Communications Biology (Oct 2024)
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives
- Taopeng Wang,
- Michael J. Roach,
- Kate Harvey,
- Javier Escudero Morlanes,
- Beata Kiedik,
- Ghamdan Al-Eryani,
- Alissa Greenwald,
- Nikolaos Kalavros,
- Felipe Segato Dezem,
- Yuling Ma,
- Yered H. Pita-Juarez,
- Kellie Wise,
- Cyril Degletagne,
- Anna Elz,
- Azi Hadadianpour,
- Jack Johanneson,
- Fiona Pakiam,
- Heeju Ryu,
- Evan W. Newell,
- Laurie Tonon,
- Andrew Kohlway,
- Tingsheng Drennon,
- Jawad Abousoud,
- Ryan Stott,
- Paul Lund,
- Jens Durruthy,
- Andres F. Vallejo,
- Wenyan Li,
- Robert Salomon,
- Dominik Kaczorowski,
- Joanna Warren,
- Lisa M. Butler,
- Sandra O’Toole,
- Jasmine Plummer,
- Ioannis S. Vlachos,
- Joakim Lundeberg,
- Alexander Swarbrick,
- Luciano G. Martelotto
Affiliations
- Taopeng Wang
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Michael J. Roach
- Adelaide Centre for Epigenetics, University of Adelaide
- Kate Harvey
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Javier Escudero Morlanes
- KTH Royal Institute of Technology, Science for Life Laboratory
- Beata Kiedik
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Ghamdan Al-Eryani
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Alissa Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science
- Nikolaos Kalavros
- Department of Pathology, Beth Israel Deaconess Medical Center
- Felipe Segato Dezem
- Center for Spatial Omics, St. Jude Children’s Research Hospital
- Yuling Ma
- Department of Pathology, Beth Israel Deaconess Medical Center
- Yered H. Pita-Juarez
- Department of Pathology, Beth Israel Deaconess Medical Center
- Kellie Wise
- Adelaide Centre for Epigenetics, University of Adelaide
- Cyril Degletagne
- CRCL Core facilities, Centre de Recherche en Cancérologie de Lyon (CRCL) INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard
- Anna Elz
- Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center
- Azi Hadadianpour
- Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center
- Jack Johanneson
- Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center
- Fiona Pakiam
- Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center
- Heeju Ryu
- Vaccine and Infectious Disease Division, Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center
- Evan W. Newell
- Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center
- Laurie Tonon
- CRCL Core facilities, Centre de Recherche en Cancérologie de Lyon (CRCL) INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard
- Andrew Kohlway
- 10X Genomics
- Tingsheng Drennon
- 10X Genomics
- Jawad Abousoud
- 10X Genomics
- Ryan Stott
- 10X Genomics
- Paul Lund
- 10X Genomics
- Jens Durruthy
- 10X Genomics
- Andres F. Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton
- Wenyan Li
- Children’s Cancer Institute, UNSW Lowy Cancer Research Centre
- Robert Salomon
- Children’s Cancer Institute, UNSW Lowy Cancer Research Centre
- Dominik Kaczorowski
- Cellular Genomics Platform, Garvan Institute of Medical Research
- Joanna Warren
- Cellular Genomics Platform, Garvan Institute of Medical Research
- Lisa M. Butler
- South Australian Immunogenomics Cancer Institute, University of Adelaide
- Sandra O’Toole
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Jasmine Plummer
- Center for Spatial Omics, St. Jude Children’s Research Hospital
- Ioannis S. Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center
- Joakim Lundeberg
- KTH Royal Institute of Technology, Science for Life Laboratory
- Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research
- Luciano G. Martelotto
- Adelaide Centre for Epigenetics, University of Adelaide
- DOI
- https://doi.org/10.1038/s42003-024-07043-2
- Journal volume & issue
-
Vol. 7,
no. 1
pp. 1 – 12
Abstract
Abstract 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.
