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REsolution: opening the gates for new medicines

Overall concept of proposed activities in REsolution (© Tatjana Hirschmugl / REsolution).

The new REsolution consortium is a public-private research partnership, supported by the Innovative Medicines Initiative (IMI), with nine partners from academia and the pharmaceutical industry. Starting on June 1, 2021 and with a duration of 2 years, the project aims to understand how genetic variants in humans affect the function of hundreds of cellular transporters.  

How do molecules such as vitamins, nutrients and drugs enter our organs and cells? Why do some of us take up certain molecules more easily than others? The REsolution consortium studies how differences in the genetic makeup of so-called transporter genes, encoding proteins that allow molecules to pass cellular membranes, may account for those differences. The REsolution consortium includes universities, research institutes, a small-medium-sized enterprise, and European Federation of Pharmaceutical Industries and Associations (EFPIA) members. The project, led by Pfizer and the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, has received funding through the IMI joint undertaking consisting of €1 million from the H2020 Programme of the European Union and €1 million from in-kind contributions of industry partners.  

Solute carriers (SLCs) are transport proteins located on cellular membranes and can be seen as cellular “gates”. With more than 400 proteins, they constitute the largest family of transporters in the human genome and represent a largely untapped source of potential novel drug targets. They are essential for a cell’s well-being and often genetically associated with human diseases – such as amyotrophic lateral sclerosis (ALS), autism, Alzheimer's disease, schizophrenia, diabetes, metabolic and cardiovascular diseases, and several types of cancer – and play an integral role in drug absorption into specific organs.
“In the last decade, the amount of data on human genetic variations has skyrocketed,” says the academic coordinator Giulio Superti-Furga from CeMM. “The REsolution initiative offers the chance of interpreting what these variations mean in terms of transporter functions and our individual ability to access molecules from the environment. It should create a large impact on medical and, particularly, pharmacological research.”

REsolution aims at gathering publicly available datasets and combining them with novel experimental data on genetic variants of SLCs. To that end, REsolution will build on the ongoing project RESOLUTE, which is working efficiently on a systematic campaign to increase the knowledge on SLCs by creating tools and datasets and making them available to the scientific community.
“REsolution is the natural evolution of our collective work to advance a more holistic view of the SLC protein family,” said Claire Steppan, the EFPIA project lead from Pfizer. “Through the development of this rich dataset, we hope to enhance the broader scientific community’s understanding of SLCs and ultimately accelerate the development of promising therapeutics for patients in need.”  
RESOLUTE and REsolution together have the potential to create an unprecedented SLC database. This resource could act as a “compass” to allow the medical community and drug discoverers to prioritize those targets most clearly involved in specific human diseases.

For more information visit: https://re-solute.eu/resolution and follow us on Twitter @RESOLUTE_IMI.

Funding:

The REsolution project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101034439. This Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA.

The IMI is a partnership between the European Union and the European pharmaceutical industry. Since 2008, IMI has facilitated open collaboration in research to advance the development of, and accelerate patient access to, personalised medicines for the health and wellbeing of all, especially in areas of unmet medical need. www.imi.europa.eu

 

Scientists develop “scifi-RNA-seq” method for ultra-high-throughput RNA sequencing in single cells

Study authors Paul Datlinger, André F. Rendeiro and Christoph Bock. ©Klaus Pichler, CeMM

Molecular analysis of single cells provides an important basis for precision medicine. Five years ago, scientists around the world came together to pursue the “Human Cell Atlas” project, with the aim of cataloging all cells in the human body. These data have helped, for example, to identify those cell types that the coronavirus can infect particularly well. To accelerate and improve the creation of such cell catalogs, Paul Datlinger and André F. Rendeiro from Christoph Bock’s research group at CeMM developed a new method that enables single-cell RNA sequencing in a very large number of individual cells at the same time.

This method, which is called “scifi-RNA-seq” (for: “single-cell combinatorial fluidic indexing”), marks the RNA of many cells with specific barcodes, before the cells are loaded on a microfluidic chip and their RNA is prepared for single-cell sequencing. These additional barcodes overcome an important problem with existing methods for single-cell sequencing, where single cells are packed into tiny emulsion droplets and assigned cell-specific barcodes. When several cells land in the same droplet, they receive the same barcode and can no longer be distinguished. Therefore, the single cell suspension is loaded onto the microfluidic chip at low concentrations, which means that most of the emulsion droplets remain empty, and the reagents are used very inefficiently.

