Integrated Mechanisms of Cellular Identity and Homeostasis
Diamond Jubilee Conference
26-27 June 2008
Babraham, Cambridge

Organisers:

Anne Corcoran, The Babraham Institute, Cambridge, UK
Martin Turner, The Babraham Institute, Cambridge, UK
Raghu Padinjat, The Babraham Institute, Cambridge, UK

Draft Report

Summary

This conference was convened to celebrate the 60th anniversary of the contribution of the Babraham Institute to international science. In the post genomic era of functional genomics, two key areas have taken centre stage: epigenetics and systems biology of signalling. These are two of the main convergent and evolving strands of the Institute's research, and the aim of the conference was to explore these themes, and to foster crosstalk between them to develop future areas of research in the coming decade. This aim evolved from our vision of the need for integrative approaches both inside and outside the nucleus, and for cross-disciplinary approaches to incorporate and exploit the large-scale experimental and computational information being generated in the post-genomic era. The conference brought together eighteen key international leaders in epigenetics, signalling and immunology to discuss two topics that embrace these themes: Epigenetic mechanisms in development and Cellular responses to the environment. The ‘Epigenetic mechanisms in development' theme addressed the key ‘hot' topics in epigenetics and epigenomics. These included the epigenetic factors and processes that control stem cell reprogramming (Azim Surani, Austin Smith, Yehudit Bergman, Amanda Fisher, Myriam Hemberger), higher order chromatin structure and dynamic nuclear organization of the genome (Wendy Bickmore, Tom Misteli), roles of DNA methylation in health and disease (Adrian Bird, Robert Feil),X chromosome inactivation (Edith Heard). The ‘Cellular Responses to the Environment' component of the conference focussed on large-scale integrative strategies for understanding cellular signalling, with talks by several world-leaders currently applying systems biology approaches to complex signalling questions. These included Kevin Shokat (chemical genetics of protein kinases); Anjano Rao (genome-wide mouse and Drosophila RNAi screen identifying novel regulators of calcium and immune signalling); Dennis Bray (systems biology pioneer, mathematical modeling of signalling pathways in bacteria); Julian Downward (genome wide screening of critical growth regulators in human oncogenesis). Several speakers presented work which spanned the two themes, including Nicholas Spitzer (genetic programmes and calcium signalling in neuronal stem cells) and Nullin Divecha (cytoplasmic and nuclear phosphoinositide signalling). They are complemented by Briggitta Stockinger, Steve Jameson and Doreen Cantrell, who discussed various aspects of T cell homeostasis in health and disease, and the role of integrated signalling pathways therein. The speakers were two-thirds European, including several former Babraham Institute scientists (Surani, Feil, Divecha, Stockinger, Jameson). Overall the conference provided an authoritative overview of the key questions in each topic and the cutting-edge technologies being used to address them, and provided a lively and interactive cross-disciplinary forum in which numerous possibilities for future integrative directions were discussed.

Scientific Content

The conference was attended by 154 delegates, 100 from the Babraham Institute, and 54 external delegates, including 31 students, and 43 postdocs. The external delegates included several from industry and representatives of prominent journals, as well as other academic settings, thus providing an extremely diverse interest base. The scientific programme consisted of a session each day on each theme - epigenetics and signalling, and the invited speakers were given the remit of making their research accessible to a wide-ranging audience. Thus talks were 40 mins, which gave ample time to instruct the audience on the important elements of the discipline with which they were less familiar. The programme was limited to nine speakers each day, to give maximum opportunity for in-depth discussion and interaction. In addition two short talks, one for each theme, were chosen from abstracts. One of these was given by a PhD student from the Babraham Institute. The speakers emphasised the cross-disciplinary nature of their research and throughout the two days there was a stimulating exchange of ideas and integrative solutions which provided delegates with an excellent overview of emerging systems biology and functional genomics approaches in both disciplines, and the consequent sea-change in scientific direction that will occur in the next decade. The conference also benefited greatly from the active participation of the four Session Chairs (Sir Mike Berridge, Sir John Gurdon, Robin Irvine and Anne Ferguson-Smith), all world-leaders in their fields.

