Best Poster Awards – The Non-Coding Genome

Taking place for the third time,  the EMBO|EMBL Symposium: The Non-Coding Genome (16 – 19 October 2019) brought together 305 RNA experts to discuss the roles of non-coding RNAs in both prokaryotes and eukaryotes, gene regulation and function. 

A total of 189 posters were presented, from which two were singled out as the winners by popular vote.

Characterization of the genomic and splicing features of long non-coding RNAs using bioinformatics approaches

Monah Abou Alezz is a Ph.D student in genetics, molecular and cellular biology at the University of Pavia, Italy. PHOTO: Monah Abou Alezz

Authors: Monah Abou Alezz, Ludovica Celli, Giulia Belotti, Silvia Bione, Institute of Molecular Genetics L. L Cavalli-Sforza – National Research Council, Italy

Recent developments in deep sequencing approaches have simulated the continuous discovery of a significantly large number of novel long non-coding RNA (lncRNA) genes loci in the genomes. Long non-coding RNAs are recognized as a new class of regulatory molecules despite very little is known about their functions in the cellular processes. Due to their overall low expression level and tissue-specificity, the identification and annotation of lncRNA genes still remains challenging. The characterization of lncRNAs’ features is crucial to understand and get functional insights on their mechanisms of action. We exploited recent annotations by the GENCODE compendium to characterize the genomic and splicing features of long non-coding genes, in comparison to protein-coding ones, in the human and mouse genome by using bioinformatics approaches. Our analysis highlighted differences between the two classes of genes in terms of gene architecture regarding exons and introns length, GC-content, and the combinatorial patterns of chromatin marks and states. Moreover, significant differences in the splice sites usage were observed between long non-coding and protein-coding genes. While the frequency of non-canonical GC-AG splice junctions represents about 0.8% of total splice sites in protein-coding genes, we identified a remarkable enrichment of the GC-AG splice sites in long non-coding genes, both in human (3.0%) and mouse (1.9%). In addition, we identified peculiar characteristics of the GC-AG introns in terms of donor and acceptor splice sites strength, poly-pyrimidine tract, intron length, and a positional bias of GC-AG junctions being enriched in the first intron. Genes containing at least one GC-AG intron were found conserved in many species across large evolutionary distances, more prone to alternative splicing and a functional analysis pointed toward their enrichment in specific biological processes such as
DNA repair.

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MirGeneDB 2.0: The metazoan microRNA complement

Bastian Fromm is a Senior Researcher at Science for Life Laboratory, Stockholm University, Sweden. PHOTO: Bastian Fromm

Authors: Bastian Fromm (1), Diana Domanska (2), Eirik Hoye (3), Vladimir Ovchinnikov (4), Wenjing Kang (5), Ernesto Aparicio-Puerta (6), Morten Johansen (7), Kjersti Flatmark (3), Anthony Mathelier (8), Hovig
Eivind (3), Michael Hackenberg (6), Marc Friedländer (5), Kevin Peterson (9)

Non-coding RNAs (ncRNA) have gained substantial attention due to their roles in human disorders and animal development. microRNAs (miRNAs) are unique within this class as they are the only ncRNAs with individual gene sequences conserved across the animal kingdom. Bona fide miRNAs can be clearly distinguished from the myriad small RNAs generated in cells by a set of unique criteria. Unfortunately, recognition and utilization of these clear and mechanistically well understood features is not a  common practice. We addressed this by extensively expanding our curated miRNA gene database MirGeneDB to 45 organisms that represent the breadth of Metazoa. By consistently annotating and naming more than 11,000 miRNA genes in these organisms, we show that previous miRNA annotations contained not only many false positives, but surprisingly many false negatives as well. Indeed, curated miRNA complements of closely related organisms are very similar and can be used to reconstruct evolution of miRNA genes, families and biogenesis across more than 1 billion years of evolution. MirGeneDB represents a robust platform for providing deeper and more significant insights into the biology of miRNAs, possible sources of mis-regulation, and evolutionary mechanisms. MirGeneDB is publicly and freely available under http://mirgenedb.org/.