In the scifi-RNA-seq method, the cells are marked in advance with an additional barcode. As a result, the emulsion droplets can be loaded with many cells at the same time, while it is still possible to analyze individual cells. Study author Paul Datlinger explains: “On the popular 10x Genomics system, we use this method to measure 15 times more individual cells. The additional barcode also allows the user to mark and combine thousands of samples in advance, and to process those samples together in a single microfluidic analysis. As part of our study, we performed a CRISPR screen with single-cell RNA sequencing readout in human T cells. In the future, our method may, among other things, help to improve immunotherapies for the treatment of cancer.”

An efficient high-throughput method with a wide range of applications

Projects that need to apply single-cell RNA sequencing to very large numbers of cells or very many samples will particularly benefit from the new method. Project leader Christoph Bock explains: “scifi-RNA-seq enables efficient RNA sequencing for millions of individual cells, which facilitates the characterization of complex tissues, organs, and entire organisms. Moreover, in biomedicine it is often useful to analyze many single cells, for example to discover rare stem cells in tumors or cancer cells in the blood. Finally, scifi-RNA-seq will contribute to the trend that drug screens and CRISPR screens are increasingly combined with high-resolution single-cell sequencing readouts. “

The study “Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing” was published in Nature Methods on 31 Mai 2021 (online ahead of print), DOI: 10.1038/s41592-021-01153-z

Authors: Paul Datlinger, André F. Rendeiro, Thorina Boenke, Martin Senekowitsch, Thomas Krausgruber, Daniele Barreca, Christoph Bock

Funding: This work was conducted in the context of two Austrian Science Fund (FWF) Special Research Program grants (FWF SFB F6102; FWF SFB F7001). Thomas Krausgruber was supported by a Lise Meitner fellowship from the Austrian Science Fund (FWF M2403). Christoph Bock is supported by an ERC Starting Grant (European Union’s Horizon 2020 research and innovation program, grant agreement no. 679146).

Blood test detects childhood tumors based on their epigenetic profiles

Extracting tumor epigenetics from blood (© Tatjana Hirschmugl).

A new study exploits the characteristic epigenetic signatures of childhood tumors to detect, classify and monitor the disease. The scientists analyzed short fragments of tumor DNA that are circulating in the blood. These "liquid biopsy" analyses exploit the unique epigenetic landscape of bone tumors and do not depend on any genetic alterations, which are rare in childhood cancers. This approach promises to improve personalized diagnostics and, possibly, future therapies of childhood tumors such as Ewing sarcoma. The study has been published in Nature Communications.

A study led by scientists from St. Anna Children’s Cancer Research Institute (St. Anna CCRI) in collaboration with CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences provides an innovative method for “liquid biopsy” analysis of childhood tumors. This method exploits the fragmentation patterns of the small DNA fragments that tumors leak into the blood stream, which reflect the unique epigenetic signature of many childhood cancers. Focusing on Ewing sarcoma, a bone tumor of children and young adults with unmet clinical need, the team led by Eleni Tomazou, PhD, St. Anna CCRI, demonstrates the method’s utility for tumor classification and monitoring, which permits close surveillance of cancer therapy without highly invasive tumor biopsies.

In tumors, cancer cells constantly divide, with some of the cancer cells dying in the process. These cells often release their DNA into the blood stream, where it circulates and can be analyzed using genomic methods such as high-throughput DNA sequencing. Such “so-termed liquid biopsy” analyses provide a minimally invasive alternative to conventional tumor biopsies that often require surgery, holding great promise for personalized therapies. For example, it becomes possible to check frequently for molecular changes in the tumor. However, the use of liquid biopsy for childhood cancers has so far been hampered by the fact that many childhood tumors have few genetic alterations that are detectable in DNA isolated from blood plasma.

Exploiting tumor-specific epigenetic patterns

Cell-free DNA from dying tumor cells circulates in the blood in the form of small fragments. Their size is neither random nor determined solely by the DNA sequence. Rather, it reflects how the DNA is packaged inside the cancer cells, and it is influenced by the chromatin (i.e., complex of DNA, protein and RNA) structure and epigenetic profiles of these cells. This is very relevant because epigenetic patterns – sometimes referred to as the “second code” of the genome – are characteristically different for different cell types in the human body. Epigenetic mechanisms lead to changes in gene function that are not based on changes in the DNA sequence but are passed on to daughter cells. The analysis of cell-free DNA fragmentation patterns provides a unique opportunity to learn about the epigenetic regulation inside the tumor without having to surgically remove tumor cells or even know whether and where in the body a tumor exists.

