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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.
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MINFLUX is a promising new development in single-molecule localization microscopy, claiming a resolution of 1-3 nm in living and fixed biological specimens. While MINFLUX can achieve very high localisation precision, quantitative analysis of reported results leads us to dispute the resolution claim and question reliability for imaging sub-100-nm structural features, in its current state.
Although directed evolution has been remarkably successful at expanding the chemical and functional boundaries of biology, it is limited by the robustness and flexibility of available selection platforms - traditionally designed around a single desired function with limited scope for alternative applications. We report SNAP as a quantitative reporter for bacterial cell display, which enabled fast troubleshooting and systematic development of the selection platform. In addition, we demonstrate that even weak interactions between displayed proteins and nucleic acids can be harnessed towards specific labelling of bacterial cells, allowing functional characterisation of DNA binding proteins and enzymes. Together, this establishes bacterial display as a viable route towards the systematic engineering of all ligands and enzymes required for the development of XNA molecular biology.
T cells typically recognize their ligands using a defined cell biology - the scanning of their membrane microvilli to palpate their environment - while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise as well as a tractable means to study the interplay between receptor affinity, microvillar dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize microvillar scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing the affinity and/or avidity of binding brought synapse microvillar dynamics into natural ranges, normalized synapse resolution and improved downstream effector function. This work highlights the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.
Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), couples the measurement of surface marker proteins with simultaneous sequencing of mRNA at single cell level, which brings accurate cell surface phenotyping to single cell transcriptomics. Unfortunately, multiplets in CITE-seq datasets create artificial cell types and complicates the automation of cell surface phenotyping. We propose CITE-sort, an artificial-cell-type aware surface marker clustering method for CITE-seq. CITE-sort is aware of and is robust to multiplet-induced artificial cell types. We benchmarked CITE-sort with real and simulated CITE-seq datasets and compared CITE-sort against canonical clustering methods. We show that CITE-sort produces the best clustering performance across the board. CITE-sort not only accurately identifies real biological cell types but also consistently and reliably separates multiplet-induced artificial-cell-type droplet clusters from real biological-cell-type droplet clusters. In addition, CITE-sort organizes its clustering process with a binary tree, which facilitates easy interpretation and verification of its clustering result and simplifies cell type annotation with domain knowledge in CITE-seq.
We present the first example of in vivo high-resolution mass spectrometry (HRMS) for subcellular molecular systems biology of proteins and metabolites. With light microscopy, we identified the left-dorsal and left-ventral animal cells in cleavage-stage non-sentient Xenopus laevis embryos. Using precision-translated fabricated microcapillaries, the subcellular content of each cell was double-probed, each time collecting <5% of cell volume (~10 nL) swiftly (<5 s/event). The proteins and metabolites were analyzed by custom-built ultrasensitive capillary electrophoresis electrospray ionization employing Orbitrap and time-of-flight HRMS. Label-free detection of ~150 metabolites (57 identified) and 738 proteins found proteo-metabolomic networks with differential quantitative activities between the cell types. Spatially and temporally scalable sampling the technology preserved the integrity of the analyzed cells, the neighboring cells, and the embryo. 95% of the analyzed embryos developed into sentient tadpoles that were indistinguishable from their wild-type siblings based on anatomy and visual function in a background color preference assay.
Advances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challenging for individual scientists to effectively integrate and understand this data. We have developed a new data retrieval and indexing framework that allows us to integrate publicly available data from different sources and to combine publicly available data with new or bespoke datasets. Beyond a database search, our approach empowered testable hypotheses of new synthetic lethal gene pairs, genes associated with sex disparity, and immunotherapy targets in cancer. Our approach is straightforward to implement, well documented and is continuously updated which should enable individual users to take full advantage of efforts to map cancer cell biology.
Cell type atlases organize biological complexity by compressing high-dimensional molecular profiles into discrete cell types that can be mapped across tissues. Yet a principled theory of what constitutes a cell type remains lacking. Here, I introduce an information-theoretic framework in which molecularly defined cell type classifications are evaluated by the information content of the spatial maps they produce. The optimal taxonomy maximizes spatial information, constrained by molecular data, by balancing the entropy of the cell type code against the spatial entropy of the resulting map. The framework generalizes naturally to higher-order spatial partitions, including tissue regions defined by local cellular composition. Applied to a whole-brain mouse spatial transcriptomic dataset, this approach identifies optimal cell-type and region-level taxonomies that balance coding complexity with spatial informativeness. Together, these results establish a unified information-theoretic foundation for cell-type and region-level atlas construction grounded in tissue spatial architecture.
