Biology subjects

Alon, S.

Publications and source records attributed to Alon, S..

4 recordsLinked to original sources

bioRxiv2025

Super-Resolved Spatial Transcriptomics Reveals Early Changes in RNA Localization in the 5xFAD Hippocampus

Cell-type-specific changes in gene expression and RNA localization are hallmarks of Alzheimers disease (AD) and other neurodegenerative disorders, yet spatial dysregulation in early disease stages remains poorly defined. Here, we applied Expansion Sequencing (ExSeq) to map the spatial distribution of 101 genes at super-resolution in the hippocampus of 4-week-old 5xFAD and wild-type (WT) mice, prior to overt pathology. We uncovered early alterations in RNA spatial organization and gene expression, including 23 genes showing altered localization without changes in abundance in the 5xFAD hippocampus. Using spatial expression analysis and single-cell neighborhood analysis, we identified cell-type- and region-specific molecular programs associated with synaptic function, neuroinflammation, and metabolic stress that differed between 5xFAD and WT mice. Spatial RNA velocity further revealed state differences influenced by local cell to cell interactions. Together, these results suggest that RNA positioning and transcriptional programs are perturbed at early disease stages. Finally, we provide the full super-resolution ExSeq dataset as an open resource for spatial and cell-type-specific analyses in early Alzheimers disease research. HighlightsO_LISuper-resolved transcriptomic profiling of the hippocampus at early disease stages C_LIO_LIIdentification of 23 genes with altered spatial localization without changes in abundance C_LIO_LIEarly alterations in single-cell neighborhood organization in the 5xFAD hippocampus C_LIO_LISpatial RNA velocity reveals cell-type-specific cell state differences shaped by cell-cell proximity C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/678295v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1b46cf2org.highwire.dtl.DTLVardef@5cc55eorg.highwire.dtl.DTLVardef@a1ade4org.highwire.dtl.DTLVardef@9f833e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics

Mapping and molecularly annotating mammalian neural circuits is challenging due to the inability to uniquely label cells while also resolving subcellular features such as synaptic proteins or fine cellular processes. We argue that an ideal technology for connectomics would have the following characteristics: the capacity for robust distance-independent labeling, synaptic resolution, molecular interrogation, and scalable computational methods. The recent development of high-diversity cellular barcoding with RNA has provided a way to overcome the labeling limitations associated with spectral dyes, however performing all-optical circuit mapping has not been demonstrated because no method exists to image barcodes throughout cells at synaptic-resolution. Here we show ExBarSeq, an integrated method combining in situ sequencing of RNA barcodes, immunostaining, and Expansion Microscopy coupled with an end-to-end software pipeline that automatically extracts barcode identities from large imaging datasets without data processing bottlenecks. As a proof of concept, we applied ExBarSeq to thick tissue sections from mice virally infected with MAPseq viral vectors and demonstrated the extraction of 50 barcoded cells in the visual cortex as well as cell morphologies uncovered via immunostaining. The current work demonstrates high resolution multiplexing of exogenous barcodes and endogenous synaptic proteins and outlines a roadmap for molecularly annotated connectomics at a brain-wide scale.

neuroscience↗

bioRxiv2020

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

AbstractMethods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale. One Sentence SummaryIn situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.

genomics↗

bioRxiv2018

Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses

We present Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In-Situ analysis (BOLORAMIS), a reverse-transcription (RT)-free method for spatially-resolved, targeted, in-situ RNA identification of single or multiple targets. For this proof of concept, we have profiled 154 distinct coding and small non-coding transcripts ranging in sizes 18 nucleotides in length and upwards, from over 200, 000 individual human induced pluripotent stem cells (iPSC) and demonstrated compatibility with multiplexed detection, enabled by fluorescent in-situ sequencing. We use BOLORAMIS data to identify differences in spatial localization and cell-to-cell expression heterogeneity. Our results demonstrate BOLORAMIS to be a generalizable toolset for targeted, in-situ detection of coding and small non-coding RNA for single or multiplexed applications.

cell biology↗