“We previously identified unique epigenetic signatures of Ewing sarcoma. We reasoned that these characteristic epigenetic signatures should be preserved in the fragmentation patterns of tumor-derived DNA circulating in the blood. This would provide us with a much-needed marker for early diagnosis and tumor classification using the liquid biopsy concept”, explains Dr. Tomazou, Principal Investigator of the Epigenome-based precision medicine group at St. Anna CCRI.

Machine learning increases sensitivity

The new study benchmarks various metrics for analyzing cell-free DNA fragmentation, and it introduces the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. The scientists used machine-learning classifiers to distinguish between patients with cancer and healthy individuals, and between different types of pediatric sarcomas. “By feeding these machine learning algorithms with our extensive whole genome sequencing data of tumor-derived DNA in the blood stream, the analysis becomes highly sensitive and in many instances outperforms conventional genetic analyses”, says Dr. Tomazou.

When asked about potential applications, she explains: “Our assay works well, we are very excited. However, further validation will be needed before it can become part of routine clinical diagnostics.” According to the scientists, their approach could be used for minimally invasive diagnosis and, but also as a prognostic marker, monitoring which patient responds to therapy. Additionally, it might serve as a predictive marker during neoadjuvant therapy (i.e., chemotherapy before surgery), potentially enabling dose adjustments according to treatment response. “Right now, most patients receive very high doses of chemotherapy, while some patients may be cured already with a less severe therapy, which would reduce their risk of getting other cancers later in life. There is a real medical need for adaptive clinical trials and personalized treatment of bone tumors in children.”

International scientific collaboration

This study was led by St. Anna CCRI in collaboration with CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Medical University of Vienna, collaborating with multiple institutions in Austria, Germany, Norway, and France.

About epigenetics

Epigenetics is the link between genes and their environment. It contributes to gene regulation and controls which genes are active or inactive at specific time points. Epigenetic mechanisms lead to changes in gene function that are not based on changes in the DNA sequence – for example through mutation – but are passed on to daughter cells. Since childhood cancers often harbor few genetic alterations, their epigenetic patterns are promising markers for non-invasive diagnostics using liquid biopsy.

Publication:
"Multimodal analysis of cell-free DNA whole genome sequencing for pediatric cancers with low mutational burden" was published on Nature Communications on May 28, 2021. Doi: https://doi.org/10.1038/s41467-021-23445-w

Authors:
Peter Peneder*, Adrian M Stütz*, Didier Surdez, Manuela Krumbholz, Sabine Semper, Mathieu Chicard, Nathan C Sheffield, Gaelle Pierron, Eve Lapouble, Marcus Tötzl, Bekir Erguner, Daniele Barreca, Andre F Rendeiro, Abbas Agaimy, Heidrun Boztug, Gernot Engstler, Michael Dworzak, Marie Bernkopf, Sabine Taschner-Mandl, Inge M Ambros, Ola Myklebost, Perrine Marec-Bérard, Susan Ann Burchill, Bernadette Brennan, Sandra J Strauss, Jeremy Whelan, Gudrun Schleiermacher, Christiane Schaefer, Uta Dirksen, Caroline Hutter, Kjetil Boye, Peter F Ambros, Olivier Delattre, Markus Metzler, Christoph Bock#, Eleni M Tomazou#

*Shared first authors
#Corresponding authors

Funding:
This study was funded by the Austrian National Bank’s Jubilaumsfonds (OeNB), a charitable donation from Kapsch Group and the Austrian Science Fund (FWF).

14th CeMM Landsteiner Lecture by Sarah Teichmann and the 2020 Denise P. Barlow Award Ceremony

Keynote speaker Sarah Teichmann and CeMM Scientific Director Giulio Superti-Furga.

The 14th Landsteiner Lecture was held virtually on 10 May 2021 by Sarah Teichmann, Head of Cellular Genetics at the Wellcome Sanger Institute (UK), with a special focus on the Global Human Cell Atlas Consortium, which she co-founded in 2016.

The CeMM Landsteiner Lecture series is named in honor of Karl Landsteiner, the Viennese scientist who was awarded the Nobel Prize for discovering blood groups. The invited speakers, carefully selected by CeMM Faculty, are prominent scientists whose molecular research is deemed to have had a significant impact on medicine. From 2007 to 2018, the lecture was held in the stunning 18th century frescoed festive hall of the Austrian Academy of Sciences, where once Haydn and Beethoven conducted premieres of their work.

