To understand how genes are regulated, researchers create genome-wide maps that connect regulatory proteins to their target sites on the DNA. This analysis is typically performed using “chromatin immunoprecipitation followed by sequencing” (ChIP-seq). With this method, the cell’s chromosomes are cut into small pieces, and an antibody is used to fish out those DNA fragments that are bound by the regulatory protein of interest. Unfortunately, ChIP-seq is a relatively complex protocol that requires a lot of cells, which makes it difficult to analyze some of the most interesting cell types – for example stem cells and cancer initiating cells.
Researchers in Christoph Bock’s group at CeMM have developed a new and very efficient alternative to ChIP-seq that addresses these limitations. Their approach, which is called “ChIPmentation”, combines the creation and enrichment of antibody-bound DNA fragments in a single-step reaction, making it much faster and more efficient for rare and difficult cell types. Their new paper was published in Nature Methods, which is the leading journal for new methods in biology and biomedicine, and the method is expected to substantially reduce the burden of large-scale studies on gene regulation. At CeMM, ChIPmentation will be used to dissect the role of epigenetic marks in the development and treatment of cancer.
Christian Schmidl*, André F. Rendeiro*, Nathan C. Sheffield and Christoph Bock. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nature Methods, 17 August 2015, DOI: 10.1038/nmeth.3542 (*shared first authors)
This work was supported by the European Commission (BLUEPRINT), the Austrian Science Fund (CINOCA), the Alexander von Humboldt Foundation, the Human Frontier Science Program, and the New Frontiers Programme of the Austrian Academy of Sciences.
Recent scientific insights and technical breakthroughs strongly argue for a global, efficient approach to map the gene products that manage the interface between biological systems and their environment.
The proteins that transport nutrients and drugs across cellular membranes into cells and organisms have paradoxically not been studied in an orderly, efficient fashion, despite their clear importance. Recent work at CeMM on regulation of the mTOR pathway and mechanism of cancer drug resistance has identified two members of the large group of solute carrier proteins (SLCs) as critical for these processes (Rebsamen et al, Nature 2015; Winter et al, Nature Chem Biol 2014). These discoveries generated the idea of a small workshop of scientists from academia and industry to discuss the merits of a research effort aimed at characterizing systematically the entire group of SLCs, composed of some 400 members. Together with Aled Edwards of the Structural Genomics Consortium in Toronto and Oxford and Matthias Hediger, of the University of Bern and scientists from several other laboratories in the Canada and the USA, Giulio Superti-Furga and his team now report to the large scientific readership of the prestigious journal Cell the logic that justifies the call to the scientific community for more attention to this class of proteins. First authors Adrián César-Razquin and Berend Snijder have found an unusually high degree of “asymmetric attention” so far devoted to SLCs by the scientific community. Some members, such as the target of serotonin uptake inhibitors and glucose transporters have been studied intensively and successfully, while the majority has been practically overlooked. Yet SLCs are of extraordinarily medical importance: many SLCs are linked to disease, it has been shown that SLCs can be excellent drug targets, and many drugs require SLCs to access cells and tissues. Because nutrient transport is linked by the complex and intertwined networks of metabolism, the paper argues that the function of SLCs should be studied taking these interactions into account. Ultimately, understanding the function and specificity of all membrane transporters promises substantial benefits for medicine and pharmacology.
Adrián César-Razquin, Berend Snijder, Tristan Frappier-Brinton, Ruth Isserlin, Gergely Gyimesi, Xiaoyun Bai, Reinhart A.F. Reithmeier, David Hepworth, Matthias A. Hediger, Aled M. Edwards and Giulio Superti-Furga, A Call for Systematic Research on Solute Carriers. Cell 162, July 30 2015.