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Fromm, B. et al. MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Research, gkz885, (2019), https://doi.org/10.1093/nar/gkz885

(1) Science for Life Laboratory, Sweden
(2) Department of Informatics, University of Oslo, Oslo, Norway
(3) Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
(4) School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, United Kingdom
(5) Stockholm University, SciLifeLab, Sweden
(6) Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
(7) Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
(8) Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
(9) Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America


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Best Poster Awards – EMBO Workshop: Tools for Structural Biology of Membrane Proteins

183 researchers convened at the Centre for Structural Systems Biology (CSSB) in Hamburg, Germany, for the recent EMBO Workshop: Tools for Structural Biology of Membrane Proteins (7 – 9 October 2019) to present and discuss new technologies and approaches applied in studying membrane protein structure, dynamics and functions.

Out of the 82 posters presented, 6 were awarded a poster prize based on popular vote. Here we present the poster abstracts of four of the winners.

Structural insights into the role of the conserved ATPase component, EccC, in the mycobacterial T7SS

Katherine Beckham is a postdoctoral fellow in Matthias Wilmanns’ group at EMBL Hamburg. PHOTO: Katherine Beckham

Authors: Katherine Beckham (1), Luciano Ciccarelli (1), Mandy Rettel (2), Mikhail Savitski (2), Jan Kosinski (1), Annabel
Parret (1), Matthias Wilmanns (1)

Mycobacteria have a unique membrane structure with a complex hydrophobic outer-membrane rich in mycolic acids. To transport substances across this impermeable barrier, mycobacteria rely on a highly specialised translocation machinery – the Type VII secretion system (T7SS). Pathogenic mycobacteria encode up to five distinct T7SSs ESX-1 to 5 [1]. Our previous work characterised the structure of the of the inner-membrane complex of the ESX-5 T7SS from Mycobacterium xenopi using negative stain electron microscopy, revealing a hexameric 1.8 MDa complex comprising the four conserved core components: EccB5, EccC5, EccD5 and EccE5 [2]. The large cytosolic domain of EccC5, an FtsK/SpoE-like ATPase, is absent in our current EM map due to its conformational flexibility, which may be required to accommodate a range of protein substrates. Our current work aims to understand the role of EccC5 in secretion. In isolation this component can oligomerise into a hexameric ring-like conformation, as observed for other ATPases in this family. In addition, chemical cross-linking of the ESX-5 complex coupled with mass spectrometry (XL-MS) supports the oligomerisation of EccC5 in the secretion complex, suggesting that it may form a channel or ‘translocation tunnel’. Thus, we propose that EccC5 may exist in two conformational states: an extended, flexible monomeric state and a more compact hexameric state. Using an integrative structural biology approach, we are combining structures of isolated proteins derived from X-ray crystallography and electron microscopy studies with XL-MS data. Together these data aim to further elucidate the secretion pathway across the mycobacterial cell envelope.

References:
[1] Houben, E. N. G., et al. Take five — Type VII secretion systems of Mycobacteria. Biochim. Biophys. Acta – Mol. Cell Res.1843, 1707–1716 (2014).
[2] Beckham, K. S. H. et al. Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis. Nat. Microbiol.2, 17047 (2017).

(1) EMBL Hamburg, Germany, (2) EMBL Heidelberg, Germany

Poster currently not available


Dissection of protonation sites for antibacterial recognition and transport in QacA, a multidrug efflux transporter

Puja Majumder is a Ph.D student at the Indian Institute of Science. PHOTO: Puja Majumder

Authors: Puja Majumder (1), Shashank Khare (1), Arunabh Athreya (1), Nazia Hussain (1), Ashutosh Gulati (2), Aravind Penmatsa (1)

Emergence of multidrug-resistance poses serious threat to the society. One of the effective way by which bacteria gain drug resistance is through active efflux of antibiotics and other antibacterial compounds using multidrug efflux transporters. Among the battery of efflux pumps present in pathogenic bacteria, our work is focused on QacA, a drug-proton anitiporter (DHA) with 14-transmembrane helices that provide resistance to methicillin resistant Staphylococcus aureus (MRSA) strain, with homologs present in other pathogenic organisms. QacA is a highly promiscuous transporter, capable of effluxing diverse array of monovalent and divalent cationic antibacterial compounds and dyes. This study using a homology model, dissects the role of six protonatable residues present in the transport vestibule of QacA. Systematic mutagenesis resulted in identification of D34 (TM1) and E407 (TM13) as crucial residues and D323 (TM10) and D411 (TM13) as conditional residues needed for transport process of QacA. Whole cells, inside-out vesicles, substrate-induced proton release and microscale thermophoresis based assays were used to investigate the transport and binding properties of the transporter and its mutants. The activity of purified protein was checked with reconstituted QacA in a proteoliposome using substrate-induced proton transport assay. We identify two sites, D34 and D411 playing vital role in recognition of most of the substrates tested while E407 facilitates substrate efflux as a protonation site. It was also observed that E407 has an additional role as a recognition site for the transport of dequalinium, a divalent quaternary ammonium compound. These observations rationalize the promiscuity at the residue level of QacA for diverse substrates. The study identifies the role of acidic residues in QacA with implications for substrate recognition, promiscuity and processive transport in multidrug efflux transporters, related to QacA.

