Tomas Kirchhausen

Cell entry of nonenveloped animal viruses requires translocation of a macromolecular assembly across a cellular membrane. Double-stranded RNA viruses introduce into the target cell an inner capsid particle that does not uncoat further. Instead, it extrudes capped viral mRNA by virtue of polymerase and capping activities within it. As described here, we used cryogenic electron tomography to visualize the full course of rhesus rotavirus entry, from cell attachment and virion uptake to release of the subviral particle. The cryo-tomograms and subtomogram averaging of classified subparticles link high-resolution structures of the virion and its components with time series from live-cell fluorescence microscopy. We outline the mechanism of each step in the entry process, including the membrane perforation step that transfers a subviral particle into the cytosol.

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling tradeoffs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present Multimodal Optical Scope with Adaptive Imaging Correction (MOSAIC), a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution and multiphoton, all equipped with adaptive optics. MOSAIC enables noninvasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

Phosphorothioate-modified antisense oligonucleotides (ASOs) enter cells, but their site of productive escape remains uncertain. We combined live-cell imaging and ratiometric pH measurements to follow a Malat1 -targeting ASO internalized without a delivery vehicle. In U2OS cells, less than 4% of internalized ASO reached the nucleus under conditions that reduced Malat1 RNA by >90%. Most ASO accumulated in late endosomes, endolysosomes and lysosomes as foci and broadly distributed luminal signal. These compartments underwent neutralization without detectable membrane rupture or galectin-3 recruitment. ASO foci showed constrained motion, consistent with association with endolysosomal constituents. L-leucyl-L-leucine methyl ester-induced membrane damage or Ca²⁺-dependent lysosome exocytosis released dextran while retaining luminal ASO. Loss of the stress-granule scaffolding proteins G3BP1/2 modestly enhanced ASO activity without detectable endolysosomal damage. Tantalosin, a small molecule that perturbs endosomal recycling, redistributed the ESCRT-III protein IST1 to endosomes. It enhanced early escape of SYTOX Green and ASOs, detected by nuclear accumulation, and increased Malat1 knockdown, with cell-type-dependent responses. Tantalosin did not detectably increase nuclear ASO accumulation after sequestration in late compartments. These findings place productive ASO escape early in endocytic trafficking, most likely in early or recycling endosomes, before sequestration in largely nonproductive late compartments. GRAPHICAL

Enveloped viruses enter cells by membrane fusion. The viral membrane fuses with a host membrane, either at the cell surface or within endocytic compartments. For endocytic entry, fusion is typically triggered by low pH and often requires proteolytic priming by compartment-specific host proteases, which together define the site and mechanism of fusion and shape viral tropism. Inhibition of the lipid kinase PIKfyve, which generates PI(5)P and PI(3,5)P ₂ in late endosomes and lysosomes, swells those compartments and blocks infection by a subset of enveloped viruses, including Ebola virus, Marburg virus, coronaviruses (SARS-CoV-2), and VSV chimeras bearing Ebola, SARS-CoV-2, or Lassa glycoproteins, while showing minor effects on H1N1 influenza and no effect on VSV or VSV-rabies chimeras. In the work reported here, we have determined the basis for selectivity. We show that swelling of late endosomes/lysosomes, independent of changes in lipid composition or altered virion trafficking, is sufficient to block virus–endosome fusion and genome release, even when endosomal acidity is preserved. Acute PIKfyve inhibition with apilimod or brief hypotonic treatment produced endosomal swelling and impaired infection by interrupting a late endosomal entry step. Live-cell three-dimensional lattice light-sheet fluorescence microscopy imaging tracked fluorescent virions accumulating and arresting in late endosomes prior to fusion, and single-cell, single-round assays confirmed loss of infectivity. These data support a simple biophysical mechanism: endo-lysosomal swelling, likely increasing endosomal membrane tension, creates an energy barrier to fusion and genome release. Inducing such swelling may offer a general strategy to inhibit viruses that depend on late endosomal entry.

