The epidermis is the first barrier of protection of living organisms against external attacks. It is constantly renewed throughout life, through a process called "homeostasis", which ensures that every cell lost on its surface is replaced by new ones. Recent studies have shown that this balance is ensured by a hierarchy of stem cells (SC) and progenitors that perform 3 types of cell divisions, each having a fixed probability. Although the epidermis has been extensively studied during homeostasis, little is known about the cellular dynamics taking place when the epidermis must expand its surface. Are these probabilities of division immutable or can they change? In this project, we focused on two conditions of epidermal expansion: postnatal growth and wound healing. Using the mouse tail epidermis as a model, we show that the re-epithelialization after a wound is achieved via the formation of two transient compartments that are spatially and molecularly distinct :a leading edge and a proliferative hub. We show that the leading edge cells have a specific transcriptional signature that is independent of their quiescent state and we propose new markers not previously described. Using the technique of "lineage tracing", coupled with clonal analysis and mathematical modeling, we highlight the proliferation dynamics of SCs and progenitors during healing. We show that different populations of cells residing in different compartments, the hair follicle infundibulum and the interfollicular epidermis, acquire a similar dynamics and re-activate their SC while the progenitors increase their rate of proliferation without changing their division probabilities. This similar proliferation dynamics in two compartments of the epidermis suggests that division probabilities are not dictated by the cell of origin. Interestingly, cell dynamics is different during postnatal growth. Using lineage tracing, clonal analysis and single-cell transcriptional analysis, we demonstrate that the post-natal epidermis is composed of a homogeneous population of equipotent progenitors which ensure a harmonious tissue growth through a constant imbalance towards self-renewing divisions and an ever decreasing proliferation rate. On the other hand, we show that basal cells in the adult epidermis display a greater molecular heterogeneity and that this heterogeneity is acquired progressively at the end of growth. Finally, by coupling in vivo measurements and in vitro micro-patterning experiments, we show that the orientation of cell division of equipotent progenitors is locally influenced by the alignment of the collagen fibers of the underlying dermis. These data suggest that SC specification occurs late in postnatal development and that proliferation dynamics are not immutable and could therefore be influenced by extrinsic factors. / L’épiderme est la première barrière de protection des organismes vivants contre des attaques extérieures. Il est constamment renouvelé au cours de la vie, via un processus appelé « homeostasie », qui assure que chaque cellule perdue à sa surface soit remplacée par de nouvelles. Des études récentes ont montré que cet équilibre était assuré par une hiérarchie de cellules souches (CS) et de progéniteurs qui réalisent 3 types de divisions cellulaires, chaque type de division ayant une probabilité fixe. Bien que l’épiderme ait été intensivement étudié durant l’homeostasie, peu de choses sont connues concernant la dynamique cellulaire prenant place lors de phénomènes où l’épiderme doit grandir. Ces probabilités de division sont-elles immuables ou peuvent-elles au contraire changer ?Dans ce projet, nous nous sommes intéressés à deux conditions d’expansion de l’épiderme :la croissance post-natale et la cicatrisation des plaies. En utilisant l’épiderme de la queue de souris comme modèle, nous montrons que la ré-épithélialisation d’une plaie est réalisée via la formation de deux compartiments cellulaires transitoires distincts spatialement et du point de vue moléculaire :un front de migration et un centre prolifératif. Nous montrons que les cellules du front de migration ont une signature transcriptionnelle spécifique qui est indépendante de leur état de quiescence et proposons de nouveaux marqueurs non décrits auparavant. En utilisant la technique du « lineage tracing », couplée à une analyse clonale et à de la modélisation mathématique, nous mettons en évidence la dynamique de prolifération des CS et des progéniteurs lors de la cicatrisation. Nous montrons que différentes populations de cellules résidant dans