Systems Biology of Cellular Regulation
3-5 May, 2011
Dresden, Germany

Organisers:

Draft Report

Summary

The international symposium “Systems Biology of Cellular Regulation” focused on technological aspects of systems biology. New advances, such as high-throughput technologies obtained with genomic approaches, have been the source of biological insights, which were presented for the first time. The meeting featured international, high-profile speakers from the areas of stem cell biology, regenerative medicine, systems genetics and cellular stress.

The agenda consisted of four central topics: systems biology of embryonic stem cells, genome-scale methods for systems biology, statistical genetics, and oxidative stress. Embryonic stem (ES) cells have been developed in culture and induced to differentiate into any tissue type. Mouse ES cells can be used to generate new mice from single embryonic stem cells.

Complexes between particular proteins and other proteins or DNA are isolated by introducing labelled molecules into the cell, or by using antibodies to detect the endogenous proteins directly. Once the protein and its associated complex can be derived biochemically, mass spectrometry can be used to work out what other members the complex contains. This can predict where on the genome a particular transcription factor could bind. The interactions that do occur can be identified directly and characterised further.

Statistical genetics develops ways to associate genetic variations with phenotypes. Recently, genome-wide association studies (GWAS) have identified genetic loci associated with complex diseases and many other medically relevant phenotypes. This research is a key to personalised medicine, and also for identifying genetic risks, which may lead to the development of improved clinical management.

In addition to clinical GWAS, many have been conducted in model species, such as panels of inbred mouse strains. The meeting focused on systematic genetic studies, using mainly mouse and different yeasts. The session presented experimental and computational technologies that depict statistical genetics screens understandably.

Oxidative stress plays a part in many important diseases such as cancer and neurodegeneration. This special session of the meeting presented proteomics, deep sequencing and statistical genetics to reveal the molecular pathways invoked in oxidative stress. It emphasized how natural genetic variation affects whether cells can effectively respond to chemical stress such as reactive oxygen species. Different polymorphisms, such as SNPs, may interact in combination to produce extreme sensitivity or resistance to oxidative stress.

Scientific Content

At the “Systems Biology of Cellular Regulation” symposium, international experts presented the latest developments in genomic technologies. These included mass-spectrometry-based proteomics, deep sequencing, RNA interference, and computational biology. Presentations were focused on stem cell biology, preclinical regenerative medicine, the effects of cellular stress, and statistical genetics. The results presented were the outcome of work that combined new techniques of determining molecular interactions with new depictions of cellular regulation. Thus, the symposium addressed the following focus areas of the FFG programme: functional genomics technologies, biomedicine, bioinformatics, systems biology, and biotechnology.

Systems analysis of biology has especially progressed through the development of high-throughput methods for labelling and selectively ablating gene products by recombinant DNA engineering (recombineering). Using sequence-based genome-wide association studies we can now map interactions by labelling (tagging) technology. This has enabled a much more comprehensive analysis of genomic topology and combinatorial responses to extracellular signalling. The advantage of the present meeting has been incorporating systems analysts who can interpret and depict the interactive data that biochemical studies have derived.

The participants emphasised the role of noncoding regulatory sequence elements (enhancers, silencers) and transcription factor proteins in combinatorial coregulatory complexes. The hierarchical expression of key transcription factors was shown to be the major determinant of cell expression repertoire as tissues develop. Posttranscriptional modification of transcription factors and their cofactors was also shown to be a major control mechanism in cell regulation.

The individual cellular expression pattern was also shown as the outcome of extracellular events in the case of immediate response genetic outputs. Genome-wide analyses of transcription start sites and promoters identified a promoter type generally bound by transcription factors and their associated complexes. These are associated with cell-type-specific responsiveness to signals.

A different type of promoter element was associated with metabolic functions consistently performed in the cell. The active or repressed state of those promoters is maintained throughout cell division (epigenetically) in cells committed to a particular lineage-specific gene expression pattern. These were usually gene products relevant to continued maintenance of cell type, in contradistinction to immediate stress-response transcriptional output.