The event opened with a beautiful musical prelude performed by Austrian musicians Anna Lang and Doris Freimüller, as a tribute to the 250th anniversary of Ludwig van Beethoven's birth, followed by the welcome address by CeMM Scientific Director Giulio Superti-Furga. Then the Denise P. Barlow Award Ceremony took place, a yearly academic talent prize in memory of former CeMM Principal Investigator Denise Barlow, and launched by the four Viennese institutions she was connected to: IMP, Max Perutz Labs, IMBA and CeMM. The prize intends to promote the academic career of young scientists and awards the best PhD thesis on topics that cover basic cell biological, biochemical, molecular biological, structural and computational work, with an emphasis on new biological mechanisms. The 2020 awardee was Anete Romanauska for her thesis entitled “Lipid metabolism at the inner nuclear membrane”, which she conducted under the supervision of Prof. Alwin Köhler from the Max Perutz Labs in Vienna. The awardees in 2019, Julia Batki and Matthias Muhar, who are currently pursuing their postdoctoral career, also joined the event.

After another musical interlude, the invited keynote speaker Sarah Teichmann introduced the Human Cell Atlas (HCA), a project which was born thanks to a collaborative community of world-leading scientists who came together to discuss how to build a high-resolution and comprehensive collection of maps that would serve as a basis for both understanding human health and diagnosing, monitoring, and treating disease. Cells are the most fundamental unit of life, yet they vary enormously within the body, and express different sets of genes. Surprisingly there is little knowledge about them and without comprehensive maps of the different types and locations within the body, it is not possible to describe all their functions and gain a better understanding of the biological networks that direct their activities.

We would like to warmly thank Sarah Teichmann for delivering such an insightful virtual 14th CeMM Landsteiner Lecture! We also congratulate Anete Romanauska for her award and thank the 300  participants who joined us virtually from all over the world!

If you could not join the event, watch the full recording here.

Do purines influence cancer development?

First author Kai-Chun Li and last author Giulio Superti-Furga (© Laura Alvarez / CeMM)

Numerous disease development processes are linked to epigenetic modulation. One protein involved in the process of modulation and identified as an important cancer marker is BRD4. A recent study by the research group of Giulio Superti-Furga, Principal Investigator and Scientific Director at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, now shows that the supply of purines as well as the purine synthesis of a cell can influence BRD4 activity and thus play a role in the carcinogenesis process. The findings were published in Nature Metabolism.

Chromatin is a central component of the cell nucleus. It refers to the complex of the approximately two-meter-long human DNA with proteins that organize it so that – depending on the cell type – certain genes are activated or deactivated. In order to be able to adapt to diverse situations and influences, cells read the information relevant to them from the DNA. If this process is disturbed, diseases such as cancer develop. Scientists have been researching for many years what influences this process. The protein BRD4, which makes a decisive contribution to the unpacking and packaging of DNA in chromatin, was identified as a marker for cancer. Since then, scientists have been investigating how BRD4 can be modulated. A recent study by scientist Kai-Chun Li and the research group of CeMM Scientific Director Giulio Superti-Furga makes an important contribution to answering this question. She investigated how certain externally supplied nutrients, so-called purines, influence BRD4 and thus the development process of various cancer diseases. Purines are basic building blocks of the cell. Disturbances of the purine metabolism in the cell have already been associated with some disease patterns in the past. The study showed, on the one hand, that inhibiting purine supply as well as disturbing purine synthesis can trigger a functional disturbance of BRD4 and thus impact chromatin accessibility. On the other hand, BRD4 functionality could be restored by adding adenine.

Analysis of the transport pathways

Giulio Superti-Furga’s research group focuses particularly on those transport proteins in the genome that transport numerous important substances such as nutrients and metabolites into and out of the cell – so-called solute carriers (SLC). First author Kai-Chun Li explains: “Our aim was to investigate the involvement of SLC-mediated purine uptake and cellular metabolism in the modulation of cellular epigenetic states, because purine metabolism plays an essential role in cell metabolism.” With the help of SLCs, the scientists were able to modulate the purine supply for their study and observe the direct effects. They used both a genetic screening based on a CRISPR/Cas9 library focused on transporters, and a drug screening using a compound library mainly consisting of cellular metabolites and drugs, both to track down the modulation of BRD4-dependent chromatin states in myeloid leukemia cells. The scientists compared “normal” cancer cells with those cancer cells in which the SLCs that transport purines were inhibited. In addition, purines were added to or omitted from the growth medium of the cells in various experiments, thus modulating purine biosynthesis in the cells.

