Federico Vaggi

An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology

Insulin-like peptides (ILPs) play highly conserved roles in development and physiology. Most animal genomes encode multiple ILPs. Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse processes, including development, reproduction, longevity and several specific stress responses. Our systematic studies identify an ILP-based combinatorial code for these phenotypes characterized by substantial functional specificity and diversity rather than global redundancy. Notably, we show that ILPs regulate each other transcriptionally, uncovering an ILP-to-ILP regulatory network that underlies the combinatorial phenotypic coding by the ILP family. Extensive analyses of genetic interactions among ILPs reveal how their signals are integrated. A combined analysis of these functional and regulatory ILP interactions identifies local genetic circuits that act in parallel and interact by crosstalk, feedback and compensation. This organization provides emergent mechanisms for phenotypic specificity and graded regulation for the combinatorial phenotypic coding we observe. Our findings also provide insights into how large hormonal networks regulate diverse traits.

Spatial segregation of polarity factors into distinct cortical clusters is required for cell polarity control

Cell polarity is regulated by evolutionarily conserved polarity factors whose precise higher-order organization at the cell cortex is largely unknown. Here we image frontally the cortex of live fission yeast cells using time-lapse and super-resolution microscopy. Interestingly, we find that polarity factors are organized in discrete cortical clusters resolvable to ~50–100 nm in size, which can form and become cortically enriched by oligomerization. We show that forced co-localization of the polarity factors Tea1 and Tea3 results in polarity defects, suggesting that the maintenance of both factors in distinct clusters is required for polarity. However, during mitosis, their co-localization increases, and Tea3 helps to retain the cortical localization of the Tea1 growth landmark in preparation for growth reactivation following mitosis. Thus, regulated spatial segregation of polarity factor clusters provides a means to spatio-temporally control cell polarity at the cell cortex. We observe similar clusters in Saccharomyces cerevisiae and Caenorhabditis elegans cells, indicating this could be a universal regulatory feature.

The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation

There is a body of literature that describes the geometry and the physics of filopodia using either stochastic models or partial differential equations and elasticity and coarse-grained theory. Comparatively, there is a paucity of models focusing on the regulation of the network of proteins that control the formation of different actin structures. Using a combination of in-vivo and in-vitro experiments together with a system of ordinary differential equations, we focused on a small number of well-characterized, interacting molecules involved in actin-dependent filopodia formation: the actin remodeler Eps8, whose capping and bundling activities are a function of its ligands, Abi-1 and IRSp53, respectively; VASP and Capping Protein (CP), which exert antagonistic functions in controlling filament elongation. The model emphasizes the essential role of complexes that contain the membrane deforming protein IRSp53, in the process of filopodia initiation. This model accurately accounted for all observations, including a seemingly paradoxical result whereby genetic removal of Eps8 reduced filopodia in HeLa, but increased them in hippocampal neurons, and generated quantitative predictions, which were experimentally verified. The model further permitted us to explain how filopodia are generated in different cellular contexts, depending on the dynamic interaction established by Eps8, IRSp53 and VASP with actin filaments, thus revealing an unexpected plasticity of the signaling network that governs the multifunctional activities of its components in the formation of filopodia.

Models of Breast Morphogenesis Based on Localization of Stem Cells in the Developing Mammary Lobule

Summary Characterization of normal breast stem cells is important for understanding their role in breast development and in breast cancer. However, the identity of these cells is a subject of controversy and their localization in the breast epithelium is not known. In this study, we utilized a novel approach to analyze the morphogenesis of mammary lobules, by combining one-dimensional theoretical models and computer-generated 3D fractals. Comparing predictions of these models with immunohistochemical analysis of tissue sections for candidate stem cell markers, we defined distinct areas where stem cells reside in the mammary lobule. An increased representation of stem cells was found in smaller, less developed lobules compared to larger, more mature lobules, with marked differences in the gland of nulliparous versus parous women and that of BRCA1/2 mutation carriers versus non-carriers.

Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network

The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify ‘linker’ proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted ‘linkers’ also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.

