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
2. twitter.com/sanghokwon17/status/1650589385379962881 from 2023-04-24 Sang Ho Kwon @sanghokwon17 DOI: 10.1101/2023.04.20.537710 #Visium_SPG_AD
3. DOI: 10.1038/s41593-020-00787-0 twitter.com/lcolladotor/status/1233661576433061888 from 2020-02-29
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
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
6. Visium spatial clustering works for variables with high % variance explained. But what about other ones? DOI: 10.1038/s41593-020-00787-0
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
8. Hypothesis Local tissue microenvironments in close proximity to AD-related neuropathology have distinct cellular and molecular signatures. Sang Ho Kwon
9. Visium Spatial Proteogenomics (Visium-SPG) Visium-SPG = Visium SRT + immunofluorescence (using identical tissue samples) Sang Ho Kwon
10. Experimental design & study overview Braak V-VI & CERAD frequent Sang Ho Kwon
11. AD pathology signal is too small to detect by spatially-resolved gene expression alone research.libd.org/Visium_SPG_AD/
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
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
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 +
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
16. Estimating pathological burden per spot to generate transcriptome-scale maps of AD pathology
17. Identifying transcriptional signatures of AD-related neuropathology Principal component analysis Sang Ho Kwon
18. Identifying transcriptional signatures of Abeta-related neuropathology Sang Ho Kwon
19. Validation study design using RNAscope FISH-IF Sang Ho Kwon
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
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:
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
24. Identifying transcriptional signatures of Abeta microenvironment VS Neural plasticity* Previously not significant Sang Ho Kwon
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
26. Visium + RNAscope to provide additional insights into spatial gene expression gradients Sang Ho Kwon