Adenine brings BRD4 back into balance

The study shows that an imbalance of intracellular purine pools leads to a dysfunction of BRD4-dependent transcriptional modulation of chromatin, which means that the correct reading of DNA information is disturbed. “These results demonstrate a pharmacologically effective axis between purine metabolism and BRD4-dependent chromatin states,” explains study leader Giulio Superti-Furga. Drugs that influence BRD4 have already been developed in the past. At the same time, some cancer types also became resistant to such BET inhibitors. “With our study, we show another way to modulate BRD4 – by influencing the purine metabolism.” The scientists also found an answer to the question of how BRD4 functionality could be restored: they were able to show that adenine, a purine-derived compound, plays a strong role in BRD4 interaction. “Our results suggest that adenylates (adenine, ATP, etc.) are important for healthy cells. This could be a significant starting point for developing new therapies against BRD4-induced cancer types,” says Superti-Furga.



The study “Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent 2 chromatin states” was published in Nature Metabolism on May 10, 2021, DOI: 10.1038/s42255-021-00386-8.

Authors: Kai-Chun Li, Enrico Girardi, Felix Kartnig, Sarah Grosche, Tea Pemovska, Johannes W. Bigenzahn, Ulrich Goldmann, Vitaly Sedlyarov, Ariel Bensimon, Sandra Schick, Jung-Ming G. Lin, Bettina Gürtl, Daniela Reil, Kristaps Klavins, Stefan Kubicek, Sara Sdelci, Giulio Superti-Furga

Funding: CeMM and the Superti-Furga and Kubicek laboratories are supported by the Austrian Academy of Sciences. They were supported by third-party funds from the Austrian Science Fund, the European Research Council, the European Commission (Marie 437 Skodowska-Curie Action Fellowship) and an EMBO long-term Fellowship. Sarah Grosche is supported by the Peter and Traudl Engelhorn Foundation. Research in the Kubicek lab is supported by the Austrian Science Fund (FWF F4701) and the European Research Council under the European 440 Union’s Horizon 2020 research and innovation programme (ERC-CoG-772437).
 

10th CeMM S.M.A.R.T. Lecture with Prof. Orly Goldwasser

CeMM Scientific Director Giulio Superti-Furga with Prof. Orly Goldwasser (©Laura Alvarez / CeMM).

On 27 April 2021, CeMM hosted its 10th S.M.A.R.T. Lecture with Orly Goldwasser, Professor of Egyptology at the Hebrew University of Jerusalem and an Honorary Professor at the University of Göttingen.

The S.M.A.R.T. lecture series is an initiative launched by CeMM dedicated to diverse topics around the fields of science, medicine, art, research, and technology. They address contemporary challenges of science in an interdisciplinary manner and at the interface of science and society, with the aim of establishing an open dialogue with the broader public. Once a year CeMM invites an international speaker renowned for having made extraordinary achievements in their fields.

This year in an online format, Prof. Goldwasser talked about one of the greatest and lasting inventions in history: the alphabet. Interestingly, the alphabet was invented only once: all alphabetic scripts of all languages of the world originated from one single invention.

During her talk, Prof. Goldwasser introduced the history of how the alphabet was invented from hieroglyphs, dating back to C. 1840 BCE in the Sinai Desert. She explained how ancient inscriptions that were discovered in the mines during this period of history were made by the Canaanites, which were the people originally from Israel, Palestine and Lebanon who spoke a Semitic language, the mother language of the modern Hebrew and Arabic used nowadays. The essence of the invention of the alphabet lied in identify the meaning of the picture in the hieroglyph, naming it in Canaanite, extracting only the first sound of the picture and discard then the meaning of the picture entirely. Each sign became then one single sound.

In the past, there was no agreement in the international scientific community about where and when exactly was the alphabet invented. Prof. Goldwasser’s research work has been paramount in the reconstruction of the invention process. She made a breakthrough contribution by suggesting hieroglyphic models in the Sinai repertoire of Egyptian hieroglyphs that could have served as models for the inventors. She also identified through her work that the inventors were indeed illiterate Canaanites working in the mines of the Sinai desert.

We would like to thank Prof. Goldwasser for a very insightful talk and for carrying us with her talk to a very interesting time in history!

Watch the full Zoom video recording here.

