Frontiers in Biomedical Research
20-21 September
Basel, Switzerland

Organisers:

Draft Report

Summary

On September 20 & 21, 2010, the FMI celebrated its 40th Anniversary with a world-class Anniversary Symposium, that opened the Basel Life Sciences Week. The Symposium took place in Basel at the Congress Center and attracted more than 800 participants coming from Switzerland, Europe and even overseas. The programme covered the topics which have been the focus of past or present research at the FMI, such as neurobiology, epigenetics, growth control, signaling or cancer. The invited speakers came from all over the world as well as from the FMI and a keynote lecture was delivered by Prof. Susumu Tonegawa, Nobel Laureate and Director of the Picower Institute at MIT. The very high interest raised by the Symposium was evidenced by the numerous professors from Basel or other Universities who attended and at times three Nobel Laureates were in the audience. Also many colleagues from the local biotech and pharmaceutical companies made their way to the FMI Anniversary Symposium. The second day of the Symposium was co-sponsored by the Biovalley network and was dubbed the Biovalley Science Day. More than 150 posters were presented in two sessions which allowed young scientists to discuss their results with a broad audience. In addition, the best posters were awarded the Biovalley Poster Prizes which were presented by Susan Gasser from the FMI and Peter Meier-Abt from the University of Basel.

This Symposium has been a unique occasion to bring together many friends of the FMI, coming from Basel and all over the world, in the context of a truly outstanding scientific meeting.

Scientific Content

On September 20 - 21, 2010, the Friedrich Miescher Institute for Biomedical Research celebrated its 40th Anniversary with a world-class scientific meeting which was also the opening for the Basel Life Sciences Week. The FMI Anniversary Symposium “Frontiers in Biomedical Research” took place in honor of the long-standing dialogue between FMI and the research community, the University of Basel and the local pharmaceutical industry.

About twenty talks were given by FMI group leaders as well as invited scientists from all over the world and the programme was arranged in sessions that reflected the current and also past strengths of the FMI.

Neuronal Circuitry and Behaviour

The Symposium was opened by Catherine Dulac, from Harvard University, who discussed genomic imprinting, a process which results in preferential expression of the paternally or the maternally inherited allele of certain genes. Catherine Dulac and her group used a genome-wide approach to characterise the repertoire of imprinted genes in the mouse embryonic and adult male and female brain. The presented study uncovered over 1000 new loci with imprinted features, some of them sexually dimorphic, suggesting that imprinting is a major mode of epigenetic regulation in the brain which had not been appreciated yet. Next, Silvia Arber from the FMI and University of Basel presented work on the assembly of neuronal networks involved in controlling motor behavior. Dedicated circuits exist in the spinal cord at the core of regulating phasic motor bursting patterns essential to move. The work presented used sophisticated mouse genetics in combination with transsynaptic viruses to label specific connections, in order to visualise interneuronal network organization in the spinal cord. The results revealed the widespread yet highly specific connectivity of motor circuits, and thereby provide evidence for anatomical traces of functional specificity in the control of behavior. Selected from the submitted abstracts, a talk by Volker Busskamp, discussed new technologies for treating retinitis pigmentosa, a diverse group of hereditary diseases that lead to incurable blindness. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. Volker Busskamp and his colleagues showed that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. This was then extended to human ex vivo retinas, where they could show that halorhodopsin can reactivate light-insensitive human photoreceptors.

The following presentation was by Barry J. Dickson, who is the Director of the Institute for Molecular Pathology in Vienna, who uses Drosophila courtship as a model to study how innate neural circuits generate complex adaptive behaviors. They showed that courtship behavior is intimately linked to the sex-specific splicing of the fruitless (fru) gene and the ~2000 neurons in which it is expressed. They have used genetic methods to dissect these neurons into 100 distinct classes, which were characterised anatomically and assembled into a cellular-resolution wiring diagram for the “fru circuit”. Finally, Andreas Lüthi of the FMI, discussed the synaptic and cellular mechanisms underlying learning, extending the neuronal circuits to auditory fear conditioning in the live animal. Andreas Lüthi and his group performed 2-photon calcium imaging and targeted patch clamp recordings from identified cell types in the auditory cortex of anesthetised mice, finding that during fear conditioning, sensory processing is dis-inhibited by a specific subpopulation of GABAergic interneurons receiving cholinergic input from the basal forebrain.