des compartiments différents, l’infundibulum du follicule pileux et l’épiderme interfolliculaire, acquièrent une dynamique similaire et ré-activent leur CS tandis que les progéniteurs augmentent leur taux de prolifération sans changer leur probabilité de division. Cette dynamique de prolifération similaire dans deux compartiments de l’épiderme suggère que les probabilités de divisions ne sont pas dictées par la cellule d’origine. De façon intéressante, la dynamique cellulaire est par contre différente durant la croissance post-natale. En utilisant le lineage tracing, l’analyse clonale et des analyses transcriptionnelles sur cellule unique, nous démontrons que l’épiderme post-natal est composé d’une population homogène de progéniteurs équipotents qui présentent un constant déséquilibre envers des divisions d’auto-renouvèlement et un taux de prolifération décroissant, assurant une croissance harmonieuse de l’épiderme. En revanche, les cellules basales de l’épiderme adulte montrent une plus grande hétérogénéité moléculaire et cet hétérogénéité est acquise progressivement à la fin de la croissance. Enfin, en couplant des mesures in vivo et des expériences de micro-patterning in vitro, nous montrons que l’orientation de la division cellulaire des progéniteurs équipotents est localement influencée par l’alignement des fibres de collagène du derme sous-jacent. Ces données suggèrent que la spécification des CS survient tardivement au cours du développement post-natal et que la dynamique de prolifération n’est pas immuable et pourraient donc être influencée par des facteurs extrinsèques. / Doctorat en Sciences biomédicales et pharmaceutiques (Pharmacie) / info:eu-repo/semantics/nonPublished

Kallikrein-related peptidases (KLKs) constitute a highly conserved serine protease family. Based on in vitro experiments, KLKs are predicted to play an important role in a number of physiolog- ical and pathophysiological processes. However, their role in vivo remains not fully understood, partially due to a lack of suitable animal models. In this work, we aim to prepare a KLK5 and KLK14 double-deficient mouse model. Both KLK5 and KLK14 were proposed to be involved in epidermal proteolytic networks critical for maintaining skin homeostasis. However, both KLK5 and KLK14 single-deficient mouse models show minimal or no phenotype, likely due to similar substrate specificity resulting in functional compensation. Double-deficient mice cannot be easily obtained by crossing due to localization of the Klk5 and Klk14 genes within the same locus on chromosome 7. We report that KLK5 and KLK14 double-deficient mice were success- fully generated, mediated by transcription activator-like effector nucleases (TALENs) targeting Klk14 by microinjection of TALEN mRNA into KLK5-deficient zygotes. Furthermore, we show that KLK5 and KLK14 double-deficient mice are viable and fertile. We believe that these novel mouse models may serve as a useful experimental tool to study KLK5 and KLK14 in vivo.

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The nucleus of epidermal keratinocytes (KCs) is a complex and highly compartmentalized organelle, whose structure is markedly changed during terminal differentiation and transition of the genome from a transcriptionally active state seen in the basal and spinous epidermal cells to a fully inactive state in the keratinized cells of the cornified layer. Here, using multicolor confocal microscopy, followed by computational image analysis and mathematical modeling, we demonstrate that in normal mouse footpad epidermis, transition of KCs from basal epidermal layer to the granular layer is accompanied by marked differences in nuclear architecture and microenvironment including the following: (i) decrease in the nuclear volume; (ii) decrease in expression of the markers of transcriptionally active chromatin; (iii) internalization and decrease in the number of nucleoli; (iv) increase in the number of pericentromeric heterochromatic clusters; and (v) increase in the frequency of associations between the pericentromeric clusters, chromosomal territory 3, and nucleoli. These data suggest a role for nucleoli and pericentromeric heterochromatin clusters as organizers of nuclear microenvironment required for proper execution of gene expression programs in differentiating KCs, and provide important background information for further analyses of alterations in the topological genome organization seen in pathological skin conditions, including disorders of epidermal differentiation and epidermal tumors.

