Research and Scientific Services

The programme’s scientific highlights in 2017 included the development of the Capture Long Seq (CLS) methodology to exhaustively characterise the transcript diversity of long non-coding RNAs, the development of nextflow, a domain-specific language that enables scalable and reproducible scientific workflows using software containers, the uncovering of a sexual cycle and a recent association with the human host in the emerging fungal pathogen Candida glabrata and the Global Score algorithm to predict protein interactions with large transcripts.

Several groups in the programme are participating in a number of large-scale genomic projects, such as ENCODE, GTEx, PanCancer, I5K, F1K, WebOfLife and IASIS (first grant in Catalonia for personalised medicine).

The programme has continued to deploy and support the European Genome-phenome Archive (EGA) in collaboration with the European Bioinformatics Institute (EBI). EGA has been selected as an ELIXIR Core Data Resource and as an ELIXIR Recommended Deposition Database. It has also been selected as one of the Global Alliance for Genomics and Health (GA4GH) Driver Projects. EGA is also one of the European Open Science Cloud (EOSC) Science pilot demonstrators.

In 2017, Malhotra’s lab discovered a di-acidic motif necessary for the secretion of superoxide dismutase (SOD)1, which is secreted without the conventional endoplasmic reticulum-Golgi pathway of protein export. Modulation of this sequence could help in understanding neurotoxicity associated with mutant SOD1 in amyotrophic lateral sclerosis. This lab also discovered that a protein called TANGO1, which is required for the export of bulky collagens, assembles into a ring at ER exit sites, thereby compartmentalizing ER into specific regions for folding and export of bulky collagens from the rest of the ER. Another finding of considerable interest is the demonstration of sphingomyelin in organizing the shape and the function of Golgi membranes. Isabelle Vernos’s lab continued to dissect the mechanism of spindle dynamics and discovered a new mitotic partner of a specific kinesin motor and their role in microtubule and chromosome alignment. Sebastian Maurer succeeded in reconstituting RNA migration on microtubules in vitro. This tour de force approach is the first of its kind and a major achievement for understanding the mechanism of kinesin-dependent cargo transport on microtubules. Manuel Mendoza discovered a new mechanism of cell cycle progression via asymmetric division. Solon’s lab provided a first description of the evolutionary modulations in the process of epithelial sealing between different fly species. They found an evolutionary transition leading to a simplification of the sealing process in dorsal closure and identified a conserved essential role of the microtubule cytoskeleton in epithelial sealing.

These findings attest to this department’s overall interest in addressing the mechanisms underlying cell compartmentation, cell division and tissue organisation.

2017 witnessed the departure of a junior group leader, Manuel Mendoza, who moved to the Institute of Genetics and Molecular and Cellular Biology-IGBMC (Strasbourg, France) as group leader. During his spell at the CRG, Manuel’s lab revealed a fascinating mechanism for the modulation of nuclear pore complexes during cell division and the role of this process in controlling differential cell cycle progression in mother and daughter cells. His findings also revealed a challenging connection of exocytosis and abscission and the mechanism by which cells control abscission to ensure normal chromosomal segregation. We are proud of Manuel’s achievements and wish him continued success in his new position in France. His collegiality, generosity and scholarly discussions will be sorely missed.

Finally, we would like to welcome two new group leaders. Elvan Boke has joined the department as a Junior Group Leader. She is leading the Oocyte Biology & Cellular Dormancy lab. During her post-doc at Harvard, Elvan discovered that oocytes cluster and segregate mRNA, mitochondria, ER, Golgi, endosomes and lysosomes through a large disordered protein called Xvelo. The Xvelo-mediated creation of this mega sub-compartment called the Balbiani body is a major breakthrough and holds great promise for understanding the basic principles in oocyte development and the overall process of fertilisation. Boke’s leading discovery and objectives are recognised by the award of a starting ERC grant. Verena Ruprecht was recruited following her brilliant research at IST in Austria. As a post-doc at IST, Verena discovered how cortical contractile activity leads to rapid amoeboid cell motility. This process of amoeboid migration is witnessed in numerous developmental and cancer metastases, although the mechanism is unclear. Verena’s findings opened a brand-new chapter in cell migration and have made this process of fundamental importance amenable to molecular analysis. Verena’s expertise in physics and imaging brings new approaches to addressing cell migration, and we look forward to many new discoveries.