It was shown moreover that potential responsivity to a signal that may occur is also a trait that cells may confer epigenetically. Most implicated in epigenetic cell determination were the Set-domain histone modifying complexes and other histone modifiers that affect gene expression.

The totipotential capacity of cultured embryonic stem cells was defined in practical terms. Chemical inhibition of the cell signalling response to culture conditions (high-oxygen monolayer) allows embryonic stem cells to be maintained as undifferentiated cultures despite their natural tendency to differentiate.

Protein complexes important for maintaining the undifferentiated state have been identified. These were found by high-throughput analysis combined with literature-modified statistical analysis. As well as the maintenance of stem-cell self-renewal, the poised change to differentiated expression output was also extensively addressed.

As an example and a useful indicator of cell commitment, the inactivation of one X chromosome in females has been intensively studied. More details of the mechanism of X-inactivation were presented. Other speakers described further examples of regulation by noncoding RNAs.

Members of coactivator or corepressor protein complexes are subject to phosphorylation, acetylation or other modifications. These regulatory cofactor complexes were identified as signal integrators within the cell.

In the immediate response to stress, protein activation rather than expression changes were shown to be the major events. The transduction of signals is controlled by the structural interaction of multiprotein complexes so that transfer of modifying molecules is limited and controlled.

Whereas phosphorylation events are the most prominent short-term responses, the acetylation of proteins has the most significance for long-term functional changes. The challenging task of dissecting the reciprocal interactions between opposing signal modifiers can now be approached using deletion analyses and bioinformatics analysis.

Specific systems were presented in detail, with analysis of the latest results in haematopoietic differentiation in peripheral and bone marrow blood-forming cells, and in the neuronal system.

The derivation of pure cultures of specific neuronal subtypes is a significant advance, since it will allow study of these cell types by biochemical methods not applicable to whole tissue samples containing a wide diversity of cell types.

Cellular responses to stress were extensively discussed in the context of the Phenoxigen consortium, which co-organised the ESF forum along with the SyBoSS consortium. So far, most of the systems analysis of gene expression has been done in yeast. The most sophisticated mathematical models presented were of yeast subtypes, and included predictive analyses of knockout phenotypes. Systematic analysis of epigenetic resetting, especially by acetylation of cofactors, yielded a great resource of data. Dissection of this information allowed quantitative mapping of loci that have an impact on the expression of other genes (QTL mapping).

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

The Biotec Forum Systems Biology of Cellular Regulation united two systems biology research consortia (SyBoSS and Phenoxigen) in an open free symposium that covered the whole range of contemporary issues in gene expression regulation, combinatory interactive relationships and determination of cellular and organism phenotype. By inviting cell biologists and molecular physiologists along with internationally accredited mathematicians and systems analysts dedicated to the topic, a truly remarkable collaborative network has been established.

The scientific discussion progressed from specific details of stem cells to analysis of gene transcription then on to derive general principles from a systems analytical view. As a specific example, the response of cells to oxidative stress was portrayed. This was particularly relevant to the practical issues of growing stem cells in culture for medical applications, and also to the innate regenerative response to stress in tissues.

Using model species has provided a basis for developing new technologies that can later be applied to humans. A prominent example is screening for expression quantitative trait loci (eQTL), which was first developed using yeast and mouse populations and is now also being applied in humans.

Despite the ethical restraints on attempting whole animal generation from human ES cells, there is a great potential in developing multipotentiality in human cells. New advances in the techniques of culturing stem cells have allowed a more physiological milieu to be recreated, so that populations of committed stem cells can reliably be derived. With sophisticated analysis of the biochemical interactions in cells that are in various conditions at various times, we can gradually document how the composition of regulatory protein complexes changes, and how this affects transcription of the genome.