The effects of an editor serving as one of the reviewers during the peer-review process

Background Publishing in scientific journals is one of the most important ways in which scientists disseminate research to their peers and to the wider public. Pre-publication peer review underpins this process, but peer review is subject to various criticisms and is under pressure from growth in the number of scientific publications. Methods Here we examine an element of the editorial process at eLife, in which the Reviewing Editor usually serves as one of the referees, to see what effect this has on decision times, decision type, and the number of citations. We analysed a dataset of 8,905 research submissions to eLife since June 2012, of which 2,750 were sent for peer review, using R and Python to perform the statistical analysis. Results The Reviewing Editor serving as one of the peer reviewers results in faster decision times on average, with the time to final decision ten days faster for accepted submissions (n=1,405) and 5 days faster for papers that were rejected after peer review (n=1,099). There was no effect on whether submissions were accepted or rejected, and a very small (but significant) effect on citation rates for published articles where the Reviewing Editor served as one of the peer reviewers. Conclusions An important aspect of eLifes peer-review process is shown to be effective, given that decision times are faster when the Reviewing Editor serves as a reviewer. Other journals hoping to improve decision times could consider adopting a similar approach.

Process Modeling and Rendering of Biochemical Structures: Actin

We propose stochastic process models as a means for studying and rendering unbounded biological structures, involving mechanisms that extend over geometric space. As an example, we discuss a case study of actin polymerization dynamics, which plays a key role in many cellular activities and enjoys a rich struc- ture.Weprovideacomparativereviewofvariousapproachesintheliteratureformod- eling actin. We then illustrate on actin models how otherwise challenging structures can be modeled. In these models the complexity of the structures are incrementally increased with respect to the biological data. We present a geometric representa- tion of these models that we use to generate movies reflecting their dynamics while preserving formal cleanliness as well as loyalty to the biological data.

A network approach to mixing delegates at meetings

Delegates at scientific meetings can come from diverse backgrounds and use very different methods in their research. Promoting interactions between these ‘distant’ delegates is challenging but such interactions could lead to novel interdisciplinary collaborations and unexpected breakthroughs. We have developed a network-based ‘speed dating’ approach that allows us to initiate such distant interactions by pairing every delegate with another delegate who might be of interest to them, but whom they might never have encountered otherwise. Here we describe our approach and its algorithmic implementation.

Reconstructing regulatory pathways by systematically mapping protein localization interdependency networks

A key goal of functional genomics is to elucidate how genes and proteins act together in space and time, wired as pathways, to control specific aspects of cell biological function. Here, we develop a method to quantitatively determine proteins’ localization interdependencies at high throughput. We show that this method can be used to systematically obtain weighted, signed and directional pathway relationships, and hence to reconstruct a detailed pathway wiring. As proof-of-principle, we focus on 42 factors that control cell polarity in fission yeast (Schizosaccharomyces pombe) and use high-throughput confocal microscopy and quantitative image analysis to reconstruct their Localization Interdependency Network (LIN). Through this approach we identify 554 pairwise interactions across the factors, including 98% putative new directed links. Validation of an unexpected interaction between two polarity factor subgroups - the polarity landmark proteins and the cell integrity pathway components - by orthogonal phenotyping demonstrates the power of the LIN approach in detecting subtle, systems-level causal connections.

“Keystone Species” of Molecular Interaction Networks

Abstract Network theory is widely used to find the most important elements of ecological networks. Removal of “keystone species” from the system could cause a rapid collapse of the network and various network measures are used to identify such important members of the system. In the spirit of such analysis we investigate molecular interaction networks responsible for various biological functions and use network measures to identify the most important genes that control the biological process under investigation. These genes may play a major role in integrating the multiplicity of processes. We develop a workflow where molecular interaction networks of genes associated with a given biological process are collected. These networks are studied using the tools of network analysis. Results using various network measures are compared and based on the example of cell cycle regulation, biological conclusions are drawn. Furthermore, the conservation of the putative “keystone species” among evolutionary distant yeast species is investigated.