Research highlights in the programme in 2017 include important insights into the role of the three-dimensional arrangement of chromatin in regulating gene expression. Members of the ERC 4D Genome Synergy project reported the fundamental roles of local genomic context in the latency of HIV virus, the expression of genes in Drosophila cells and how genome topology influences – and is influenced by – the activity of transcription factors during cell reprogramming. Additional work by other groups in the programme unveiled transcriptional networks with key roles in the regulation of embryonic stem cell identity, somatic cell reprogramming and organ regeneration by cell fusion. These processes are also being characterised using super-resolution microscopy, supported by FET grants. Progress was also made in understanding molecular mechanisms of anti-tumour drugs targeting the splicing machinery and efforts to develop novel modulators of this process have been supported by laCaixa Impulse and ERC PoC grants. Finally, Bernhard Payer’s group initiated a collaboration with the Eugin fertility clinic, also involving CNAG-CRG, to explore the molecular basis of human oocyte ageing.

2017 witnessed the departure of two of our group leaders.  Matthieu Louis, a junior group leader, moved to the University of California at Santa Barbara, and James Sharpe, a senior group leader, became the first director of EMBL Barcelona.  During their time at the CRG, Matthieu’s lab completed an absolute tour de force of technology development to establish the Drosophila larva as a premier system in which to quantitatively study sensory perception and animal behaviour.  The lab discovered new behaviours, developed methods to study them, elucidated the wiring diagram of the larva olfactory system, studied its evolution, and, through the use of a closed-loop optogenetic tracker, developed and tested a multi-level model for how the animal integrates dynamic olfactory signals.

James’ lab has been part of the program since it started in 2006 and James was coordinator of the program from 2011 to 2017 and so contributed enormously to the culture of the program and the style of the science we do.  The lab’s major achievement whilst at CRG was the demonstration that the mechanism that specifies mammalian digits is a molecular Turing system.  A vast amount of technology development underlies this major achievement, and the lab continued to develop microscopes and modelling approaches throughout its time at CRG.   They also published a fascinating body of work exploring the design space of dynamic gene networks, and, in collaboration with a former program member, Mark Isalan, built some of these patterning networks in bacteria.  We may have five digits, but it turns out there are six mechanisms for three genes to interpret a morphogen gradient to build a stripe!  We are very excited that James will direct the new site EMBL Barcelona.  The institute will focus on the biology of tissues and organs and will bring an additional 6-7 systems biology labs to the PRBB, giving the building an unrivalled concentration of quantitative and integrative biology labs in Europe.

We are very proud of the achievements of both Matthieu’s and James’ labs – theirs is exactly the kind of original, ambitious, difficult, and long-term quantitative science that we aim to develop in the program.   We wish them luck in their new homes and expect to hear great things coming out of their labs for many years to come. We will miss their scientific vision, friendship, and support.

2017 has been quite a productive year for the program.  Ben Lehner’s lab published their discovery of a long-lasting and chromatin-associated transgenerational epigenetic memory of the environment in C. elegans, as well as their discovery that maternal age is a major influence on phenotypic variation in this species.  These two studies continue the lab’s long-running interest in understanding the causes of phenotypic variation amongst genetically identical individuals.   The lab also showed that the signatures of clustered mutations in >1,000 human tumours can be used to identify the molecular mechanisms that cause mutations, including the discovery of a new mutation process that targets mutations to active genes in tumours associated with carcinogen exposure, including alcohol consumption.  Luis Serrano’s lab continued to develop Mycoplasma pneumonia as a ‘therapeutic chassis’. They also published the structure of the Mycoplasma chromosome at 10 kb resolution and used random mutagenesis and deep-sequencing to determine key sequences of promoter and untranslated regions that influence transcription and translation efficiency in this bacterium.  Mara Dierssen’s lab continued their work on understanding the changes in neuronal architecture and connectivity that disrupt cortical and hippocampal function in genetic cognitive disorders.  They also showed that Neurotrophin-3 infusion rescues fear extinction impairment in a mouse model of pathological fear.  Manuel Irimia’s lab published the most comprehensive database of alternative splicing events released to date.  They also elucidated the role and evolution of Esrp-dependent splicing programs in morphogenesis.  In addition, by molecularly characterising the development of the amphioxus neural tube, they presented an important new model for vertebrate brain organization and evolution.

