PerturbSpace: Spatially resolved, multimodal in vivo Perturb-seq using antibody-based cell hashing

Added: 2026-05-27

[00:00:01]My name is Alex Neveu and I'm a senior scientist on the in vivo functional genomics team at Arc.

[00:00:08]Today we're releasing a preprint on Perturb-seq, which is a spatially resolved single-cell workflow that enables organ scale profiling of perturbed tissue. Perturb-seq uses microwells on an array. Each microwell contains a uniquely barcoded antibody that labels cells.

[00:00:26]Following spatial tagging, you take your sample through a standard single-cell RNA-seq workflow that includes tissue dissociation and optional flow cytometry to enrich for populations of interest.

[00:00:40]Perturb-seq enables transcriptome wide gene expression just as you would expect with single-cell RNA sequencing. It's also easy to label on multimodal readouts including proteins with Cite-seq and CRISPR perturbations.

[00:00:55]We use Perturb-seq in two different experimental paradigms. First, in the regenerating spleen, we perturb 40 epigenetic regulators in immune progenitor cells ex vivo. We then transplant those cells into an irradiated mouse and profile the splenic colony forming units that are formed.

[00:01:15]Here we show how Perturb-seq can visualize the colony forming units. We can zoom in to specific colonies and see their cell type composition in both physical space and UMAP space.

[00:01:29]We then use this data to compare across our different perturbations to look for changes in colony size and composition.

[00:01:37]For example, we find perturbations that produce larger colonies than expected by proliferation rate alone.

[00:01:45]In our second paradigm, we use Perturb-seq to detect the extrinsic effects of perturbations, which has been challenging with existing technologies.

[00:01:54]We express either interferon gamma or control peptide and assess the liver where immune cells are more rare.

[00:02:03]We found that cells in the same spatial neighborhood as interferon gamma expressing cells exhibit an interferon gamma specific gene signature illustrating that we can detect extrinsic effects using perturb space.

[00:02:17]If you're interested in using perturb space for your own research, please read the preprint and reach out if you have any questions.