The Superti-Furga laboratory at CeMM is part of a new crowdsourcing initiative, a wiki site called www.chemicalprobes.org that recommends appropriate chemical probes for biological targets, provides guidance on their use, and documents their limitations. Chemical probes are chemical tool compounds that enable scientists to study proteins in living cells without genetic modifications and which may be interesting drug targets to treat diseases like cancer. Many chemical probes produce spurious results that can lead researchers to wrong conclusions about the proteins and drug molecules they are studying. The use of optimal and well-documented probes and the exchange of best practices will help to improve the quality of research, will save time and money, and might have a huge impact on the understanding of fundamental biology and the identification of new therapeutic opportunities.
For more information please read the following publication, or visit the chemical probes website.
Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak D, Edwards AM, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Roth B, Ross R, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ. The promise and peril of chemical probes. Nat Chem Biol. 2015 Jul 21;11(8):536-41. doi: 10.1038/nchembio.1867.
www.chemicalprobes.org is supported by the Wellcome Trust
Through the investigation of specific interaction partners of the leukemia-associated, truncated variant of C/EBPa, the research group of Giulio Superti-Furga, Scientific Director at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, has gained new mechanistic insights into the molecular details of oncogenic transformation by C/EBPa mutant proteins. Florian Grebien, postdoctoral fellow in Superti-Furga´s team and since 2014 group leader at the Ludwig Boltzmann Institute for Cancer Research, found that the short, leukemic C/EBPa mutant can exert its oncogenic functions through a selective interaction with Wdr5, a critical constituent of histone-methyltransferase complexes that promote gene activation. Genetic inactivation of Wdr5 alleviated the differentiation block in myeloid cells and restored normal maturation in C/EBPa-mutant AML cells. In collaboration with the Structural Genomics Consortium (SGC) Toronto, the researchers at CeMM characterized a novel small molecule that was able to antagonize cellular functions of Wdr5 by disrupting specific protein-protein interactions. This novel chemical compound selectively inhibited the proliferation of AML cells and induced myeloid differentiation in cells from AML patients with N-terminal C/EBPa mutations. Therefore, interfering with Wdr5 represents a new therapeutic strategy for AML with C/EBPa mutations, which warrants attention for clinical development.
10 % of patients with acute myeloid leukemia (AML), a common form of blood cancer in adults, express a shortened form of the transcription factor C/EBPa that lacks a significant portion of the N-terminus of the protein. This short, mutant protein can induce leukemia development by preventing normal myeloid differentiation of blood cells.
Florian Grebien, Masoud Vedadi, Matthäus Getlik, Roberto Giambruno, Amit Grover, Roberto Avellino, Anna Skucha, Sarah Vittori, Ekaterina Kuznetsova, David Smil, Dalia Barsyte-Lovejoy, Fengling, Gennadiy Poda, Matthieu Schapira, Hong Wu, Aiping Dong, Guillermo Senisterra, Alexey Stukalov, Kilian V M Huber, Andreas Schönegger, Richard Marcellus, Martin Bilban, Christoph Bock, Peter J Brown, Johannes Zuber, Keiryn L Bennett, Rima Al-awar, Ruud Delwel, Claus Nerlov, Cheryl H Arrowsmith and Giulio Superti-Furga. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPa N-terminal leukemia. Nature Chemical Biology, doi:10.1038/nchembio.1859.
CeMM gratefully acknowledges funding from the Austrian Academy of Sciences, the European Research Council and the Austrian Science Fund FWF.
An unexpected order in the molecular regulation of the constituents of the fat part of our cells is revealed in two simultaneous publications appearing from the laboratory of Prof. Giulio Superti-Furga in the renowned scientific journals Cell and Cell Reports. The two studies, from scientists at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences investigated the role of lipids in the immune response. Marielle Köberlin, Berend Snijder, Leonhard Heinz and colleagues discovered that the regulation of lipids in the cell membrane follows a surprising circular, ring-like organizational pattern and that this pattern is linked to various cellular functions. In particular, the scientists found that the ability of cells to mount an immediate immune response is influenced by the cell’s lipid composition to a degree that far exceeds what had been known to date and can be predicted by this new regulatory “code”.
