No / Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma.

No / 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.

No / The skin produces bioactive lipids that participate in physiological and pathological states, including homeostasis, induction, propagation, and resolution of inflammation. However, comprehension of the cutaneous lipid complement, and contribution to differing roles of the epidermal and dermal compartments, remains incomplete. We assessed the profiles of eicosanoids, endocannabinoids, N-acyl ethanolamides, and sphingolipids, in human dermis, epidermis, and suction blister fluid. We identified 18 prostanoids, 12 hydroxy-fatty acids, 9 endocannabinoids and N-acyl ethanolamides, and 21 non-hydroxylated ceramides and sphingoid bases, several demonstrating significantly different expression in the tissues assayed. The array of dermal and epidermal fatty acids was reflected in the lipid mediators produced, whereas similarities between lipid profiles in blister fluid and epidermis indicated a primarily epidermal origin of suction blister fluid. Supplementation with omega-3 fatty acids ex vivo showed that their action is mediated through perturbation of existing species and formation of other anti-inflammatory lipids. These findings demonstrate the diversity of lipid mediators involved in maintaining tissue homeostasis in resting skin and hint at their contribution to signaling, cross-support, and functions of different skin compartments. Profiling lipid mediators in biopsies and suction blister fluid can support studies investigating cutaneous inflammatory responses, dietary manipulation, and skin diseases lacking biomarkers and therapeutic targets.

No

Yes / The maintenance of a proper nuclear architecture and 3D organization of the genes, enhancer elements and transcription machinery plays an essential role in tissue development and regeneration. Here we show that in the developing skin, epidermal progenitor cells of mice lacking p63 transcription factor display alterations in the nuclear shape accompanied by marked decrease in expression of several nuclear envelop-associated components (Lamin B1, Lamin A/C, SUN1, Nesprin-3, Plectin) compared to controls. Furthermore, ChIP-qPCR assay showed enrichment of p63 on Sun1, Syne3 and Plec promoters, suggesting them as p63 targets. Alterations in the nuclei shape and expression of nuclear envelope-associated proteins were accompanied by altered distribution patterns of the repressive histone marks H3K27me3, H3K9me3 and heterochromatin protein 1- alpha in p63-null keratinocytes. These changes were also accompanied by downregulation of the transcriptional activity and relocation of the keratinocyte-specific gene loci away from the sites of active transcription towards the heterochromatin-enriched repressive nuclear compartments in p63-null cells. These data demonstrate functional links between the nuclear envelope organization, chromatin architecture and gene expression in keratinocytes and suggest nuclear envelope-associated genes as important targets mediating p63-regulated gene expression programme in the epidermis.

