MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue
- 1Harvard University / HHMI
Abstract
Genetic perturbations can reshape both the state of a targeted cell and the behavior of neighboring cells. Measuring these effects systematically in intact tissues requires pooled screening methods that jointly identify perturbations, molecular phenotypes, and spatial context of individual cells. Here, we report an imaging-based pooled screening method that detects perturbation identities and endogenous RNAs without enzymatic amplification. Relative to our previous enzymatic-amplification-based workflow, amplification-free MERFISH detection with direct hybridization increased recovery of perturbation barcodes by ~10-fold and endogenous transcripts by 2.5-fold, improving perturbation assignment as well as molecular profiling of both perturbed and neighboring cells. Applying this method to a genetic mosaic mouse liver screen targeting ~200 genes in hepatocytes, we profiled 1.5 million cells in intact tissues and mapped both cell-autonomous responses of perturbed hepatocytes and cell non-autonomous changes in neighboring immune and vascular populations. These included localized accumulation of pDC-like cells near hepatocytes with impaired V-ATPase function and angiogenic responses in vascular cells near Vhl-perturbed hepatocytes with hypoxia activation. Our method provides a simplified, scalable approach to linking genetic perturbations with cell state, multicellular response, and tissue organization.
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BibTeX
@misc{jin2026merfishbased,
title = {{MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue}},
author = {K. Jin and R. A. Saunders and J. Zhang and J. Lu and A. A. Halpern and J. Sandhu and X. Pan and C. Y. Wang and A. M. Li and W. E. Allen and J. S. Weissman and X. Zhuang},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.06.756924},
url = {https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue
AU - K. Jin
AU - R. A. Saunders
AU - J. Zhang
AU - J. Lu
AU - A. A. Halpern
AU - J. Sandhu
AU - X. Pan
AU - C. Y. Wang
AU - A. M. Li
AU - W. E. Allen
AU - J. S. Weissman
AU - X. Zhuang
PY - 2026
DA - 2026/10/06
PB - bioRxiv
DO - 10.64898/2026.10.06.756924
UR - https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1
AB - Genetic perturbations can reshape both the state of a targeted cell and the behavior of neighboring cells. Measuring these effects systematically in intact tissues requires pooled screening methods that jointly identify perturbations, molecular phenotypes, and spatial context of individual cells. Here, we report an imaging-based pooled screening method that detects perturbation identities and endogenous RNAs without enzymatic amplification. Relative to our previous enzymatic-amplification-based workflow, amplification-free MERFISH detection with direct hybridization increased recovery of perturbation barcodes by ~10-fold and endogenous transcripts by 2.5-fold, improving perturbation assignment as well as molecular profiling of both perturbed and neighboring cells. Applying this method to a genetic mosaic mouse liver screen targeting ~200 genes in hepatocytes, we profiled 1.5 million cells in intact tissues and mapped both cell-autonomous responses of perturbed hepatocytes and cell non-autonomous changes in neighboring immune and vascular populations. These included localized accumulation of pDC-like cells near hepatocytes with impaired V-ATPase function and angiogenic responses in vascular cells near Vhl-perturbed hepatocytes with hypoxia activation. Our method provides a simplified, scalable approach to linking genetic perturbations with cell state, multicellular response, and tissue organization.
ER -