Schwann cells are critical for the proper development and function of the peripheral nervous system, where they form a mutually beneficial relationship with axons. Past studies have highlighted that a pair of proteins called the prohibitins play major roles in Schwann cell biology. Prohibitins are ubiquitously expressed and versatile proteins. We have previously shown that while prohibitins play a crucial role in Schwann cell mitochondria for long-term myelin maintenance and axon health, they may also be present at the Schwann cell-axon interface during development. Here, we expand on this work, showing that drug-mediated modulation of prohibitins in vitro disrupts myelination and confirming that Schwann cell-specific ablation of prohibitin 2 (Phb2) in vivo results in early and severe defects in peripheral nerve development. Using a proteomic approach in vitro, we identify a pool of candidate PHB2 interactors that change their interaction with PHB2 depending on the presence of axonal signals. Furthermore, we show in vivo that loss of Phb2 in mouse Schwann cells causes ineffective proliferation and dysregulation of transcription factors EGR2 (KROX20), POU3F1 (OCT6) and POU3F2 (BRN2) that are necessary for proper Schwann cell maturation. Schwann cell-specific deletion of Jun, a transcription factor associated with negative regulation of myelination, confers partial rescue of the development defect seen in mice lacking Schwann cell Phb2. This work develops our understanding of Schwann cell biology, revealing that Phb2 may directly or indirectly modulate the timely expression of transcription factors necessary for proper peripheral nervous system development, and proposing candidates that may play a role in PHB2-mediated integration of axon signals in the Schwann cell.
Optogenetics enables experiments in out-of-equilibrium conditions to clarify biological mechanisms and quantify biophysical parameters. However, modelling and control techniques to study mammalian cell biology under optogenetic perturbation remain underutilised. Here, we benchmark these methods within mammalian cells by steering nucleocytoplasmic transport via the optogenetic LEXY protein in outcome-driven microscopy. First, we employ system identification to obtain models that predict transport dynamics by minimising the prediction error. We quantify this prediction accuracy for one biophysical model and two black-box models. Second, we evaluate closed-loop control efficacy by steering transport along a predefined trajectory using model-free Proportional Integral (PI) control, model-based Linear Quadratic Regulation (LQR) and Model Predictive Control (MPC). Both the predictive models and the applied control techniques demonstrate robust performance against cell-to-cell variation. This biological variation is quantified by the parameter distributions obtained from model identification with single-cell trajectories. While we show that model-free techniques such as PI and gain-scheduled PI achieve steering without explict model knowledge, predictive architectures offer better performance under this cell-to-cell variation and time-varying setpoints. Moreover, black-box predictive accuracy suggests that this model-based control is possible, even when explicit mechanistic understanding is missing. Ultimately, we demonstrate that predictive modelling and optogenetics enable quantitative characterisation and precise manipulation of mammalian cells, while offering practical guidelines for the implementation of these techniques. SIGNIFICANCEOptogenetics provides the unique ability to steer cellular processes with light. Variable and localised light inputs allow us to extract more data and guide living cells to specific states. Despite this potential, application of predictive modelling and control techniques with optogenetics remain underutilised in mammalian cell biology. Here, we benchmark these techniques within mammalian cells to steer nucleocytoplasmic transport. Benchmarking these techniques demonstrates their direct applicability to mammalian systems, enabling the extraction of new biological insight in outcome-driven microscopy.
Transmission of malaria relies on the formation of sporozoites in the mosquito midgut and their subsequent invasion of the salivary gland. Despite their importance, our understanding of the cell biology of sporozoite formation and salivary gland invasion is limited. Here, we apply a technique called Mosquito Tissue Ultrastructure Expansion Microscopy (MoTissU-ExM), which physically expands infected mosquito tissues while preserving both host and parasite ultrastructure. Using MoTissU-ExM we are able to observe a range of parasite structures and organelles including features previously seen only by electron microscopy as well as structure not observed before. We leverage MoTissU-ExM to investigate a number of cell biology events during sporozoite formation and salivary gland invasion. In particular we focus on the rhoptries, a secretory organelle important for host cell invasion. We establish a timeline for sporozoite rhoptry biogenesis, show that two rhoptries are used up during salivary gland invasion, and provide the first evidence that rhoptry pairs are specialized for different invasion events. Building on this new knowledge, we characterize the rhoptry protein RON11 and identify it as the first protein involved in sporozoite rhoptry biogenesis. Disruption of RON11 led to the production of sporozoites that specifically fail to invade the salivary gland epithelial cell, thereby blocking transmission of these parasites.