Quantitative, time-resolved 3D fluorescence microscopy can reveal complex cellular dynamics in living cells and tissues. Broader use remains limited by the difficulty of identifying, segmenting, and tracking objects of different size and shape in crowded intracellular environments in low-contrast, anisotropic, monochromatic image volumes. Objects overlap, deform, appear and disappear, and span wide ranges of size and intensity. Classical segmentation pipelines typically require high signal-to-noise data and rely on intensity heuristics with hand-tuned postprocessing that generalize poorly. Supervised deep learning methods require extensive voxel-level annotations that are costly, inconsistent across phenotypes, and rapidly become obsolete as imaging conditions change. We introduce SpatialDINO, a fully automated self-supervised method that trains a native 3D vision transformer, based on a modified version of DINOv2 (1). SpatialDINO yields robust semantic feature maps from single channels of multi-channel microscopy that, irrespective of object shape, support object detection and segmentation directly from naïve 3D images across z-spacings and numbers of planes and different imaging modalities, without retraining or voxel annotations. We trained SpatialDINO on a small set of confocal volumes acquired by live-cell fluorescent 3D lattice light-sheet microscopy, spanning targets of different size and shape located in crowded cellular environments, from diffraction-limited clathrin coated pits and clathrin coated vesicles to bigger structures including endosomes and lysosomes, and endosomes and lysosomes pharmacologically enlarged to highlight endosomal membrane profiles. Post-processing of the features generated by SpatialDINO allows detection and unique object identification of these objects in naïve 3D images. It also enables detection of significantly different previously unseen object classes, such as cellular plasma membranes and nuclei and even tumors in MRI scans. Finally, we illustrate its value by tracking endosomes in 3D time series, combining SpatialDINO-derived feature similarity with spatial proximity to improve association through occlusion, abrupt appearance changes, and dense packing, all conditions that have been challenging for existing methods. SpatialDINO therefore lowers a major barrier to quantitative analysis of heterogeneous, monochromatic objects in crowded 3D cellular environments. SUMMARY: Lavaee et al. have developed SpatialDINO to surmount the difficulties presented by attempting to identify, segment, and track objects in crowded volumes. SpatialDINO is a self-supervised, native 3D vision transformer trained directly on unlabeled fluorescence volumes acquired by live-cell 3D lattice light-sheet microscopy. By learning dense volumetric representations without voxel-level supervision, SpatialDINO generates features that enable fully automated detection, segmentation, and tracking of subcellular structures across a wide range of sizes and morphologies in crowded, anisotropic 3D/4D datasets acquired with different microscopy modalities. The approach generalizes across targets and imaging conditions without further training, reducing dependence on manual annotation while maintaining performance in complex cellular environments. SIGNIFICANCE: SpatialDINO brings a self-supervised foundation model for analyzing 3D fluorescence microscopy images by adapting DINOv2-style joint-embedding training to learn dense volumetric features directly from unlabeled 3D datasets. By exploiting true 3D context rather than slice-wise “2.5D” aggregation, it enables automated detection and segmentation in crowded, anisotropic, low-contrast volume and enables tracking in 4D time-lapse data. SpatialDINO generalizes across targets and imaging conditions without voxel-level annotation or retraining.

Enveloped viruses enter cells by membrane fusion. The viral membrane fuses with a host membrane, either at the cell surface or within endocytic compartments. For endocytic entry, fusion is typically triggered by low pH and often requires proteolytic priming by compartment-specific host proteases, which together define the site and mechanism of fusion and shape viral tropism. Inhibition of the lipid kinase PIKfyve, which generates PI(5)P and PI(3,5)P₂ in late endosomes and lysosomes, swells those compartments and blocks infection by a subset of enveloped viruses, including Ebola virus, Marburg virus, coronaviruses (SARS-CoV-2), and VSV chimeras bearing Ebola, SARS-CoV-2, or Lassa glycoproteins, while showing minor effects on H1N1 influenza and no effect on VSV or VSV–rabies chimeras. In the work reported here, we have determined the basis for selectivity. We show that swelling of late endosomes/lysosomes, independent of changes in lipid composition or altered virion trafficking, is sufficient to block virus–endosome fusion and genome release, even when endosomal acidity is preserved. Acute PIKfyve inhibition with apilimod or brief hypotonic treatment produced endosomal swelling and impaired infection by interrupting a late endosomal entry step. Live-cell 3D lattice light-sheet fluorescence microscopy imaging tracked fluorescent virions accumulating and arresting in late endosomes prior to fusion, and single-cell, single-round assays confirmed loss of infectivity. These data support a simple biophysical mechanism: endo-lysosomal swelling, likely increasing endosomal membrane tension, creates an energy barrier to fusion and genome release. Inducing such swelling may offer a general strategy to inhibit viruses that depend on late endosomal entry. SIGNIFICANCE STATEMENT: Why does inhibiting the endosomal lipid kinase PIKfyve, which generates PI(5)P and PI(3,5)P ₂ , block entry of some enveloped viruses but spare VSV-G? Using single-round infectivity and live-cell 3D imaging, we show that acute PIKfyve inhibition traps incoming VSV chimeras bearing SARS-CoV-2 spike or Ebola GP in swollen late endosomes/lysosomes before fusion and genome release. Hypotonic swelling phenocopies the block, and removing glutamine prevents apilimod-induced swelling and largely restores infection, arguing that swelling—not altered phosphoinositides—restricts entry. We propose a physical mechanism: increased endosomal membrane tension raises the energetic barrier for fusion-pore formation and genome release. Modulating endolysosomal volume may therefore inhibit viruses that rely on late endosomal entry.

