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Supplementary Figure Legends

Tumour phenotypes in Prss56Cre, R26tdTom, Nf1flox/flox and Prss56Cre, R26tdTom, Nf1flox/- mice

Supplementary Materials and Methods

Supplementary Figures S1-S6

Central nervous system (CNS) lesions are a leading cause of death and disability worldwide. Three-dimensional neural cultures in biomaterials offer more physiologically relevant models for disease studies, toxicity screenings or in vivo transplantations. Herein, we describe the development and use of pullulan/dextran polysaccharide-based scaffolds for 3D neuronal culture. We first assessed scaffolding properties upon variation of the concentration (1%, 1.5%, 3% w/w) of the cross-linking agent, sodium trimetaphosphate (STMP). The lower STMP concentration (1%) allowed us to generate scaffolds with higher porosity (59.9 ± 4.6%), faster degradation rate (5.11 ± 0.14 mg/min) and lower elastic modulus (384 ± 26 Pa) compared with 3% STMP scaffolds (47 ± 2.1%, 1.39 ± 0.03 mg/min, 916 ± 44 Pa, respectively). Using primary cultures of embryonic neurons from PGKCre, Rosa26tdTomato embryos, we observed that in 3D culture, embryonic neurons remained in aggregates within the scaffolds and did not attach, spread or differentiate. To enhance neuronal adhesion and neurite outgrowth, we then functionalized the 1% STMP scaffolds with laminin. We found that treatment of the scaffold with a 100 μg/mL solution of laminin, combined with a subsequent freeze-drying step, created a laminin mesh network that significantly enhanced embryonic neuron adhesion, neurite outgrowth and survival. Such scaffold therefore constitutes a promising neuron-compatible and biodegradable biomaterial.

Patients carrying an inactive NF1 allele develop tumors of Schwann cell origin called neurofibromas (NF). Genetically engineered mouse models have significantly enriched our understanding of plexiform forms of NFs (pNF). However, this has not been the case for cutaneous neurofibromas (cNF), observed in all NF1 patients, as no previous model recapitulates their development. Here, we show that conditional Nf1 inactivation in Prss56-positive boundary cap cells leads to bona fide pNFs and cNFs. This work identifies subepidermal glia as a likely candidate for the cellular origin of cNFs and provides insights on disease mechanisms, revealing a long, multistep pathologic process in which inflammation-related signals play a pivotal role. This new mouse model is an important asset for future clinical and therapeutic investigations of NF1-associated neurofibromas. Significance: Patients affected by NF1 develop numerous cNFs. We present a mouse model that faithfully recapitulates cNFs, identify a candidate cell type at their origin, analyze the steps involved in their formation, and show that their development is dramatically accelerated by skin injury. These findings have important clinical/therapeutic implications. This article is highlighted in the In This Issue feature, p. 1

Summary Astrocyte dysfunction and neuroinflammation are detrimental features in multiple pathologies of the CNS. Therefore, the development of methods that produce functional human astrocytes represents an advance in the study of neurological diseases. Here we report an efficient method for inflammation-responsive astrocyte generation from induced pluripotent stem cells (iPSCs) and embryonic stem cells. This protocol uses an intermediate glial progenitor stage and generates functional astrocytes that show levels of glutamate uptake and calcium activation comparable with those observed in human primary astrocytes. Stimulation of stem cell-derived astrocytes with interleukin-1β or tumor necrosis factor α elicits a strong and rapid pro-inflammatory response. RNA-sequencing transcriptome profiling confirmed that similar gene expression changes occurred in iPSC-derived and primary astrocytes upon stimulation with interleukin-1β. This protocol represents an important tool for modeling in-a-dish neurological diseases with an inflammatory component, allowing for the investigation of the role of diseased astrocytes in neuronal degeneration., Graphical Abstract, Highlights • Reliable method for generation of astrocytes from human iPSCs and ESCs • Generated astrocytes are functional and inflammation-responsive • Generated astrocytes share properties with primary astrocytes in vitro • This method is a valuable tool for disease modeling of neuroinflammation, In this article, Gage and colleagues developed a reliable method for generating functional astrocytes from human pluripotent stem cells. This protocol uses an intermediate glial progenitor stage and generates inflammation-responsive astrocytes, providing an important tool to model neurological diseases in-a-dish, enabling the study of neurological disorders with an inflammatory component.

