With the emergence of VisiumHD and other spatial transcriptomics datasets, HiVis facilitates exploring intra-cellular mRNA localization patterns across tissues and conditions. Great work by Roy Novoselsky and Ofra Golani.

HiVis also enables automated nucleus and cytoplasmic segmentation from H&E images, facilitating extraction of nuclear-cytoplasmic localization.

We also perform VisiumHD of mouse liver sections and identify mRNAs that are polarized towards the sinusoidal facing basal cell compartment.

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.

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.

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.

EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology Mammalian genomes are pervasively transcribed into long noncoding RNAs (lncRNAs), whose functions and modes of action remain poorly understood. EPB41L4A-AS1 is an evolutionary conserved, broadly and h...

New preprint 📜 from @AlanMonziani in the lab – EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology www.biorxiv.org/content/10.1... . A🧵

Hadas Keren-Shaul, Liat Fellus-Alyagor, Dana Hirsch, Chen Mayer, Ron Pery, Niv Pencovich, Timucin Taner, Ido Nachmany, Weizmann Institute, Sheba Medical Center, Mayo Clinic.

7/ Huge shoutout to the amazing team behind this:
Oran Yakubovsky, Amichay Afriat, Adi Egozi, Keren Bahar Halpern, Tal Barkai, Yotam Harnik, Yael Korem Kohanim, Roy Novoselsky, Ofra Golani, Inna Goliand, Yoseph Addadi, Merav Kedmi,

6/ Our data, including Loupe files for Visium & VisiumHD, is open access for exploration:
Zenodo: zenodo.org/records/1479...
Web browser: itzkovitzwebapps.weizmann.ac.il/webapps/home...

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.

4/ Key hepatic functions show pericentral shifts in humans, including: Mitochondrial gluconeogenesis (PCK2), Urea cycle (NAGS, OTC), Respiration genes and the Key TF HNF4A.

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.

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.

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.

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...

Intracellular polarization of RNAs and proteins in the human small intestinal epithelium The intestinal epithelium is a polarized monolayer of cells and both proteins and mRNAs have been shown to have global basal-apical polarization in mice. These authors perform a systematic analysis of...

What a cool new story by @shalevitzkovitz.bsky.social! They show which proteins and RNAs are expressed in the apical vs basal sides of intestinal epithelial cells (mice and humans). Some really interesting phenomenons
@plosbiology.bsky.social @npariente.bsky.social
journals.plos.org/plosbiology/...