Imaging-based spatial transcriptomics technologies such as Multiplexed error-robust fluorescence in situ hybridization (MERFISH) can capture cellular processes in unparalleled detail. However, rigorous and robust analytical tools are needed to unlock their full potential for discovering subcellular biological patterns. We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. InSTAnT employs specialized statistical tests and algorithms to detect gene pairs and modules exhibiting intriguing patterns of co-localization, both within individual cells and across the cellular landscape. We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. We perform rigorous statistical assessment of discovered co-localization patterns, find supporting evidence from databases and RNA interactions, and identify associated subcellular domains. We uncover several cell type and region-specific gene co-localizations within the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.
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http://dx.doi.org/10.1038/s41467-024-49457-w | DOI Listing |
Microbiol Res
December 2024
Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla ES-41013, Spain; Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla ES-41013, Spain. Electronic address:
The Gram-negative bacterium Pseudomonas putida bears a tuft of flagella at a single cell pole. New flagella must be assembled de novo every cell cycle to secure motility of both daughter cells. Here we show that the coordinated action of FimV, FlhF and FleN sets the location, timing and number of flagella assembled.
View Article and Find Full Text PDFJ Am Chem Soc
December 2024
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.
Cellular activity is spatially organized across different organelles. While several structures are well-characterized, many organelles have unknown roles. Profiling biomolecular composition is key to understanding function but is difficult to achieve in the context of small, dynamic structures.
View Article and Find Full Text PDFMol Biol Cell
December 2024
Department of Neuroscience, Jefferson Center for Synaptic Biology, Vickie and Jack Farber Institute for Neuroscience, Sydney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107.
Development of neuronal connections is spatially and temporally controlled by extracellular cues which often activate their cognate cell surface receptors and elicit localized cellular responses. Here, we demonstrate the use of an optogenetic tool to activate receptor signaling locally to induce actin-mediated growth cone remodeling in neurons. Based on the light-induced interaction of light between Cryptochrome 2 (CRY2) and CIB1, we generated a bicistronic vector to co-expresses CRY2 fused to the intracellular domain of a guidance receptor and a membrane-anchored CIB1.
View Article and Find Full Text PDFACS Synth Biol
December 2024
Department of Biomedical Engineering, Rowan University, 201 Mullica Hill Rd, Glassboro, New Jersey 08028, United States.
Transmembrane receptors that endow mammalian cells with the ability to sense and respond to biomaterial-bound ligands will prove instrumental in bridging the fields of synthetic biology and biomaterials. Materials formed with thiol-norbornene chemistry are amenable to thiol-peptide patterning, and this study reports the rational design of synthetic receptors that reversibly activate cellular responses based on peptide-ligand recognition. This transmembrane receptor platform, termed Extracellular Peptide-ligand Dimerization Actuator (EPDA), consists of stimulatory or inhibitory receptor pairs that come together upon extracellular peptide dimer binding with corresponding monobody receptors.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
European Molecular Biology Laboratory, Cell Biology and Biophysics, Heidelberg, Germany.
MINFLUX is a super-resolution fluorescence microscopy technique that enables single-molecule tracking in live cells at a single-nanometer spatial and sub-millisecond temporal resolution. This chapter describes a method for tracking fluorescently labeled human kinesin-1 in live cells using MINFLUX and analyzing kinesin stepping dynamics.
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