Les aquaporines (AQPs) sont des petites protéines formant des canaux hydriques àtravers les membranes cellulaires. Les AQPs 0, 1, 2 ,4 ,5 ,6 et 8 assurent le transport sélectif de l’eautandis que les AQPs 3, 7, 9 et 10 permettent également le passage du glycérol. Nous avons étudié leurexpression dans l’épiderme, la couche supérieure de notre peau supposée imperméable. Dans lesmélanocytes, des cellules dendritiques responsables de la pigmentation, seule l’AQP1 est exprimée.Nous avons montré que les kératinocytes, les cellules majoritaires de l’épiderme, expriment enprolifération les AQPs 3 et 10, alors que les kératinocytes différenciés expriment les AQPs 3 et 9. Lalocalisation de l'AQP3 a été précédemment rapportée à la membrane plasmique des kératinocytes, de lacouche basales à la couche épineuse. Nous avons localisé l'AQP9 dans les kératinocytes différenciés dela couche granuleuse au contenu riche en glycérol et réduit en eau. De fait nous pensons que l'AQP9 ysert de transporteur de glycérol. Enfin contrairement à d'autres auteurs, nous n’avons pu mettre enévidence de lien entre prolifération tumorale et expression des aquaporines. / Aquaporins (AQPS) are a family of small proteins forming water channels across cell membranes.AQPs 0, 1, 2, 4, 5, 6 and 8 are strictly water channel whereas AQPs 3, 7, 9 and 10 allow transport ofwater and glycerol. We have studied their expression in the epidermis, the outer-most water-impermeablelayer of the skin. In melanocytes, dendritic cells responsible for pigmentation, only AQP1 is expressed, invitro and ex vivo. We have shown that keratinocytes, principal cells of the epidermis, express AQPs 3 and10 in proliferation, whereas differentiated keratinocytes express AQPs 3 and 9. The localisation of AQP3to plasma membrane of keratinocytes was previously reported from the basal layer to the spinous layer ofthe skin. We localised AQP9 in the fully differentiated keratinocytes of the granular layer, where there is ahigh glycerol and low water content. So we think that AQP9 likely functions as a glycerol transporter.Unlike other authors, we were unable to identify a link between tumorous proliferation and the expressionof aquaporins.

The structure, function and accessibility of epidermal skin provide aunique opportunity to study the DNA damage response (DDR) of a normaltissue. The in vivo response can be examined in detail, at a molecularlevel, and further associated to the structural changes, observed at atissue level. We collected an extensive skin biopsy material frompatients undergoing fractionated radiotherapy for 5 to 7 weeks. Several end-points inthe DDR pathways were examined before, during and after the treatment. Quantification of DNA double strand break (DSB) signalling focirevealed a hypersensitivity to doses below 0.3Gy. Furthermore, aconsiderable amount of foci persisted between fractions. The low dosehypersensitivity was observed throughout the treatment and was alsoobserved for several key parameters further downstream in the DDR-pathway, such as p21-associated checkpoint activation, apoptosisinduction and reduction in basal keratinocyte density (BKD).Furthermore, for dose fractions above 1.0 Gy, a distinct acceleration inDDR was observed half way into treatment. This was manifested as anaccelerated loss of basal keratinocytes, mirrored by a simultaneousincrease in DSBs and p21 expression. Quantifications of mitotic events revealed a pronounced suppression ofmitosis throughout the treatment which was clearly low dosehypersensitive. Thus, no evidence of accelerated repopulation could beobserved for fraction doses ranging from 0.05 to 2Gy. Our results suggest that the keratinocyte response primarily isdetermined by checkpoints, which leads to pre-mitotic cell elimination by permanent growth arrest and apoptosis. A comparison between the epidermal and dermal sub-compartments revealsa consistent up-regulation of the DDR response during treatment. Adifference was however observed in the recovery phase after treatment,where miR-34a and p21 remain up-regulated in dermis more persistentlythan in epidermis. Our observations suggest that the recovery phaseafter treatment can provide important clues to understand clinicalobservations such as the early and late effects observed in normaltissues during fractionated radiotherapy.

