Data availability

Sequencing data were deposited into the NCBI Gene Expression Omnibus under GSE273803.

Code availability

The open-source software, tools, and packages used for data analysis in this study, as well as the version of each program, were R (v3.6.1), PIPseeker (v1.0.0), Seurat R package (v4.3.0), scGate R package (v1.6), ScType R package (v1.0), and SingleR R package (v1.0)57. No custom software, tools, or packages were used.

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Acknowledgments

This work was supported by grants R01AI149699 and R01NS130876. I.F-M. was supported by a postgraduate fellowship from the La Caixa Foundation, a Momentum Fellowship from the Mark Foundation for Cancer Research, a Scholarship of Excellence Rafael del Pino, and an NCI F99 award (CA284253-01). R.L.B. was supported by a Damon Runyon-Sohn Fellowship and the NCI (K99CA248460). R.L.L. was supported by a Memorial Sloan Kettering Cancer Center Support Grant/Core Grant P30 CA088748, an R35 grant from the National Institute of Cancer (CA197594), and a collaborative U01 Research Project grant from the National Institute of Aging—the U01 grant was jointly received with the laboratory of Jennifer Trowbridge at the Jackson Laboratories (U01AG077925; 210374-0622-02). We are grateful to members of the Abate laboratory for helpful discussions. We thank Eric Chow and the staff of the UCSF Center for Advanced Technology for their technical support, the members of the Flow Cytometry and the Integrated Genomics Operation (IGO) cores at Memorial Sloan Kettering Cancer Center for their advice and technical help, Kristina Fontanez, Autumn Cholger and Bob Wikle from Fluent BioSciences for their advice and support.

Author information

Author notes

These authors contributed equally: Sixuan Pan, Inés Fernández-Maestre.

Authors and Affiliations

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA

Sixuan Pan, Kai-Chun Chang & Adam R. Abate 1.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Inés Fernández-Maestre, Matthew G. Wereski & Ross L. Levine 1.

Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Inés Fernández-Maestre 1.

Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Stéphane Van Haver 1.

Tow Center for Developmental Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Stéphane Van Haver 1.

Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA

Alexandra M. Haugh, Katy K. Tsai & Adil I. Daud 1.

Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

Robert L. Bowman 1.

Departments of Radiation Oncology and Neurological Surgery, University of California San Francisco, San Francisco, CA, USA

Harish N. Vasudevan 1.

Department of Medicine, Weill Cornell Medical College, New York, NY, USA

Ross L. Levine 1.

Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Ross L. Levine

Authors

1. Sixuan Pan
2. Inés Fernández-Maestre
3. Kai-Chun Chang
4. Stéphane Van Haver
5. Matthew G. Wereski
6. Alexandra M. Haugh
7. Katy K. Tsai
8. Adil I. Daud
9. Robert L. Bowman
10. Harish N. Vasudevan
11. Ross L. Levine
12. Adam R. Abate

Contributions

S.P., K.C., and A.R.A. designed the study; S.P. and K.C. optimized the PURE-seq workflow; I.F.-M. designed and performed the experiments for all mouse studies; S.P., A.M.H, K.K.T, A.I.D., and H.N.V. conducted the CTC study; I.F.-M, K.C., and S.P. analyzed scRNA-seq data; S.V.H. provided bioinformatic and data curation support; M.G.W. assisted with mouse dissections and sample processing; R.L.B. provided input on data visualization; S.P. and I.F.-M. wrote the manuscript; A.R.A. and R.L.L. supervised the work and revised the manuscript; all authors read, reviewed, and approved the manuscript.

Corresponding authors

Correspondence to Ross L. Levine or Adam R. Abate.

Ethics declarations

Competing interests

R.L.L. is on the Supervisory board of Qiagen (compensation/equity), a co-founder/board member at Ajax (equity), and is a scientific advisor to Mission Bio, Syndax, Scorpion, Zentalis, Auron, Prelude, and C4 Therapeutics; for each of these entities, he receives equity/compensation. He has received research support from the Cure Breast Cancer Foundation, Calico, Zentalis and Ajax, and has consulted for Jubilant, Goldman Sachs, Incyte, AstraZeneca and Janssen. The remaining authors declare no competing interests.

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Pan, S., Fernández-Maestre, I., Chang, KC. et al. PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells. Nat Commun (2026). https://doi.org/10.1038/s41467-025-68146-w

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Received: 05 August 2024

Accepted: 19 December 2025

Published: 21 January 2026

DOI: https://doi.org/10.1038/s41467-025-68146-w