Nowdays there is a plethora of evidence for H₂O₂-mediated oxidative stress in the epidermis as well as in the system in patients with vitiligo (for review see (Schallreuter, Bahadoran et al. 2008). Xanthine dehydrogenase/xanthine oxidase (XDH/XO) catalyses the oxidative hydroxylation of hypoxanthine to xanthine followed by xanthine to uric acid, the last two steps in purine degradation pathway. Under oxidative conditions, XDH is converted to XO. The reactions catalysed by this enzyme generate H₂O₂ and O₂̇⁻, yielding in the presence of ROS accumulation, allantoin from uric acid. Therefore XO has been considered a major biologic source of oxygen-derived free radicals in many organs. The presence of XO in the human epidermis has not been shown so far. In this study several techniques were utilised to nail the presence and activity of XO in epidermal melanocytes and keratinocytes. The enzyme is regulated by H₂O₂ in a concentration dependent manner, where concentrations of 10-6M upregulate activity. Importantly, the results showed that the activity of XO is little affected by H₂O₂ in the mM range. H₂O₂-mediated oxidation of tryptophan and methionine residues in the sequence of XO yields only subtle alterations in the enzyme active site. These findings are in agreement with enzyme kinetics in the presence of 10-3M H₂O₂. Since uric acid is the end product of XO activity and this can be oxidised to allantoin by H₂O₂, we wanted to know whether allantoin is formed in the epidermis of patients with vitiligo. In order to address this issue, we utilised HPLC/mass spectrometry analysis. Analysis of epidermal cell extracts from suction blister tissue identified the presence of allantoin in patients with acute vitiligo, while this product was absent in healthy controls. In conclusion, our results provide evidence for functioning epidermal XO in the human epidermis which 4 can be a major source for the production of H₂O₂ contributing to oxidative stress in vitiligo. In addition, this thesis also demonstrates for the first time the presence of XO in melanosomes, and we showed that both 7BH4 and 7-biopterin inhibit XO activity in a concentration dependent manner. Moreover, XO has the potential to bind to 6/7BH4 and 6/7-biopterin from the pterin/tyrosinase inhibitor complex. This discovery adds another receptor independent mechanism for regulation of tyrosinase within the melanocyte similar to α/ß-MSH as shown earlier (Moore, Wood et al. 1999; Spencer, Chavan et al. 2005). Since the entire epidermis of patients with vitiligo is under H₂O₂-mediated oxidative stress, oxidative DNA damage would be highly expected. This thesis shows for the first time that epidermal 8-oxoG levels as well as plasma level of this oxidised DNA base are significantly increased in patients compared to healthy controls. We have shown that epidermal cells from patients with vitiligo respond to oxidative DNA damage via the overexpression of p21 and Gadd45α leading to a functioning increased short-patch base-excision repair (BER), while increased apoptosis can be ruled out due to lower caspase 3 and cytochrome c response compared to healthy controls. Our results show that patients develop effective DNA repair machinery via hOgg1, APE1 and DNA polymeraseß. Taking into consideration that these patients do not have an increased prevalence for solar-induced skin cancers, our data suggest that BER is a major player in the hierarchy to combat H₂O₂-mediated oxidative stress preventing ROS-induced tumourigenesis in the epidermis of these patients.

3 domaines cellulaires définissent l'épiderme de la queue de Ciona intestinalis. Le domaine des lignes médianes, donne naissance à deux structures différenciées larvaires, la nageoire et système nerveux périphérique. Il a été montré que les voies de signalisation BMP et FGF sont respectivement les inducteurs des lignes médianes ventrale et dorsale. Ce travail a consisté en la caractérisation des mécanismes moléculaires, situés à l'interface des signaux inducteurs et des processus de différenciation, définissant l'identité cellulaire des lignes médianes. L'identification des relations épistatiques reliant 7 facteurs de transcription impliqués dans ce processus suggère un fonctionnement en réseau hiérarchisé et place Msxb comme gène clé. Cette hiérarchie est validée par: un atlas d'expression spatio-temporelle, la perte de fonction de Msxb, l'analyse des régions cis-régulatrices de la transcription. Nous avons identifié 2 types d'enhancers, contrôlant respectivement les gènes précoces et tardifs du réseau. L'expression précoce de Msxb dans les précurseurs dorsaux est controlée par un enhancer distinct régulé par la voie FGF relayée par Otx et Nodal. Cette signature transcriptionnelle est retrouvée dans les enhancers de gènes co-exprimés, et chez l'orthologue de Msxb chez une autre ascidie. Enfin, nous montrons que la partie la plus postérieure des lignes médianes constitue un troisième compartiment, déployant un programme génétique distinct. Ce travail nous renseigne sur la structure, les mécanismes moléculaires de formation des lignes médianes, l'existence d'une signature transcriptionnelle évolutivement conservée pour le gène clé de l'acquisition de ce destin cellulaire. / Ciona intestinalis tail epidermis has 8 rows of cells defining 3 domains. One of them, the midline domain, gives rise to differentiated cells which form the larval fin and part of peripheral nervous system. Previous work has shown that BMP and FGF signalling are the inducers of ventral and dorsal midlines respectively. My work consisted in the identification of molecular events which lead epidermal cells to adopt midline fate, from induction to tail differentiation. We identified 7 transcription factors involved in this process. Identification of epistatic relationships suggest that these genes are in a hierarchical network where Msxb is a key gene. This hierarchy is validated by 1) a spatio-temporal expression atlas, 2) loss of function of Msxb, 3) cis-regulatory regions analysis for each network gene. We identified 2 types of enhancers, one capable to decouple ventral / dorsal signals used by early genes, and the other used by later genes, acting as a global response in both midlines. We showed that the early expression of Msxb in dorsal precursors is controled by a distinct enhancer, regulated by FGF9/16/20 via Otx and Nodal. This transcriptional signature is found in enhancers of co-expressed genes and in Msxb orthologue in another ascidian. Finally, we showed the most posterior part of the midlines is controlled by a distinct genetic program than the one used in dorsal and ventral midlines. This work gives insight into midlines structure, the mechanisms involved in their formation and a conserved transcriptional signature for the key gene involved in midline cell fate.