VR visualization supports research on molecular networks

Last author Jörg Menche and first author Sebastian Pirch (© Michael Sazel/CeMM)

Networks offer a powerful way to visualize and analyze complex systems. However, depending on the size and complexity of the network, many visualizations are limited. Protein interactions in the human body constitute such a complex system that can hardly be visualized. Jörg Menche, Adjunct Principal Investigator at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Professor at the University of Vienna and research group leader at Max Perutz Labs (Uni Wien/MedUni), and his team developed an immersive virtual reality (VR) platform that solves this problem. With the help of VR visualization of protein interactions, it will be possible in the future to better recognize correlations and identify those genetic aberrations that are responsible for rare diseases.

The larger and more complex networks are, the more difficult their visualization on the screen becomes. Conventional computer programs quickly reach their limits. This challenge was addressed by network scientist Jörg Menche and his research group at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. They developed a VR platform for exploring huge amounts of data and their complex interplay in a uniquely intuitive fashion.

The body as a network

The representation of complex data can be particularly important in the search for the cause of rare diseases, because the human body, with its approximately 20,000 proteins that are encoded in the human genome and interact with each other, represents a huge complex network. Whether movement or digestion – at the molecular level, all biological processes are based on the interaction between proteins. If the protein interactions are illustrated in a network, a barely representable picture of about 18,000 dots – proteins – and about 300,000 lines between these dots will be created. Menche and his research group used the virtual reality (VR) platform they developed to make this image “readable” and, in collaboration with St. Anna Children’s Cancer Research, succeeded in making the entirety of protein interactions visible for the first time. This makes it possible to interactively explore the vast and complex network.

Approaching the cause of rare immune diseases

For their study, published in Nature Communications, first author Sebastian Pirch and Menche’s research group identified connection patterns between different protein complexes in the human body and linked them to their biological functions. In addition, the scientists used global databases to identify specific protein complexes associated with a particular disease. “While conventional forms of representation would look like a proverbial ‘hairball’, the 3-dimensional representation enables the precise analysis and observation of the different protein complexes and their interactions,” says study author Pirch. This can be particularly important in the identification of rare genetic defects and crucial for therapeutic measures. “On the one hand, our study represents an important proof of concept of our VR platform; on the other hand, it directly demonstrates the enormous potential of visualizing molecular networks,” says project leader Menche. “Especially in rare diseases, severe immune diseases, protein complexes associated with specific clinical symptoms can be analyzed in more detail to develop hypotheses about their respective pathobiological mechanisms. This facilitates the approach to disease causes and subsequently the search for targeted therapeutic measures.”

About the VR platform

The platform developed by Menche’s research group is designed for maximum flexibility and extensibility. Key features include the import of user-defined code for data analysis, easy integration of external databases, and a high degree of design freedom for arbitrary elements of user interfaces. The researchers were able to draw on technology normally used in the development of 3D computer games, such as the globally popular game Fortnite. By publishing the source code, the researchers hope to convince other developers of the potential of virtual reality for analyzing scientific data.

The study "VRNetzer: A Virtual Reality Network Analysis Platform" was published in the journal Nature Communications on April 23, 2021. DOI: 10.1038/s41467-021-22570-w.

Authors: Sebastian Pirch, Felix Müller, Eugenia Iofinova, Julia Pazmandi, Christiane V. R. Hütter, Martin Chiettini, Celine Sin, Kaan Boztug, Iana Podkosova, Hannes Kaufmann & Jörg Menche

Funding: This work was supported by the Vienna Science and Technology Fund (WWTF) through projects VRG15-005 and NXT19-008, and by an Epic MegaGrant.

 

Immune cells out of control: how lethal hyperinflammation emerges from a novel gene defect

Artem Kalinichenko and Kaan Boztug. / © St. Anna Children's Cancer Research Institute.

Scientists from CeMM Adjunct PI Kaan Boztug's Group at St. Anna Children's Cancer Research Institute, together with their collaborators from Finland and Sweden, discover a novel subtype of a genetic disease: genetically determined deficiency of the protein RhoG abrogates the normal cytotoxic function of specific immune cells, causing hemophagocytic lymphohistiocytosis (HLH). These new findings may help with the genetic diagnosis for patients with a clinical suspicion of HLH. Published in the high-ranked scientific journal Blood, the study provides a basis for both a deeper understanding of the biology of HLH and the exploration of new therapeutic approaches.

As part of an international collaborative effort, the scientists illuminate a new etiology of a disease called familial hemophagocytic lymphohistiocytosis (HLH). Occurring usually in early childhood, familial or genetically-determined HLH is one of the most dramatic hematologic disorders. It is characterized by the inability of specific immune cells, namely T lymphocytes and natural killer (NK) cells, to kill an infected (e.g., virus-infected) target cell. As a consequence, the body may secrete biological messengers (so-called cytokines) that generate massive immune activation and hyperinflammation throughout the entire body. “If untreated, the hyperinflammation associated with HLH can be lethal in a short period of time”, says Kaan Boztug, MD, Scientific Director of St. Anna CCRI and senior author of the study.