Bipolar disorder (BD) is a progressive psychiatric disorder with more than 3% prevalence worldwide. Affected individuals experience recurrent episodes of depression and mania, disrupting normal life and increasing the risk of suicide greatly. The complexity and genetic heterogeneity of psychiatric disorders have challenged the development of animal and cellular models. We recently reported that hippocampal dentate gyrus (DG) neurons differentiated from induced pluripotent stem cell (iPSC)-derived fibroblasts of BD patients are electrophysiologically hyperexcitable. Here we used iPSCs derived from Epstein-Barr virus-immortalized B-lymphocytes to verify that the hyperexcitability of DG-like neurons is reproduced in this different cohort of patients and cells. Lymphocytes are readily available for research with a large number of banked lines with associated patient clinical description. We used whole-cell patch-clamp recordings of over 460 neurons to characterize neurons derived from control individuals and BD patients. Extensive functional analysis showed that intrinsic cell parameters are very different between the two groups of BD neurons, those derived from lithium (Li)-responsive (LR) patients and those derived from Li-non-responsive (NR) patients, which led us to partition our BD neurons into two sub-populations of cells and suggested two different subdisorders. Training a Naïve Bayes classifier with the electrophysiological features of patients whose responses to Li are known allows for accurate classification with more than 92% success rate for a new patient whose response to Li is unknown. Despite their very different functional profiles, both populations of neurons share a large, fast after-hyperpolarization (AHP). We therefore suggest that the large, fast AHP is a key feature of BD and a main contributor to the fast, sustained spiking abilities of BD neurons. Confirming our previous report with fibroblast-derived DG neurons, chronic Li treatment reduced the hyperexcitability in the lymphoblast-derived LR group but not in the NR group, strengthening the validity and utility of this new human cellular model of BD.

International audience; Figure 1. Le trouble bipolaire est une mala-die psychiatrique relevant des troubles de l'humeur. Les troubles de l'humeur se dis-tribuent selon un spectre, en fonction de la durée et l'intensité des épisodes dépressifs et maniaques. Le trouble unipolaire, ou dépression majeure, présente seulement des épisodes dépressifs ; le trouble bipo-laire de type II présente en plus des épi-sodes hypomaniaques ; le trouble bipolaire de type I comporte des phases dépressives et maniaques sévères. La cyclothymie est caractéri-sée par une succession de phases dépressives et euphoriques de faible intensité. La dysthymie correspond à un état dépressif chronique, moins intense que la dépression majeure.

Schwann cells (SC) enter the central nervous system (CNS) in pathophysiological conditions. However, how SC invade the CNS to remyelinate central axons remains undetermined. We studied SC migratory behavior ex vivo and in vivo after exogenous transplantation in the demyelinated spinal cord. The data highlight for the first time that SC migrate preferentially along blood vessels in perivascular extracellular matrix (ECM), avoiding CNS myelin. We demonstrate in vitro and in vivo that this migration route occurs by virtue of a dual mode of action of Eph/ephrin signaling. Indeed, EphrinB3, enriched in myelin, interacts with SC Eph receptors, to drive SC away from CNS myelin, and triggers their preferential adhesion to ECM components, such as fibronectin via integrinβ1 interactions. This complex interplay enhances SC migration along the blood vessel network and together with lesion-induced vascular remodeling facilitates their timely invasion of the lesion site. These novel findings elucidate the mechanism by which SC invade and contribute to spinal cord repair. Electronic supplementary material The online version of this article (10.1007/s00401-019-02011-1) contains supplementary material, which is available to authorized users.

Patients carrying an inactive

International audience; Although cardiac neural crest cells are required at early stages of arterial valve development, their contribution during valvular leaflet maturation remains poorly understood. Here, we show in mouse that neural crest cells from pre-otic and post-otic regions make distinct contributions to the arterial valve leaflets. Genetic fate-mapping analysis of Krox20-expressing neural crest cells shows a large contribution to the borders and the interleaflet triangles of the arterial valves. Loss of Krox20 function results in hyperplastic aortic valve and partially penetrant bicuspid aortic valve formation. Similar defects are observed in neural crest Krox20-deficient embryos. Genetic lineage tracing in Krox20(-/-) mutant mice shows that endothelial-derived cells are normal, whereas neural crest-derived cells are abnormally increased in number and misplaced in the valve leaflets. In contrast, genetic ablation of Krox20-expressing cells is not sufficient to cause an aortic valve defect, suggesting that adjacent cells can compensate this depletion. Our findings demonstrate a crucial role for Krox20 in arterial valve development and reveal that an excess of neural crest cells may be associated with bicuspid aortic valve.

