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The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule, yet technical limitations impeded reconstructing similar global spatial maps of other hepatocyte features. Here, we show how zonated surface markers can be used to sort hepatocytes from defined lobule zones with high spatial resolution. We apply transcriptomics, miRNA array measurements and mass spectrometry proteomics to reconstruct spatial atlases of multiple zonated features. We demonstrate that protein zonation largely overlaps with mRNA zonation, with the periportal HNF4α as an exception. We identify zonation of miRNAs such as miR-122, and inverse zonation of miRNAs and their hepatocyte target genes, highlighting potential regulation of protein levels through zonated mRNA degradation. Among the targets we find the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstructing spatial atlases of multiple cellular features in the liver and other structured tissues. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

No abstract

In metal-enhanced fluorescence (MEF), the localized surface plasmon resonances of metallic nanostructures amplify the absorption of excitation light and assist in radiating the consequent fluorescence of nearby molecules to the far-field. This effect is at the base of various technologies that have strong impact on fields such as optics, medical diagnostics, and biotechnology. Among possible emission bands, those in the near-infrared (NIR) are particularly intriguing and widely used in proteomics and genomics due to its noninvasive character for biomolecules, living cells, and tissues, which greatly motivates the development of effective and, eventually, multifunctional NIR-MEF platforms. Here, we demonstrate NIR-MEF substrates based on Au nanocages micropatterned with a tight spatial control. The dependence of the fluorescence enhancement on the distance between the nanocage and the radiating dipoles is investigated experimentally and modeled by taking into account the local electric field enhancement and the modified radiation and absorption rates of the emitting molecules. At a distance around 80 nm, a maximum enhancement up to 2–7 times with respect to the emission from pristine dyes (in the region 660–740 nm) is estimated for films and electrospun nanofibers. Due to their chemical stability, finely tunable plasmon resonances, and large light absorption cross sections, Au nanocages are ideal NIR-MEF agents. When these properties are integrated with the hollow interior and controllable surface porosity, it is feasible to develop a nanoscale system for targeted drug delivery with the diagnostic information encoded in the fluorophore.

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Imprinted, distributed feedback lasers are demonstrated on individual, active electrospun polymer nanofibers. In addition to advantages related to miniaturization, optical confinement and grating nanopatterning lead to a significant threshold reduction compared to conventional thin-film lasers. The possibility of imprinting arbitrary photonic crystal geometries on electrospun lasing nanofibers opens new opportunities for realizing optical circuits and chips.

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Single-cell RNA sequencing combined with spatial information on landmark genes enables reconstruction of spatially-resolved tissue cell atlases. However, such approaches are challenging for rare cell types, since their mRNA contents are diluted in the spatial transcriptomics bulk measurements used for landmark gene detection. In the small intestine, enterocytes, the most common cell type, exhibit zonated expression programs along the crypt-villus axis, but zonation patterns of rare cell types such as goblet and tuft cells remain uncharacterized. Here, we present ClumpSeq, an approach for sequencing small clumps of attached cells. By inferring the crypt-villus location of each clump from enterocyte landmark genes, we establish spatial atlases for all epithelial cell types in the small intestine. We identify elevated expression of immune-modulatory genes in villus tip goblet and tuft cells and heterogeneous migration patterns of enteroendocrine cells. ClumpSeq can be applied for reconstructing spatial atlases of rare cell types in other tissues and tumors.