Genetic recording and in situ readout of single-cell signaling memory
Creators
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1.
University of California, Los Angeles
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2.
California Institute of Technology
Abstract
Intensity and duration of biological signals encode a few pathways to direct diverse cellular behaviors, yet quantifying these features in single cells remains difficult. To address this challenge, we developed INSCRIBE, which uses a CRISPR base editor to mutate genomic targets at rates proportional to signaling activity. Edits are recovered at the endpoint through a new ratiometric readout strategy from images of two fluorescence channels. We engineered human cells to record WNT and BMP activity. Following defined exogenous stimulations, INSCRIBE accurately recovered signal intensity in dose–response experiments and exposure duration in time-course experiments. Applying INSCRIBE revealed a persistent memory in the BMP pathway, where progeny of high-responding cells remained more sensitive to subsequent BMP stimulation for up to 3 weeks. Together, our results establish a scalable platform for genetic recording and in situ readout of signaling activity in single cells, advancing quantitative analysis of cell–cell communication during development and disease.
Copyright and License
© 2026, The Author(s), under exclusive licence to Springer Nature America, Inc.
Acknowledgement
We thank the members of the laboratory of A.A., especially Z. Samadi for helpful discussions and approaches for data analysis. We thank L. Sanchez-Guardado for insightful discussions. We are grateful to M. Elowitz and the Elowitz laboratory, especially M. Tran and D. Chadly, for critical feedback and for sharing plasmids with signal-responsive elements. This work was supported by a grant from the National Eye Institute (R00EY031782 to A.A.) and the University of California, Los Angeles, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Transformative Technology Development Pilot Award, including support from The Rose Hills Foundation Innovator Grant Program (to A.A.).
Data Availability
The INSCRIBE barcode array amplicon sequencing datasets are deposited at the National Center for Biotechnology Information’s Sequence Read Archive, under accession number PRJNA1232380. The sequences of primers, probes and constructs used in this study are listed in Supplementary Data Set 1. The exact quantified sample sizes for each experimental condition are listed in Supplementary Data Set 2. Due to the large size of the raw imaging files, public deposition in open data repositories was not feasible. However, all raw data are available from the corresponding author upon request. Source data are provided with this paper.
Code Availability
All the custom scripts were written in Python Jupyter Notebook, and processed source data required to replicate our analysis and demonstration pipelines are available at Zenodo via https://doi.org/10.5281/zenodo.18307130
Conflict of Interest
K.H and A.A. have filed a patent on recording and detection of cellular signals (The Regents of the University of California, PCT/US25/47952). The other authors declare no competing interests.
Supplemental Material
Supplementary Data Set 1 (download XLSX )
Complete sequences of all plasmids, oligonucleotide probes and genetic constructs used in this study.
Supplementary Data Set 2 (download XLSX )
Exact sample sizes for all experimental conditions used in this study.
Additional details
Identifiers
- PMID
- 41813882
Related works
- Describes
- Journal Article: https://rdcu.be/e9dO0 (URL)
Dates
- Available
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2026-03-11Version of record
Caltech Custom Metadata
- Caltech groups
- Division of Biology and Biological Engineering (BBE)
- Publication Status
- Published