EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expr...

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Published in:	Cell Vol. 184; no. 26; p. 6361
Main Authors:	Wang, Yuhan, Eddison, Mark, Fleishman, Greg, Weigert, Martin, Xu, Shengjin, Wang, Tim, Rokicki, Konrad, Goina, Cristian, Henry, Fredrick E, Lemire, Andrew L, Schmidt, Uwe, Yang, Hui, Svoboda, Karel, Myers, Eugene W, Saalfeld, Stephan, Korff, Wyatt, Sternson, Scott M, Tillberg, Paul W
Format:	Journal Article
Language:	English
Published:	United States 22.12.2021
Subjects:	Animals Biomarkers - metabolism Gene Expression Profiling Gene Expression Regulation Hypothalamic Area, Lateral - cytology Hypothalamic Area, Lateral - metabolism Imaging, Three-Dimensional In Situ Hybridization, Fluorescence Male Mice Mice, Inbred C57BL Neurons - metabolism Neuropeptides - metabolism Proto-Oncogene Proteins c-fos - metabolism RNA - metabolism RNA-Seq Single-Cell Analysis Transcription, Genetic expansion microscopy RNA brain anatomy Fluorescence in situ hybridization lateral hypothalamus transcriptomics 3D segmentation cell type brain
ISSN:	1097-4172, 1097-4172
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Abstract	Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.
AbstractList	Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization. Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.
Author	Wang, Tim Saalfeld, Stephan Sternson, Scott M Henry, Fredrick E Korff, Wyatt Rokicki, Konrad Weigert, Martin Yang, Hui Schmidt, Uwe Myers, Eugene W Fleishman, Greg Xu, Shengjin Wang, Yuhan Lemire, Andrew L Svoboda, Karel Tillberg, Paul W Eddison, Mark Goina, Cristian
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Keywords	expansion microscopy RNA brain anatomy Fluorescence in situ hybridization lateral hypothalamus transcriptomics 3D segmentation cell type brain
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SubjectTerms	Animals Biomarkers - metabolism Gene Expression Profiling Gene Expression Regulation Hypothalamic Area, Lateral - cytology Hypothalamic Area, Lateral - metabolism Imaging, Three-Dimensional In Situ Hybridization, Fluorescence Male Mice Mice, Inbred C57BL Neurons - metabolism Neuropeptides - metabolism Proto-Oncogene Proteins c-fos - metabolism RNA - metabolism RNA-Seq Single-Cell Analysis Transcription, Genetic
Title	EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization
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