Pathogenic tau assemblies propagate by templated seeding. For endocytosed fibrils to initiate aggregation of endogenous tau, a breach must occur in the limiting membrane of an endosome or lysosome. To study the route by which internalized tau seeds access cytosolic monomers and to identify the site of aggregate growth, we imaged live human iPSC-derived neurons (iNs) expressing tau P301L–eGFP after exposure to recombinant tau pre-formed fibrils (PFFs) or Alzheimer’s disease (AD) brain–derived oligomers or fibrils. We detected seeded tau P301L– eGFP aggregation within late endosomes/lysosomes of iNs but not in undifferentiated iPSCs. Colocalization with a Dextran pH biosensor showed that the aggregates remained within the lumen of an intact, low-pH compartment. Reporters of endolysosomal injury and repair (endolysosomal recruitment cytosolic galectin-3 and the ESCRT-III component IST1) did not change during seeding. Volume focused-ion-beam scanning electron microscopy showed fibrillar material exclusively inside membrane-bounded endolysosomes, with no membrane discontinuities in the fibril-containing compartments and with no evidence of cytosolic aggregates. Because tau and α-synuclein can cross-seed, we adapted a HaloTag pulse–chase assay to test for the persistence of trans-membrane access. AD fiber–containing endolysosomes progressively recruited cytosolic α-synuclein–Halo over days, with heterogeneous incorporation histories consistent with recurrent, self-limited access events rather than persistent rupture or terminal sealing. Pharmacologic inhibition of the endolysosomal lipid kinase PIKfyve with apilimod suppressed seeded tau aggregation and prevented neuronal toxicity. These data indicate that templated conversion proceeds within acidic, membrane-intact endolysosomes; tau seeding in neurons is enabled by transient, self-limited endolysosomal perforations yet remains confined to the endolysosomal lumen, and it requires PIKfyve- dependent PI(3,5)P₂.

The architecture of ER exit sites (ERES), the first sites of membrane remodeling in protein secretion, remains unclear, with descriptions ranging from vesicular clusters to extended tubular structures. We addressed this divergence by visualizing ERES in cells not overexpressing secretory cargo using large-scale volume-focused ion beam scanning EM (FIB-SEM) after high-pressure freeze substitution. Automated segmentation in EM (ASEM), our 3D U-Net pipeline trained with sparsely labeled 50–70-nm COPI vesicles near the Golgi, accurately detected them in HeLa, SVG-A, and iPSC-derived neurons. Using the same model, we identified abundant clusters of ∼5–40 larger vesicles (∼65–85 nm) confined within ∼250 nm3 regions adjacent to flattened ER domains, consistent with vesicular ERES. Similar assemblies also appeared alongside tubular networks and varicosities extending from enlarged ER domains, previously described as the sole ERES in HeLa cells. These findings reveal that vesicular ERES are widespread and morphologically diverse, resolving longstanding contradictions in early secretory pathway organization.

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling trade-offs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present MOSAIC, a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution, and multi-photon, all equipped with adaptive optics. MOSAIC enables non-invasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues, and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

Subcellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with unprecedented precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the subcellular environment is labor intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework integrated in an analysis software, to interpret the diffusional two- or three-dimensional temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying endosomal organelles, clathrin-coated pits and vesicles among others with F1 scores of 81%, 82% and 95%, respectively, and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone illustrates that besides structure, motion encodes function at the molecular and subcellular level.