Human epidermis relies on a population of adult stem cells to maintain its homeostasis. Stem cells transit from a dormant to an active state and undergo a tightly regulated process of differentiation that replenishes the tissue according to its needs. This process either replaces cells that get shed away, or contributes to tissue healing upon injuries, such as wounding. Distinct molecular mechanisms are required to keep human epidermal stem cells localized in their niche and for their active proliferation and mobilization, while others regulate their differentiation status. However, little is known about the proper global chromatin modifications that ensure the correct transition between these stem cell states. This work shows that Cbx4, a Polycomb Repressive Complex-1 (PRC1)-associated protein, maintains human epidermal stem cells slow-cycling and undifferentiated, while protecting them from senescence. Interestingly, abrogating the polycomb activity of Cbx4 impairs its anti-senescent function without affecting stem cell differentiation, indicating that differentiation and senescence are independent processes in human epidermis. Conversely, Cbx4 inhibits stem cell activation and differentiation through its SUMO ligase activity. Global transcriptome and chromatin occupancy analyses indicate that Cbx4 regulates modulators of epidermal homeostasis and represses factors, such as Ezh2, Dnmt1, and Bmi1, to prevent the active stem cell state. Interestingly, Cbx4 also represses genes required for neuronal fate repression, suggesting that it might have a role in ectoderm patterning during development. Cbx proteins are differently expressed during epidermal differentiation and the activity of Cbx4 towards promoting human epidermal stem cell quiescence is unique among the Cbx proteins. This suggests that different Polycomb complexes are assembled, based on the availability of its core member, and balance epidermal stem cell dormancy and activation, while continually preventing senescence and differentiation. / La homeostasis de la epidermis humana depende de una población de células troncales adultas (CTAs). Las CTAs alternan ciclos de quiescencia y actividad, seguidos por una regulación estricta de su diferenciación, según las necesidades celulares del tejido. Este proceso es esencial para repoblar el tejido de células envejecidas o dañadas. Cada estadío por el que transita una CTA está regulado por procesos moleculares específicos. Sin embargo, aún sabemos poco sobre los procesos que regulan la reorganización de la cromatina necesarios para mediar dichas transiciones en la población de las CTAs. Estos resultados demuestran que la proteina Cbx4, pertenciente al complejo Polycomb Repressive Complex-1 (PRC1), es necesaria para mantener a las CTAs de la epidermis humana quiescentes, indiferenciadas, y protegidas de la senescencia. A nivel molecular, la actividad polycomb de Cbx4 es únicamente necesaria para su función antisenescente, pero es dispensable para la regulación de la proliferación y diferenciación de las CTAs. La inhibición de la proliferación y diferenciación celular sin embargo depende de la activdad E3 SUMO ligasa de Cbx4. Analisis del transcriptoma global y de unión a la cromatina (ChIP), demuestran que Cbx4 regula la expresión de moduladores esenciales de la homeostasis de la epidermis, y reprime la expresión de factores necesarios para la activación de las CTAs, tales como Ezh2, Dnmt1 y Bmi1. Cabe destacar que Cbx4 también reprime la expresión de genes que determinam el linage neuronal, lo que sugiere que Cbx4 pueda ser importante para separar el neuroectodermo entre ectodermo y neuronas, durante el desarrollo embrionario. Cbx4 es la única proteina Cbx capaz de inducir entrada en quiescencia de las CTAs, y el resto de proteinas Cbx se expresa de forma diferente durante la diferenciación en la epidermis. Por lo tanto, nuestros estudios sugieren que la actividad de distintos complejos Polycomb actúa en los sucesivos estadíos de quiescencia, proliferación y diferenciación de las CTAs, a la vez que impiden su senescencia de forma constante.