The first Epigenetics Mechanisms in Development session was opened by a Plenary lecture given by Azim Surani, who gave a fascinating overview of the epigenetic mechanisms underlying germ cell reprogramming, and the similarities and differences between pluripotent embryonic stem cells and epiblast-derived germ cells. He highlighted the seminal discovery from his group that BLIMP-1 was the key determinant of primordial germ cell development. He presented evidence that every pluripotent stem cell in mice is a potential germ cell, and proposed that advances in knowledge of the mouse germ cell lineage may contribute more generally to a deeper understanding of the pluripotent state, as well as towards manipulation of cell fates, and to regenerative potential in mammals. This set the stage for the following speakers, Austin Smith, Yehudit Bergman, Myriam Hemberger and Amanda Fisher, who all expanded on various aspects of pluripotency. Austin Smith described some elegant experiments suggesting that capturing stem cell pluripotency can be achieved by targeted inhibition of mitogen–activated protein kinase signalling, as a complementary strategy to previous approaches in which particular factors have been used to induce a pluripotent state. Myriam Hemberger described the earliest differentiation step after fertilization, when the trophoblast and embryonic lineages separate. They have found that differential DNA methylation plays a key role in this differentiation. Using a genome-wide screen for promoter DNA methylation differences, they identified a gatekeeper gene, which is unmethylated and expressed in the trophoblast, and repressed in the embryonic lineage. This is the earliest example developmentally of a major epigenetic restriction of cell lineage fate. Yehudit Bergman approached the challenge of pluripotency from the standpoint of the mechanisms that suppress it and prevent embryonic reprogramming. Using micrarray analysis, they have identified the SET-domain protein G9a as a master regulator of irreversible gene silencing as pluripotency is lost, and have determined that it has a dual role in this process. Its Set domain generates heterochromatin, while its ANK domain recruits DNA methyltransferases to effect DNA methylation. Amanda Fisher described a heterokaryon cell fusion system they have developed which has enabled them to determine the dominant players in cellular reprogramming, in particular elucidating the central role of the polycomb complexes in this process.

The first Cellular Responses to the Environment session commenced with a talk from Julian Downward, who described a systems biology approach to identify novel targets of the Ras oncogene. Comparative genome-wide RNA interference libraries screening 20,000 genes from Ras-dependent and independent cell lines have identified genes that cause apoptosis in Ras dependent cells. This approach has identified several pathways important specifically for survival of Ras-transformed cells, and several potential therapeutic targets for treatment of Ras-dependent cancers. Nullin Divecha gave the first of several talks that powerfully illustrated the convergence of the two themes of the conference. His presentation on phosphoinositide signalling in the nucleus drew attention to the regulatory enzymes shared with the cytoplasmic phosphoinositides, and the shared and divergent targets and mechanisms of action between the two cellular subcompartments. Priya Chandra, a student from the Babraham Institute, presented elegant live imaging data to demonstrate that formation of autophagosomes is spatially connected to the endoplasmic reticulum and to support a model in which this connection enables the ER to provide important components for phagosome formation. Nicholas Spitzer then gave a presentation on calcium signalling in early neuronal specification and development. Again this talk illustrated the convergence of signalling and epigenetics. He described the profound effect that electrical stimulation of calcium transients has on expression of specific neurotransmitters in the embryonic spinal cord, which in turn select the appropriate receptor from a pre-existing post-synaptic repertoire. The Plenary Lecture which closed this session was given by Kevan Shokat, who expertly guided the audience through one of the most advanced developments of systems biology – chemical genetics. He described the large-scale combination of chemical synthesis, X-ray crystallography, and kinome-level selectivity profiling, which have enabled his group to identify therapeutic compounds within a single group that can inhibit oncogenic proteins from two families ie the tyrosine kinases, and the phosphoinositide-3-kinases.

The talks were complemented by a very well-attended Poster Session on the first evening, which gave the opportunity to students and postdocs to interact with invited speakers and external delegates. This was followed by the Conference Dinner, providing further opportunities for discussion. The former Director of the Babraham Institute, Richard Dyer, currently Chief Executive Officer of the Biosiences Federation, gave a thought-provoking speech, in which he emphasized the need for biological scientists to realize their place in the wider world, and the necessity of engaging the support of the general public by educating them about the importance of current scientific advances.