Signalling and Cancer

The session on cancer was opened by George Thomas, a former FMI scientist who discussed Target of Rapamycin Complex1 (mTORC1) and its downstream effectors, 40S ribosomal protein S6 Kinase 1 (S6K1). Owing to its central role in these basic cellular signaling processes, dysfunctional mTORC1 signalling is associated with a number of human pathologies including diabetes, obesity, neurodegenerative disease and cancer. Inhibitors of mTORC1 signalling have proven efficacious in the treatment of renal cell carcinoma, and are being considered as single agents for the treatment of neuroendocrine (NET) tumours and subependymal giant cell astrocytoma (SEGA). George and his colleagues have examined whether the rapamycin derivatives are simply slowing the growth of tumours or whether they are circumvented by inherent mechanisms of tumor resistance, using Neurofibromatosis type 1 (NF1), and in Tuberous Sclerosis Complex (TSC). They have found in mouse models that tumours initially respond to treatment with Affinitor®, but with time such tumours begin to proliferate at a rate equal to that of controls treated with the vehicle alone. The same resistance mechanisms are starting to appear in human tumours.

The next presentation was by Tony Hunter, on protein phosphorylation which occurs as a result of mutations or epigenetic variations in human diseases, such as cancer. Tony Hunter and his colleagues devised a rank-ordering system to define which protein kinase mutations are most likely to play a role in cancer, and have begun to investigate several of these for their involvement in carcinogenesis. Specifically they analysed cancer-associated mutations in DAPK3 and two isoforms of PKC and found that they decrease kinase activity, suggesting that these kinases normally play tumor suppressor roles and are mutationally inactivated in some cancers. In response to DNA double-strand breaks (DSBs), cells sense the DNA ends at the break and then activate the protein kinase ATM to initiate a signalling cascade that is driven by phosphorylation and ubiquitylation and known as the checkpoint response. Tony also reported that the tumor suppressor protein CtIP is essential downstream of ATM for resection of the 5’ end at DSBs to generate a 3’ single strand. This was followed by FMI researcher Brian A. Hemmings, who gave a fascinating overview on kinases and their importance in biology. Regulation of protein kinases temporally, spatially and quantitatively is crucial to the correct maintenance of all aspects of cell biology from metabolism to transcription, cell growth, shape, migration, survival and differentiation. These enzymes phosphorylate one-third of all intracellular proteins, making them key regulators in signalling. The mammalian genome encodes about 518 different protein kinases, and in cancer cells, mutations in key regulatory enzymes result in permanently upregulated proliferation and survival signalling pathways. Integrating knowledge of these pathways gained from molecular biology, biochemistry, animal models and patient samples may lead to specific therapeutic targets and treatments.