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(1) Indian Institute of Science, India, (2) Stockholm University, Sweden


Biophysical analysis of circularized MSP nanodiscs for structural studies

Melina Daniilidis is a Ph.D student in Prof. Dr. Franz Hagn’s group at the Bavarian NMR Center (BNMRZ) of the Technical University of Munich. PHOTO: Melina Daniilidis

Authors: Melina Daniilidis (1), Ralf Stehle (1), Franz Hagn (1,2)

Structure and dynamics of membrane proteins are crucial aspects for understanding functional properties of this protein class. Unfortunately, stabilizing them in their isolated form is still difficult. By incorporating membrane proteins into nanodiscs, they can be studied in a native-like
environment using biochemical and structural methods. However, thermal and long-term stability of small nanodiscs limit these studies and make it difficult to carry out nuclear magnetic resonance spectroscopy (NMR) measurements at elevated temperatures. Circularized membrane scaffold proteins (MSPs) produced via split-inteins have been shown to be more stable and homogenous than their linear counterparts. However, their biophysical properties, as well as suitability for membrane protein insertion and structural studies have not yet been assessed in a systematic manner. Thus, we examined circular and linear nanodiscs of varying size using several biophysical methods. An important issue for NMR structural studies is that the size and shape of circular nanodiscs do not expand above the phase transition temperature, increasing their homogeneity and reducing their size as compared to linear nanodiscs at high temperatures. 1H,15N-TROSY experiments could demonstrate that circular MSP1D1 nanodiscs with incorporated VDAC-1 are stable at higher temperatures, making it possible to obtain high-resolution NMR spectra of superior quality. Furthermore, NMR relaxation experiments were carried out to compare rotational correlation times of VDAC-1 in circular and linear nanodiscs, respectively. Despite the higher molecular weight, the circular nanodiscs showed lower rotational correlation times, which corroborated the biophysical results on the temperature-dependecy of the nanodisc diameter and homogeneity. The presented data demonstrate that these very stable circularized MSPs are well applicable to the study of membrane proteins in a lipid environment by NMR, but also other structural methods like electron microscopy.

(1) Technical University of Munich, Germany, (2) Helmholtz Zentrum München, Germany

Poster currently not available


Reconstitution of the activity of RND efflux pumps into proteoliposomes

Dhenesh Puvanendran is a Ph.D student at the Institute of Physical and Chemical Biology in Paris, France. PHOTO: Dhenesh Puvanendran

Authors: Dhenesh Puvanendran, Quentin Cece, Martin Picard, IBPC, France

Efflux pumps are the major systems in bacterial resistance against antibiotics. They are classified by the energy needed to be active (ATP hydrolysis or ion counter-transport). Efflux pumps from the RND (Resistance, Nodulation, and cell Division) family use a proton gradient to be active and are composed of three proteins: a membrane fusion protein (MFP) and a transporter (RND) in the inner membrane, and an Outer Membrane Factor (OMF) localized in the outer membrane. We focus on the MexA-MexB-OprM efflux pump from Pseudomonas aeruginosa.The overall goal of my research is to measure in vitro the velocity of transport by efflux pumps. To that end, we reconstitute MexA and MexB as one population of proteoliposome, and OprM as another population of proteoliposome. The whole tripartite pump forms upon association of the respective populations of liposomes. The proof of concept of this method has already been described, leading to a qualitative monitoring of transport. We now work at defining a reconstitution procedure amenable to now quantify the rate of transport. To do so we take extreme care to precisely determine the efficiency of protein reconstitution and the type of lipids component used to perform liposomes. I will present the roadmap towards the rational, step-by-step, reconstitution of the MexA-MexB-OprM efflux pump as well as the methodologies that are undertaken to measure the velocity of transport, and possible perspectives regarding the screening of efflux pump inhibitors.