Essential to our immune system are so-called macrophages that act as sentinels and can ‘eat’ and destroy pathogens. The first contact between an invading pathogen and macrophages occurs at the cell surface of the macrophage. As for all cells in the human body, this cell surface is made up of two oppositely oriented layers of lipids, called a lipid membrane, and membrane proteins, including receptors that recognize pathogens. While much is known about the role of the many proteins involved in this process, cellular membranes contain hundreds of chemically distinct lipids, for which little is known in terms of regulation and function, and in particular their possible influence on the cell’s immune response.
Membrane lipids follow a higher-level organization
The team around Giulio Superti-Furga at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, has been interested in the organizational principle of biological matter, such as cell constituents, and in processes related to the primary response of cells to pathogens.
In the systematic study published in Cell, the team discovered that the amount and composition of lipids of different lipid types, follows a higher-level organization. The authors report that in cells certain lipids increase or decrease together with other lipids, a process they call lipid co-regulation. Visualization of the regulatory interdependence between hundreds of different lipid species, revealed that the organization forms a near perfect circular network of co-regulated lipids, exposing for the first time a “code” underlying the cellular lipids, or the “lipidome”.
Interestingly, based on the “circular lipidome” the researchers are now able to decipher the role of hundreds of different lipid species in the immune response, revealing which lipids act to stimulate and which act to dampen the inflammatory response of macrophages. The predictive power of the circular lipidome was put to test with cells from patients suffering from lipid storage disorders, caused by inherited mutations in genes involved in lipid metabolism. The authors found that they could accurately predict the inflammatory response of cells of these patients, only based on the measured differences in lipid composition.
Further insights into the lipid´s role in the immune response
In their second study published in the journal Cell Reports, the team provides a detailed functional characterization of a protein called SMPDL3B, a lipid-modifying enzyme. In a collaborative effort involving researchers from CeMM, the Medical University of Vienna and the National University of Singapore, the authors discovered that SMPDL3B is located on the surface of macrophages where it strongly affects the cellular lipid composition, thereby providing a novel mode of regulation for the immune response.
Senior Author Giulio Superti-Furga, who is Principal Investigator at CeMM and Professor for Medical Systems Biology at the Medical University of Vienna says: “Not only do these studies reveal a wide, unexpected role for lipids in innate immune signaling, but establish that global studies, looking at many molecules at the same time, can reveal new fundamental principles on how biological matter is organized. The circularity of lipid co-regulation discovered at CeMM is likely to enter the biochemistry textbooks.”
A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses. Marielle S. Köberlin, Berend Snijder, Leonhard X. Heinz, Christoph L. Baumann, Astrid Fauster, Gregory I. Vladimer, Anne-Claude Gavin and Giulio Superti-Furga
Cell 162, July 2, 2015: 1-14. DOI: http://dx.doi.org/10.1016/j.cell.2015.05.051
The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity. Leonhard X. Heinz, Christoph L. Baumann, Marielle S. Köberlin, Berend Snijder, Riem Gawish, Guanghou Shui, Omar Sharif, Irene M. Aspalter, André C. Müller, Richard K. Kandasamy, Florian P. Breitwieser, Andreas Pichlmair, Manuela Bruckner, Manuele Rebsamen, Stephan Blüml, Thomas Karonitsch, Astrid Fauster, Jacques Colinge, Keiryn L. Bennett, Sylvia Knapp, Markus R. Wenk, and Giulio Superti-Furga
Cell Reports 11, June 30, 2015: 1–10. DOI: http://dx.doi.org/10.1016/j.celrep.2015.05.006
CeMM gratefully acknowledges funding from the Austrian Academy of Sciences, the Medical University of Vienna, the European Research Council, the European Union, EMBO, the Swiss National Science Foundation, and the Austrian Science Fund FWF.