Epidermal wound healing requires the coordinated involvement of complex cellular and biochemical processes. In the case of epidermal wounds associated with burns, the healing process may be less than optimal and may take a significant amount of time, possibly resulting in infection and scarring. An innovative method to assist in the repair of the epidermis (the outer layer of skin) is to use an aerosolised apparatus. This method involves taking skin cells from an area of the patient's undamaged skin, culturing the cells in a laboratory, encouraging them to rapidly proliferate, then harvesting and separating the cells from each other. The cells are then sprayed onto the wound surface. We investigate this novel treatment strategy for the healing of epidermal wounds, such as burns. In particular, we model the application of viable cell colonies to the exposed surface of the wound with the intent of identifying key factors that govern the healing process. Details of the evolution of the colony structure are explored in this two-dimensional model of the wound site, including the effect of varying the initial population cluster size and the initial distribution of cell types with different proliferative capacities. During injury, holoclones (which are thought to be stem cells) have a large proliferative capacity while paraclones (which are thought to be transient amplifying cells) have a more limited proliferative capacity. The model predicts the coverage over time for cells that are initially sprayed onto a wound. A detailed analysis of the underlying mathematical models yields novel mathematical results as well as insight into phenomena of healing processes under investigation. Two one-dimensional systems that are simplifications of the full model are investigated. These models are significant extensions of Fisher's equation and incorporate the mixed clonal population of quiescent and active cells. In the first model, an active cell type migrates and proliferates into the wound and undergoes a transition to a quiescent cell type that neither migrates nor proliferates. The analysis yields the identification of the key parameter constraints on the speed of the healing front of the cells on this model and hence the rate of healing of epidermal wounds. Approximations for the maximum cell densities are also obtained, including conditions for a less than optimal final state. The second model involves two active cell types with different proliferative capacity and a quiescent cell type. This model exhibits two distinct behaviours: either both cell types coexist or one of them dies out as the wound healing progresses leaving the other cell type to fill the wound space. Conditions for coexistence are explored.

Chez les vertébrés, le battement coordonné des cils motiles présents par centaines à la surface apicale des cellules multiciliées (MCC) est requis pour propulser directionnellement les fluides biologiques à l’intérieur de certains organes (voies respiratoires, ventricules cérébraux, trompes utérines ou certaines structures embryonnaires). De nombreuses pathologies humaines sont associées à des défauts ciliaires ou à une perte des MCC (dyskinésies ciliaires, mucoviscidose, asthme,...). Dans ce contexte, mon travail de thèse a consisté à élucider les mécanismes complexes contrôlant la différenciation des MCC et donc la formation des cils motiles (multiciliogenèse). Par des approches de génomiques fonctionnelles à partir de deux modèles d’épithéliums multiciliés évolutivement éloignés (épithélium respiratoire humain et épiderme d’embryon de Xénope) nous avons identifié la famille des microARN (petits ARN non-codants régulateurs de l’expression génique) miR-449 comme majoritairement exprimée dans les MCC. Nous avons montré que miR-449 contrôle la multiciliogenèse i) en bloquant le cycle cellulaire, ii) en réprimant directement la voie de signalisation Notch et iii) en inhibant l’expression de la petite GTPase R-Ras. Enfin, nos travaux montrent que l’ensemble de ces mécanismes est conservé chez les vertébrés. En conclusion, miR-449 est un nouveau régulateur clé de la multiciliogenèse conservé au cours de l’évolution. Nos résultats pourraient ouvrir la voie à de nouvelles stratégies thérapeutiques utilisant des petits ARN régulateurs dans le traitement de certaines pathologies associées à des défauts ciliaires. / In vertebrates, the coordinated beating of hundreds of motile cilia present at the apical surface of multiciliated cells (MCC) is required for propel directionally flow of biological fluids inside some organs (airways, cerebral ventricles, fallopian tubes or some embryonic structures). Many human diseases are associated with ciliary defects or loss of MCC (ciliary dyskinesia, cystic fibrosis, asthma ...). In this context, my thesis has sought to elucidate the complex mechanisms that control the differentiation of MCC and thus the formation of motile cilia (multiciliogenesis). By functional genomic approaches from two evolutionarily distant models of multiciliated epithelia (human respiratory epithelium and epidermis of Xenopus embryo) we identified the miR-449 family of microRNAs (small non-coding RNAs regulating gene expression) as mainly expressed in MCC. Then, we showed that miR-449 controlled multiciliogenesis by i) blocking the cell cycle ii) directly suppressing the Notch pathway and iii) by inhibiting the expression of the small GTPase R-Ras. Finally, we have demonstrated that all these mechanisms were conserved in vertebrates. In conclusion, miR-449 is a new key and conserved regulator of multiciliogenesis. Our findings could pave the way for new therapeutic strategies using small regulatory RNAs in the treatment of several diseases associated with ciliary defects.