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Biology subjects

Engel, L.

Publications and source records attributed to Engel, L..

11 recordsLinked to original sources

HIDE-Deconv: A hierarchical deconvolution framework for multiscale characterization of cellular remodeling

Most deconvolution methods estimate cellular composition at a single level of cellular resolution despite biological processes often manifesting within fine-grained cellular subpopulations. We present HIDE-Deconv, a hierarchical deconvolution framework that jointly optimizes cellular compositions across multiple levels of a cell-type hierarchy while maintaining consistency between resolutions. In benchmark experiments, HIDE-Deconv achieved the highest overall predictive performance among evaluated methods. Analyses of lung adenocarcinoma, sepsis, COVID-19 and systemic lupus erythematosus revealed biologically relevant cellular remodeling that remained concealed at broader levels of cellular resolution. HIDE-Deconv is available as an open-source framework at https://github.com/dvoelkl/HIDE-deconv.

bioinformatics↗

Gold Electron Microscopy Grids with Anisotropic Foil Geometry Enable On-Grid Contact Guidance

All-gold electron microscopy (EM) grids reduce beam-induced motion relative to conventional holey carbon supports and provide biocompatible substrates for cellular cryo-EM. However, placing customizable all-gold grid fabrication in the hands of researchers requires accessible processes based on standard microfabrication tools. We report a wafer-scale process using microfabrication techniques available in most academic cleanrooms such as lift-off metallization, electroplating, and sacrificial layer release to fabricate 594 all-gold grids per 4-inch wafer without individual grid handling. A numerical electroplating model provides a quantitative framework to relate gold deposition, grid-bar thickness, and tilt-compatible grid geometry. We show that oval 2 {micro}m x 6 {micro}m foil holes bias on-grid actin organization by substrate geometry alone, without chemical micropatterning. The EM grids supported a 2.15 [A] apoferritin single-particle reconstruction on a 200 kV cryo-TEM and are compatible with protein micropatterning and cell culture. This platform establishes an accessible route to programmable, application-specific all-gold cryo-EM supports that couple high-resolution structural imaging with engineered control of cellular organization.

Cell Biology↗

Cryo-ET reveals nanoscale thick filamentdisorganization in MYH7 P710R hypertrophiccardiomyopathy cardiomyocytes

Hypertrophic cardiomyopathy (HCM) is the most common monogenic inherited heart disease and is a major cause of sudden death in individuals under 35 years of age. HCM is associated with progressive tissue-level disarray and subcellular disorganization in individual cardiomyocytes. Mutations in {beta}-cardiac myosin (MYH7), the second most common genetic cause of HCM, commonly result in changes in sarcomeric force production, but how this leads to altered cell- and tissue-level organization is unclear. Here, we use cryo-electron tomography (cryo-ET) to bridge the molecular and cellular scales by visualizing the nanoscale organization of individual myosin-containing thick filaments within sarcomeres of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Compared to isogenic wild-type controls, hiPSC-CMs expressing P710R MYH7 exhibit pronounced disruption of the hexagonal packing of thick filaments within individual sarcomeres, which would be difficult to visualize using conventional light microscopy or even room-temperature electron microscopy. We also observe ribosome infiltration into areas of sarcomeric disorder for both wild-type and P710R MYH7 hiPSC-CMs, suggesting that disordered regions may be sites of local proteostasis or remodeling. Together, these data illuminate how altered myosin activity can propagate to yield dramatic changes in sarcomeric organization in HCM.

cell biology↗

Cryogenic Electron Tomography Redefines Herpesvirus Capsid Assembly Intermediates Inside the Cell Nucleus.

Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been characterized, but their roles in herpesvirus replication remain controversial. The status of the capsid vertex-specific component (CVSC), essential for capsid stability and dsDNA packaging and retention, is also unclear. By integrating cryogenic focused ion beam milling with electron tomography and subtomogram averaging, we derived atomic models for all protein components, including the CVSC, across different herpesvirus capsid types within infected cell nuclei. Focused classification of pentonal vertex densities revealed differences in CVSC occupancy between genome-filled capsids and capsids lacking dsDNA, highlighting structural heterogeneity and providing insight into distinct capsid assembly stages in situ. These intra-nuclear findings redefine the maturation model of herpesvirus capsid assembly, advancing the understanding of herpesvirus replication, and demonstrate the effectiveness of in situ electron imaging by studying virus assembly within host cells.

microbiology↗

DynaMiCs - Dynamic cell-type deconvolution ensembles for Mapping in mixed Conditions

Single-cell techniques facilitate the molecular analysis of individual cells, providing insights into cellular diversity, function, and the complexity of biological systems. However, their application is typically limited to small-scale studies involving individual or a few dozen samples, as a consequence of costs and experimental requirement. This complicates the inference of robust conclusions about populations. Bulk transcriptomics offers cost-efficient measurements with low experimental requirements. However, the cellular resolution is lost and only a complex linear combination of signals from multiple cells is observed. Thus, gene expression changes cannot be attributed to individual cells or cell populations. Cell-type deconvolution methods infer cellular compositions from bulk transcriptomics data. State-of-the-art approaches use single-cell data to build molecular reference profiles and identify powerful cell-type markers for improved deconvolution. In this context, we propose Dynamic cell-type deconvolution ensembles for Mapping in mixed Conditions (DynaMiCs) for the integration of single-cell and bulk transcriptomics data. Specifically, DynaMiCs dynamically extracts information from single-cell experiments to (1) provide more accurate estimates of cellular compositions, and (2) establish a mapping between bulk and single-cell data. Consequently, DynaMiCs enables the investigation of how cell populations change in both quantity and molecular characteristics between different phenotypes, informed by single-cell experiments.

bioinformatics↗

An engineered platform to study the influence of extracellular matrix nanotopography on cell ultrastructure

Nanoscale fabrication techniques have played an essential role in revealing the impact of extracellular matrix (ECM) nanotopography on cellular behavior. However, the mechanisms by which nanotopographical cues from the ECM influence cellular function remain unclear. To approach these questions, we have engineered a novel class of nanopatterned ECM constructs suitable for cryogenic electron tomography (cryo-ET), the highest resolution modality for imaging frozen hydrated cells in 3D. We electrospun aligned and randomly oriented ECM fibers directly onto transmission electron microscopy (TEM) supports to generate fibrous scaffolds that mimic physiological ECM in healthy (organized ECM) and diseased (disorganized ECM) states. We produced fibers from gelatin without toxic additives and crosslinked them to maintain structural stability in aqueous environments. The electrospun fibers had an average fiber diameter of hundreds of nanometers, within the physiological range. We confirmed that the TEM supports can serve as viable cell culture substrates that can influence cell organization and demonstrated their compatibility with plunge freezing and cryo-ET. By enabling nanoscale structural analysis inside cells on substrates with programmable topographies, this platform can be used to study the physical cues necessary for healthy endothelial tissue formation and pathologies that are linked to endothelial dysfunction in diseases such as peripheral arterial disease.

biophysics↗

Cryo-electron tomography reveals the structural diversity of cardiac proteins in their cellular context

Cardiovascular diseases are a leading cause of death worldwide, but our understanding of the underlying mechanisms is limited, in part because of the complexity of the cellular machinery that controls the heart muscle contraction cycle. Cryogenic electron tomography (cryo-ET) provides a way to visualize diverse cellular machinery while preserving contextual information like subcellular localization and transient complex formation, but this approach has not been widely applied to the study of heart muscle cells (cardiomyocytes). Here, we deploy an optimized cryo-ET platform that enables cellular-structural biology in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Using this platform, we reconstructed sub-nanometer resolution structures of the human cardiac muscle thin filament, a central component of the contractile machinery. Reconstructing the troponin complex, a regulatory component of the thin filament, from within cells, we identified previously unobserved conformations that highlight the structural flexibility of this regulatory complex. We next measured the impact of chemical and genetic perturbations associated with cardiovascular disease on the structure of troponin. In both cases, we found changes in troponin structure that are consistent with known disease phenotypes--highlighting the value of our approach for dissecting complex disease mechanisms in the cellular context.

biophysics↗

Extracellular filaments revealed by affinity capture cryo-electron tomography of lymphocytes

