The fluid covering the surface of airway epithelia represents a first barrier against pathogens. The chemical and physical properties of the airway surface fluid are controlled by the activity of ion channels and transporters. In cystic fibrosis (CF), loss of CFTR chloride channel function causes airway surface dehydration, bacterial infection, and inflammation. We investigated the effects of IL-17A plus TNF-α, 2 cytokines with relevant roles in CF and other chronic lung diseases. Transcriptome analysis revealed a profound change with upregulation of several genes involved in ion transport, antibacterial defense, and neutrophil recruitment. At the functional level, bronchial epithelia treated in vitro with the cytokine combination showed upregulation of ENaC channel, ATP12A proton pump, ADRB2 β-adrenergic receptor, and SLC26A4 anion exchanger. The overall result of IL-17A/TNF-α treatment was hyperviscosity of the airway surface, as demonstrated by fluorescence recovery after photobleaching (FRAP) experiments. Importantly, stimulation with a β-adrenergic agonist switched airway surface to a low-viscosity state in non-CF but not in CF epithelia. Our study suggests that CF lung disease is sustained by a vicious cycle in which epithelia cannot exit from the hyperviscous state, thus perpetuating the proinflammatory airway surface condition.

Proliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells. However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times. Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and predict a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could be relevant therapeutic targets to control cell proliferation.

The genetic changes sustaining the development of cancers of unknown primary (CUP) remain elusive. The whole‐exome genomic profiling of 14 rigorously selected CUP samples did not reveal specific recurring mutation in known driver genes. However, by comparing the mutational landscape of CUPs with that of most other human tumor types, it emerged a consistent enrichment of changes in genes belonging to the axon guidance KEGG pathway. In particular, G842C mutation of PlexinB2 (PlxnB2) was predicted to be activating. Indeed, knocking down the mutated, but not the wild‐type, PlxnB2 in CUP stem cells resulted in the impairment of self‐renewal and proliferation in culture, as well as tumorigenic capacity in mice. Conversely, the genetic transfer of G842C‐PlxnB2 was sufficient to promote CUP stem cell proliferation and tumorigenesis in mice. Notably, G842C‐PlxnB2 expression in CUP cells was associated with basal EGFR phosphorylation, and EGFR blockade impaired the viability of CUP cells reliant on the mutated receptor. Moreover, the mutated PlxnB2 elicited CUP cell invasiveness, blocked by EGFR inhibitor treatment. In sum, we found that a novel activating mutation of the axon guidance gene PLXNB2 sustains proliferative autonomy and confers invasive properties to stem cells isolated from cancers of unknown primary, in EGFR‐dependent manner.

Skeletal muscles exhibit notable morphological diversity, yet the developmental mechanisms specifying distinct identities are unclear. Using Drosophila leg muscles, we show that naïve mesodermal precursors undergo stepwise specification orchestrated by epithelial morphogens. Wg/Wnt1 and Dpp/BMP first restrict multipotent precursors into proximal and distal lineages. Within the distal lineage, successive fate bifurcations generate distinct muscle subtypes and a separate nonmuscle lineage of neuronal lamella cells. Focusing on one lineage, we demonstrate that Wg and Dpp act again to control the spatiotemporal deployment of transcription factors, ensuring that groups of myoblasts destined to fuse to produce a specific muscle share a coordinated transcriptional identity. Thus, epithelial morphogens not only pattern the epithelium but also synchronize myoblast specification, enabling the emergence of diverse muscles from syncytial fibers. Our findings provide a framework for the developmental and evolutionary origins of appendicular muscles and may help explain the selective vulnerability of specific muscles in muscular dystrophies.

Transcription reactivation kinetics and chromatin structure reorganization after mitosis: Dans cette thèse, nous avons tenté de découvrir le lien existant entre l'organisation tridimensionnelle de la chromatine et la régulation de la machinerie transcriptionnelle, en combinant des analyses informatiques et la modélisation mathématique de données provenant d'expériences à haut débit telles que le RNA-Seq et le Hi-C. Ces recherches visent principalement à mettre en évidence les principaux régulateurs responsables de la réactivation de la transcription à la sortie de la mitose, et à identifier les facteurs les plus importants de la réorganisation structurelle de la chromatine dans le cycle cellulaire.

SUMMARY: Skeletal muscles display remarkable morphological diversity, but the developmental mechanisms specifying distinct muscle morphology remain poorly understood. Using Drosophila leg muscles as a model, we uncover how naïve mesodermal precursors progressively acquire lineage-restricted identities through a stepwise specification program guided by epithelial morphogens. Initially, multipotent mesodermal precursors become spatially and transcriptionally restricted into two broad lineages - proximal and distal - under the combined influence of Wg/Wnt1 and Dpp/BMP signals from the overlying epithelium. By tracing mesodermal precursors that eventually give rise to distal leg muscles, we reveal a second sequence of fate bifurcations that generate distinct muscle subtypes prior to myoblast fusion, as well as a separate lineage producing neuronal lamella cells. Focusing on a single muscle lineage, we show that Wg and Dpp act again during a second phase to control the spatial and temporal deployment of specific transcription factors, ultimately specifying a unique muscle identity. These findings demonstrate that epithelial morphogens not only pattern the epithelium but also orchestrate muscle diversity by promoting stepwise mesodermal specification. Mesodermal precursors translate morphogen signals over time and space to activate distinct transcriptional programs that operate in parallel with the general program of myogenesis, enabling the emergence of distinct muscle and non- muscle lineages whose unique identities underpin their specialized functions.