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The other award-winning posters are:

Novel antigen-binding chimeric proteins as tolls in crystallography and cryo-EM of membrane proteins presented by Thomasz Uchanski, Vrije Universiteit Brussel, Belgium

Cryo-Electron tomography of synaptic vesicle fusion junctions presented by Lucy Ginger, MRC Laboratory of Molecular Biology, United Kingdom


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Best Poster Awards – EMBO|EMBL Symposium: Systems Genetics: From Genomes to Complex Traits

The first EMBO|EMBL Symposium: Systems Genetics: From Genomes to Complex Traits (29 Sep – 2 Oct 2019) brought together over 150 international researchers to discuss how genetic variation alters molecular mechanisms to cause phenotypic changes amongst individuals, including quantitative traits and human disease. 

From the 77 posters that were presented on-site, 3 were selected as the winners after a shortlist round by popular vote, followed by a selection round by the conference organisers.

Resolving noise-control conflict by gene duplication

Michal Chapal is a PhD student in Naama Barkai’s lab at the Weizmann Institute of Science in Israel. PHOTO: Michal Chapal

Authors: Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai, Weizmann Institute of Science, Israel

Gene duplication promotes adaptive evolution in two principle ways: allowing one duplicate to evolve a new function and resolving adaptive conflicts by splitting ancestral functions between the duplicates. In an apparent departure from both scenarios, low-expressing transcription factor duplicates commonly regulate similar sets of genes and act in overlapping conditions. To examine for possible benefits of such apparently redundant duplicates, we examined the budding yeast duplicated stress regulators Msn2 and Msn4. We show that Msn2,4 indeed function as one unit, inducing the same set of target genes in overlapping conditions, yet this two-factor composition allows its expression to be both  environmental-responsive and with low-noise, thereby resolving an adaptive conflict that inherently limits expression of single genes. Our study exemplified a new model for evolution by gene duplication whereby duplicates provide adaptive benefit through cooperation, rather than functional divergence: attaining two-factor dynamics with beneficial properties that cannot be achieved by a single gene.

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Deep learning on single-cell ATAC-seq data to decipher enhancer logic

Ibrahim Taskiran is a PhD student in Stein Aerts’ lab at the VIB & KU Leuven Center for Brain & Disease Research. PHOTO: Ibrahim Taskiran

Authors: Ibrahim Ihsan Taskiran, Liesbeth Minnoye, Carmen Bravo Gonzalez-Blas, Sara Aibar Santos, Gert Hulselmans, Valerie Christiaens, Stein Aerts
KU Leuven – VIB, Belgium

Single-cell ATAC-seq provides new opportunities to study gene regulation in heterogeneous cell populations such as complex tissues or dynamic processes. We recently developed a probabilistic topic modeling approach, called cisTopic, to predict regulatory topics and sets of co-accessible enhancers from scATAC-seq data. Here, we apply deep learning approaches to analyze these sets of co-accessible enhancers, with the goal to predict the spatiotemporal pattern of enhancer accessibility directly from the enhancer sequence. We trained different types of Artificial Neural Networks, including a hybrid model that combines Convolutional and Recurrent Neural Networks. By applying this approach to a cohort of melanoma patient samples and Drosophila eye disc, we show that key transcription factors can be identified from the convolutional filters. In addition, we use the trained model to analyze the motif architecture in enhancers, such as motif combinations and relationship to nucleosome preferences. We furthermore exploit network explaining methods to predict the impact of somatic mutations, using publicly available SNP databases and in-house whole genome sequencing of inbred fly lines. Currently, to validate our models we are testing (mutated) synthetic cell state specific enhancers using massively parallel enhancer reporter assays (MPRA). In conclusion, training deep learning models on single-cell epigenomics data sets has multiple applications to understand the underlying enhancer logic and decipher gene expression programs.

