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shalevitzkovitz.bsky.social

@shalevitzkovitz.bsky.social
55 followers 23 following 24 posts
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
Finally, ~7% of epithelial cells completely lost enterocyte identity and exhibited gastric metaplasia.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
We found that this abnormal co-expression arises from spatial overlap of morphogen gradients: BMP signals from the villus tip and WNT signals from the crypt base now intersect due to the reduced distance between their sources.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
Surprisingly, in Celiac Disease, enterocytes adopted a new cellular state. Rather than losing specific zones, remaining enterocytes co-expressed gene programs that, in healthy tissue, are restricted to distinct villus zones.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
To address this, we applied spatial transcriptomics (VisiumHD) to human small intestinal tissue, together with matched single-cell RNA-seq, to analyze enterocyte zonal identity. In the healthy pediatric intestine, enterocytes displayed pronounced zonation along the villus axis.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
We asked: does villus flattening cause loss of specific zonal populations, proportional scaling of zonation or a breakdown of spatial organization.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
Enterocytes exhibit different cellular states depending on their height along the small intestine villus axis, a phenomenon known as ‘zonation’. In Celiac Disease, autoimmune destruction of enterocytes leads to villus flattening.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 18/02/2026
Happy to share our new preprint: Spatial Rewiring of Enterocyte Identity in Celiac Disease. We describe unexpected changes in enterocyte zonation in Celiac Disease.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 10/09/2025
HiVis also enables automated nucleus and cytoplasmic segmentation from H&E images, facilitating extraction of nuclear-cytoplasmic localization.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 10/09/2025
We also perform VisiumHD of mouse liver sections and identify mRNAs that are polarized towards the sinusoidal facing basal cell compartment.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 10/09/2025
HiVis facilitates both tissue-level zonation reconstruction, and automated or guided detection of sub-cellular compartments to extract intra-cellular mRNA localization patterns. We demonstrate this by resolving apical-basal mRNA polarization in mouse intestinal epithelium.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 10/09/2025
Intracellular mRNA polarization is hard to study in intact tissues. We developed HiVis: pypi.org/project/HiVis/, a computational Python package that combines image processing with transcriptomics to extract these features from VisiumHD datasets.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 10/09/2025
Happy to share our new preprint: Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics: www.biorxiv.org/content/10.1... We utilize VisiumHD to extract intra-cellular mRNA polarization patterns in epithelial tissues.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
5/ We also developed AI-based lipid classification for Visium spots, revealing dynamic expression changes in early steatosis: First, early steatotic hepatocytes build lipids (↑ FASN, MLXIPL). Then, they shift to increased insulin & adiponectin receptor expression.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
4/ Key hepatic functions show pericentral shifts in humans, including: Mitochondrial gluconeogenesis (PCK2), Urea cycle (NAGS, OTC), Respiration genes and the Key TF HNF4A.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
3/ Most human hepatocyte genes are zonated, but zonation patterns in humans differ dramatically from those in mice and even large mammals (cow, pig, boar) which we also profiled.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
2/ Using Visium, VisiumHD, and MERFISH on 16 patients, we uncovered striking differences between live donor liver and the commonly used 'adjacent normal' liver samples. Live donor liver shows lower immune gene expression and higher hepatocyte program expression.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
1/ The liver's remarkable regenerative capacity allowed us to study gene expression programs in live healthy donors (LHDs) - a unique opportunity to understand human liver biology.
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shalevitzkovitz.bsky.social @shalevitzkovitz.bsky.social · 24/02/2025
Happy to share our new preprint: A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver: www.biorxiv.org/content/10.1...
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