GDB2023-Visium_SPG_AD

Transcript

1. @lcolladotor
   lcolladotor.github.io
   lcolladotor.github.io/bioc_team_ds
   Applying Visium Spatial
   Proteogenomics (Visium-SPG) to
   study Alzheimer’s Disease
   Leonardo Collado Torres #Visium_SPG_AD
   May 17th 2023
   #GBD23
   Slides available at speakerdeck.com/lcolladotor
   

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2. twitter.com/sanghokwon17/status/1650589385379962881 from 2023-04-24
   Sang Ho Kwon
   @sanghokwon17
   DOI: 10.1101/2023.04.20.537710
   #Visium_SPG_AD
   

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3. DOI: 10.1038/s41593-020-00787-0
   twitter.com/lcolladotor/status/1233661576433061888 from 2020-02-29
   

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4. DOI: 10.1038/s41593-020-00787-0
   twitter.com/lcolladotor/status/1233661576433061888 from 2020-02-29
   DOI 10.1093/bioinformatics/btac299
   Since Feb 2020
   spatialLIBD::fetch_data()
   provides access to
   SpatialExperiment
   R/Bioconductor objects
   

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5. DOI: 10.1038/s41593-020-00787-0
   twitter.com/lcolladotor/status/1233661576433061888 from 2020-02-29
   twitter.com/CrowellHL/status/1597579271945715717
   DOI 10.1093/bioinformatics/btac299
   Since Feb 2020
   spatialLIBD::fetch_data()
   provides access to
   SpatialExperiment
   R/Bioconductor objects
   

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6. Visium spatial clustering works for variables with high %
   variance explained. But what about other ones?
   DOI: 10.1038/s41593-020-00787-0
   

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7. Alzheimer’s disease related neuropathology
   Adopted and modified from B Wang (2018) and the Brain from the Top to Bottom in McGill University
   20 um
   Sang Ho Kwon
   Amyloid beta
   pTau
   

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8. Hypothesis
   Local tissue microenvironments in close proximity to AD-related
   neuropathology have distinct cellular and molecular signatures. Sang Ho Kwon
   

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9. Visium Spatial Proteogenomics (Visium-SPG)
   Visium-SPG = Visium SRT + immunofluorescence
   (using identical tissue samples)
   Sang Ho Kwon
   

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10. Experimental design & study overview
    Braak V-VI & CERAD frequent
    Sang Ho Kwon
    

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11. AD pathology signal is too small to detect by
    spatially-resolved gene expression alone research.libd.org/Visium_SPG_AD/
    

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12. Visium
    * ~5k spots in honeycomb
    * gene expression per spot
    * tissue (H&E staining)
    Immunofluorescence (IF)
    * multi-channel (6) images
    * identifies morphological features of interest
    * large: might be broken in tiles
    Channel 1
    * triangle feature
    Channel 2
    * cloud feature
    Channel 6
    * xyz feature
    Tissue (bright field image)
    Visium spot
    Channel 1 feature
    Channel 2 feature
    +
    Visium Spatial Proteogenomics (Visium-SPG / IF) raw data: 2 types
    

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13. Spot ID Gene 1 Gene 2 Gene X
    spot0001 0 12 39
    spot0002 4 0 27
    Spot ID Gene 1 Gene 2 Gene X In Tissue # cells
    spot0001 0 12 39 true 3
    spot0002 4 0 27 false 0
    * spaceranger
    * Loupe Browser
    * VistoSeg on H&E bright
    field image
    Visium Analysis
    @MadhaviTippani
    @HeenaDivecha
    cell
    VistoSeg DOI:
    10.1101/2021.08.04.452489
    

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14. Feature ID X center Y center type intensity
    feat0001 5 102 triangle 130.4
    feat0002 10 30 cloud 99.1
    Max (X, Y)
    Min (X, Y)
    Area
    ...
    SPG / IF Image Analysis
    * segment each
    channel
    * find features
    Challenges:
    * morphological
    features can be
    quite diverse
    * images are large
    * multiple tiles
    +
    

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15. Spot ID # Triangle # Cloud % triangle % cloud
    spot0001 0 12 0 17
    spot0002 4 0 27 0
    Merge Visium & IF
    IF
    Spot ID Gene 1 Gene 2 Gene X In Tissue # cells
    spot0001 0 12 39 true 3
    spot0002 4 0 27 false 0
    Visium
    downstream
    * QC
    * analyses
    spatialLIBD DOI:
    10.1186/s12864-022-08601-w
    VistoSeg DOI:
    10.1101/2021.08.04.452489
    Check version 2!!
    @MadhaviTippani
    

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16. Estimating pathological burden per spot
    to generate transcriptome-scale maps of AD pathology
    

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17. Identifying transcriptional signatures of AD-related neuropathology
    Principal component analysis
    Sang Ho Kwon
    

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18. Identifying transcriptional signatures of Abeta-related neuropathology
    Sang Ho Kwon
    

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19. Validation study design using RNAscope FISH-IF
    Sang Ho Kwon
    

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20. bioconductor.org/packages/spatialLIBD
    Pardo et al, 2022 DOI 10.1186/s12864-022-08601-w
    Maynard, Collado-Torres, 2021 DOI 10.1038/s41593-020-00787-0
    Brenda Pardo Abby Spangler
    @PardoBree @abspangler
    Louise A. Huuki-Myers
    @lahuuki
    Check her #GDB2023
    poster for more!
    Session 1: #7
    

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21. Conclusions
    • Visium-SPG can identify local transcriptional signatures of late-stage AD pathology
    • RNAscope FISH-IF can further explore spatial gene expression patterns of a few select
    features
    • Proof-of-concept study: our work lays the groundwork. Can now use Visium-SPG for other
    diseases too
    • Future studies are needed to produce mechanistic insights
    • Explore our code & data at research.libd.org/Visium_SPG_AD & download it with
    spatialLIBD::fetch_data()
    ○ There’s lots more to explore with this data!
    Sang Ho Kwon
    Slide adapted from:
    

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22. Contributors for this project
    Investigation
    Data analysis
    Mentorship
    Web resources
    Sang Ho Kwon
    @sanghokwon17
    #Visium_SPG_AD
    In collaboration with
    Slides available at
    speakerdeck.com
    /lcolladotor
    Download data with
    spatialLIBD::fetch_data()
    Madhavi Tippani
    Keri Martinowich Kristen Maynard
    Sowmya Parthiban Jashandeep Lobana
    Stephanie Hicks Stephanie Page
    Heena Divecha
    Nicholas Eagles
    

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24. Identifying transcriptional signatures of Abeta microenvironment
    VS
    Neural plasticity*
    Previously not significant
    Sang Ho Kwon
    

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25. 6 Abeta-associated DEGs on RNAscope FISH-IF
    (Kruskal-Wallis test,
    *p<0.05, &p<0.005, and #p<0.0001)
    Sang Ho Kwon
    

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26. Visium + RNAscope
    to provide additional insights into spatial gene expression gradients
    Sang Ho Kwon
    

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