In an international study scientists from Kaan Boztug´s team at CeMM and the Medical University of Vienna, in close collaboration with the groups of Luigi Notarangelo at Boston Children’s Hospital, and Jean-Laurent Casanova at Rockefeller University, New York , have elucidated the molecular cause of a hitherto unrecognized inherited disorder of the immune system (primary immunodeficiency). Performing genetic and cellular immunological studies, the researchers identified biallelic mutations in DOCK2, a gene encoding a protein of critical importance for the cytoskeleton. Patients affected by this rare disease exhibit broad defects of immunity, including defective cellular motility and effector function of various types of leukocytes. The findings have been published online, on 18th June, 2015, in the New England Journal of Medicine.
According to the EU-wide definition, a disease is classified as rare if it occurs in no more than five people per 10,000 inhabitants. Often, far fewer people suffer a rare disease, of which there are estimated to be up to 8,000 different ones. To foster better diagnostics, research, and clinical care of patients with rare diseases, the Medical University of Vienna together with CeMM have recently established the Vienna Center for Rare and Undiagnosed Diseases (CeRUD) in Vienna. Although a number of primary immunodeficiencies have been identified, a large number remains elusive. Accordingly, a scientific focus at CeRUD lies in the investigation of undefined immunodeficiency disorders, conducted by Kaan Boztug, whose research group has identified several novel types of immunodeficiency disorders since his relocation to Vienna in 2011. Recognition of such disorders has a huge impact beyond the individual patient, as it allows for a molecular understanding of the hierarchical composition of the human immune system and its core components as well as their involvement in molecular networks. From the molecular characterization of these diseases, patients may profit through more specific diagnostics and the development of targeted therapeutic approaches in the future.
In their publication, CeMM PhD student Cecilia Domínguez Conde along with shared first authors Kerry Dobbs, Sheng-Ying Zhang and Silvia Parolini used a next generation sequencing-based approach to identify autosomal recessive mutations in DOCK2 in five unrelated families. The patients were characterized by a history of life-threatening bacterial and viral infections during infancy and early childhood. DOCK2 is an activator of the signaling molecule Rac1 which regulates cytoskeletal rearrangements and signaling events. Adequate control of the cytoskeleton is particularly important for immune cells, since they critically depend on regulated actin dynamics to enable migration and immune cell signaling. The defects resulting from DOCK2 mutations included impaired chemokine-induced migration in B and T cells and cytotoxic activity of NK cells. In addition, the authors identify an unexpected role for DOCK2 in non-hematopoietic cells including deficient antiviral immunity, which may explain the marked susceptibility to viral infections in these patients. Due to the severity of the disease, the authors find that allogeneic hematopoietic stem cell transplantation should be performed early after detection, and may be efficient in providing long-term immune reconstitution.
Inherited DOCK2 Deficiency in Patients with Early-Onset Invasive Infections.
Kerry Dobbs*, Cecilia Domínguez Conde*, Shen-Ying Zhang*, Silvia Parolini*, et al.,
Jean-Laurent Casanova#, Kaan Boztug#, and Luigi D. Notarangelo#
New England Journal of Medicine, AOP 18 June 2015. DOI: 10.1056/NEJMoa1413462.
* Shared first authors
# Shared senior and corresponding authors
We thank the following organisations for funding
ÖAW and MUW, NIH, Manton Foundation, European Research Council, Austrian Science Fund START programme, NCRR, NCATS, German Research Foundation Cluster of Excellence REBIRTH, New England Newborn Screening Program, Scientific and Technological Research Council of Turkey, Union Chimique Belge Celltech and Baxter Healthcare.
