Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4520 - 4545

Published: Aug. 1, 2024

Language: Английский

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Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 11, 2025

SUMMARY Here, we report the spatial organization of RNA transcription and associated enhancer dynamics in human spinal cord at single-cell single-molecule resolution. We expand traditional multiomic measurements to reveal epigenetically poised bivalent active transcriptional states that define cell type specification. Simultaneous detection chromatin accessibility histone modifications nuclei reveals previously unobserved cell-type specific cryptic activity, which activation is uncoupled from accessibility. Such enhancers both stable identity transitions between cells undergoing differentiation. also glial gene regulatory networks reorganize along rostrocaudal axis, revealing anatomical differences regulation. Finally, identify into distinct cellular organizations address functional significance this observation context paracrine signaling. conclude diversity best captured through lens state intercellular interactions drive state. This study provides fundamental insights healthy cord.

Language: Английский

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A scoping study of the whole-cell imaging literature: a foundational corpus, potential for data-mining and research synthesis, and a call for standardization of an emerging field

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 4, 2025

ABSTRACT The level of cellular organization bridging the mesoscale and whole-cell scale is coming into focus as a new frontier in cell biology. Great progress has been made unraveling complex physical functional interconnectivity organelles, but how entire organelle network spatially arranges within cytoplasm only beginning to be explored. Drawing on cross-disciplinary research synthesis methods, we systematically curated volumetric imaging literature through 3 rounds screening involving independent reviewers, resulting 89 top hits 38 “borderline” studies. We describe trajectory current state field (2004-2024). A broad characterization, or “scoping review”, bibliometrics, study design, reporting practices shows accelerating technological development output. find high variability design practices, including modality, model organism, contexts, organelles imaged, analyses. Due laborious, low-throughput nature most trends toward small sample sizes (<30 cells) types. common quantitative analyses across studies, ratios inter-organelle contact Our dataset now enables future aggregate comparative potentially reveal larger patterns generate more generalized hypotheses. This work establishes growing data, motivates call for standardized reporting, data sharing practices. More broadly, showcase potential rigorous secondary methods strengthen biology’s review reproducibility toolkit, create avenues discovery, promote open that support data-reuse integration.

Language: Английский

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Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions

Published: March 11, 2025

A current challenge in bioimaging for immunology and immunotherapy research lies analyzing multimodal multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed high-performance, end-to-end analysis of image-based vitro immune assays. Purpose-built multicondition, 2D multichannel time-lapse microscopy mixed populations, Celldetective is optimized the needs The seamlessly integrates AI-based segmentation, Bayesian tracking, automated single-cell event detection, all within intuitive graphical interface supports interactive visualization, annotation, training capabilities. We demonstrate its utility with original on effector activating surface, mediated by bispecific antibodies, further showcase potential extensive sets pairwise antibody-dependent cytotoxicity events.

Language: Английский

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Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions

Published: March 11, 2025

A current challenge in bioimaging for immunology and immunotherapy research lies analyzing multimodal multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed high-performance, end-to-end analysis of image-based vitro immune assays. Purpose-built multicondition, 2D multichannel time-lapse microscopy mixed populations, Celldetective is optimized the needs The seamlessly integrates AI-based segmentation, Bayesian tracking, automated single-cell event detection, all within intuitive graphical interface supports interactive visualization, annotation, training capabilities. We demonstrate its utility with original on effector activating surface, mediated by bispecific antibodies, further showcase potential extensive sets pairwise antibody-dependent cytotoxicity events.

Language: Английский

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Representing Mitochondrial Dynamics with Abstract Algebra

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 18, 2025

This paper addresses the increasing need for comprehensive mathematical descriptions of cell organization by examining algebraic structure mitochondrial network dynamics. Mitochondria are cellular structures involved in metabolism that take form a membrane-based tubes undergo continuous re-arrangement set morphological processes, including fission and fusion, carried out protein-based machinery. Because their structure, mitochondria can be represented as graphs, operations place cell, referred to dynamics, changes graphs. Prior studies have classified graphs based on graph-theoretic features, but an alternative approach is focus not themselves inducing since this may provide simpler representation. Moreover, what determine will generated biological system. Here we show dynamics single connected mitochondrion constitute groupoid includes automorphism group each graph. For multi-component define graph encapsulates Using these formalisms distance metric similarity between edit distance. In course defining motivation new experimental questions regarding fusion impacts division morphology. work points general strategy formulating state-space, shapes structures, relations dynamic produce them.