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ROADdt: Regulation network remodeling along disease development trajectories

Celine Sin is a Postdoctoral Fellow in Jörg Menche’s Group at the CeMM Research Center for Molecular Medicine, Austria. PHOTO: Celine Sin

Authors: Celine Sin, Jörg Menche
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria

The human body is comprised of over 200 different cell types varying in size, shape, and function. The differentiation and subsequent maintenance of these different phenotypic states are governed by complex gene regulatory networks that dynamically orchestrate the activation and deactivation of genes. Abnormalities in these networks may lead to dysfunctional expression programs, e.g. uncontrolled cell proliferation. In order to understand the conditions resulting in disease, we must understand the underlying gene regulatory networks governing
the gene expression program. As cells move through the differentiation space, the networks that govern gene regulation are remodeled in order to achieve the appropriate gene expression program. While statistical physics and network theory have demonstrated numerous relationships between the structure of networks and the dynamic processes that act on them,
few studies link these mathematically rigorous principles to gene regulatory networks, none at the level of cell-trajectory-states. The overall goal of this project is to understand the fundamental architecture of gene regulatory networks associated with cell differentiation processes in disease. We hypothesize that the gene regulatory networks of different
cell-trajectory-states along the differentiation trajectory – e.g. transitory, branching, or terminal states – are each characterized by distinct structural features. I will present our first steps in this direction, starting from single-cell RNA seq profiles of tumors. Ultimately, we expect that detailed characterization of the gene regulatory networks in these disease processes will reveal basic principles applicable to other diseases and cell  developmental processes.

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Creating is Understanding: Synthetic Biology Masters Complexity – Best Poster Awards

The recent EMBO Workshop: Creating is Understanding: Synthetic Biology Masters Complexity (22 – 25 Sep) covered various themes that are geared toward basic research while being at the forefront of synthetic biology.

110 researchers came together at the EMBL Advanced Training Centre in Heidelberg, Germany for 3,5 days of talks, posters and networking. Here we present the work of 4 scientists who received best poster awards at the conference by popular vote.

Engineering portability of the CcaSR light switch for the control of biofilm formation in Pseudomonas putida

Angeles Hueso-Gil is a PhD researcher at the Spanish National Centre for Biotechnology in Madrid.

Authors: Angeles Hueso-Gil (1), Ákos Nyerges (2), Csaba Pál (2), Belén Calles (1), Victor de Lorenzo (1)

Two of the technical challenges faced by contemporary microbiology involve controlling gene expression using light and regulating bacterial biofilm formation, determined by the intracellular levels of the secondary messenger c-di-GMP. CcaSR system is one of the light switches repeatedly used for transcription induction in Escherichia coli. This two-component system represented a good candidate for its adaptation to Pseudomonas putida. Previous attempts have tried to use this microorganism as chassis for the implementation of new pathways, being biofilm formation an important function to control. To this end, we unified CcaSR components in one single construct and randomly mutagenized their regulatory regions to find a clone with a balanced expression of the system key parts inside P. putida. The combination of this novel mutagenization process with a proper screening, which included a first sorting of the libraries and the later isolation of colonies, lead us to a clone with a much improved induction by green light. The selected variant had a notable capacity in response to green light. Finally, optimized CcaSR was used to control the expression of super-efficient variant of PleD, a diguanylate cyclase of Caulobacter which allowed a tight control of c-di-GMP levels, and therefore, of biofilm production.

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(1) National Centre for Biotechnology, Spain
(2) Biological Research Centre of the Hungarian Academy of Sciences, Hungary

Designer membraneless organelles enable orthogonal translation in eukaryotes

Christopher Reinkemeier is a PhD student at EMBL Heidelberg, JGU Mainz and IMB Mainz, Germany

Christopher Reinkemeier (1,2,3), Gemma Estrada Girona (3), Edward A. Lemke (1,2,3)

Genetic code expansion is a powerful tool to study and control protein function with single-residue precision. It is widely used to e.g. perform labeling for microscopy or to photocontrol proteins. This is achieved by introducing an orthogonal tRNA/synthetase suppressor pair into the host, to recode a stop codon to incorporate a noncanonical amino acid (ncAA) into the nascent chain. This technique is codon-specific, but it cannot select specific mRNAs, so naturally occurring stop codons could be suppressed leading to potential interference with housekeeping translation. Nature avoids cross-talk between cellular processes by confining specific functions into organelles. We aimed to design an organelle dedicated to protein engineering, but as translation is a complex process requiring hundreds of factors to work together, membrane-encapsulation would not be feasible. Inspired by the concept of phase separation we hypothesized that such an organelle could instead be designed membraneless. Phase separation can generate high local concentrations of proteins and RNAs in cells and has recently gained attention owing to its role in the formation of specialized organelles such as nucleoli or stress granules. Despite being membraneless and constantly exchanging with the cytoplasm/nucleoplasm, these organelles still perform complex tasks, such as transcription. We combined phase separating proteins with microtubule motor proteins to generated orthogonally translating organelles in living cells that contain an RNA-targeting system, the stop codon suppression machinery and ribosomes. These large organelles enable site- and mRNA-specific ncAA incorporation, decoding one specific codon exclusively in the mRNA of choice. Our results demonstrate a simple yet effective approach to the generation of semi-synthetic eukaryotic cells containing artificial organelles to harbor two
distinct genetic codes, providing a route towards customized orthogonal translation and protein engineering.