Le récepteur à l'IGF1 (IGF-1R) ainsi que ses voies de régulation sous-jacentes ont été largement étudié pour leur importance au cours du développement et leur rôle mitotique sur divers types cellulaires. A l'échelle de la peau, l'IGF-1R contribue à l'homéostasie épidermique et est souvent associé au compartiment basal pour son effet pro-prolifératif. Très peu d'études ont montré son implication au niveau de la différenciation épidermique et celles-ci présentent des résultats contradictoires. Au cours du vieillissement, la peau s'amincit et la barrière épidermique présente des défauts de perméabilité. Parallèlement, l'activité de l'IGF- 1R, maximale à l'adolescence, diminue avec l'âge. Cette étude a contribué à éclaircir le rôle de l'IGF-1R sur la différenciation épidermique et à montrer un lien entre vieillissement, perte en qualité de la peau et diminution d'activité de l'IGF-1R. L'élaboration de modèles 2D et 3D mimant le vieillissement par diminution d'activité de l'IGF-1R, nous a permis de confirmer le rôle mitotique de l'IGF-1R sur les kératinocytes et les progéniteurs et de démontrer son effet régulateur sur la différenciation épidermique par augmentation ou diminution de ces marqueurs. L'IGF-1R renforce l'adhésion cellulaire sur différentes matrices, impliquant de possibles interactions avec les intégrines α6 et β1. Ces résultats ont été corrélés aux observations de biopsies de peaux jeunes et âgées. Nous avons aussi montré que l'IGF-1R conférait un état sénescent aux cellules soumises à de fortes doses d'H2O2. Ces travaux montrent ainsi que l'IGF-1R est nécessaire pour le processus de différenciation épidermique et pour en assurer sa protection face au stress oxydant / Insulin-like growth factor 1 receptor (IGF-1R) and its signaling pathway have been widely studied for their growth promoting role on many cell types and their implication in development. On skin, the IGF-1R function has been associated to basal proliferation and contributes to epidermal morphogenesis, but very little is known about its involvement on keratinocytes differentiation and the few studies existing depict contradictory results. IGF-1R activity is maximal during teenage and tend to decrease during aging. Aged skin depicts major thinning and defects in permeability of skin barrier. Our work consisted in clarifying IGF-1R role on epidermal differentiation process and emphasized a correlation between aging, loss of skin quality and IGF-1R activity. By building 2D and 3D aging like models with low IGF-1R activity, we confirmed IGF-1R mitogenic role on both basal and progenitor-like keratinocytes. We demonstrated that IGF-1R activity regulated keratinocytes differentiation by either enhancing or slowing down differentiation markers deposition. More importantly, we highlighted the importance of IGF-1R activity for keratinocytes adhesion on both laminin-332 and collagen I/IV coatings, implying possible interactions with α6 and β1 integrins. This relationship was further correlated on skin biopsies of young and aged donors. In a parallel study, we showed that IGF-1R could induce cell senescence under acute H2O2 stress. Taken together, IGF-1R is necessary for the epidermal differentiation process and protects epidermis from acute oxidative stress induced damages

