snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.

Paraffin Embedding / methods Humans Sequence Analysis, RNA / methods Tissue Fixation / methods Single-Cell Analysis / methods Formaldehyde / chemistry Transcriptome Gene Expression Profiling / methods Workflow

Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
16 Oct 2024
Historique:
received: 31 10 2023
accepted: 10 10 2024
medline: 17 10 2024
pubmed: 17 10 2024
entrez: 16 10 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s42003-024-07043-2 PMID: 39414943
pubmed: 39414943
doi: 10.1038/s42003-024-07043-2
pii: 10.1038/s42003-024-07043-2
doi:

Substances chimiques

Formaldehyde 1HG84L3525

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1340

Subventions

Organisme : Department of Health | National Health and Medical Research Council (NHMRC)
ID : APP2004774

Informations de copyright

© 2024. The Author(s).

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Auteurs

Taopeng Wang (T)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
ORCID: 0000-0002-9184-609X

Michael J Roach (MJ)

Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, Australia.
South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia.
College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
ORCID: 0000-0003-1488-5148

Kate Harvey (K)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
ORCID: 0000-0002-2155-5203

Javier Escudero Morlanes (JE)

KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden.

Beata Kiedik (B)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
ORCID: 0000-0001-8517-5253

Ghamdan Al-Eryani (G)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.

Alissa Greenwald (A)

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
ORCID: 0000-0001-5428-9645

Nikolaos Kalavros (N)

Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
ORCID: 0000-0001-5503-9808

Felipe Segato Dezem (FS)

Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.

Yuling Ma (Y)

Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.

Yered H Pita-Juarez (YH)

Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Kellie Wise (K)

Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, Australia.
South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia.

Cyril Degletagne (C)

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, Lyon, France.

Anna Elz (A)

Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Azi Hadadianpour (A)

Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Jack Johanneson (J)

Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center, Seattle, WA, USA.
ORCID: 0009-0002-7612-1290

Fiona Pakiam (F)

Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Heeju Ryu (H)

Vaccine and Infectious Disease Division, Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Evan W Newell (EW)

Fred Hutch Innovation Lab, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Vaccine and Infectious Disease Division, Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA.
ORCID: 0000-0002-2889-243X

Laurie Tonon (L)

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, Lyon, France.
Fondation Synergie Lyon Cancer, Plateforme de Bioinformatique Gilles Thomas, Centre Léon Bérard, Lyon, France.
ORCID: 0009-0005-8794-7276

Andrew Kohlway (A)

10X Genomics, Pleasanton, CA, USA.

Tingsheng Drennon (T)

10X Genomics, Pleasanton, CA, USA.
ORCID: 0000-0002-8106-7981

Jawad Abousoud (J)

10X Genomics, Pleasanton, CA, USA.

Ryan Stott (R)

10X Genomics, Pleasanton, CA, USA.

Paul Lund (P)

10X Genomics, Pleasanton, CA, USA.
ORCID: 0000-0003-0496-1434

Jens Durruthy (J)

10X Genomics, Pleasanton, CA, USA.

Andres F Vallejo (AF)

Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK.
ORCID: 0000-0002-4688-0598

Wenyan Li (W)

Children's Cancer Institute, UNSW Lowy Cancer Research Centre, Kensington, NSW, Australia.
School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.

Robert Salomon (R)

Children's Cancer Institute, UNSW Lowy Cancer Research Centre, Kensington, NSW, Australia.
School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.
ORCID: 0000-0003-4504-2901

Dominik Kaczorowski (D)

Cellular Genomics Platform, Garvan Institute of Medical Research, Sydney, NSW, Australia.
ORCID: 0000-0002-9205-1934

Joanna Warren (J)

Cellular Genomics Platform, Garvan Institute of Medical Research, Sydney, NSW, Australia.

Lisa M Butler (LM)

South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia.
Solid Tumour Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
ORCID: 0000-0003-2698-3220

Sandra O'Toole (S)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
School of Medicine, University of Western Sydney, Sydney, NSW, Australia.

Jasmine Plummer (J)

Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, TN, USA.
ORCID: 0000-0001-7263-350X

Ioannis S Vlachos (IS)

Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
ORCID: 0000-0002-8849-808X

Joakim Lundeberg (J)

KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden.
ORCID: 0000-0003-4313-1601

Alexander Swarbrick (A)

Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. a.swarbrick@garvan.org.au.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia. a.swarbrick@garvan.org.au.
ORCID: 0000-0002-3051-5676

Luciano G Martelotto (LG)

Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, Australia. luciano.martelotto@adelaide.edu.au.
South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia. luciano.martelotto@adelaide.edu.au.
ORCID: 0000-0002-9625-1183

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Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Techniques de laboratoire clinique › Techniques histologiques › Techniques de préparation histocytologique › Inclusion de tissu › Inclusion en paraffine › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Techniques d'investigation › Techniques de laboratoire clinique › Techniques histologiques › Techniques de préparation histocytologique › Fixation tissulaire › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse sur cellule unique › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Composés chimiques organiques › Aldéhydes › Formaldéhyde › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › snPATHO-seq, a versatile FFPE single-nucleus...
questionsmedicales.fr › Sciences de l'information › Analyse des systèmes › Flux de travaux › snPATHO-seq, a versatile FFPE single-nucleus...