The second session on Epigenetic Mechanisms in Development focused first on nuclear organization with a series of talks by Tom Misteli, Wendy Bickmore and Edith Heard. All of these used sophisticated fluorescent microscopy techniques to visualize dynamic nuclear events. Tom Misteli reported on an experimental system which can introduce DNA double strand breaks at a single defined genomic site, and follow the fate of the broken DNA ends in real time in living cells. Their findings that broken DNA ends are immobile, provides insight into their previous findings that chromosomal translocations occur preferentially between neighbouring chromosomes. Remarkably this system has revealed that the cellular DNA damage response can be activated in the absence of DNA lesions, which has profound implications for our understanding of how cancer translocations occur. Wendy Bickmore presented elegant data to visually demonstrate the differential roles of linker histone H1 and polycomb repressive complexes PRC1 and 2 in global chromatin compaction, and compaction of developmentally regulated genes including hox genes, respectively. Edith Heard described the genomic regulation effected by pairing of chromosomes, by demonstrating the association of the two X chromosomes that enables inactivation of one of them, and the elements and epigenetic mechanisms involved. This was a powerful example of an emerging general process in which both homologous and non-homologous chromosomes regulate each other by physical interaction in the nucleus. Overall, the factors and elements involved in sensing other chromosomes and in physical movement within the nucleus are poorly understood, and are likely to require increasingly sophisticated imaging methods to resolve. A common theme was that large-scale functional genomics approaches, while undoubtedly powerful, often suffered from providing an average view of a cell population, and relied on interpretation when defining molecular interactions. Conversely microscopy techniques while visualizing ‘real cells/nuclei' were limited by the number of parameters they could use. Thus a key aim for the future should be to develop methods to increase the power of both live and static imaging. Robert Feil and Adrian Bird spoke about DNA methylation, the key epigenetic mark. Robert Feil focused on genomic imprinting and presented his group's work on the role of repressive histone methylation and its complex relationship with DNA methylation, in particular highlighting emerging differences between imprinting and global gene silencing. Adrian Bird illustrated the critical importance of understanding the functions of epigenetic regulators, focusing on the MeCP2 protein discovered by their group, which binds methylated DNA and initiates a cascade of gene silencing epigenetic alterations. Mutations in this protein, leading to loss of expression in neurons, cause Rett syndrome, a severe autism spectrum disorder. He presented exciting data from a mouse model in which the neuronal defects and associated disease symptoms can be reversed by re-expression of MeCP2, raising the future possibility of disease reversal in the human disease with the advent of effective gene therapy.

The second session on Cellular Responses to the Environment focused largely on T cell signalling and homeostasis. Anjana Rao gave a broad-ranging talk illustrating the power of functional genomics approaches in both Drosophila and mouse. She described several genome-wide RNAi screens which have been used to address previously intractable questions. Examples included genome-wide screens for regulators of CD45 splicing in mouse T cells, and for novel components of store-operated calcium entry channels. Several new factors have been identified initially in Drosophila RNAi and proteomic screens. These have been confirmed to have a conserved function by targeted deletion in mice, and the talk stressed the importance of continuity and synergy between the two approaches. Dennis Bray presented his pioneering studies developing methods of ‘virtual' systems biology. Their work has used a combination of experimental data and computer simulations to determine how bacterial chemotaxis operates, and to generate virtual ‘surrogate' bacteria. They have used the responses of these bacteria to reveal novel features of chemotactic behaviour that would not be possible to detect experimentally. This perspective was of wide-spread interest as the possible ‘next-generation' approach that will utilize large genomic and proteomic datasets. Brigitta Stockinger, Steve Jameson and Doreen Cantrell focused on T cell homeostasis and the complex mechanisms that regulate T cell responses to the environment and differentiation to different subsets. Brigitta Stockinger reported the discovery of a new T cell subset, Th9, adding to a growing list of T cell subsets recently discovered by their group and others, indicating that T cell plasticity is a key response to different environmental challenges. Doreen Cantrell described the nutrient sensing phosphoinositide-3-kinases and mTOR (mammalian target of rapamycin) and their regulation of T lymphocyte trafficking and effective function by controlling chemokine receptor and adhesion molecule expression. One of their targets is the transcription factor KLF2, and Steve Jameson continued this theme by expanding on the essential role of this factor in providing the normal balance of T cell subsets. The absence of KLF2 has profound effects both on KLF2-deficient cells and on bystander T cells, due both to its role in expression of trafficking molecules, and also cytokine production.