Queratinócitos são um veículo bastante atrativo para a transferência gênica ex vivo e liberação sistêmica uma vez que as proteínas secretadas por estas células podem atingir a circulação via um mecanismo similar ao processo natural. Um eficiente vetor retroviral (LXSN) contendo o gene do hormônio de crescimento de camundongo (mGH) foi utilizado para transduzir queratinócitos humanos primários. Os queratinócitos transduzidos apresentaram um nível de secreção in vitro alto e estável atingindo até 11 g mGH/106 células/dia. Os epitélios formados por estes queratinócitos geneticamente modificados apresentaram, porém, uma queda na taxa de secreção > 80 % quando foram retirados da placa de cultura utilizando um procedimento clássico. A substituição desta metodologia clássica por uma cultura organotípica resolveu completamente este problema. Camundongos anões imunodeficientes (lit/scid) implantados com estes enxertos organotípicos foram acompanhados durante 4 meses, e apresentaram um aumento de peso significativo (P<0,05) nos primeiros 40 dias. Níveis circulatórios de mGH atingiram um pico de 21 ng/mL 1 h após o implante, mas estes níveis rapidamente atingiram níveis basais (~2 ng/mL). Os queratinócitos humanos primários apresentaram portanto altos níveis de expressão in vitro e os maiores níveis circulatórios, porém por um breve período de tempo, reportados até o momento para GH neste tipo de células. Em conjunto com resultados que mostraram uma recuperação considerável da eficiência de secreção de mGH em cultura por enxertos organotípicos retirados dos animais, foram discutidos os fatores que ainda impedem a utilização clínica deste modelo promissor de terapia gênica cutânea. / Keratinocytes are a very attractive vehicle for ex vivo gene transfer and systemic delivery, since proteins secreted by these cells may reach the circulation via a mechanism which mimics the natural process. An efficient retroviral vector (LXSN) encoding the mouse growth hormone gene (mGH) was used to transduce primary human keratinocytes. Organotypic raft cultures were prepared with these genetically modified keratinocytes and were grafted onto immunodeficient dwarf mice (lit/scid). Transduced keratinocytes presented a high and stable in vitro secretion level of up to 11 g mGH/106cells/day. Conventional epidermal sheets made with these genetically modified keratinocytes, however, showed a drop in secretion rates of > 80% simply due to detachment of the epithelium from its substratum. Substitution of conventional grafting methodologies with organotypic raft cultures completely overcame this problem. The stable long-term grafting of such cultures onto immunodeficient dwarf (lit/scid) mice could be followed for more than 4 months, and a significant weight increase (P<0.05) over the control group was observed in the first 40 days. Circulating mGH levels revealed a peak of 21 ng/mL just 1h after grafting, but unfortunately these levels rapidly fell to baseline values (~ 2 ng/mL). mGH-secreting primary human keratinocytes presented the highest in vitro expression and peak circulatory levels reported to date for a form of GH with this type of cells. Together with data showing that excised implants can recover in culture a remarkable fraction of their original in vitro mGH secretion efficiency, the factors that might still hamper the success of this promising model of cutaneous gene therapy are discussed. SUMÁRIO