Planarian flatworms are popular invertebrate models for basic research on stem cell biology and regeneration. These animals are commonly maintained on a diet of homogenized calf liver or boiled egg yolk in the laboratory, introducing a source of uncontrolled experimental variability. Here, we report the development of defined diets, prepared entirely from standardized, commercially sourced ingredients, for the freshwater species Schmidtea mediterranea, Dugesia japonica, and Girardia dorotocephala. These food sources provide an opportunity to test the effects of specific nutritional variables on biological phenomena of interest. Defined diet consumption was not sufficient for growth and only partially induced the increase in stem cell division that normally accompanies feeding, suggesting these responses are not solely determined by caloric intake. While our defined diet formulations do not support long-term planarian maintenance, they do enable delivery of double-stranded RNA for gene knockdown in a manner that provides unique advantages in some experimental contexts. We also present a new approach for preserving tissue integrity during hydrogen peroxide bleaching of liver-fed animals. These tools will empower research on the connections between diet, metabolism, and stem cell biology in the experimentally tractable planarian system.
Single-cell detection of multiple target analytes is an important goal in cell biology. However, due to the spectral overlap of common fluorophores, multiplexed fluorescence imaging beyond two-to-three targets inside living cells remains a technical challenge. Herein, we introduce a multiplexed imaging strategy that enables live-cell target detection via sequential rounds of imaging-and-stripping process, which is named as "sequential Fluorogenic RNA Imaging-Enabled Sensor" (seqFRIES). In seqFRIES, multiple orthogonal fluorogenic RNA aptamers are genetically encoded inside cells, and then the corresponding cell membrane permeable dye molecules are added, imaged, and rapidly removed in consecutive detection cycles. As a proof-of-concept, we have identified in this study five in vitro orthogonal fluorogenic RNA aptamer/dye pairs (>10-fold higher fluorescence signals), four of which can be used for highly orthogonal and multiplexed imaging in living bacterial and mammalian cells. After further optimizing the cellular fluorescence activation and deactivation kinetics of these RNA/dye pairs, the whole four-color semi-quantitative seqFRIES process can now be completed in [~]20 min. Meanwhile, seqFRIES-mediated simultaneous detection of two critical signaling molecules, guanosine tetraphosphate and cyclic diguanylate, was also achieved within individual living cells. We expect our validation of this new seqFRIES concept here will facilitate the further development and potential broad usage of these orthogonal fluorogenic RNA/dye pairs for highly multiplexed and dynamic cellular imaging and cell biology studies.
Maternally inherited bacteria can profoundly impact animal biology. A notable example is the induction of thelytokous parthenogenesis: the asexual production of female offspring. Despite decades of symbiont-mediated parthenogenesis documented across diverse arthropods, the underlying cell biological mechanisms remain poorly understood. In some species of parasitic wasps, Wolbachia causes a chromosome segregation failure during the first mitotic division in unfertilized haploid embryos. This diplodizes the embryo and facilitates asexual reproduction of females. To elucidate the mechanism of mitotic failure and understand how the animal continues development, we compared meiosis and early embryonic mitoses of the parasitoid wasp, Trichogramma pretiosum, with and without their parthenogenesis-inducing Wolbachia symbiont. We show that meiosis in these animals is anastral, and embryos undergo de novo microtubule organizing center (MTOC) biogenesis prior to the first embryonic mitosis, regardless of Wolbachia. During the first mitosis, embryos with Wolbachia had increased numbers of MTOCs associated with the oocyte nucleus and formed multipolar spindles in a modified metaphase, after which chromosome segregation failed. A restitution nucleus formed, and mitotic slippage enabled the diploid nucleus to transition to interphase and replicate. Subsequent mitotic divisions inherited supernumerary MTOCs, but formed pseudo-bipolar spindles and segregated normally. These results demonstrate that Wolbachia-mediated parthenogenesis stems from altered MTOC biology, provide a structural basis for mitotic failure and the subsequent restitution. Symbiont-mediated parthenogenesis offers unique opportunities to uncover the cell biology of asexual reproduction and a fascinating model for understanding mitosis more broadly.