Until recently, four subtypes of familial HLH had been known, caused by mutations in genes involved in regulating the immune defense. “Now we discovered a new type of this disease, caused by inherited mutations in the gene that encodes the protein RhoG”, explains the first author of the study, Artem Kalinichenko, PhD, Senior Postdoctoral researcher at St. Anna CCRI and Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD).
The researchers show how deficiency of RhoG specifically impairs the cytotoxic function of T lymphocytes and NK cells. This results in their uncontrolled activation and ultimately causes HLH.

In particular, RhoG deficiency impairs the process of exocytosis in specific immune cells and disables their killing ability. Immune cells like T and NK cells use exocytosis to release cytotoxic molecules to attack and kill infected or tumor cells. When RhoG deficiency abrogates this function in immune cells, they cannot kill their target cells as intended. “We will explore in more detail, how this potentially affects the propensity to develop cancer”, says Dr. Kalinichenko.

RhoG regulates lymphocyte cytotoxicity

In their study, the scientists investigated an infant who developed severe HLH at the age of four months. While the disease was associated with impaired cytotoxicity of T and NK cells, no mutations were found in known HLH-associated genes. Further genetic analysis revealed deleterious mutations in the gene encoding RhoG. By experimental ablation of RhoG, the scientists confirmed the previously unknown role of RhoG in the cytotoxic function of human lymphocytes. Despite a drastic and specific effect on cytotoxic function, RhoG deficiency does not affect other functions of immune cells that play an important role for the disease development.

“In our study we discovered a pivotal role of RhoG interaction with an exocytosis protein called Munc13-4, essential for anchoring of cytotoxic granules to the plasma membrane”, explains Dr. Boztug. This docking is a critical step in exocytosis. It is required for further fusion of the vesicles with the plasma membrane and the release of the cytotoxic granules.
“Thus, our study illuminates RhoG as a novel essential regulator of human lymphocyte cytotoxicity, and provides the molecular pathomechanism behind this previously unreported genetically determined form of hemophagocytic lymphohistiocytosis”, concludes Dr. Boztug.

Shorter screening process for patients

Based on the understanding of the underlying molecular mechanism of familial HLH, the researchers are looking forward to an improved prognosis and treatment of the disease in the long-term. As a short-term consequence, the here discovered RhoG deficiency can help HLH patients by enabling a genetic diagnosis. “We hope that our understanding of the molecular pathomechanisms of HLH may impact disease management and prognosis”, comments Dr. Boztug.

This study is an exciting breakthrough that brings up new important scientific questions. “The discovery of RhoG deficiency has opened up new insights into the molecular functions of this protein and revealed highly relevant questions. We have found that RhoG regulates both, the ‘cell skeleton’ and the exocytosis machinery. Now we are very keen to know how RhoG coordinates their activity in space and time”, says Dr. Kalinichenko.

Collaborative research on rare diseases

This scientific work was possible thanks to a collaboration of St. Anna CCRI with the LBI-RUD, the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, the Medical University of Vienna, and international partners. Special thanks go to the co-senior authors Janna Saarela (Institute for Molecular Medicine Finland, Helsinki, Finland and Centre for Molecular Medicine Norway, Oslo, Norway) and Mikko R.J. Seppänen (Rare Diseases Center, Children’s Hospital, University of Helsinki, Finland) as well as Yenan T. Bryceson (Karolinska Institute, Stockholm, Sweden). The patient was enrolled in the ongoing FINPIDD study series and is under medical treatment at the Helsinki University Hospital.


