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. 2024 Oct;55(10):e266-e268.
doi: 10.1161/STROKEAHA.124.047907. Epub 2024 Aug 29.

Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics

Melanie Walker  1   2   3 , Emma Federico  1   2 , Josh L Espinoza  3 , Christopher L Dupont  3
Affiliations

Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics

Melanie Walker et al. Stroke. 2024 Oct.
No abstract available

Keywords: atherosclerosis; middle cerebral artery; stroke; thrombectomy; thrombosis.

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Conflict of interest statement

None.

Figures

Figure 1.
Figure 1.. Spatial Transcriptomic Analysis of Cerebral Thrombi.
Panel A shows a representative selection from 23 ROIs using a geometric method based on cellular cluster patterns identified with traditional stains and morphology markers. In Panel B, data are sorted by sample type on the y-axis and show the signal-to-noise ratio, calculated as counts divided by the LOQ on the x-axis, highlighting the assay’s performance across various samples. Panels C and D feature Volcano plots that show differential gene expression, where gene significance is plotted against fold change; Panel C compares 8 LAA core ROIs against 7 LAA periphery ROIs, while Panel D compares 4 LAA core ROIs against 4 similarly located CE core ROIs. Panels E and F display GSEA results; Panel E shows significant enrichment of genes associated with extracellular matrix organization in LAA thrombus, and Panel F highlights predominant neutrophil degranulation in the CE thrombus core compared to LAA. In Panels E and F, the enrichment score is plotted on the y-axis, which represents the degree to which a gene set is overrepresented at the top or bottom of a ranked list of genes, and the rank is plotted on the x-axis, indicating the position of genes in the ordered list. A fourth (CE) thrombus did not meet quality control checks and was excluded from analysis.
See this image and copyright information in PMC

References

    1. Bergholtz H, Carter JM, Cesano A, Cheang MCU, Church SE, Divakar P, Fuhrman CA, Goel S, Gong J, Guerriero JL, et al. Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler. Cancers [Internet]. 2021;13. Available from: 10.3390/cancers13174456 - DOI - PMC - PubMed
    1. Adams HP Jr, Bendixen BH, Kappelle LJ, Biller J, Love BB, Gordon DL, Marsh EE 3rd. Classification of subtype of acute ischemic stroke. Definitions for use in a multicenter clinical trial. TOAST. Trial of Org 10172 in Acute Stroke Treatment. Stroke. 1993;24:35–41. - PubMed
    1. Liu X, Jiang Y, Song D, Zhang L, Xu G, Hou R, Zhang Y, Chen J, Cheng Y, Liu L, et al. Clinical challenges of tissue preparation for spatial transcriptome. Clin. Transl. Med 2022;12:e669. - PMC - PubMed
    1. Zhang L, Chen D, Song D, Liu X, Zhang Y, Xu X, Wang X. Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther. 2022;7:111. - PMC - PubMed
    1. Bingham GC, Lee F, Naba A, Barker TH. Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. Matrix Biol. 2020;91–92:152–166. - PMC - PubMed

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