In recognition of their achievements, Manu Irimia was elected as an EMBO Young Investigator, Ben Lehner was elected as an EMBO Member, and Mara Dierssen received both the BigVang Medal and the Trifermed Social Impact of Healthcare Award.

Finally, Nick Stroustrup joined the program as a junior group leader.  Nick’s Dynamics of Living Systems Lab will develop experimental and computational methods to characterize where, when, and why aging occurs, and how we might effectively intervene in its progression.  Whilst at Harvard, Nick developed the ‘Lifespan Machine’, which allows researchers to track tens of thousands of nematodes throughout their entire lifespan and he used this to discover a universal scaling law for how interventions alter lifespan. Nick continues the program traditions of hosting groups with an engineering-driven approach and groups tackling a well-established question from a very original (orthogonal) angle.  Welcome Nick!

The Core Facilities programme currently comprises seven Core Units: Genomics, Proteomics, Advanced Light Microscopy, Biomolecular Screening & Protein Technologies, FACS, Bioinformatics, and Tissue Engineering. The programme also comprises the Histology Service and the Storage and Computing Unit that are only accessible to PRBB users, or internal users, respectively.

All units work towards implementing new technologies and applications in response to both our user needs and the future directions in their respective fields. The most prominent new technologies set up in 2017 include:

• Isolation of single virus by flow cytometry (for single-virus genomics and the study of the marine virosphere)
• Identification and isolation of extracellular vesicles by flow cytometry for the study of the vesicle cargo
• Generation of Pseudostratified mucociliary epithelium from normal human bronchial epithelium and of Retina pigmented epithelium from human ES cells
• Derivation and culture of intestine organoids
• New workflow for the elucidation of protein complexes and structural features using chemical crosslinkers
• Protocol for error correction of sequencing reads to allow high sensitivity of mutation detection
• Globin depletion protocol from blood RNA samples during a normal mRNA library prep
• Implementation of most standard bioinformatics pipelines in NextFlow

In order to anticipate future needs in life science research, we are also working towards a further integration of facilities by implementing new cross-facility methodologies that require the collaboration of several units. More particularly, we are setting up genome engineering by CRISPR/Cas9 directly in embryos, deciphering the proteome of extracellular vesicles or generating a full set of in-house-produced enzymes for NGS library preparation.

Additionally, we are focusing our efforts on collaboration with the Industry for technology scouting. In 2017, we performed the application-testing of the latest Leica STED objective and organised several scouting events to assess the latest technologies on the market.

The CRG core facilities are not only well-established locally, with users from different institutions in Spain and abroad, but are also recognised partners in European initiatives. The Advanced Light Microscopy Unit is a partner in the ESFRI initiative EuroBioimaging (EuBI), and its head, Timo Zimmerman, the national coordinator for biological imaging. The Genomics and Proteomics Units are members of MERIL, the European Research Infrastructure portal listing facilities with more-than-national relevance (CRG being the only Spanish Proteomics Facility).

The Core Facilities are members of the Core Facilities Excellence Alliance “Core For Life” (www.coreforlife.eu), as described in the ‘National and International Dimension’ section.