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(1) Johannes Gutenberg University Mainz, Germany
(2) Institute of Molecular Biology, Germany
(3) EMBL Heidelberg, Germany

Metabolic perceptrons for neural computing in biological systems

Paul Soudier is a PhD Student at the French National Institute of Agricultural Research, France

Amir Pandi (1), Mathilde Koch (1), Peter Voyvodic (2), Paul Soudier (1), Jerome Bonnet (2), Manish Kushwaha (1), Jean-Loup Faulon(1)

Synthetic biological circuits are promising tools for developing sophisticated systems for medical, industrial, and environmental applications. So far, circuit implementations commonly rely on gene expression regulation for information processing using digital logic. Here, we present a new approach for biological computation through metabolic circuits designed by computer-aided tools, implemented in both whole-cell and cell-free systems. We first combine metabolic transducers to build an analog adder, a device that sums up the concentrations of multiple input metabolites. Next, we build a weighted adder where the contributions of the different metabolites to the sum can be adjusted. Using a computational model fitted on experimental data, we finally implement two four-input of metabolite combinations by applying model-predicted weights to the metabolic perceptron. The perceptron-mediated neural computing introduced here lays the groundwork for more advanced metabolic circuits for rapid and scalable multiplex sensing.

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(1) French National Institute of Agricultural Research, France
(2) INSERM, France

Programmed uptake of biomacromolecules into protocells

Wiggert Altenburg is a PhD student at the Eindhoven University of Technology, The Netherlands

Wiggert Altenburg, Amy Yewdall, Daan Vervoort, Alex Mason, Jan van Hest

The bottom up recreation of cellular processes into synthetic compartments has, in recent years, emerged as an exciting line of research with which to study biological processes in a controlled environment. However, the interior of a living cell is a difficult milieu to mimic in bottom-up synthetic cells, as it is an environment crowded with high concentrations of many different biomacromolecules. In this work, we describe the development of a powerful new tool to more accurately emulate the cell cytosol in discrete coacervate-based protocells. The coacervate core utilized herein not only provides an inherently crowded and highly charged microenvironment, but has also been chemically modified to interact specifically with recombinantly expressed proteins. Our method leverages the well-established binding of His-tagged proteins to Ni2+-nitrilotriacetic acid, which ensures that macromolecules are taken up in a highly efficient, yet gentle manner, thus preserving biological activity. The straightforward method allowed for both control over the amount taken up and an increased local concentration. Moreover, the engineered uptake of proteins was then employed to study two key aspects: the effect of the Ni-NTA interaction on the diffusivity of incorporated proteins, and the enhancement in activity of an encapsulated two-enzyme cascade. This direct and targeted method of protein uptake into a discrete, membrane bound platform is a significant step forward for synthetic cells, and will enable the engineering of highly complex enzyme and signaling networks with increasingly life-like properties.

Poster currently not available

Eindhoven University of Technology, The Netherlands

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Multiomics to Mechanisms Symposium – Best Poster Awards

The recent EMBO|EMBL Symposium: Multiomics to Mechanisms – Challenges in Data Integration (11-13 Sep 2019) addressed ways of integrating large-scale biological data across the different omics fields.

258 researchers from various fields gathered in Heidelberg last week to listen to 36 talks and engage with 146 poster presenters. Here we present the posters of 5 scientists who received best poster awards at the conference by popular vote.

Benchmarking of multi-omics joint  dimensionality reduction (DR) approaches for cancer study

Laura Cantini is a CNRS Research Scientist at IBENS in France.

