<p>The liver is composed of diverse cell populations that coordinate essential metabolic and immune functions. Single-cell transcriptomics has advanced characterization of liver cellular composition, but dissociation of tissue to single-cells can introduce biases through the enrichment or depletion of cell types. Spatial transcriptomics is a complementary approach to avoid inherent bias for cell populations and to add important spatial context. The Visium HD spatial transcriptomics technology from 10X Genomics enables high-resolution spatial mapping of gene expression in tissue samples with a bin width of 2 µm enabling quantification of transcripts at a sub-cellular resolution. We applied Visium HD to three healthy human liver donor samples, from two adult and one pediatric donor. We identified cell types by clustering 8 µm bins and integration with single-cell reference maps. Differential expression analyses identified spatially distinct gene expression resulting in development of a high-resolution map of the liver. This resource provides cell-level and spatially-resolved insights into the cellular and anatomical heterogeneity of the liver to serve as a resource for researchers to identify disease-specific spatial signatures and novel therapeutic targets.</p>

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High-resolution spatial transcriptomics of adult and pediatric human liver with Visium HD

  • Faizan Hasan,
  • Rachel D. Edgar,
  • Jawairia Atif,
  • Diana Nakib,
  • Cornelia Thoeni,
  • Amanda Ricciuto,
  • Blayne A. Sayed,
  • Ian McGilvray,
  • Gary D. Bader,
  • Sonya A. MacParland

摘要

The liver is composed of diverse cell populations that coordinate essential metabolic and immune functions. Single-cell transcriptomics has advanced characterization of liver cellular composition, but dissociation of tissue to single-cells can introduce biases through the enrichment or depletion of cell types. Spatial transcriptomics is a complementary approach to avoid inherent bias for cell populations and to add important spatial context. The Visium HD spatial transcriptomics technology from 10X Genomics enables high-resolution spatial mapping of gene expression in tissue samples with a bin width of 2 µm enabling quantification of transcripts at a sub-cellular resolution. We applied Visium HD to three healthy human liver donor samples, from two adult and one pediatric donor. We identified cell types by clustering 8 µm bins and integration with single-cell reference maps. Differential expression analyses identified spatially distinct gene expression resulting in development of a high-resolution map of the liver. This resource provides cell-level and spatially-resolved insights into the cellular and anatomical heterogeneity of the liver to serve as a resource for researchers to identify disease-specific spatial signatures and novel therapeutic targets.