Data availability The RNA sequencing datasets (GSE117930) and the single cell RNA sequencing datasets (GSE131508) are deposited in the Gene Expression Omnibus (GEO, NCBI) repository. The proteomic datasets are deposited in PRoteomics IDEntifications (PRIDE) repository (PXD010597). Author Contribution L.O. designed and performed most of the experiments, analysed and interpreted the data and contributed to the manuscript preparation. E.N. assisted with data collection, performed all the 3D-scaffold co-culture experiments, the in vivo Wisp1 experiments, the scRNA sequencing, interpreted and analysed the data and contributed to the manuscript preparation. I.K. performed the qPCR analysis, some of the tissue IF staining and analysed the data. A.M. and J.H.L. performed some of the tissue IF staining, all the lung organoid experiments, interpreted and analysed the data. V.B. performed some of the tissue IF staining. P.C. and S. H. performed bioinformatics analysis. I.H., J.K. and A.O. performed the proteomic and analysed the data. E.G.G. helped with the collection of Ly6G + cells for proteomics. G.M. performed the 3D-scaffold co-culture to analyse CD104 + cells. A.W. and L.C. performed the electron microscopy experiments. E.H. and V.S. provided human samples. L.O., E.N., I.K., V.B. and J.H.L., critically reviewed the manuscript. J.H.L., supervised the lung organoid experiments. I.M. designed and supervised the study, interpreted the data and wrote the manuscript.

Griscelli syndrome (GS) patients and the corresponding mouse model ashen exhibit defects mainly in two types of lysosome-related organelles, melanosomes in melanocytes and lytic granules in CTLs. This disease is caused by loss-of-function mutations in RAB27A, which encodes 1 of the 60 known Rab GTPases, critical regulators of vesicular transport. Here we present evidence that Rab27a function can be compensated by a closely related protein, Rab27b. Rab27b is expressed in platelets and other tissues but not in melanocytes or CTLs. Morphological and functional tests in platelets derived from ashen mice are all within normal limits. Both Rab27a and Rab27b are found associated with the limiting membrane of platelet-dense granules and to a lesser degree with α-granules. Ubiquitous transgenic expression of Rab27a or Rab27b rescues ashen coat color, and melanocytes derived from transgenic mice exhibit widespread peripheral distribution of melanosomes instead of the perinuclear clumping observed in ashen melanocytes. Finally, transient expression in ashen melanocytes of Rab27a or Rab27b, but not other Rab's, restores peripheral distribution of melanosomes. Our data suggest that Rab27b is functionally redundant with Rab27a and that the pathogenesis of GS is determined by the relative expression of Rab27a and Rab27b in specialized cell types.

Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, remains the world's deadliest infectious disease. Sterilising chemotherapy requires at least six months of multidrug therapy. Difficulty visualising the subcellular localisation of antibiotics in infected host cells means that it is unclear whether antibiotics penetrate into all mycobacteria-containing compartments in the cell. Here, we combine correlated light, electron and ion microscopy to image the distribution of Bedaquiline in infected human macrophages at sub-micrometre resolution. Bedaquiline accumulated primarily in host cell lipid droplets, but heterogeneously in mycobacteria within a variety of intracellular compartments. Furthermore, lipid droplets did not sequester antibiotic but constituted a transferable reservoir that enhanced antibacterial efficacy. Thus, strong lipid binding facilitated drug trafficking by host organelles to an intracellular target during antimicrobial treatment.Mycobacterium tuberculosis (Mtb) can persist in multiple intracellular niches within human * Correspondence to: max.

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Xenophagy is an important cellular defence mechanism against cytosol invading pathogens, such as Mycobacterium tuberculosis (Mtb). Activation of xenophagy in macrophages targets Mtb to autophagosomes, however how Mtb is targeted to autophagosomes in human macrophages at a high spatial and temporal resolution is unknown. Here, we use human induced pluripotent stem cell derived macrophages (iPSDM) to study the human macrophage response to Mtb infection induced by the ESX-1 Type-VII secretion system. Using RNA-seq, we identify ESX-1 dependent transcriptional responses in iPSDM after infection with Mtb. This analysis revealed differential inflammatory responses and dysregulated pathways such as Eukaryotic Initiation Factor 2 (eIF2) signalling and protein ubiquitination. Moreover, live cell imaging revealed that Mtb infection in human macrophages induces dynamic ESX-1-dependent, LC3B positive tubulovesicular autophagosomes (LC3-TVS). Through a correlative live cell/FIB SEM approach, we show that upon phagosomal rupture Mtb induces the formation of LC3-TVS, from which it is able to escape to reside in the cytosol. Thus, iPSDM represent a valuable model for studying spatiotemporal dynamics of human macrophage-Mtb interactions and that Mtb is able to evade capture by autophagic compartments.

Enterovirus genome replication occurs at virus-induced structures derived from cellular membranes and lipids. However, the origin of these replication organelles (ROs) remains uncertain. Ultrastructural evidence of the membrane donor is lacking, suggesting that the sites of its transition into ROs are rare or fleeting. To overcome this challenge, we combined live-cell imaging and serial block-face scanning electron microscopy of whole cells to capture emerging enterovirus ROs. The first foci of fluorescently labeled viral protein correlated with ROs connected to the endoplasmic reticulum (ER) and preceded the appearance of ROs stemming from the trans-Golgi network. Whole-cell data sets further revealed striking contact regions between ROs and lipid droplets that may represent a route for lipid shuttling to facilitate RO proliferation and genome replication. Our data provide direct evidence that enteroviruses use ER and then Golgi membranes to initiate RO formation, demonstrating the remarkable flexibility with which enteroviruses usurp cellular organelles. IMPORTANCE Enteroviruses are causative agents of a range of human diseases. The replication of these viruses within cells relies on specialized membranous structures termed replication organelles (ROs) that form during infection but whose origin remains elusive. To capture the emergence of enterovirus ROs, we use correlative light and serial block-face scanning electron microscopy, a powerful method to pinpoint rare events in their whole-cell ultrastructural context. RO biogenesis was found to occur first at ER and then at Golgi membranes. Extensive contacts were found between early ROs and lipid droplets (LDs), which likely serve to provide LD-derived lipids required for replication. Together, these data establish the dual origin of enterovirus ROs and the chronology of their biogenesis at different supporting cellular membranes.

The presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here, we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glial markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.