May 11, 2020

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

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

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

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

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

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

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

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

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

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

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

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

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

May 05, 2020

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

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

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

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

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

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

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

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

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

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

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

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

May 05, 2020

Join the CeMM Alumni Network

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

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

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

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

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

April 20, 2020

A Soundtrack of Research – CeMM Research Report 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

 

April 02, 2020

Obituary Michael Wakelam

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

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


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


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


Michael Wakelam 1955 – 2020

March 27, 2020

Mutational Dynamics of SARS-CoV-2 in Austria

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RNA sample preparation and genome sequencing at CeMM / © CeMM

As a leading biomedical research institute, CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, is committed to advancing our molecular understanding of the COVID-19 pandemic and the causative pathogen, SARS-CoV-2. Biomedical research on the virus and the disease will contribute substantially to informed policy decisions and, ultimately, the development of new treatments.

An interdisciplinary team at CeMM under the project leadership of virologist Andreas Bergthaler and computational biologist Christoph Bock will investigate SARS-CoV-2 genome evolution in patients by deep sequencing and sophisticated computational analyses. This will result in rapid open sharing of SARS-CoV-2 genomes from Austria, inform epidemiologists to reconstruct transmission chains, and offer invaluable insights into the molecular dynamics of the ravaging viral pandemic.

The work is part of a collaboration network with Elisabeth Puchhammer-Stöckl from the Center for Virology of the Medical University of Vienna as primary partner. The network is open to additional collaborations and especially welcomes contributions from clinical virologists and diagnostics laboratories across Austria. First collaborations with evolution biologists, population geneticists and virologists have already started. Integration of Austria’s contribution into an emerging world-wide map of SARS-CoV-2 mutations will help decipher the mutational dynamics underlying the pandemic.

CeMM is focusing efforts to soon openly share the first SARS-CoV-2 genomes from Austria with the world. We encourage the scientific community and industry to use these results to accelerate research to fight the coronavirus, and hope the data will support policy makers and epidemiologists to better understand how the virus is spreading”, says Giulio Superti-Furga, CeMM Director.

* * *

Mutationsdynamik von SARS-CoV-2 in Österreich

Als führendes biomedizinisches Forschungsinstitut engagiert sich CeMM, das Forschungszentrum für Molekulare Medizin der Österreichischen Akademie der Wissenschaften, für das bessere molekulare Verständnis der COVID-19-Pandemie und des Erregers SARS-CoV-2. Die biomedizinische Erforschung des Virus wird wesentlich zu fundierten politischen Entscheidungen und letztendlich zur Entwicklung neuer Therapien beitragen.

Ein interdisziplinäres Team am CeMM unter der Projektleitung von Andreas Bergthaler, Virologe, und Christoph Bock, Bioinformatiker, wird die SARS-CoV-2-Genomentwicklung bei Patienten mittels ausgereifter Sequenzier- und Analysemethoden untersuchen. Dies wird zu einer raschen, frei zugänglichen Veröffentlichung von SARS-CoV-2-Genomen aus Österreich führen, Epidemiologen bei der Rekonstruktion von Übertragungsketten unterstützen und wertvolle Einblicke in die molekulare Dynamik der verheerenden Viruspandemie liefern.

Die Forschungsarbeit am CeMM ist Teil eines Netzwerks, und Elisabeth Puchhammer-Stöckl vom Zentrum für Virologie der Medizinischen Universität Wien eine essentielle Kooperationspartnerin. Das Netzwerk ist offen für weitere Kooperationen und begrüßt insbesondere Beiträge von klinischen Virologen und Diagnostiklabors aus ganz Österreich. Erste Kooperationen mit Evolutionsbiologen, Populationsgenetikern und Virologen haben bereits begonnen. Der österreichische Beitrag zu einer weltweiten Karte von SARS-CoV-2-Mutationen ist ein wichtiger Schritt, die Mutationsdynamik der Pandemie zu entschlüsseln.

CeMM fokussiert sich darauf, die ersten SARS-CoV-2-Genome aus Österreich bald offen mit der Welt zu teilen. Wir ermutigen die Wissenschaft und Industrie, diese Ergebnisse zu nutzen, um die Forschung zur Bekämpfung des Coronavirus zu beschleunigen. Wir hoffen, dass die Daten politische Entscheidungsträger und Epidemiologen dabei unterstützen, die Ausbreitung des Virus besser zu verstehen“, sagt Giulio Superti-Furga, CeMM-Direktor.

March 11, 2020

CeMM events and seminars postponed

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Due to the latest developments in the corona virus (COVID-19) and as a preventive health measure, CeMM has decided to cancel all public events and seminars until 13 April 2020. Events will be rescheduled to a later date.

Please check the CeMM website where the new dates will be announced.

Should you have any questions, do not hesitate to contact us at info(at)cemm(dot)at

March 09, 2020

Uncovering novel relationships between solute carrier transporters and cytotoxic drugs in human cells

Last author Giulio Superti-Furga and first author Enrico Girardi (© Klaus Pichler / CeMM)

Researchers at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences have studied how Solute Carriers (SLCs), a large family of membrane transport proteins, influence the activity and potency of cytotoxic drugs, such as those used in the treatment of leukemia and other cancers. Their study, published in the journal Nature Chemical Biology, uncovers the dependency of most drugs studied on the function of at least one SLC. In some cases, the drug required the transporter to enter into the cell, in other cases, it provided small molecules (metabolites), which are crucial to the drug’s activity or the cell response to it. These findings shed new light onto the biological roles of transporters and open the path to the development of future precision therapies.

