Whole-body integration of gene expression and single-cell morphology

Abstract

Animal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology. This is reflected by cell type-specific transcription factors and downstream effector genes implementing functional specialisation. Here, we establish and explore the link between cell type-specific gene expression and subcellular morphology for the entire body of the marine annelid Platynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to gene expression or morphological parameters. We show that collective gene expression most efficiently identifies spatially coherent groups of cells that match anatomical boundaries, which indicates that combinations of regionally expressed transcription factors specify tissue identity. We provide an integrated browser as a Fiji plugin to readily explore, analyse and visualise multimodal datasets with remote ondemand access to all available datasets. Figure 1: Ultrastructure of a whole Platynereis by serial block-face scanning electron microscopy.A: The 3D SBEM dataset can be observed in multiple orientations, either along the acquisition plane (transversal plane, top row) or as orthogonal projections (horizontal plane, bottom row; scale bar: 50 µm). B-E: fine ultrastructure is revealed when exploring the datasets at native resolution (10 nm pixel-size x/y; scale bars: 2 µm). B: epithelial cell, interfacing the cuticle and the underlying muscle. Bundles of cytoskeletal filaments (arrowhead) form part of the attachment complex (inset). C: the adult eye forms a pigment cup composed of pigment cells (PiC) and rhabdomeric photoreceptors (rPRC). The photoreceptors extend a distal segment made by microvillar projections (mi) for light detection. In the centre of the pigment cup is the vitreous body (vb). D: longitudinal muscle fibres are cut transversally displaying cross-sections of the sarcomere as well as of the sarcoplasmic reticulum that contacts the plasma membrane (inset). E: cross section of the distal part of the nephridia, highlighting the autocell junction (arrow) which forms a lumen. The lumen houses a bundle of motile cilia (identified by the 9+2 microtubule arrangement, inset), which are contributed by each cell of the nephridium, noted by the presence of basal bodies. Panels B to E are snapshots selected from the full volume and can be retrieved directly from the PlatyBrowser "Bookmark" function. Supplementary Figure 2A). Figure 2 gives a few examples of the achieved segmentation quality for epidermal cells (B), muscles (C) and nephridia (D). We measured nuclei sizes to range from 33.6 to 147.5 cubic microns, and cell sizes from 59.8 to 1224.6 cubic microns. Note that neurites in the neuropil have not been segmented, as they are not sufficiently preserved in the EM volume for automated segmentation. Figure 2: Segmentation of nuclei, cells, tissues and body parts.A. Cells and nuclei ar...

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

“…We employed an integrative imaging analysis and generated an unprecedented repository of 3D structure information of virus-induced substructures and whole-cell volumes, deduced from a FIB-SEM dataset and around 250 tomograms. All these data will be shared with the scientific community for download through the EMPIAR platform and for smooth online visualization through MoBIE (Vergara et al, 2020). This data-rich resource will support the global investigative effort to study how SARS-CoV-2 interacts with its host and become an important tool to unveil novel antiviral targets for the development of host-targeting drugs suppressing viral replication as well as virus-induced cell damage.…”

The connectome of the Caenorhabditis elegans pharynx

“…Our analysis of the pharyngeal nervous system connectome, a selfcontained, autonomously acting unit within the C. elegans nervous system, reveals numerous novel insights into the function of individual neuron types and demonstrates themes of neuronal circuit organization, inviting speculation about neuronal circuit development and evolution. The pharyngeal wiring diagram adds to connectomic literature which increasingly represents a diversity of species and nervous system structures, including both sexes of C. elegans (Cook et al, 2019;Jarrell et al, 2012;White et al, 1986), Pristionchus pacificus pharyngeal (Bumbarger et al, 2013;Bumbarger & Riebesell, 2015) and amphidial circuits (Hong et al, 2019), multiple developmental stages of Drosophila melanogaster (Eichler et al, 2017;Zheng et al, 2018), Platynereis dumerilii (Verasztó et al, 2017;Vergara et al, 2020), larval…”

OME-NGFF: scalable format strategies for interoperable bioimaging data

“…Table 1 We have defined an image specification for multiscale NGFFs on top of these formats with the hope that it will also be applicable to HDF. Implementations for writing NGFF formats exist in bioformats2raw, and for reading in ome-zarr-py which has been integrated into the napari viewer 16 , in Fiji via the MoBIE plugin 17 , and finally via Viv-based vizarr for access in the browser 18 . Figure 2 shows an example of implementing a permanent conversion of a public dataset available in IDR into Zarr, storing the converted file in a public S3 object storage bucket and then viewing it directly using each of these tools.…”