Nancy E. Hynes gave an update on the work of her group on breast cancer. The molecular understanding of genetic alterations in breast cancer has increased significantly over the past years, allowing about 25% of breast tumours to be successfully targeted by antibody-based approaches and tyrosine kinase inhibitors. Nancy Hynes has set out to identify proteins essential for breast tumour cell migration, and identified Memo (mediator of ErbB2-driven cell motility) as a protein required for ErbB2induced tumour cell migration. Memo levels are elevated in approximately 30% of breast cancer cases, and it is correlated with ErbB2-overexpression. Memo expression is higher in the invasive cells at the tumor edge. To study the role of Memo in normal physiology, Nancy Hynes and her colleagues generated a mouse strain allowing to ablate the Memo gene conditionally, and when combined with pCX-CreERTM they achieve ubiquitous Memo deletion upon tamoxifen treatment. Surprisingly, loss of Memo led to the rapid onset of a premature aging phenotype accompanied by alterations in insulin and glucose metabolism, which may be reflecting the role of Memo as a novel regulator of FGFR signaling. Josef Jiricny presented studies on the mismatch repair (MMR) system which has evolved to correct errors of DNA replication and to prevent illegitimate recombination. Joe Jiricny and his colleagues carried out a series of biochemical pull-down experiments, using human cell lines stably expressing tagged MMR proteins, and identified the interactome of MLH1 and PMS2 by proteomic analysis. The strongest interactions were verified by reciprocal pull-down experiments and by western blots. Interestingly, some of the principal interactors were proteins involved in the processing of ICLs. This was very puzzling, given that MMR-deficient cells do not generally display markedly different sensitivity to cross-linking agents such as cisplatin and mitomycin C and that cells defective in ICL processing are not known to have a mutator phenotype. Interestingly, one of the interacting partners of MLH1, encoded by a gene named KIAA1018, turned out to be a nuclease that protects cells from ICL-generating agents. This enzyme associates with the Fanconi anemia D2/I heterodimer, which recruits it to arrested replication forks, where it presumably cleaves the cross-linked substrate to release the block. The protein was named FANCD2-associated nuclease, FAN1.

Next, Ruth Chiquet-Ehrismann demonstrated that homeostasis of epithelial tissues depends on the presence of the underlying stromal cells and the basement membrane separating the two cell types. The same holds true for the growth of solid cancers. The stromal compartment or microenvironment of tumours is the site of angiogenesis that brings blood to nurture cancer cells and provides an escape route for metastatic cells. Dr Chiquet studies tenascin-C which is enriched at the invasive front of a primary tumour and seems to promote local invasion and metastasis, and tenascin-W, which is not expressed by brain cancer cells, but it is present in brain cancer blood vessels. Tenascin W seems to be implicated in angiogenesis of oligoendrogliomas as well as highly invasive glioblastomas. The prominent presence of tenascin-C and –W in tumours is currently being used for targeted immunotherapy, and the increased serum levels of tenascin-W seem to be predictive of recurrence. Finally William (Bill) Sellers, global head of oncology research at NIBR in Cambridge, gave a presentation illustrating where cutting-edge industrial cancer research stands today. The advent of complete genome sequencing along with an increasing array of technologies for analysing protein and RNA constituents of cancer cells promises to yield a detailed view of the genetic and functional drivers of the cancer process. The fundamental inability to drug certain classes of oncogenes (e g transcription factors) argues that single agent therapy will have a limited ability to achieve a high degree of efficacy in blocking tumour growth. Highly active combination regimens will be needed and pre-clinical cancer models, must be improved to robustly predictg the translation of research drug discovery effort into successful clinical trials.

Keynote Lecture: Molecular and circuit mechanisms for hippocampal memory

The Keynote lecture was given by Susumu Tonegawa, Nobel Laureate who worked in Basel for several years at the Basel Institute for Immunology. Dr Tonegawa spoke on memory, which is crucial not only for intelligent behaviour but also for daily routines. Susumu Tonegawa and his colleagues have been studying the molecular, cellular and circuit mechanisms underlying memories of events and facts by applying genetic engineering to the hippocampus of a mouse model. They designed and generated a variety of mutant mouse lines in which a specific gene encoding a receptor, channel or enzyme is deleted or modified in a highly restricted type of neurons, or a specific neuronal circuit is blockable in a temporally controllable manner. These mutant mouse strains are then analysed in comparison to normal counterparts by a variety of methods that permit an identification of impairments or deficits in the mutants at various levels of complexity: molecular, cellular, physiological, circuit and behavioral. The overall aim of this approach is to demonstrate the causal relationship among these impairments and deficits by analysing animals with highly specific and reproducible interventions. This fascinating lecture gave a glimpse of the exciting developments in brain research using these multi-disciplinary approaches.