Solute carriers (SLCs) represent the largest family of transmembrane transporters in the human genome, with over 400 members arranged into 65 families. They have a key role in determining cellular metabolism and control essential physiological functions, including nutrient uptake, ion transport and waste removal. SLCs are vital for maintaining a stable internal state of the human body (known as homeostasis), but the presence of genetic variation (polymorphisms) in SLCs are associated with several diseases, such as gout or diabetes, while gene mutations are associated with literally hundreds of disorders including many metabolic deficiencies and orphan diseases.

Solute carriers have been shown to act as drug targets, as well as constitute paths for drug absorption into specific organs. However, despite of decades of studies, there is still a lack of systematic surveys of transporter-drug relationships in human cells. Uncovering how particular drugs enter human cells and how the cell metabolism affects them is key to gaining a better understanding of the side effects and limitations of current drugs and thus developing more effective drug therapies in the future.

Expanding on a previous study (Winter et al. Nat Chem Biol, 10, pp 768-773, 2014), which uncovered how a single solute carrier (SLC35F2) is necessary in the uptake of the cytotoxic compound YM-155, Giulio Superti-Furga and his group at CeMM now performed a more systematic investigation on  the role of solute carriers in determining the activity of a large and diverse set of cytotoxic compounds. Their goal was to survey on the “how often” and “how” SLC transporters would lose or a affect the activity of a certain drug.

In their study, CeMM researchers built a CRISPR/Cas9-focused library specifically targeting 394 solute carriers and applied it to identify SLCs affecting the activity of a panel of 60 chemically diverse, most of them clinically approved, cytotoxic compounds. They determined that approximately 80% of the screened drug set shows a dependency with at least one solute carrier. To further validate these results, the scientists individually validated a subset of SLC-drug interactions and employed uptake assays and transcriptomics approaches to investigate how some of the SLCs affected drug uptake and activity. “The use of a custom-made, SLC-focused library was instrumental in allowing us to screen a large number of compounds, revealing hundreds of SLC-drug associations and providing many novel insights into SLC biology and drug mechanisms”, says Enrico Girardi, CeMM senior postdoctoral fellow and first author of the study.

The present study is the result of a cross-disciplinary collaboration with researchers from the University of Vienna Pharmacoinformatics Research Group of Gerhard Ecker as well as the group of Stefan Kubicek at CeMM. It provides not only a strong validated argument to demonstrate the requirement of solute carriers in cellular uptake and drug’s activity, but also an experimentally validated set of SLC-drug associations for several clinically relevant compounds. The evidence provided by CeMM researchers opens the pathway to further investigations of the genetic determinants of drug activity and especially uptake in human cells. “This study raises strong doubts that the generally accepted idea that most drugs can enter cells by simply diffusing through its membrane is correct and highlights the increasingly appreciated need to systematically studying the biological roles of solute carriers”, says Giulio Superti-Furga, CeMM Scientific Director and last author of the study. Gaining further insights into how the transporters affect the uptake and activity of drugs in tumors and tissues allows scientists to predict and counteract resistance mechanisms to design the most effective precision therapies. Furthermore, understanding the relationship between the expression of SLCs, cellular/organismal metabolism and nutrition is likely to allow the opening of novel therapeutic avenues in the future.

The study “A widespread role for SLC transmembrane transporters in resistance to cytotoxic drugs” was published in Nature Chemical Biology on 9 March 2020. DOI: 10.1038/s41589-020-0483-3

Authors:
Enrico Girardi, Adrián César-Razquin, Sabrina Lindinger, Konstantinos Papakostas, Justyna Konecka, Jennifer Hemmerich, Stefanie Kickinger, Felix Kartnig, Bettina Gürtl, Kristaps Klavins, Vitaly Sedlyarov, Alvaro Ingles-Prieto, Giuseppe Fiume, Anna Koren, Charles-Hugues Lardeau, Richard Kumaran Kandasamy, Stefan Kubicek, Gerhard F. Ecker, Giulio Superti-Furga

Funding:
The study was funded with support by the Austrian Academy of Sciences, the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 695214, awarded to Giulio Superti-Furga), the Austrian Science Fund (FWF I2192-B22 ERASE; FWF P29250-B30 VITRA) and by a Marie Sklodowska-Curie fellowship to Enrico Girardi (MSCA-IF-2014-661491).
Research in the Kubicek laboratory is supported by the Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology, and Development, the Austrian Science Fund (FWF) F4701 and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC-CoG-772437).
The Pharmacoinformatics Research Group (Ecker lab) acknowledges funding provided by the Austrian Science Fund FWF AW012321 MolTag.

March 06, 2020

AustroVirology Symposium 2020

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Participants at the AustroVirology Symposium 2020 | Photo credit: CeMM / CCRI

On 5 March 2020, the first AustroVirology Symposium took place at the St. Anna Kinderkrebsforschung (CCRI) in Vienna. The event, organized by CeMM PI Andreas Bergthaler and Karin Kosulin (CCRI), brought together 75 virologists from 12 institutions across Austria. The goal was to capture the rich diversity of academic, clinical and industrial virological research and to provide a platform to meet colleagues and forge new collaborations in the field.

The symposium kicked off by an inspiring keynote lecture about the co-evolution of phages and bacteria by Martin Polz, Professor at the Massachusetts Institute of Technology (MIT) and the Universität Wien. The programme included 10 short talks which covered diverse subdisciplines of virology, including structural biology, immunology, organoids, clinical diseases and biotechnological applications. Finally, the event was concluded with an open discussion and a poster session with additional networking opportunities.

The successful AustroVirology Symposium gave a vibrant demonstration of the existing excellent virus research in Austria and fostered intense networking. Considering the current SARS-CoV2 epidemics and COVID-19, the virology research community continues to play an ever-important role for our understanding of basic biology, the fight of infectious diseases and the development of novel solutions such as innovative vaccines.