Adult neurogenesis in the mammalian brain is restricted to specific regions, such as the dentate gyrus (DG) in the hippocampus and the subventricular zone (SVZ) in the walls of the lateral ventricles. Here, we used a mouse line carrying a knock-in of Cre recombinase in the Prss56 gene, in combination with two Cre-inducible fluorescent reporters (Rosa26 mTmG and Rosa26 tdTom ), to perform genetic tracing of Prss56-expressing cells in the adult brain. We found reporter-positive cells in three neurogenic niches: the DG, the SVZ and the hypothalamus ventricular zone. In the prospective DG, Prss56 is expressed during embryogenesis in a subpopulation of radial glia. The pattern of migration and differentiation of reporter-positive cells during development recapitulates the successive steps of DG neurogenesis, including the formation of a subpopulation of adult neural stem cells (NSC). In the SVZ, Prss56 is expressed postnatally in a subpopulation of adult NSC mainly localized in the medial-ventral region of the lateral wall. This subpopulation preferentially gives rise to deep granule and Calbindin-positive periglomerular interneurons in the olfactory bulb. Finally, Prss56 is also expressed in a subpopulation of α2-tanycytes, which are potential adult NSCs of the hypothalamus ventricular zone. Our observations suggest that some α2-tanycytes translocate their soma into the parenchyma and may give rise to a novel cell type in this territory. Overall, this study establishes the Prss56 Cre line as an efficient and promising new tool to study multiple aspects of adult neurogenesis in the mouse.

Frutos, Cristina A. de et al., The neocortex undergoes extensive developmental growth, but how its architecture adapts to expansion remains largely unknown. Here, we investigated how early born Cajal-Retzius (CR) neurons, which regulate the assembly of cortical circuits, maintain a dense superficial distribution in the growing neocortex. We found that CR cell density is sustained by an activity-dependent importation of olfactory CR cells, which migrate into the neocortex after they have acted as axonal guidepost cells in the olfactory system. Furthermore, using mouse genetics, we showed that CR cell density severely affects the architecture of layer 1, a key site of input integration for neocortical networks, leading to an excitation/inhibition ratio imbalance. Our study reveals that neurons reenter migration several days after their initial positioning, thereby performing sequential developmental roles in olfactory cortex and neocortex. This atypical process is essential to regulate CR cell density during growth, which in turn ensures the correct wiring of neocortical circuitry. Video Abstract, We are grateful to B. Mathieu and the IBENS Imaging Facility (France BioImaging, supported by ANR-10-INBS-04, ANR-10-LABX-54 MEMO LIFE, and ANR-11-IDEX-0001-02 PSL∗ Research University, “Investments for the future”; NERF N°2011-45; FRM DGE 20111123023; and FRC Rotary International France). We also thank N. Boggetto and the Flow Cytometry platform of the ImagoSeine facility (France BioImaging, supported by ANR-10-INSB-04, “Investments for the future”). C.A.F. was supported by the IEF Marie Curie program and the Labex Memolife, “Investements for the future” (ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL∗ Research University). G.B. was funded by Labex Memolife, FRM, and Région Ile de France. Y.A. was the recipient of a fellowship from ARC and FRM. The work in P.C. group was supported by FRM (DEQ20121126545) and work in A.P. group by grants from the ANR (ANR-2011-BSV4-023-01) and FRM (DEQ20130326521). This work was supported by grants from MRT, CNRS, INSERM, and the EURYI program to S.G. S.G. is an EMBO YIP awardee and part of the ENP program.