Epigenetics and Stem Cells

The session on Epigenetics and Stem Cells was opened by Erich A. Nigg, who presented studies on the mechanisms of chromosome duplication in cellular division. The error-free segregation of duplicated chromosomes during cell division is crucial to the development and health of all organisms. In humans, extra or missing copies of chromosomes (aneuploidies) are common causes of genetic disorders and birth defects, and are likely to favor not only tumour development but also the emergence of resistance to anti-cancer therapy. Central to chromosome segregation is a highly dynamic microtubule-based mitotic spindle, whose bipolarity depends on correct numbers of microtubule organising centers (centrosomes). To understand the multiprotein complexes and regulatory circuits that control chromosome segregation in time and space, Erich Nigg and his colleagues dissected the human spindle using proteomics and in depth analyses of individual components. The emphasis has been on the spindle assembly checkpoint and the centrosome duplication cycle and in particular on cell cycle- regulatory protein kinases, many of which are considered as potential targets for the development of novel anti-cancer therapeutics.

The next series of talks focused on cellular reprogramming. Amanda Fisher presented experiments showing that differentiated uni-potent cells can be converted back to a multi-potent state by different experimental means – including nuclear transfer into enucleated oocytes. The success rates are low even after optimisation (1-2%) and therefore Amanda Fisher has formed transient heterokaryons between differentiated cells (such as lymphocytes or fibroblasts), and pluripotent stem cells. Under these conditions the nucleus of the differentiated cell is rapidly restructured and chromatin remodeled to resemble that of a pluripotent cell, prior to the initiation of a pluripotent gene expression program and silencing of differentiation-associated genes. They have used this approach with conditional ES mutants and RNAi-based approaches, to directly dissect the factors and mechanisms required for lineage conversion. After this, Dirk Schübeler from the FMI presented recent work on the role of chromatin modifications and DNA methylation in gene regulation during embryonic stem cell differentiation into neuronal cell types. Their comprehensive analysis allowed them to identify genomic sites that change their epigenetic status in a cell-state specific manner. The results obtained suggest that the DNA sequence of regulatory regions is the main determinant of dynamic chromatin states.

This theme was carried further by Antoine H.F.M. Peters, who presented work on transgenerational epigenetic control of mammalian early embyogenic development. Acquisition of totipotency occurs upon the remodeling of chromatin states of the two parental germ cell genomes and zygotic genome activation. He has examined the epigenetic information inherited from the germline. He found that transmission of histone H3 lysine 9 tri-methylation, established in oocytes by the Suv39h Histone Methyltransferase, is required for maintaining the canonical constitutive heterochromatic state at pericentromeric major satellite repeats of the maternal genome in mouse early embryos. In the absence of this germ-line signal, e.g. in the paternal genome, an alternative repressive chromatin state is formed by Polycomb group (PcG) proteins in early embryos. Loss of PcG protein function causes aberrant differentiation and impairment of embryonic development.

Looking at a different aspect of cell type determination, Susan Gasser, presented her work on 3dimensional organisation of chromatin in the cell nucleus and its impact on gene regulation during differentiation. To test whether the association of heterochromatin with the nuclear lamina is important during cell differentiation, Susan Gasser and her colleagues have exploited the LacO- LacI-GFP interaction to visualise developmentally controlled promoters in C. elegans. During cellular differentiation, a spatial segregation of tagged genes that depends strictly on their transcriptional status was observed: active tissue-specific genes are moved to the nuclear interior when active and to the nuclear envelope when repressed. RNAi of the unique worm lamin gene, or of genes encoding both Emerin and Man1 homologues, derepressed and delocalised heterochromatic arrays from the nuclear envelope. In contrast, a lamin point mutation that confers Emery Dreifuss Muscular Dystrophy (EDMD) in humans was introduced into an extra copy of worm lamin, and was shown to prevent release of a muscle-specific promoter array from the nuclear envelope in muscle cells only. This led to EDMD-like phenotypes in the worms, and a morphological misalignment of actin fibers and sarcomeres. These experiments thus reconstituted a human disease in C. elegans and argue that nuclear organisation is not only cell-type specific but necessary for appropriate transcription in differentiated tissues.