Les cellules souches de l’épiderme interfolliculaire humain, appelées cellules souches kératinocytaires (CSK), assurent l’homéostasie et le renouvellement du tissu durant toute la vie d’un individu grâce à leur importante capacité d’autorenouvellement. Ma thèse de doctorat a porté sur l’étude des effecteurs moléculaires impliqués dans la balance entre prolifération et quiescence dans un modèle in vitro de CSK, isolées de manière clonale et définies par le terme holoclone. Je me suis tout d’abord intéressée à la réponse des holoclones à l’effet d’un régulateur important de la prolifération et de la quiescence des cellules souches adultes : le facteur de croissance TGF β1. Mon travail s’est ensuite focalisé sur l’étude d’un gène agissant en aval de la voie de signalisation TGF β, le facteur de transcription Klf4, et dont le rôle dans la biologie des cellules souches adultes reste largement méconnu. Klf4 est en effet surtout décrit pour son rôle dans la reprogrammation des cellules somatiques en cellules iPS. Le maintien de la sensibilité des holoclones aux signaux inhibiteurs de la croissance constitue un gage de la normalité des CSK. Notre étude de la réponse des holoclones à l’effet antiprolifératif du TGF β1 montre que les holoclones, dotés d’un fort potentiel de croissance, caractéristique des CSK, conservent leur sensibilité à l’effet du TGF β1. Ces résultats nous ont permis de valider les holoclones comme constituant un modèle pertinent pour caractériser la biologie normale des CSK et décrypter les contrôles moléculaires de l’état souche. Le modèle des holoclones a été exploité dans le cadre d’une approche de génomique fonctionnelle visant à déterminer le rôle du facteur de transcription Klf4 dans les CSK. L’utilisation de vecteurs lentiviraux exprimant un shARN dirigé contre l’ARNm de Klf4 nous a permis d’étudier l’impact d’une modulation fine du niveau d’expression de Klf4 sur les propriétés des holoclones. La répression transcriptionelle de Klf4, d’environ un facteur 2, favorise de manière significative l’expansion du compartiment clonogénique au sein des holoclones. Ce gain de fonction concerne à la fois les potentiels de croissance et de reconstruction épidermique des holoclones. Un aspect important de ce travail a concerné la recherche des réseaux moléculaires régulés par Klf4 dans les holoclones. Une analyse du transcriptome nous a permis de montrer que Klf4 participe au contrôle des mécanismes de cycle cellulaire et de différenciation. Klf4 interviendrait également dans la régulation des voies de signalisation TGF β/BMP et Wnt, connues pour exercer des rôles clés dans la biologie des cellules souches. Klf4 constituerait donc un censeur de l’activité du compartiment immature dans l’épiderme interfolliculaire. Il participerait aux mécanismes de régulation du cycle cellulaire et serait susceptible d’intervenir dans le contrôle de l’autorenouvellement du compartiment souche. / Stem cells present within the human interfollicular epidermis, which are defined as keratinocytes stem cells (KSC), ensure the homeostasis and renewal of the tissue throughout the whole individual life. These functions are related to their important self-renewal capacity. My PhD project was focused on the knowledge of the molecular effectors involved in the control of the balance between proliferation and quiescence in KSC. This scientific question was investigated in an in vitro model of KSC which were clonally derived and characterized as holoclones. Holoclones are controlled by mitogenic growth factors and also by antiproliferative signals. One of these regulators is the growth factor TGF β1 which plays an important role in the control of quiescence and cell proliferation within several adult stem cell systems. In the context of growth inhibition by TGF β1, I have studied the role of a downstream gene of the TGF β pathway, the transcription factor Klf4, whose role in adult stem cell biology remains unclear. In fact, Klf4 is mostly described for its involvement in the reprogramming process of somatic cells into iPS cells. The maintenance of holoclone sensitivity to cell growth inhibitors is a critical parameter of KSC normal physiology. Holoclones possess an extensive growth capacity, which is characteristic of KSC. Despite this high proliferation rate, holoclones are still responsive to the antiproliferative effect of TGF β1. These results allowed us to validate the use of holoclone as a relevant model of non-transformed KSC suitable for the characterization of the role of candidate stemness genes in KSC biology, such as Klf4. The holoclone model was exploited to perform a functional genomic approach to investigate the role of Klf4 in KSC. We have developed a shRNA-based gene knock-down method using lentiviral vectors to assess the impact of Klf4 down-modulation on holoclone functional properties. Our results show that Klf4 down modulation controls the expansion of the clonogenic compartment present within holoclone progeny. This gain-of-function, which is maintained at the long term level, leads to an increase in holoclone 3D epidermis reconstruction capacity. A major point of this project was to elucidate the molecular networks controlled by Klf4 in holoclones. Microarray data show that Klf4 regulates the expression of several genes related to pathways involved in the control of stem cell fate. In particular, we identified many transcripts related to TGF β/BMP and Wnt signallings. Interestingly, the majority of the modulated transcripts are involved in the regulation of cell cycle and in keratinocyte differentiation process. All together these results suggest a critical role Klf4 as a stemness censor of the most immature compartment activity. Klf4 is likely to be involved in cell cycle regulation of KSC compartment and in the control of KSC self-renewal process.