Deciphering the ways in which somatic mutations and germline susceptibility variants cooperate to promote cancer is challenging. Ewing sarcoma is characterized by fusions between EWSR1 and members of the ETS gene family, usually EWSR1-FLI1, leading to the generation of oncogenic transcription factors that bind DNA at GGAA motifs1–3. A recent genome-wide association study4 identified susceptibility variants near EGR2. Here we found that EGR2 knockdown inhibited proliferation, clonogenicity and spheroidal growth in vitro and induced regression of Ewing sarcoma xenografts. Targeted germline deep sequencing of the EGR2 locus in affected subjects and controls revealed 291 Ewing-associated SNPs. At rs79965208, the A risk allele connected adjacent GGAA repeats by converting an interspaced GGAT motif into a GGAA motif, thereby increasing the number of consecutive GGAA motifs and thus the EWSR1-FLI1–dependent enhancer activity of this sequence, with epigenetic characteristics of an active regulatory element. EWSR1-FLI1 preferentially bound to the A risk allele, which increased global and allele-specific EGR2 expression. Collectively, our findings establish cooperation between a dominant oncogene and a susceptibility variant that regulates a major driver of Ewing sarcomagenesis.

This HDR thesis presents my work on transcriptional regulation in metazoans (animals). As a computational biologist, my research activities cover both the development of new bioinformatics tools, and contributions to a better understanding of biological questions. The first part focuses on transcription factors, with a study of the evolution of Hox and ParaHox gene families across meta- zoans, for which I developed HoxPred, a bioinformatics tool to automatically classify these genes into their groups of homology. Transcription factors regulate their target genes by binding to short cis-regulatory elements in DNA. The second part of this thesis introduces the prediction of these cis-regulatory elements in genomic sequences, and my contributions to the development of user- friendly computational tools (RSAT software suite and TRAP). The third part covers the detection of these cis-regulatory elements using high-throughput sequencing experiments such as ChIP-seq or ChIP-exo. The bioinformatics developments include reusable pipelines to process these datasets, and novel motif analysis tools adapted to these large datasets (RSAT peak-motifs and ExoProfiler). As all these approaches are generic, I naturally apply them to diverse biological questions, in close collaboration with experimental groups. In particular, this third part presents the studies uncover- ing new DNA sequences that are driving or preventing the binding of the glucocorticoid receptor. Finally, my research perspectives are introduced, especially regarding further developments within the RSAT suite enabling cross-species conservation analyses, and new collaborations with exper- imental teams, notably to tackle the epigenomic remodelling during osteoporosis., Cette thèse d’HDR présente mes travaux concernant la régulation transcriptionelle chez les métazoaires (animaux). En tant que biologiste computationelle, mes activités de recherche portent sur le développement de nouveaux outils bioinformatiques, et contribuent à une meilleure compréhension de questions biologiques. La première partie concerne les facteurs de transcriptions, avec une étude de l’évolution des familles de gènes Hox et ParaHox chez les métazoaires. Pour cela, j’ai développé HoxPred, un outil bioinformatique qui classe automatiquement ces gènes dans leur groupe d’homologie. Les facteurs de transcription régulent leurs gènes cibles en se fixant à l’ADN sur des petites régions cis-régulatrices. La seconde partie de cette thèse introduit la prédiction de ces éléments cis-régulateurs au sein de séquences génomiques, et présente mes contributions au développement d’outils accessibles aux non-spécialistes (la suite RSAT et TRAP). La troisième partie couvre la détection de ces éléments cis-régulateurs grâce aux expériences basées sur le séquençage à haut débit comme le ChIP-seq ou le ChIP-exo. Les développements bioinformatiques incluent des pipelines réutilisables pour analyser ces jeux de données, ainsi que de nouveaux outils d’analyse de motifs adaptés à ces grands jeux de données (RSAT peak-motifs et ExoProfiler). Comme ces approches sont génériques, je les applique naturellement à des questions biologiques diverses, en étroite collaboration avec des groupes expérimentaux. En particulier, cette troisième partie présente les études qui ont permis de mettre en évidence de nouvelles séquences d’ADN qui favorisent ou empêchent la fixation du récepteur aux glucocorticoides. Enfin, mes perspectives de recherche sont présentées, plus particulièrement concernant les nouveaux développements au sein de la suite RSAT pour permettre des analyses basées sur la conservation inter-espèces, mais aussi de nouvelles collaborations avec des équipes expérimentales, notamment pour éudier le remodelage épigénomique au cours de l’ostéoporose.