Returning to the question of cancer, Gerhard Christofori presented studies on cancer cell migration and its dependence the epithelial-mesenchymal transition (EMT), which involves the loss of E-cadherin and the gain of N-cadherin expression (the cadherin switch). Gene expression profiling experiments together with biochemical analysis revealed that the distinct stages of EMT are tightly regulated by epistatic cascades of transcriptional control circuits involving activation and repression of a large number of genes that modulate the migratory and invasive behavior of tumor cells. Recently, Gerhard Christofori discovered that the expression of podoplanin, a small mucin-like protein, is upregulated in a number of human carcinomas, in particular in the invasion front of squamous cell carcinomas. Podoplanin induces tumor cell spreading, migration and invasion in vitro and in vivo by a novel molecular pathway that does not involve the loss of E-cadherin function or EMT. It rather induces actin cytoskeleton rearrangement. They propose the existence of at least two distinct mechanisms of metastatic tumour cell invasion and dissemination: single cell invasion involving a process of EMT and collective cell migration in the absence of full EMT.

Reflecting past strengths of FMI in plant genetics, Barbara Hohn presented work on how plants respond to environmental stresses on the level of the plant genomic structure. Barbara Hohn and her colleagues examined responses of plants to environmental factors, like UV, viruses, fungal pathogens and bacterial, which increase the frequency of DNA rearrangements. These influences contribute to the quantitative and qualitative variation of genotypes that are subsequently exposed to environmental selection. Interestingly, environmental factors were shown to increased genomic flexibility even in successive, untreated generations. This phenomenon may lead to increased potential for adaptation.

Next, Witold Filipowicz talked on recent advances in our understanding of the action of miRNAs in mammals. MiRNAs regulate gene expression post-transcriptionally by causing translational repression or mRNA degradation. Proteins of the GW182 family are involved in miRNA repression in metazoan by interacting with Ago proteins, key components of miRNPs, and as being part of P-bodies, structures implicated in translational repression and mRNA degradation. Deletion analysis of the human GW182 protein TNRC6C and Drosophila dGW182 revealed these domains are necessary for repression of protein synthesis. He also reported on the characterization of miRNAs regulated during light and dark adaptation in the mouse retina, independent of circadian time. Continuing the theme of RNA, Françoise Stutz, showed that accumulation of PHO84 antisense RNAs in the absence of the exosome component Rrp6 is accompanied by the recruitment of the Hda1/2/3 histone deacetylase complex and PHO84 gene repression through deacetylation of the promoter region. This can be extended to a plasmid borne gene by cosuppression. The presented data highlight the importance of non-coding RNAs in mediating RNAi-independent transcriptional gene silencing.

Prof Ueli Schibler reported on the cell-autonomous and self-sustained circadian oscillators that are operative in virtually all body cells of mammalian organisms. Although these clocks are remarkably robust, they must be synchronised periodically by a master circadian pacemaker residing in the suprachiasmatic nucleus (SCN) of the brain. Schibler described novel experimental strategies allowing the identification of signaling pathways that participate in the synchronisation of circadian clocks by oscillating blood-borne signals and body temperature rhythms. Using STAR-PROM (for Synthetic Tandem Repeat Promoter screening he discovered 14 artificial promoters containing binding sites for IETFs that respond differentially to human and/or rat plasma samples collected at 3-4-hour intervals around the clock. These IETFs are proposed to respond to signalling pathways that are stimulated by cyclic systemic signals regulated by the circadian master pacemaker in the SCN. By using MEFs from the relevant knockout mice and by performing RNA interference in NIH3T3 cells they could demonstrate that both the heat shock transcription factor HSF1 and the cold-inducible RNA binding protein CIRP are required for the efficient phase entrainment by body temperature rhythms.