Assessment of the results & impact of the event

One of the main take-home messages was the realisation that large-scale approaches are the way forward at present, but that in many cases, these methods can identify many interesting genes/proteins/molecules, which then need detailed individual analysis in specialized systems which can only deal with small numbers eg gene-targetted mouse models. An important future direction for both of these approaches to science will be to interact more with the other. The large-scale approach ultimately needs the more detailed approach again at later stages, while the more focused scientists would benefit from mining the data from large-scale studies in a more thorough fashion. A recurrent message from those producing large-scale datasets was that they didn't have the resources or the expertise to follow up on all interesting candidates, while others felt daunted by the sheer volume of data produced. In both cases they invited collaboration with interested scientists with the right expertise.

As the dynamics of nuclear organisation and epigenetic regulation becomes more clearly understood, hierarchical signalling pathways are beginning to emerge. Thus a major future direction for this field will be to learn from and adapt the systems biology approaches already in place in the signalling disciplines to map all of the components and interactions involved.

Furthermore there was much discussion of next-generation approaches to utilise large functional genomics and proteomics resource, with a great deal of interest in exploring possibilities for computer modeling of complex pathways.

Overall the conference provided a global insight into some of the major large-scale technological and conceptual advances in biology in recent years, and the directions in which they would guide research in the next decade. For participants from each of the two interest groups - Epigenetics and Signalling - it gave a series of authoritative overviews of some of the key questions and directions of their own field and the other field with which they were less familiar. It served to break down barriers of lack of confidence with unfamiliar areas, as evidenced by the large amount of cross-disciplinary interactions, both in questions to speakers and in informal discussions.

Programme
Thursday 26th June

08:30 Registration (Conference Centre)

08:55 Introduction: Michael Wakelam, Director of the Babraham Institute

Session One: Epigenetic mechanisms in development
Chair: John Gurdon

09.00 Azim Surani (Plenary Lecture) Germ cells: The route to totipotency and immortality
10.00 Austin Smith Capturing Pluripotency
10.40 Coffee Break (Conference Centre)
11.10 Myriam Hemberger Key decisions in early development: Epigenetic control of cell lineage differentiation
11.25 Yehudit Bergmann (EMBO lecture) G9a-mediated de novo methylation prevents reprogrammingof embryonically silenced genes
12.05 Amanda Fisher (London Technology Network Lecture) (Provisional title) Epigenetic mechanisms regulating cell fate
12.45 Lunch (Marquee)

Session Two: Cellular responses to the environment
Chair: Michael Berridge

14.00 Julian Downward PI 3-kinase and Ras signalling networks in oncogenic transformation
14.40 Nullin Divecha Regulation of nuclear phosphoinositides
15.20 Priya Chandra Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum
15.35 Tea Break (Conference Centre)
16.05 Nick Spitzer Making the match: calcium signaling regulates neurotransmitter specification and receptor selection
16.45 Kevan Shokat (Plenary Lecture) Chemical genetic analysis of protein kinase cascades
17.45 Poster Session and pre-Dinner drinks (Marquee)
19.00 Dinner After dinner speaker Richard Dyer: Previous Director of the Babraham Institute
22.30 Close  

Friday 27th June

08:55 Announcements

Session Three: Epigenetic mechanisms in development
Chair: Anne Ferguson-Smith

09.00 Tom Misteli (Genetics Society Lecture) Spatial genome organization in the formation of cancer translocations and DNA repair
09.40 Wendy Bickmore Polycomb repressive complexes are required to maintain compact chromatin structure at Hox loci
10.20 Coffee Break (Conference Centre)
10.50 Robert Feil Genomic imprinting in mammalian development: role of histone methylation
11.30 Adrian Bird Epigenetics and genetic diseases: MeCP2 and Rett Syndrome as an example
12.10 Edith Heard Nuclear and chromatin dynamics during X-chromosome inactivation
12.50 Lunch (Marquee)

Session Four: Cellular responses to the environment
Chair: Robin Irvine

14.00 Anjana Rao (Society for Endocrinology Lecture) Calcium/ NFAT signalling in lymphocytes
14.40 Dennis Bray (Science Lecture) Computer-based Analysis of Bacterial Chemotaxis
15.20 Tea Break (Conference Centre)
15.50 Steve Jameson (British Society of Immunology Lecture) Regulation of T cell homeostasis and trafficking by KLF2
16.30 Briggitta Stockinger Functional development and plasticity in helper T cell subsets
17.10 Doreen Cantrell Matching lymphocyte metabolism and migration
17.50 Closing remarks - Michael Wakelam
18.00 Close