicity of drugs targeting the IL-6R. The results were published on June 24, 2019 in the Journal of Experimental Medicine.
The Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD) was launched by the Ludwig Boltzmann Gesellschaft in April 2016 together with its partner institutions CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, the Medical University of Vienna, and the Children’s Cancer Research Institute (CCRI) of the St. Anna Children’s Hospital Vienna. Its research remit is the thorough analysis of rare diseases of the hematopoietic system, the immune system and the nervous system – as such not only dedicated to provide research for the development of personalized therapeutics for affected patients, but with similar efforts dedicated to unravel novel insights into human biology. Benefitting from full access to the infrastructure of its partner institutions, LBI-RUD has established a coordinated research programme, integrating and considering scientific, sociologic, ethical and economical aspects of rare diseases. http://rud.lbg.ac.at/
Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses, Journal of Experimental Medicine, DOI 10.1084/jem.20190344.
The study has been supported by the European Research Council (ERC StG 310857), the Austrian Science Fund (FWF 29951-B30), the Austrian Academy of Sciences (ÖAW DOC Fellowship), the Medical Research Council und Cancer Research UK.
A research group from MedUni Vienna and CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences has discovered a new mechanism by which cells communicate in inflammatory processes. This involves endogenous mitochondria released from white blood cells turning into initiators of inflammation. It is as if friends turn into enemies. The results have been published in the journal Circulation Research.
In collaboration with other partners, Christoph Binder from the Department of Laboratory Medicine of MedUni Vienna and CeMM, and his group members Taras Afonyushkin and Florian Puhm have investigated how monocytes (a subset of white blood cells) belonging to the immune system react under stress. Monocytes shed parts of their cell membrane in the form of so-called microvesicles. These microvesicles are capable of transmitting alarm signals to other cells. The scientists discovered that a subset of these microvesicles contains mitochondria. Normally mitochondria are an important component of cells and are known as cellular power plants. However, compared to conventional mitochondria, these mitochondria released by stressed monocytes have an increased potential to trigger inflammation.
There are two factors that render these monocytic "stressed mitochondria" dangerous. The tumour necrosis factor (a messenger molecule of the immune system) associated with them and modified mitochondrial RNA (ribonucleic acid). Via these two factors, "stressed mitochondria" trigger tumour necrosis factor and Type 1 interferon signaling pathways in recipient cells. Notably, these are two of the major signaling pathways in chronic inflammatory diseases.
"We were able to demonstrate that activated monocytes release certain stressed mitochondria, which - even in small quantities - trigger dangerous pro-inflammatory responses in recipient cells" explains Taras Afonyushkin, one of the study's first authors.
These findings give rise to two new potential therapeutic approaches. "On the one hand, one could specifically stimulate the immune system to enhance the clearance of these released mitochondria (e.g. by means of antibodies) and thereby diminish their activity in the blood," explains Christoph Binder, "on the other hand, a better understanding of the mechanisms leading to the release of these mitochondria could help to identify molecules that specifically prevent this."
The Study: “Mitochondria Are a subset of Extracellular Vesicles Released by Activated Monocytes and Induce Type I IFN and TNF Responses in Endothelial Cells” was published in Circulation Research in May 2019, DOI: https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.118.314601
Authors: Florian Puhm*, Taras Afonyushkin*, Ulrike Resch, Georg Obermayer, Manfred Rohde, Thomas Penz, Michael Schuster, Gabriel Wagner, Andre F Rendeiro, Imene Melki, Christoph Kaun, Johann Wojta, Christoph Bock, Bernd Jilma, Nigel Mackman, Eric Boilard, and Christoph J Binder.
Funding: The study has been supported by the Special Research Program SFB-54 “InThro” of the Austrian Science Fund (FWF), the Doctoral Program CCHD “Cell Communication in Health and Disease” of the FWF, and the Christian-Doppler Laboratory for Innovative Therapy Approaches in Sepsis.
On June 5, 2019, the “1st Vienna Symposium on Machine Learning in Medicine & Biology” took place at CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences bringing together the diverse crowd of Austrian researchers in this rapidly growing field. The event was organized by Georg Langs (Medical University of Vienna) and Christoph Bock (CeMM), with support by the Austrian Platform for Personalized Medicine.
Invited talks covered new methods and exciting applications of machine learning – including deep neural networks and interpretable AI, cancer and drug toxicity, the social dimension of machine learning, and what machine learning can learn from the way our brains work.
Finally, a keynote lecture by Thomas Lengauer (Max Planck Institute for Informatics & University of Cologne) demonstrated how machine learning predicts drug resistance in HIV and improves the treatment of patients with HIV in very concrete ways.
The event was heavily oversubscribed, testimony of the great interest and strong community in this field. Indeed, (bio)medicine is consistently ranked among the areas where machine learning will have most impact – but it is among the most challenging fields and requires dedicated technology to be applicable and acceptable in the context of biomedical research and clinical practice.
Following the success of this first symposium, a follow-up event is planned for 2020. Please feel free to e-mail Christoph Bock (email@example.com) and Georg Langs (firstname.lastname@example.org) if you have any feedback or suggestions for improvements. Thank you!
RESOLUTE, an European Union IMI2 funded project with 13 partners, CeMM as academic coordinator and Pfizer as EFPIA leader, celebrated the 2nd RESOLUTE consortium meeting from June 3-5, 2019 in Krems an der Donau, near Vienna.
More than 65 participants coming from all over Europe and the US joined the meeting. This was a great chance to review the current status of the RESOLUTE project right before completing the first year of collaborations. This edition featured many young investigators presenting their progress in the generation of reagents, data and assays for solute carriers. Additionally, strategies were developed for tackling the challenges of the second year of RESOLUTE. Participants as well enjoyed the excellent weather and cultural amenities of the beautiful vineyards of the Wachau area.
Learn more about the RESOLUTE (Research Empowerment on Solute Carriers) Project: https://re-solute.eu/