In the next presentation, selected from the abstracts, Daniel Cortazar spoke on how Thymine DNA glycosylase (TDG) acts on 5-mC to control DNA methylation levels. To clarify the biological function of this multifaceted DNA repair enzyme a Tdg knockout mouse was generated. Unlike other DNA glycosylases, deficiency of TDG confers embryonic lethality. Fibroblasts (MEFs) derived from Tdg null embryos show significantly impaired gene expression due to imbalanced histone modifications and aberrant CpG island methylation in gene promoters. Using an in vitro differentiation system Daniel Cortazar and his colleagues could show that such epigenetic aberrations are not observed in TDG deficient embryonic stem cells (ESCs) but arise during cell differentiation. By chromatin immunoprecipitation they find that TDG associates physically with promoters of differentially regulated genes both in ESCs and in MEFs. They suggest that TDG supports the establishment and maintenance of active or bivalent chromatin states throughout cell differentiation, using its DNA glycosylase activity to prevent aberrant gene silencing.

The penultimate presentation of the Symposium was by Thomas Boller, who studies the mechanisms of plant defense against pathogens. They discovered the plants’ flagellin receptor, FLS2, which is a leucine-rich-repeat receptor kinase that signals the presence of bacterial flagellin and initiates the immune response in plants. While this observation first got little attention, a year late, a similar flagellin receptor was reported for mice and men, in Nature. Innate immunity is now of major interest and the FLS2 receptor associates with a protein kinase previously thought to be a central regulator in hormone signaling, the BAK1 protein kinase (brassinosteroid-receptor associated protein kinase). This established a firm molecular basis for a crosstalk between “innate immunity” and “growth and development”.

Finally, in the last talk of the Symposium Jürg Tschopp continued on the general topic of innate immunity and presented recent work on inflammation, a central process in the response to pathogens. Inflammation is also a key player in multiple diseases including cancer. The NOD-like receptors (NLR) are a family of intracellular sensors of microbial motifs and “danger signals” that have emerged as crucial components of the innate immune responses and inflammation. Several NLRs (NALPs and IPAF) form a caspase-1-activating multiprotein complex, termed the inflammasome that processes proinflammatory cytokines including IL-1beta. Amongst the various inflammasomes, the NALP3 inflammasome is particularly qualified to sense a plethora of diverse molecules, ranging from bacterial muramyldipeptide to monosodium urate crystals. The important role of the NALP3 inflammasome is emphasised by the identification of mutations in the NALP3 gene that are associated with a susceptibility to inflammatory disorders.

Assessment of the results & impact of the event on the future direction of the field

The meeting highlighted the frontiers of a number of important biomedical fields – including the molecular basis of cancer, epigenetics and cell differentiation, stem cells, neurobiology, behavioural sciences and inflammation and innate immunity. In this way it set the tone for the future years of research and revealed to the younger participants where the forefronts of these fields are headed. There were in addition, two talks by winners of the Ed Fischer and Max Burger awards, for the best PhD thesis and best postdoc paper in 2009-2010. These were also outstanding presentations on fields at the cutting edge of biomedical research. The lively participation of the audience, the extensive poster sessions and the large interest in the meeting (about 1000 inscriptions for the meeting) attest that this set of speakers addressed topics of general interest to the biomedical community of Switzerland and Europe.

The role of the Friedrich Miescher Institute for Biomedical Research in european science was illucidated and further reinforced with this symposium. The support from various sources was sincerely appreciated and was broadly advertised in the meeting materials.