Cryogenic-electron tomography (cryo-ET) has provided an unprecedented glimpse into the nanoscale architecture of cells by combining cryogenic preservation of biological structures with electron tomography. Micropatterning of extracellular matrix proteins is increasingly used as a method to prepare adherent cell types for cryo-ET as it promotes optimal positioning of cells and subcellular regions of interest for vitrification, cryo-focused ion beam (cryo-FIB) milling, and data acquisition. Here we demonstrate a micropatterning workflow for capturing minimally adherent cell types, human T-cells and Jurkat cells, for cryo-FIB and cryo-ET. Our affinity capture system facilitated the nanoscale imaging of Jurkat cells, revealing extracellular filamentous structures. It improved workflow efficiency by consistently producing grids with a sufficient number of well positioned cells for an entire cryo-FIB session. Affinity capture can be extended to facilitate high resolution imaging of other adherent and non-adherent cell types with cryo-ET.

cell biology↗

VTA dopamine neurons drive spatiotemporally heterogeneous striatal dopamine signals during learning

Environmental cues, through Pavlovian learning, become conditioned stimuli that invigorate and guide animals toward acquisition of rewards. Dopamine neurons in the ventral tegmental area (VTA) and substantia nigra (SNC) are crucial for this process. Dopamine neurons are embedded in a reciprocally connected network with their striatal targets, the functional organization of which remains poorly understood. Here, we investigated how learning during optogenetic Pavlovian cue conditioning of VTA or SNC dopamine neurons directs cue-evoked behavior and shapes subregion-specific striatal dopamine dynamics. We used a fluorescent dopamine biosensor to monitor dopamine in the nucleus accumbens (NAc) core and shell, dorsomedial striatum (DMS), and dorsolateral striatum (DLS). We demonstrate spatially heterogeneous, learning-dependent dopamine changes across striatal regions. While VTA stimulation evoked robust dopamine release in NAc core, shell, and DMS, cues predictive of this activation preferentially recruited dopamine release in NAc core, starting early in training, and DMS, late in training. Corresponding negative prediction error signals, reflecting a violation in the expectation of dopamine neuron activation, only emerged in the NAc core and DMS, and not the shell. Despite development of vigorous movement late in training, conditioned dopamine signals did not similarly emerge in the DLS, even during Pavlovian conditioning with SNC dopamine neuron activation, which elicited robust DLS dopamine release. Together, our studies show broad dissociation in the fundamental prediction and reward-related information generated by different dopamine neuron populations and signaled by dopamine across the striatum. Further, they offer new insight into how larger-scale plasticity across the striatal network emerges during Pavlovian learning to coordinate behavior.

neuroscience↗

Lattice micropatterning of electron microscopy grids for improved cellular cryo-electron tomography throughput

Cryo-electron tomography is the highest resolution tool available for structural analysis of macromolecular complexes within their native cellular environment. At present, data acquisition suffers from low throughput, in part due to the low probability of positioning a cell such that the subcellular structure of interest is on a region of the electron microscopy (EM) grid that is suitable for imaging. Here, we photo-micropatterned EM grids to optimally position endothelial cells so as to enable high-throughput imaging of cell-cell contacts. Lattice micropatterned grids increased the average distance between intercellular contacts and the thicker cell nuclei such that the regions of interest were sufficiently thin for direct imaging. We observed a diverse array of membranous and cytoskeletal structures at intercellular contacts, demonstrating the utility of this technique in enhancing the rate of data acquisition for cellular cryo-electron tomography studies.

bioengineering↗

Extracellular matrix micropatterning technology for whole cell cryogenic electron microscopy studies

Cryogenic electron tomography is the highest resolution tool available for structural analysis of macromolecular organization inside cells. Micropatterning of extracellular matrix (ECM) proteins is an established in vitro cell culture technique used to control cell shape. Recent traction force microscopy studies have shown correlation between cell morphology and the regulation of force transmission. However, it remains unknown how cells sustain increased strain energy states and localized stresses at the supramolecular level. Here, we report a technology to enable direct observation of mesoscale organization in epithelial cells under morphological modulation, using a maskless protein photopatterning method to confine cells to ECM micropatterns on electron microscopy substrates. These micropatterned cell culture substrates can be used in mechanobiology research to correlate changes in nanometer-scale organization at cell-cell and cell-ECM contacts to strain energy states and traction stress distribution in the cell.

bioengineering↗