In 2017, CNAG-CRG has further consolidated its position. The inclusion of the CRG Genomics Core Facility has allowed us to reorganise activities and instrumentation with CNAG-CRG focussing on the high-end, high-throughput applications, while the CRG Genomics Core Facility focuses more on applications such as miRNA and ChIP sequencing. Together we have continued our strategic path to offer the best-in-class support to our collaborators for their research projects. Still of particular focus are areas of patient-near research, such as in rare diseases and cancer. From an applications points of view we have extended our expertise in single cell analysis, epigenomics, translational techniques and the integration of population information. We have further developed our advanced analytical capabilities.

This year has seen many highlights. Our quality system running under ISO17025:2005 accreditation with the scope of DNA/RNA analysis by high throughput sequencing (NGS) and ISO9001:2015 certification by the Spanish national accreditation body ENAC has passed its re-accreditation and re-certification with flying colours. Additionally and after a rigorous training program, the CNAG-CRG has become the first European center to obtain Roche’s Certified Service Provider program for SeqCap EZ Target Enrichment Systems. We are in the process of adding further accreditations that will facilitate working with the clinical services in particular with a view to personalized medicine.

In 2017, we incorporated a second Illumina HiSeq4000 and retired several of the older sequencing instruments that had reached their end of life. Much effort has gone into the resolution of technical problems inherent to the newer Illumina sequencing instruments that operate with patterned flowcells. An innovative modification has been included in the sequencing protocols that allows handling this problem. On the Oxford Nanopore sequencers we have implemented direct RNA sequencing which opens several new exciting avenues for research projects. The Oxford Nanopore sequencers have turned into a major workhorse in de novo assembly projects.

The RD-Connect Genome-Phenome Analysis Platform (GPAP), developed at the CNAG-CRG, was made available to the European International Rare Disease Research Consortium investigators. It already has over 400 users and has been used in many rare disease research projects. It was crucial for the BBMRI-LPC call in which 900 exomes were sequenced. Data was analysed in the RD-Connect GPAP and biological specimens transferred to Eurobiobank. Although RD-Connect is coming to an end, the CNAG-CRG is strengthening its role in the field of rare diseases with upcoming projects such as Solve-RD. In 2017, more than half of the patient samples analysed resulted in disease gene identifications.

The Single Cell Genomics team found a way to cryopreserve biological samples without compromising gene expression profiles compared to freshly processed samples at single cell level. A game-changer result since the use of cryopreservation drastically influences sample accessibility. In addition, the team is taking an active role in the Human Cell Atlas, aimed to build a collection of maps that will describe and define the cellular basis of health and disease.

Personalized medicine is arriving and genome analysis is its major tool, as it provides unprecedented resolution for diagnosing patients. NAGEN1000, a pilot project together with Navarrabiomed funded by the Servicio Navarro de Salud-Osasunbidea and two pilot projects (MedPerCan and URDCat) together with several hospitals in Barcelona funded by the Catalan Department of Health (PERIS) started in 2017. These projects aim to bring genomic analysis into the clinic for the immediate benefit of patients. Moving forward it is clear that CNAG-CRG will play a key role in the implementation of personalized medicine into healthcare. With our sequencing platform, our sophistication in data analysis and our databases to make genomic data more user-friendly we are in a prime position to support this monumental task.

The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The data at EGA was collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project.

Since its launch, researchers from around the world have deposited and accessed data from more than 1000 studies in the EGA of various types. These studies vary from large-scale array-based genotyping experiments on thousands of samples in case-control designs or population based studies, to sequencing-based studies designed to understand changes in the genome, transcriptome or epigenome in both normal tissue and in various diseases such as cancer. As a result, the EGA has grown from about 50 TB to 3500 TB during the last five years.

The EGA team engages in several initiatives and projects, such as securing storage and distribution of human personal identifying data; analysing relationships between genomes and phenomes; evolutionary medicine; it is the driver project of the Global Alliance for Genomics and Health (GA4GH); it is the ELIXIR Core Data Resource of fundamental importance to the life science community and the long-term preservation of biological data, and it is also a major player in EXCELERATE (HORIZON 2020) projects.