ArticleNature biotechnology2023
Spatial transcriptomics for profiling the tropism of viral vectors in tissues.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 50 citations in OpenAlex.
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- Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits.Nature communications · 2026Article
- Bi-directional highways and super-seeder tissues underpin parasite dissemination in experimental Leishmania donovani infection.Nature communications · 2026Article
- Crosstalk of noradrenergic CaCell communication and signaling : CCS · 2026Article
- Review
- Defining a Midgestational Window forbioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomics and single-nucleus RNA sequencing reveal rAAV2- and rAAV9-specific transduction signatures in the mouse liver.Gene therapy · 2026Article
- Technical and biological sources of noise confound multiplexed enhancer AAV screening.Nature communications · 2026Article
- Dual AAV vectors for efficient delivery of large transgenes.Nature protocols · 2026Review
- Identification of Recombinant Adeno-Associated Virus Serotypes by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.Analytical chemistry · 2026Article
- Spatial mapping of barcoded, brain-tropic AAVs using multiplexed RNAMolecular therapy. Advances · 2026Article
- Adeno-Associated Virus (AAV) for Tracking Neural Development and Connectivity in Xenopus.Methods in molecular biology (Clifton, N.J.) · 2026Article
- CD163+ perivascular macrophages in schizophrenia: a research framework for testing macrophage-related mechanisms.Frontiers in psychiatry · 2026Article
- Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo.Nature biotechnology · 2026Article
- Targeted Intracellular Delivery via Precision Programming of ARRDC1-Mediated Microvesicles.Journal of extracellular vesicles · 2025Article
- Roadmap for direct and indirect translation of optogenetics into discoveries and therapies for humans.Nature neuroscience · 2025Review
- Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets.bioRxiv : the preprint server for biology · 2025Article
- Spatial Transcriptomics to Study Virus-Host Interactions.Annual review of virology · 2025Review
- An AAV capsid proposed as microglia-targeting directs genetic expression in forebrain excitatory neurons.Cell reports methods · 2025Article
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8 authors at 1 institution in 1 country.
Funding
Abstract
A barrier to advancing engineered adeno-associated viral vectors (AAVs) for precision access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in vivo transduction profiles. In this study, we developed an ultrasensitive, sequential fluorescence in situ hybridization (USeqFISH) method for spatial transcriptomic profiling of endogenous and viral RNA with a short barcode in intact tissue volumes by integrating hydrogel-based tissue clearing, enhanced signal amplification and multiplexing using sequential labeling. Using USeqFISH, we investigated the transduction and cell subtype tropisms across mouse brain regions of six systemic AAVs, including AAV-PHP.AX, a new variant that transduces robustly and efficiently across neurons and astrocytes. Here we reveal distinct cell subtype biases of each AAV variant, including a bias of AAV-PHP.N toward excitatory neurons. USeqFISH also enables profiling of pooled regulatory cargos, as we show for a 13-variant pool of microRNA target sites in AAV genomes. Lastly, we demonstrate potential applications of USeqFISH for in situ AAV profiling and multimodal single-cell analysis in non-human primates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.