Authors: Laura Cantini (1), Pooya Zakeri (2), Aurelien Naldi (1), Denis Thieffry (1), Elisabeth Remy (3), Anaïs Baudot (2)

Dimensionality Reduction (DR), decomposing data into low-dimensional spaces while preserving most of their information content, is among the most prevalent machine learning techniques in data mining. With the advent of high-throughput technologies, high-dimensional data have become a standard in biology, emphasizing the use of DR. This phenomenon is particularly pronounced in cancer biology, where consortia have profiled thousands of patients for multiple molecular assays (“multi-omics”), including at the emerging single-cell scale. DR approaches have been mainly applied to single omics data leading to cancer subtyping, tumor sub-clones quantification and immune infiltration quantification. Recently, DR approaches designed to jointly analyze multiple omics have been proposed. Integrative DR methods are based on various mathematical assumptions, ranging from extensions of CCA, tensors, or more general data fusion approaches, which makes difficult to chose which method to apply.
In this context, we here in-depth benchmark multi-omics DR approaches using: i) artificial multi-omics cancer data ii) multi-omics bulk data from 10 different cancer types downloaded from TCGA iii) multi-omics single-cell data from cancer cell lines In (i), the capability of the various methods to predict the clustering ground truth was found strongly sensible to the size of the clusters, with intNMF, RGCCA, MCIA and JIVE being the more robust methods. For (ii), MCIA, RGCCA, MOFA and JIVE more consistently identified factors associated to survival, clinical annotations and biological annotations. Finally in (iii), despite never being applied to single-cell data, tICA and MSFA outperformed other methods for their ability to cluster  single cells based on their cell line of origin. Overall, our results show that RGCCA, MCIA and JIVE perform consistently better across the three scenarios. This suggests that a mathematical formulation, based on the search of omic-specific factors whose inter-dependence is maximized, better approximates the nature of multi-omics data.

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(1) Institut de Biologie de l’Ecole Normale Superieure IBENS, France, (2) Aix Marseille University, INSERM, MMG, CNRS, France, (3) Aix Marseille University, CNRS, France


Single-cell transcriptome and chromatin accessibility data integration reveals cell specific signatures

Andrés Felipe is a PhD student at the German Cancer Research Center in Heidelberg, Germany.

Authors: Andres Quintero (1), Anne-Claire Kröger (2), Carl Herrmann (2)

The ability to integrate multiple layers of omics data will play an essential role in understanding the complex interplay of different molecular mechanisms that give rise to cellular diversity. In particular, single-cell multi-omics studies provide an enormously valuable source of information, allowing the characterization of different cell states under different biological contexts. However, the integration of distinct cellular modalities to disentangle the regulatory networks and pathways that explain cell identity is still a challenge.Here we introduce Integrative Iterative Non-negative Matrix Factorization (i2NMF), a computational method to dissect cell type associated signatures from multi-omics data sets. i2NMF takes full advantage of data sets with multiple modalities for the same sample or cell, defining cell type-specific features and discerning the shared and specific contribution of each omics type to the identification of different cell types. We applied i2NMF to an early human embryo single-cell multi-omics data set for which scRNA-seq and scATAC-seq profiles were available for every single cell, identifying master transcription factors at the morula and blastocyst stages. Finally, i2NMF is also able to integrate different modalities across multiple experiments. We used this functionality to extract cell-type specific molecular signatures from two complementary datasets of the mouse visual cortex, comprising scATAC-seq and scRNA-seq data. i2NMF was implemented on TensorFlow, presenting a scalable framework and allowing its efficient execution under multiple systems. Our results demonstrate that i2NMF is a useful tool to identify cell-type specific signatures and dissect their underlying molecular features.

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(1) German Cancer Research Center (DKFZ), Germany, (2) University Hospital Heidelberg, Germany


Linking signalling and metabolomic footprints with causal networks

Aurélien Dugourd is a PhD student in mechanistic modelling at JRC Combine, RWTH Aachen, Germany.