Publication:

"RhoG deficiency abrogates cytotoxicity of human lymphocytes and causes hemophagocytic lymphohistiocytosis" was publishd on Blood on 15 April 2021. DOI: https://doi.org/10.1182/blood.2020008738

Authors: Artem Kalinichenko, Giovanna Perinetti Casoni*, Loic Dupre*, Luca C. Trotta*, Jakob Huemer, Donatella Galgano, Yolla German, Ben Haladik, Julia Pazmandi, Marini Thian, Özlem Yüce Petronczki, Samuel C.C Chiang, Mervi H Taskinen, Anne Hekkala, Saila Kauppila, Outi Lindgren, Terhi Tapiainen, Michael J. Kraakman, Kim Vettenranta, Alexis J. Lomakin, Janna Saarela§ , Mikko R J Seppänen§, Yenan T Bryceson§, Kaan Boztug§‡
* these authors contributed equally
§ these authors contributed equally


Funding:
This work was supported by European Research Council through an ERC Consolidator Grant “iDysChart” (Kaan Boztug) and the Vienna Science and technology Fund (WWTF) through project LS14-031 (Kaan Boztug); Austrian Academy of Science (ÖAW) through DOC fellowship program 25365 (Jakob Huemer) and 25225 (Marini Thian); Finnish Foundation for Pediatric Research and Pediatric Research Center, Helsinki University Hospital (Mikko RJ. Seppänen), and Swedish Research Council, Cancer Foundation, Children's Cancer Foundation, and Knut and Alice Wallenberg Foundation to Yenan T. Bryceson.

New sponsored chairs arrived at the CeMM terrace

CeMM South terrace with the new chairs (© Laura Alvarez / CeMM).

After 10 years in the CeMM building, we have made some renovations in the cafeteria and our iconic terrace overlooking Vienna’s historical center. Despite the challenging times we are living, it is a priority for CeMM to provide an inviting and comfortable space for safe interactions and cooperation not only among our colleagues but also our guests.

At the end of 2020, we launched the “One Chair One for CeMM” fundraising campaign to help support the acquisition of new, high quality outdoor chairs. The campaign was a success and we received donations to cover the costs of 48 chairs. Each chair is unique and includes a dedicated label chosen by the sponsor. We are happy to announce that the new chairs have arrived at the CeMM terrace and are now available for all our colleagues.

We would like to thank all our donors and supporters for their invaluable support to our institute and helping us to keep on providing the right space for our colleagues to do their work in the best possible conditions!

Successful collaboration among 3 CeMM groups results in the development of a novel synthesis for the quinoxaline functional group

On the left, fluorescence microscopy images of the cell lines after treatment with solutions 1.5 μM in DMSO of quinoxalines (© Fabián Amaya Garcia & Miriam Unterlass). / On the right, authors of the study.

The discipline of chemistry deals with understanding (analysis) and making and transforming (synthesis) of matter. The size-range with which chemistry is most concerned with is that of molecules as building blocks of matter. Molecules are nothing but connected atoms, and when aiming at making, i.e. synthesizing, them, it is useful to chemists to subdivide them into subsets, which are so-called "functions" or "functional groups". Although every type of molecule is unique, it's subsets - the functional groups - will eventually be found in many other molecules. Therefore, approaches of generating a particular functional group may eventually benefit the synthesis of numerous molecules bearing ths functional group.

The research group of Miriam Unterlass, CeMM Adjunct Principal Investigator and Assistant Professor at the Technische Universität Wien, in collaboration with two other CeMM research groups, the Menche Lab and the Kubicek Lab, has now developed a novel synthesis for the so-called "quinoxaline" functional group, which is to date reported to be part of more than 100,000 molecules. Quinoxalines are highly important for especially pharmaceutical applications, where they are part of various drugs such as the antibiotic Echinomycin, or Brimonidine a drug to treat ocular hypertension. Furthermore, they display intriguing optoelectronic properties and therefore find application as e.g. dyes or electroluminescent materials. Classically, the quinoxaline function is made by rather harsh, harmful, and tedious routes (toxic organic solvents, expensive catalysts). In contrast, the new synthesis developed by Unterlass and colleagues employs 'hot water' as solvent and is therefore termed hydrothermal synthesis (HTS). Through the developed HTS, quinoxalines can be generated within only 10 minutes. In fact, the synthesis is the least harmful of all routes reported to date, as Amaya-García et al. show in their recently published manuscript, through a large-scale computational comparison with all existing alternatives. Moreover, the researchers show that the generated quinoxalines exhibit fluorescence and can be used to stain different cell lines.

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The study "Green hydrothermal synthesis of fluorescent 2,3-diarylquinoxalines and large-scale computational comparison to existing alternatives" was published online ahead of print on ChemSusChem on 4 March 2021. DOI: https://doi.org/10.1002/cssc.202100433

Authors: Fabián Amaya-García, Michael Caldera, Anna Koren, Stefan Kubicek, Jörg Menche, Miriam M. Unterlass

Funding: This project was funded by the Austrian Science Fund (FWF) under grant no. START Y1037‐N28 and the Vienna Science and Technology Fund (WWTF) under grant number LS17‐051.