Cell type | EPFL Graph Search

A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, that differ both in appearance and function yet have identical genomic sequences. Cells may have the same genotype, but belong to different cell types due to the differential regulation of the genes they contain. Classification of a specific cell type is often done through the use of microscopy (such as those from the cluster of differentiation family that are commonly used for this purpose in immunology). Recent developments in single cell RNA sequencing facilitated classification of cell types based on shared gene expression patterns. This has led to the discovery of many new cell types in e.g. mouse cortex, hippocampus, dorsal root ganglion and spinal cord. Animals have evolved a greater diversity of cell types in a multicellular body (10

Data-driven whole mouse brain modeling for multi-scale simulations

Dimitri Bruno Marie Rodarie

In this thesis, we present a data-driven iterative pipeline to generate, simulate and validate point-neuron models of the whole mouse brain. The ultimate goal is to replicate close loop experiments with a virtual body in a virtual world. This pipeline was origi-nally created by a PhD student of the Blue Brain Project and this pioneer work has yielded the first versions of the model and their simulations. My objective is to refine, extend and consolidate the previous version of the workflow and in particular to extend the repertoire of neuron types by integrating and consolidating available literature data.The pipeline has four main parts. First, we define a pair of reference atlases to create a spatial reference for every dataset that we want to integrate. Second, we create a cell atlas with estimates of the number and density of the major cell types in each brain region. Then, we build a connectivity atlas that describes the connections of each neuron of the mouse brain and their properties. Finally, we assign point-neuron parameters to each of the neuron types, and synaptic parameters to each of the connection types of our model to obtain a point-neuron network of the mouse brain. This network can be simulated to perform mouse brain experi-ments in-silico.In this thesis, we evaluate the quality of the different reference atlases, released by the Allen Institute for Brain Science and pro-vide methods to mitigate the impact of artifacts in the original images. We further extend the cell atlas with density estimates of more inhibitory neuron types. To do so, we introduce a new method to combine estimates of inhibitory neuron counts from the literature into a consistent framework. We also estimate inhibitory neuron density in regions where no literature data are avai-lable, using collected literature estimates and gene expression data from in situ hybridization image stacks. Our approach can be further extended to other cell types and provides a resource to build more detailed circuits of the mouse brain. Next, we refine the connectivity atlas, including literature findings on short-range connectivity. Additionally, we construct a database to store data collected on neuron types point-neuron parameters and synaptic parameters. With the results of the previous steps, we generate a new version of the whole mouse brain point-neuron network. We tested this new model against its previous version using three benchmark experiments. We explore the possibility to embed and connect detailed circuit reconstructions of the mouse brain to our point neuron model and co-simulate them. Finally, we constrain a 3D skeleton model of the mouse with joint constraints from the literature and attach muscle to its bones to create a musculoskeletal model of the mouse body that can be simulated in close-loop with our model to reproduce motor control experiments.

EPFL2022

Immunosuppressive roles of Activin-A in melanoma and characterization of its precursor cleavage