Language: Английский

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A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 21, 2024

SUMMARY Organ function requires coordinated activities of thousands genes in distinct, spatially organized cell types. Understanding the basis emergent tissue approaches to dissect genetic control diverse cellular and phenotypes vivo . Here, we develop paired imaging sequencing methods construct large-scale, multi-modal genotype-phenotypes maps with pooled perturbations. Using imaging, identify perturbations individual cells while simultaneously measuring their gene expression subcellular morphology. single-cell sequencing, measure transcriptomic responses same We apply this approach study hundreds mouse liver. Our reveals regulators hepatocyte zonation liver unfolded protein response, as well distinct pathways that cause steatosis. enables new ways interrogating complex organismal physiology provides crucial training data for emerging machine-learning models function.

Language: Английский

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Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 3, 2024

Summary Cell atlas projects have nominated recurrent transcriptional states as drivers of biological processes and disease, but their origins, regulation, properties remain unclear. To enable complementary functional studies, we developed a scalable approach for recapitulating cell in vitro using CRISPR activation (CRISPRa) Perturb-seq. Aided by novel multiplexing method, activated 1,836 transcription factors two types. Measuring 21,958 perturbations showed that CRISPRa targets within physiological ranges, epigenetic features predicted activatable genes, the protospacer seed region drove an off-target effect. Perturbations recapitulated vivo fibroblast states, including universal inflammatory identified KLF4 KLF5 key regulators state. Inducing state suppressed disease-associated highlighting its therapeutic potential. Our findings cement tool perturbing differentiated cells indicate can be elicited via perturbation, enabling studies clinically relevant ex .

Language: Английский

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Enhanced endogenous gene tagging in human induced pluripotent stem cells via AAV6-mediated donor delivery

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 25, 2024

Systematically tagging endogenous proteins with fluorescent markers in human induced pluripotent stem cells (hiPSCs) allows observation of live cell dynamics different states. However, the precise insertion into via CRISPR/Cas9-induced editing relies on homology-directed repair (HDR). The nonhomologous end-joining (NHEJ) DNA pathway often outcompetes HDR, resulting irreversible insertions and deletions (INDELs) low knock-in efficiency. Recognizing successful HDR-mediated events is an additional challenge when target gene not expressed cannot be immediately observed. To address these challenges, we used: 1) adeno-associated virus serotype 6 (AAV6) mediated donors at optimized multiplicity infection (MOI) to deliver tag payloads maximal efficiency; 2) titrated, multiplexed Cas9:gRNA ribonucleo-protein (RNP) amounts assure balanced HDR/INDEL frequency among conditions; 3) long-amplicon droplet digital PCR (ddPCR) measure HDR-generated alleles edited pools; 4) simultaneous Inference CRISPR Edits (ICE) detect thereby avoid conditions significantly saturated (>50%) INDELs. These approaches enabled us identify efficient accurate recover tagged cells, including loci cells. Together steps allowed develop methodology workflow clonally isolate directly from ideal pool optimal HDR minimized INDEL frequencies. Using this approach, achieved both monoallelic biallelic four genes that are turned during differentiation but initially hiPSCs, where direct selection based fluorescence was impossible: TBR2, TBXT, CDH2 (pro-differentiation pro-migratory genes), CDH5 (endothelial specific gene). Through a systematic evaluation various gRNA sequences RNP concentrations, identified for each high frequencies, peaking 38.6%, while also avoiding INDELs, isolation clones allele trans unedited difficult. Over-all, enhances efficiency facilitating reliable image-based cellular processes, enables recovery accurately mono- biallelically clones. We standardized yield general introducing large knock-ins hiPSCs.

Language: Английский

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The intrinsic dimension of gene expression during cell differentiation

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 6, 2024

Abstract Waddington’s epigenetic landscape has long served as a conceptual framework for understanding cell fate decisions. The landscape’s geometry encodes the molecular mechanisms that guide gene expression profiles of uncommitted cells toward terminally differentiated types. In this study, we demonstrate applying concept intrinsic dimension to single-cell transcriptomic data can effectively capture trends in trajectories, supporting framework. This approach allows us define robust potency score without relying on prior biological information. By analyzing an extensive collection datasets from various species, experimental protocols, and differentiation processes, validate our method successfully reproduce established hierarchies type potency.

Language: Английский

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