The importance of posttranscriptional modification and activation of proteins at all levels of cellular output highlighted the need for future improvements in analysing cellular regulation. Particular goals are the comparisons of complex regulatory combinations as they change with time or tissue context. Extension of the methods and principles derived from studies of yeast, cell culture and mice to human disease is a natural expectation from the work presented.

The meeting was therefore an update on the state of the art for those interested in developing innovative therapies and personalised medicine. It also included new insights into the effects of exogenous influences such as toxins, and ways of analysing the effects of environmental or pharmaceutical agents in the context of cellular regulation.
By bringing together international experts from different disciplines, the basis for future interactions and data sharing was established.

Programme
Tuesday, May 3rd, 2011
Session I - Genomic and Proteomic Technologies
Chair: Tony Hyman
09:00 - 09:30 Francis Stewart - Welcome to SyBoSS
09:30 - 10:15 Keynote - Nevan Krogan, San Francisco
Functional insights from protein-protein and genetic interaction maps
10:15 - 10:35 Alex Bird, Dresden
Molecular genetic analysis of spindle assembly using BAC transgenes
Chair- Francis Stewart
11:00 - 11:30 Bill Skarnes, Cambridge
Genome-wide functional analyses by high throughput gene targeting
11:30 - 12:00 Jesper Olson, Copenhagen
Global analysis of signalling pathways in ESCs by quantitative phosphoproteomics
12:00 - 12:30 Chunaram Choudhary, Copenhagen
Decoding signalling networks by mass spectrometry based proteomics Embryonic Stem Cells
Chair - Edith Heard
14:00 - 14:30 Austin Smith, Cambridge
Naive Pluripotency
14:30 - 15:00 Frank Buchholz, Dresden
From RNAi screens to molecular function
15:00 - 15:20 Ingmar Glauche, Dresden
Cell fate decisions in mES cells and the role of heterogeneity
15:20 - 16:45 Poster session
Chair - Mike Rudnicki,
16:45 - 17:15 Edith Heard, Paris
Nuclear dynamics and epigenetic changes during X-chromosome inactivation
17:15 - 18:00 Huck Hui Ng, Singapore
Genome-wide analyses of the key nodes of the ESC transcriptional regulatory network

Wednesday, May 4th, 2011
Session II - Somatic Stem Cells/Computational Methods
Chair - Austin Smith
09:00 - 09:45 Michael Rudnicki, Ottawa
Molecular regulation of muscle cell function
09:45 - 10:15 Frank Grosveld, Rotterdam
Transcription factors in blood
10:15 - 10:45 Boris Lenhard, Bergen
Computational genomics of promoter usage and responsiveness to enhancers in development and differentiation
Chair - Frank Grosveld
11:15 - 11:45 Søren Brunak, Lyngby
11:45 - 12:15 Andreas Beyer, Dresden
Integrated analysis of functional genetic screens and protein inetraction data
Neurons/Systematics of cellular regulation
Chair - Frank Buchholz
14:00 - 14:30 Wolfgang Wurst, Munich
Regional patterning of telencephalon during development
14:30 - 15:00 Gerd Kempermann, Dresden
Systems biology of adult neurogenesis
15:00 - 16.20 Jan Kaslin, Dresden
Progenitor potential determines brain regeneration outcome in zebrafish
16:20 - 16:45 Poster session
Chair - Wolfgang Wurst
16:45 - 17:15 Toby Gibson, Heidelberg
The nature of cell regulation and why kinases don't cascade
17:15 - 18:00 Keynote – Luis Serrano, Barcelona

Thursday, May 5th, 2011
Session III - Yeast systems biology
Chair - Andreas Beyer
09:00 - 09:45 Keynote - Aimée Dudley, Seattle
Systems genetics in yeast
09:45 - 10:15 Ruedi Aebersold, Zurich
10:15 - 10:45 Christopher Workman, Lyngby
11:15 - 11:45 Jürg Bähler, London
Genome regulation in fission yeast
11:45 - 12:05 selected from posters
12:05 - 12:50 Gaël Yvert, Lyon
Genetics and lability of intra-species epigenomic variation