Multicellular Systems Biology of Development

Embryonic development depends on the precise coordination of cell fate specification, patterning and morphogenesis. Although great strides have been made in the molecular understanding of each of these processes, how their interplay governs the formation of complex tissues remains poorly understood. New techniques for experimental manipulation and image quantification enable the study of development in unprecedented detail, resulting in new hypotheses on the interactions between known components. By expressing these hypotheses in terms of rules and equations, computational modeling and simulation allows one to test their consistency against experimental data. However, new computational methods are required to represent and integrate the network of interactions between gene regulation, signaling and biomechanics that extend over the molecular, cellular and tissue scales. In this thesis, I present a framework that facilitates computational modeling of multiscale multicellular systems and apply it to investigate pancreatic development and the formation of vascular networks. This framework is based on the integration of discrete cell-based models with continuous models for intracellular regulation and intercellular signaling. Specifically, gene regulatory networks are represented by differential equations to analyze cell fate regulation; interactions and distributions of signaling molecules are modeled by reaction-diffusion systems to study pattern formation; and cell-cell interactions are represented in cell-based models to investigate morphogenetic processes. A cell-centered approach is adopted that facilitates the integration of processes across the scales and simultaneously constrains model complexity. The computational methods that are required for this modeling framework have been implemented in the software platform Morpheus. This modeling and simulation environment enables the development, execution and analysis of multi-scale models of multicellular systems. These models are represented in a new domain-specific markup language that separates the biological model from the computational methods and facilitates model storage and exchange. Together with a user-friendly graphical interface, Morpheus enables computational modeling of complex developmental processes without programming and thereby widens its accessibility for biologists. To demonstrate the applicability of the framework to problems in developmental biology, two case studies are presented that address different aspects of the interplay between cell fate specification, patterning and morphogenesis. In the first, I focus on the interplay between cell fate stability and intercellular signaling. Specifically, two studies are presented that investigate how mechanisms of cell-cell communication affect cell fate regulation and spatial patterning in the pancreatic epithelium. Using bifurcation analysis and simulations of spatially coupled differential equations, it is shown that intercellular communication results in a multistability of gene expression states that can explain the scattered spatial distribution and low cell type ratio of nascent islet cells. Moreover, model analysis shows that disruption of intercellular communication induces a transition between gene expression states that can explain observations of in vitro transdifferentiation from adult acinar cells into new islet cells. These results emphasize the role of the multicellular context in cell fate regulation during development and may be used to optimize protocols for cellular reprogramming. The second case study focuses on the feedback between patterning and morphogenesis in the context of the formation of vascular networks. Integrating a cell-based model of endothelial chemotaxis with a reaction-diffusion model representing signaling molecules and extracellular matrix, it is shown that vascular network patterns with realistic morphometry can arise when signaling factors are retained by cell-modified matrix molecules. Through the validation of this model using in vitro assays, quantitative estimates are obtained for kinetic parameters that, when used in quantitative model simulations, confirm the formation of vascular networks under measured biophysical conditions. These results demonstrate the key role of the extracellular matrix in providing spatial guidance cues, a fact that may be exploited to enhance vascularization of engineered tissues. Together, the modeling framework, software platform and case studies presented in this thesis demonstrate how cell-centered computational modeling of multi-scale and multicellular systems provide powerful tools to help disentangle the complex interplay between cell fate specification, patterning and morphogenesis during embryonic development

Transdifferentiation of pancreatic cells by loss of contact-mediated signaling

Background: Replacement of dysfunctional beta-cells in the islets of Langerhans by transdifferentiation of pancreatic acinar cells has been proposed as a regenerative therapy for diabetes. Adult acinar cells spontaneously revert to a multipotent state upon tissue dissociation in vitro and can be stimulated to redifferentiate into beta-cells. Despite accumulating evidence that contact-mediated signals are involved, the mechanisms regulating acinar-to-islet cell transdifferentiation remain poorly understood. Results: In this study, we propose that the crosstalk between two contact-mediated signaling mechanisms, lateral inhibition and lateral stabilization, controls cell fate stability and transdifferentiation of pancreatic cells. Analysis of a mathematical model combining gene regulation with contact-mediated signaling reveals the multistability of acinar and islet cell fates. Inhibition of one or both modes of signaling results in transdifferentiation from the acinar to the islet cell fate, either by dedifferentiation to a multipotent state or by direct lineage switching. Conclusions: This study provides a theoretical framework to understand the role of contact-mediated signaling in pancreatic cell fate control that may help to improve acinar-to-islet cell transdifferentiation strategies for beta-cell neogenesis.Peer reviewe

