snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.
Authors
- Tingsheng Yu (ORCID: https://orcid.org/0000-0002-8106-7981)
- Jasmine Plummer (ORCID: https://orcid.org/0000-0001-7263-350X)
- Fiona Pakiam (ORCID: https://orcid.org/0000-0001-6292-1137)
- Jens Durruthy Durruthy
- Joanna Warren (ORCID: https://orcid.org/0000-0003-0595-0390)
- Alissa Greenwald (ORCID: https://orcid.org/0000-0001-5428-9645)
- Paul E. Lund (ORCID: https://orcid.org/0000-0003-0496-1434)
- Cyril Dégletagne (ORCID: https://orcid.org/0000-0002-5363-2381)
- Luciano G. Martelotto (ORCID: https://orcid.org/0000-0002-9625-1183)
- Kate Harvey (ORCID: https://orcid.org/0000-0002-2155-5203)
- Michael J. Roach (ORCID: https://orcid.org/0000-0003-1488-5148)
- Andrés F. Vallejo (ORCID: https://orcid.org/0000-0002-4688-0598)
- Andrew Kohlway
- Heeju Ryu (ORCID: https://orcid.org/0000-0002-4742-5415)
- Laurie Tonon (ORCID: https://orcid.org/0009-0005-8794-7276)
- Beata Kiedik (ORCID: https://orcid.org/0000-0001-8517-5253)
- Anna Elz (ORCID: https://orcid.org/0000-0002-7718-3015)
- Alexander Swarbrick (ORCID: https://orcid.org/0000-0002-3051-5676)
- Ioannis S. Vlachos (ORCID: https://orcid.org/0000-0002-8849-808X)
- Jawad Abousoud
- Sandra A O'Toole (ORCID: https://orcid.org/0000-0001-9912-0245)
- Lisa M. Butler (ORCID: https://orcid.org/0000-0003-2698-3220)
- Joakim Lundeberg (ORCID: https://orcid.org/0000-0003-4313-1601)
- Taopeng Wang (ORCID: https://orcid.org/0000-0002-9184-609X)
- Dominik C. Kaczorowski (ORCID: https://orcid.org/0000-0002-9205-1934)
- Evan W. Newell (ORCID: https://orcid.org/0000-0002-2889-243X)
- Robert Salomon (ORCID: https://orcid.org/0000-0003-4504-2901)
- Felipe Segato Dezem
- Yered Pita-Juárez (ORCID: https://orcid.org/0000-0001-6992-252X)
- Nikolaos Kalavros (ORCID: https://orcid.org/0000-0001-5503-9808)
- Ghamdan Al‐Eryani (ORCID: https://orcid.org/0000-0002-1137-1726)
- Kellie Wise (ORCID: https://orcid.org/0009-0005-8937-4352)
- Ryan Stott
- John B. Johanneson (ORCID: https://orcid.org/0009-0002-7612-1290)
- Javier Escudero Morlanes (ORCID: https://orcid.org/0009-0004-2885-2456)
- Azi Hadadianpour
- Wenyan Li (ORCID: https://orcid.org/0009-0000-6591-1073)
- Yuling Ma (ORCID: https://orcid.org/0000-0003-4046-5219)
Institutions
- Université Claude Bernard Lyon 1 (FR)
- Broad Institute (US)
- Centre National de la Recherche Scientifique (FR)
- The University of Sydney (AU)
- St. Jude Children's Research Hospital (US)
- Beth Israel Deaconess Medical Center (US)
- Harvard University (US)
- Garvan Institute of Medical Research (AU)
- Inserm (FR)
- Flinders University (AU)
- Royal Prince Alfred Hospital (AU)
- Science for Life Laboratory (SE)
- UNSW Sydney (AU)
- Fred Hutch Cancer Center (US)
- Centre Léon Bérard (FR)
- 10X Genomics (United States) (US)
- Centre de Recherche en Cancérologie de Lyon (FR)
- South Australian Health and Medical Research Institute (AU)
- Centre for Cancer Biology (AU)
- University of Southampton (GB)
- Weizmann Institute of Science (IL)
- The University of Adelaide (AU)
- Western Sydney University (AU)
- KTH Royal Institute of Technology (SE)
Publication Details
- Journal
- Communications Biology
- Published
- 2024-10-16
- DOI
- https://doi.org/10.1038/s42003-024-07043-2
- Citations
- 28
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 6.55
Funders
- Breast Cancer Research Foundation
- Fred Hutchinson Cancer Research Center
- St. Jude Children's Research Hospital
- South Australian Health and Medical Research Institute
- Broad Institute
- Australian Government
- NSW Health Pathology
- University of Southampton
- Institut National de la Santé et de la Recherche Médicale
- Weizmann Institute of Science
- University of New South Wales
- University of Western Sydney
- Flinders University
- Petre Foundation
- Ligue Contre le Cancer
- Kungliga Tekniska Högskolan
- Centre National de la Recherche Scientifique
- Science for Life Laboratory
- Centre Léon Bérard
- College of Science and Engineering, University of Minnesota
- Medical Research Council
- National Health and Medical Research Council
- Sydney Medical School