Katarina Pinjusic

Activin-A, a transforming growth factor êµ family member, is a pleiotropic cytokine with diverse functions in development, fertility, adult tissue homeostasis, and aging. Accordingly, deregulation of Activin-A signaling has been associated with many pathological conditions, including cancer and cancer-associated muscle wasting (cachexia). Activin-A was shown to signal in endocrine, but also local autocrine and paracrine manner. Its secretion in many cancer types is associated with a poor prognosis. Previous studies suggest that Activin-A expression in melanoma promotes tumor growth and metastasis indirectly by inhibiting adaptive anti-tumor immunity, leading to a decrease in the intratumoral frequency of cytotoxic CD8+ T cells (CTLs). However, the underlying mechanisms and the relevant direct target cells of Activin-A and their significance for cancer therapies remained unknown. Similar to other TGFêµ-related ligands, proActivin-A is cleaved by proprotein convertases (PCs) to release mature ligands. However, unlike other family members whose signaling is tightly regulated, Activin-A apparently does not have latency.In this thesis, I characterize proActivin-A cleavage and show that one prodomain can be cleaved independently of known PCs. The resulting hemi-cleaved Activin-A can bind activin type II receptors and induce SMAD3 signaling in reporter cells. A protein interactome screen and analysis of cleavage intermediates in plasma revealed that the hemi-cleaved Activin-A likely interacts with extracellular matrix proteins via the remaining prodomain where it promotes local signaling and regulates trafficking. Luciferase reporter assay showed that hemi-cleaved Activin-A can avoid, at least partially, inhibition by endogenous inhibitors FSTL3 and FST, and enable parallel activation of BMP and Activin signaling pathways. Finally, analysis of B16-F1 melanoma models revealed that only fully cleaved Activin-A in source cells increased tumor growth by acting locally in the tumor microenvironment suggesting that the context of Activin-A precursor processing regulates its tumor growth-promoting effect.The second part of this thesis addresses the mechanisms of Activin-induced immunosuppression in melanoma. We found that Activin-A impairs CTL function indirectly and independently of CD4+ T cell, CSF1R+ macrophages, and IL4 signaling. At least in part, anti-tumor CTL responses are impaired by the inhibitory effects of Activin-A on the secretion of critical CTL-recruiting chemokines CXCL9 and CXCL10 by macrophages and dendritic cells (DCs). Furthermore, Activin-A conferred resistance to immune checkpoint blockade therapy. Characterization of Activin-induced changes in the gene expression of tumor-infiltrating cells by Single cell RNA sequencing revealed that INHBA expression induced the most changes in DCs and least in T cells. Interestingly, the most prominently induced hallmark in Activin-secreting tumors across cell types was the IFN signature. In vitro analyses showed that Activin-A increases IFNÎ³-induced activation of STAT1 and confers resistance to cytostatic IFN signaling in cancer cells.Altogether, the findings of this thesis expand our knowledge on the regulation of Activin-A signaling by precursor cleavage and offer insights into mechanisms of Activin-induced immunosuppression in melanoma. Inhibition of Activin-A maturation thus emerges as a potential new strategy to improve responses to immunotherapies in melanoma and likely other cancers

EPFL2022

Differentiation of human embryonic stem cells to hepatocytes

Noam Beckmann

Many liver diseases involve hepatocyte malfunction. In most cases, transplantation of corrected hepatocytes would correct for disease symptoms. Liver donor shortage and hepatocyte inability to proliferate in vitro accentuate this problem. Embryonic stem and induced pluripotent stem cells proliferate indefinitely and have the capacity to differentiate into every cell type of the body. They could thus represent a solution to this organ donor shortage. In this project, we aim to differentiate ES and iPS cells to hepatocytes. First, we consider an approach to select the ES/iPS cell line showing the best potential to generate liver lineage using teratomas as a selection tool. Then we use lentiviral vectors to transduce this selected cell line with essential liver-‐specific development factors to help differentiation efficiency. Next, we developed an in vitro differentiation protocol based on existing protocols and developmental clues of liver development to generate a pool of hepatocyte precursors. Later on, we injected these differentiated cells in mice liver of Fah-‐, Rag2-‐ and Il-‐2rγ-‐deficient mice to check for engraftment and liver marker expression. Our findings show, after checking for hepatocyte-‐ specific markers in the differentiated cells, that our previous selection for the potentially best cell line seems correct. We also find that the transcription factors involved in liver development appear to have a negative effect in vitro on liver differentiation. Applying our protocol to regular ES cells results on the production of late maturity hepatocyte markers, showing correct differentiation and maturation of newly formed hepatocytes. Finally, mouse in vivo liver transplantation of these differentiated cells gives us human albumin expression detectable in blood serum of said mice

2010

Immunosuppressive roles of Activin-A in melanoma and characterization of its precursor cleavage

Katarina Pinjusic

EPFL2022

Data-driven whole mouse brain modeling for multi-scale simulations

Dimitri Bruno Marie Rodarie

EPFL2022