Aurélien Dugourd (1), Christoph Kuppe (1), Rafael Kramann (1), Julio Saez-Rodriguez (2)

Renal clear cell carcinomas (RCCC) are the result of a system-wide dysregulation of signaling and metabolic functions  originating from multiple factors. Characterizing cellular molecular machineries across multiple omic layers is a very powerful strategy to understand the cellular effects of such dysregulations. In this study, we performed metabolomics and phosphoproteomics from RCCC tissue in comparison to the non-cancerous kidney tissue in a cohort of 20 patients. In order to extract mechanistic information from these observations and to integrate both datasets, we developed a novel analysis pipeline. Phosphoproteomic abundance changes are used to estimate kinase activity changes across patients. Kinase activity estimations are then correlated with metabolite abundance changes. This points at possible interactions between signaling pathways and metabolism. We subsequently build a generic network integrating signaling pathways and metabolic reaction networks based on literature knowledge and databases. We use this signaling/metabolic network to identify paths across kinases and metabolic enzymes to link the correlated kinase activities and metabolites.
This provides potential mechanisms to explain the effect of deregulation of signaling on metabolism. Our approach was able to recover the structure canonical signaling pathway topologies and highlight specific connections between kinases and metabolite abundance deregulated in kidney tumor tissues. This pipeline allows to extract and compare mechanistic
information from metabolomic, phosphoproteomic (and potentially transcriptomic) data across many kidney cancer patients. This information can be used to select potential therapeutic targets to disrupt cancer specific cellular mechanisms, such as the SP1 kinase. Furthermore, the pipeline offers the advantage of being easily transferable in many different biological contexts.

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(1) RWTH Uniklinikum Aachen, Germany, (2) Heidelberg University, Germany


A network-based approach for the identification of multi-omics modules associated with complex human diseases

Maria Anna Wörheide is a PhD student at the Helmholtz Zentrum München in Germany.

Authors: Maria Anna Wörheide (1), Jan Krumsiek (2), Gabi Kastenmüller (1), Matthias Arnold (1)

Application of advanced high-throughput omics technologies have provided us with vast amounts of quantitative, highly valuable data. For complex, heterogeneous, and untreatable diseases such as Alzheimer’s disease (AD), the integration of different omics levels and their interconnections is desperately needed to understand the underlying molecular pathomechanisms and identify potential therapeutic targets. However, integrated, multivariable analyses of cross-omics data are not straightforward, and even if successfully applied, often lack a human comprehensible representation. Graph databases provide an intuitive and mathematically well defined framework to store and interconnect diverse biological domains in accessible network structures. Here, we propose a network-based, multi-omics framework
developed with the graph database Neo4j, that allows the large-scale integration and analysis of data on biological entities across omics, as well as results from association analysis with specific (endo) phenotypes. The backbone of this framework comes from known biological relationships and functional/pathway annotations available in public databases. It is augmented with experimental, quantitative data for single omics (e.g. tissue-specific gene expression) and across omics (e.g. eQTLs or mQTLs) derived in population-based studies. To identify modules within this network that are potentially relevant to a disease such as AD, we extend the
framework using large-scale association data for AD (e.g. from case-control GWASs). The resulting network is comprised of over 50 million nodes (entities), representing more than 30 different data types, and more than 80 million edges (relationships). We mined this comprehensive catalogue of biological information using established graph algorithms to
identify potentially disease-related modules of tightly interlinked entities, and were able to obtain several subnetworks significantly enriched for AD-associations.

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(1) Helmholtz Zentrum München, Germany, (2) Weill Cornell Medicine, United States of America


Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions

Ignacio Ibarra is a PhD student in Judith Zaugg’s lab at EMBL Heidelberg, Germany.

Authors: Ignacio Ibarra, Nele Hollmann, Bernd Klaus, Sandra Augsten, Britta Velten, Janosch Hennig, Judith Zaugg (EMBL Heidelberg)

Recent high-throughput transcription factor (TF) binding assays revealed that TF cooperativity
is a widespread phenomenon. However, we still miss global mechanistic and functional understanding of TF cooperativity. To close this gap we introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data. We identify DNA shape as driver for cooperativity, with a particularly strong effect for Forkhead-Ets pairs. Follow-up experiments revealed a local shape preference at the Ets-DNA-Forkhead interface and a decreased cooperativity once the interaction is lost. Additionally, we discovered many novel functional associations for cooperatively bound TFs. Examining the novel link between FOXO1:ETV6 and lymphomas revealed that their joint expression levels improve patient survival stratification.
Altogether, our results demonstrate that inter-family cooperative TF binding is driven by position-specific DNA readout mechanisms, which provides an additional regulatory layer for downstream biological functions.

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