On June 3rd, 2015 the CeMM Kapsel/Time Capsule a Science and Art project by Martin Walde and Giulio Superti-Furga was officially opened by Andreas Mailath-Pokorny, Vienna City Councillor for Cultural Affairs and Science. The concept of the Time Capsule is based on Martin Walde´s interaction with CeMM´s research and philosophy and with the wish to create a “docking place” for artists of all branches within a biomedical research institute. The idea was to create a place where one, two or three people at a time can seclude to think or work in peace. The artist conceived the room as a safe haven and repository for ideas and thoughts that are collected in writing in one of the 13,000 empty notebooks, with coloured sleeves, shelved in an oval bookshelf embracing the entire small room. In that sense the CeMM Time capsule serves as a “serendipity” communication platform in several ways: through intentionally or accidentally meetings of artists and scientists and through the preservation of messages left in one of the notebooks. We thank all sponsors who contributed to the CeMM Time Capsule. CeMM would particularly like to thank Martin Walde for his dedicated work and this valuable and wonderful piece of art.
On Monday, May 18, the new Research Report was presented to a selected audience.
CeMM attempts to address a wider public of culturally interested people, provides interesting artistic insides and provokes new questions. A good example for this is the yearly CeMM Research Report, which is more than a summary of the ongoing projects and activities.
The theme of this year’s report is inspired by the human genome, and by the Austrian National Library. In 2014, CeMM successfully launched the Personal Genome Project “Genom Austria” (www.genomaustria.at), together with the Medical University of Vienna, aiming to support a genetic literacy in wide sections of the population. Each of our genome is composed of about six millions of letters, of As, Ts, Gs and Cs, which corresponds to roughly a million standard pages, hundreds of books per each genome, which reminded us of large libraries. We would like to thank Director Johanna Rachinger for the permission to use the Austrian National Library as a central theme illustrating our research report, and for hosting all CeMMies during a wonderful visit. Many analogies emerged by comparing the library and the digital and non-digital data storage at CeMM, like the preservation of its documents and material, the exchange and access of information, the styles of reading and writing, the responsibility to generate and provide knowledge for future generations.
To request a hardcopy please send a message to office(at)cemm.oeaw.ac(dot)at.
On the occasion of the Feierliche Sitzung/Ceremonial Meeting of the Austrian Academy of Sciences, on May 8th, 2015, both Heinz Fischer, President of Austria and Reinhold Mitterlehner, Vice-Chancellor and Federal Minister for Science, Research and Economy emphasized the pioneering achievements of CeMM and IMBA and their importance for Austria as a top location for science. Academy President Anton Zeilinger acknowledged the appeal and confirmed the intention to work on securing the future of the life science institutes in consultations with all people concerned, for the benefit of society.
“Best of Biotech” is an international life science business plan competition organized by Life Science Austria (LISA), a program run by the Austria Wirtschaftsservice (AWS) on behalf of the Austrian Federal Ministry of Science, Research and Economy. On May 6, 2015 an international jury consisting of distinguished experts from the areas of science, industry and finance selected the winners of the competition.
CeMM congratulates its researchers for being among the top 10 teams in the “Best of Biotech” competition out of 42 applications from 11 different countries.
The project idea: During the management of patients with blood cancers, hemato-oncologists often have the choice between different treatment options but may not be able to predict which is going to be the most effective. Berend Snijder, Nikolaus Krall and Gregory Vladimer, Postdoctoral Fellows in the Giulio Superti-Furga laboratory at CeMM, in collaboration with Professor Heinz Gisslinger at the Medical University of Vienna have started an incubator project to develop an in vitro diagnostic (IVD) test that can predict which chemotherapy, out of numerous possibilities, will help a patient with blood cancer and which is likely to only have side effects, using an innovative high-content automated confocal microscopy screen that allows to monitor the response of all individual cells in the sample. The project aims to help doctors make informed treatment decisions and shall ensure that patients get the best possible care.
CeMM is committed to tackling biomedical challenges with a focus on cancer, immune disorders, and infectious diseases. In keeping with CeMM´s mission “From the clinic to the clinic” the long term goal lies on developing innovative therapeutics and diagnostics in these disease areas to assist in preparing the predictive, preventive and personalized medicine of the future.