Quantification of Nematic Cell Polarity in Three-dimensional Tissues

How epithelial cells coordinate their polarity to form functional tissues is an open question in cell biology. Here, we characterize a unique type of polarity found in liver tissue, nematic cell polarity, which is different from vectorial cell polarity in simple, sheet-like epithelia. We propose a conceptual and algorithmic framework to characterize complex patterns of polarity proteins on the surface of a cell in terms of a multipole expansion. To rigorously quantify previously observed tissue-level patterns of nematic cell polarity (Morales-Navarette et al., eLife 8:e44860, 2019), we introduce the concept of co-orientational order parameters, which generalize the known biaxial order parameters of the theory of liquid crystals. Applying these concepts to three-dimensional reconstructions of single cells from high-resolution imaging data of mouse liver tissue, we show that the axes of nematic cell polarity of hepatocytes exhibit local coordination and are aligned with the biaxially anisotropic sinusoidal network for blood transport. Our study characterizes liver tissue as a biological example of a biaxial liquid crystal. The general methodology developed here could be applied to other tissues or in-vitro organoids.Comment: 27 pages, 9 color figure

PERFIL DAS PACIENTES DO AMBULATÓRIO DA PÓS GRADUAÇÃO EM VÍDEO HISTEROSCOPIA DA FACULDADE DE CIÊNCIA MÉDICAS DE MINAS GERAIS

RESUMO: A Vídeo Histeroscopia diagnóstica tornou-se uma ferramenta valiosa e importante para o ginecologista ao permitir a avaliação direta da cavidade endometrial e o diagnóstico das doenças proliferativas e ou neoplásicas. Alguns anos atrás, isso só poderia ser realizado através de procedimentos cegos e pouco tolerado pelas pacientes. A Histeroscopia é uma ferramenta cada vez mais utilizada, o que torna a avaliação do perfil epidemiológico das pacientes submetidas a esse procedimento uma nuance importante a ser estudada. Logo, o objetivo desse trabalho é avaliar o perfil epidemiológico das pacientes atendidas pela equipe da Pós-graduação em Vídeo Histeroscopia da FCMMG no ambulatório de vídeo Histeroscopia do Hospital São José em Belo Horizonte. Este trabalho trata-se de estudo retrospectivo realizado com análise de prontuários das pacientes atendidas no período entre outubro e dezembro de 2012, e submetidas a vídeo Histeroscopia ambulatorial durante os módulos do curso de pós graduação. Os exames são realizados em caráter eminentemente ambulatorial pelos pós-graduandos sob supervisão direta dos professores. São usados equipamentos com ópticas de 2,9 mm, camisas diagnósticas e de Betochi, com preferência pela última, meio de distensão soro fisiológico, infundido com bomba Histeromat. A técnica utilizada inclui vaginoscopia, sem uso do espéculo ou pinçamento do colo. O espéculo e a instrumentalização do colo foram utilizados caso houvesse alguma dificuldade no acesso ao colo durante o procedimento. Todos os procedimentos foram realizados sem anestesia. Foram incluídos 203 pacientes encaminhadas a vídeo Histeroscopia ambulatorial. A idade média das pacientes foi de 49,7 anos, variando de 17 a 81 anos. Média de paridade 3,2 filhos e considerando sua prole definida em 70,9 % (144 pacientes). Em relação à escolaridade do grupo estudado, a maioria dos pacientes não tinha concluindo o segundo grau, 67,3%, com apenas 5 pacientes relatando ter completado nível superior (2,6%). Relatavam comorbidades à anamnese 115 pacientes (56,6%), sendo as mais relatadas Hipertensão Arterial Sistêmica (HAS) e diabetes, relatadas por 69 e 20 pacientes respectivamente. Todas as pacientes apresentavam exames ecográficos anteriores. As conclusões principais das ecografias se distribuíam: exame normal 16 pacientes (7,8%), miomas em 58 (28,5%), espessamento endometrial em 67 (33%), pólipos em 66 (32,5%). Após avaliação inicial tiveram indicação confirmada e foram submetidas ao procedimento 185 pacientes. Em ordem de frequência, foram levantadas como principais indicações: espessamento endometrial à ecografia (34,0%), sangramento uterino anormal (28,6%) e infertilidade (10,8%). Todas as pacientes deste grupo concluíram seus exames histeroscópicos e os achados identificados foram: cavidade sem alterações 64 pacientes (34,5%), espessamento focal do endométrio 17 (9,1%), sinéquias 9 (4,8%), pólipos 82 (44,3%) e miomas 13 (7,0%). As pacientes atendidas no referido ambulatório de Histeroscopia tiveram todos os atendimentos iniciais em unidade básica de saúde e em sua ampla maioria tiveram confirmada a indicação para o procedimento. Mesmo realizados dentro do contexto de ensino, a efetiva realização do exame com definição diagnóstica para a cavidade uterina foi possível para todo o grupo estudado. Seus achados apontam para uma significativa diminuição da necessidade de procedimentos cirúrgicos hospitalares uma vez que um grande número de pacientes apresentaram exames normais ou alterações focais que tem seu diagnóstico e tratamento completamente efetivados, através de biópsias e pequenas intervenções realizadas durante a Histeroscopia ambulatorial.PALAVRAS-CHAVE: perfil epidemiológico, vídeo Histeroscopia ambulatorial, pós graduaçã