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newtons laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. In this paper, we describe an approach to optimizing the use of transcription factors (TFs) in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a cell cycle synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points along the cell cycle. In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the TAD expression levels. Based on this dynamical model and known bioinformatics, such as transcription factor binding sites (TFBS) and functions, we develop a methodology for identifying the top transcription factor candidates for a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. Our data-guided methodology identifies a number of transcription factors previously validated for reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.\n\nSignificance StatementReprogramming the human genome toward any desirable state is within reach; application of select transcription factors drives cell types toward different lineages in many settings. We introduce the concept of data-guided control in building a universal algorithm for directly reprogramming any human cell type into any other type. Our algorithm is based on time series genome transcription and architecture data and known regulatory activities of transcription factors, with natural dimension reduction using genome architectural features. Our algorithm predicts known reprogramming factors, top candidates for new settings, and ideal timing for application of transcription factors. This framework can be used to develop strategies for tissue regeneration, cancer cell reprogramming, and control of dynamical systems beyond cell biology.
In vitro stem cell culture is demanding in terms of manpower and media supplements. In recent years, new protocols have been developed to expand pluripotent embryonic stem cells in suspension culture, which greatly simplifies cell handling and scalability. However, it is still unclear how suspension culture protocols with different supplements affect pluripotency, cell homogeneity and cell differentiation compared to established adherent culture methods. Here we tested four different culture conditions for mouse embryonic stem cells (mESC) and quantified chimerism and germ line transmission as well as in vitro differentiation into three-dimensional neuro-epithelia. We found that suspension culture supplemented with CHIR99021/LIF offers the best compromise between culturing effort, robust pluripotency and cell homogeneity. Our work provides a guideline for simplifying mESC culture and should encourage more cell biology labs to use stem cell-based organoids as model systems.
Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community. Significance statementSingle cells RNA sequencing has revolutionised cell biology, enabling high resolution analysis of cell types and states within human tissues. Here, we report a comprehensive spatial atlas of adult human skin across different anatomical sites and basal cell carcinoma (BCC) - the most common form of skin cancer - encompassing in vivo optical coherence tomography, single cell RNA sequencing, global spatial transcriptomic profiling and in situ sequencing. In combination these modalities have allowed us to assemble a comprehensive nuclear-resolution atlas of cellular identity in health and disease.
How cells translate growth factor (GF) signals into context-specific phenotypes remains a fundamental question in cell biology. The classical view holds that cells translate a constant concentration of a GF with specific chemical identity to a steady state activation of the underlying signaling pathway, resulting in a defined phenotypic response. However, recent findings suggest that even a single GF, when presented in a pulsatile manner, drives differential phenotypic responses depending on the frequency of stimulation. To reconcile these views, we introduce a novel conceptual framework of "signaling homeorhesis". Unlike homeostasis, homeorhesis describes the stable evolution of signaling trajectories over time. Defining this concept quantitatively using a dynamical systems framework, we use mathematical models of the Epidermal Factor Growth Receptor (EGFR) and the Tropomyosin receptor kinase A (TrkA) networks, as well as available experimental temporal protein activity recordings in PC-12 cells to demonstrate that cells classify GF signals to unique signaling trajectories that encode for distinct cell phenotypes, irrespective of the GF identity. We thereby propose that the cellular phenotype is determined in real-time, as the cell actively interprets the growth factor signals from its environment.
In order to drive productive tumor-infiltrating lymphocyte (TIL) function, myeloid populations must direct antigens to the lymph node, including to resident antigen-presenting cells (APCs) that have never touched the tumor. It has long been supposed that APCs trade antigens with one another, but the dominant cell biology underlying that remains unknown. We used in vitro and in vivo assays together with lattice light sheet and multiphoton imaging to show that myeloid cells carry tumor antigen-laden vesicles that they trade with one another as they reach distant sites. This accounts for the majority of antigen displayed to T cells and provides tumors with a mechanism to access APCs that differentially direct T cell activation away from memory phenotypes. This work defines efficient cell biology that drives the first steps of TIL generation and represents a new frontier for engineering tumoral immunity.