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years

Haematopoietic stem cells in perisinusoidal niches are protected from ageing.

With ageing, intrinsic haematopoietic stem cell (HSC) activity decreases, resulting in impaired tissue homeostasis, reduced engraftment following transplantation and increased susceptibility to diseases. However, whether ageing also affects the HSC niche, and thereby impairs its capacity to support HSC function, is still widely debated. Here, by using in-vivo long-term label-retention assays we demonstrate that aged label-retaining HSCs, which are, in old mice, the most quiescent HSC subpopulation with the highest regenerative capacity and cellular polarity, reside predominantly in perisinusoidal niches. Furthermore, we demonstrate that sinusoidal niches are uniquely preserved in shape, morphology and number on ageing. Finally, we show that myeloablative chemotherapy can selectively disrupt aged sinusoidal niches in the long term, which is linked to the lack of recovery of endothelial Jag2 at sinusoids. Overall, our data characterize the functional alterations of the aged HSC niche and unveil that perisinusoidal niches are uniquely preserved and thereby protect HSCs from ageing

Early Embryonic Vascular Patterning by Matrix-Mediated Paracrine Signalling: A Mathematical Model Study

During embryonic vasculogenesis, endothelial precursor cells of mesodermal origin known as angioblasts assemble into a characteristic network pattern. Although a considerable amount of markers and signals involved in this process have been identified, the mechanisms underlying the coalescence of angioblasts into this reticular pattern remain unclear. Various recent studies hypothesize that autocrine regulation of the chemoattractant vascular endothelial growth factor (VEGF) is responsible for the formation of vascular networks in vitro. However, the autocrine regulation hypothesis does not fit well with reported data on in vivo early vascular development. In this study, we propose a mathematical model based on the alternative assumption that endodermal VEGF signalling activity, having a paracrine effect on adjacent angioblasts, is mediated by its binding to the extracellular matrix (ECM). Detailed morphometric analysis of simulated networks and images obtained from in vivo quail embryos reveals the model mimics the vascular patterns with high accuracy. These results show that paracrine signalling can result in the formation of fine-grained cellular networks when mediated by angioblast-produced ECM. This lends additional support to the theory that patterning during early vascular development in the vertebrate embryo is regulated by paracrine signalling

Redox dysregulation, neuroinflammation, and NMDA receptor hypofunction: A "central hub" in schizophrenia pathophysiology?

Accumulating evidence points to altered GABAergic parvalbumin-expressing interneurons and impaired myelin/axonal integrity in schizophrenia. Both findings could be due to abnormal neurodevelopmental trajectories, affecting local neuronal networks and long-range synchrony and leading to cognitive deficits. In this review, we present data from animal models demonstrating that redox dysregulation, neuroinflammation and/or NMDAR hypofunction (as observed in patients) impairs the normal development of both parvalbumin interneurons and oligodendrocytes. These observations suggest that a dysregulation of the redox, neuroimmune, and glutamatergic systems due to genetic and early-life environmental risk factors could contribute to the anomalies of parvalbumin interneurons and white matter in schizophrenia, ultimately impacting cognition, social competence, and affective behavior via abnormal function of micro- and macrocircuits. Moreover, we propose that the redox, neuroimmune, and glutamatergic systems form a "central hub" where an imbalance within any of these "hub" systems leads to similar anomalies of parvalbumin interneurons and oligodendrocytes due to the tight and reciprocal interactions that exist among these systems. A combination of vulnerabilities for a dysregulation within more than one of these systems may be particularly deleterious. For these reasons, molecules, such as N-acetylcysteine, that possess antioxidant and anti-inflammatory properties and can also regulate glutamatergic transmission are promising tools for prevention in ultra-high risk patients or for early intervention therapy during the first stages of the disease