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

Wang, T; Roach, MJ; Harvey, K; Morlanes, JE; Kiedik, B; Al-Eryani, G; Greenwald, A; Kalavros, N; Dezem, FS; Ma, Y; Pita-Juarez, YH; Wise, K; Degletagne, C; Elz, A; Hadadianpour, A; Johanneson, J; Pakiam, F; Ryu, H; Newell, EW; Tonon, L; Kohlway, A; Drennon, T; Abousoud, J; Stott, R; Lund, P; Durruthy, J; Vallejo, AF; Li, W; Salomon, R; Kaczorowski, D; Warren, J; Butler, LM; O'Toole, S; Plummer, J; Vlachos, IS; Lundeberg, J; Swarbrick, A; Martelotto, LG

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

Wang, T Roach, MJ Harvey, K Morlanes, JE Kiedik, B Al-Eryani, G Greenwald, A Kalavros, N Dezem, FS Ma, Y Pita-Juarez, YH Wise, K Degletagne, C Elz, A Hadadianpour, A Johanneson, J Pakiam, F Ryu, H Newell, EW Tonon, L Kohlway, A Drennon, T Abousoud, J Stott, R Lund, P Durruthy, J Vallejo, AF Li, W Salomon, R

Kaczorowski, D Warren, J Butler, LM O'Toole, S Plummer, J Vlachos, IS Lundeberg, J Swarbrick, A Martelotto, LG

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Publisher:: NATURE PORTFOLIO
Publication Type:: Journal Article
Citation:: Commun Biol, 2024, 7, (1), pp. 1340
Issue Date:: 2024-10-16

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Field	Value	Language
dc.contributor.author	Wang, T
dc.contributor.author	Roach, MJ
dc.contributor.author	Harvey, K
dc.contributor.author	Morlanes, JE
dc.contributor.author	Kiedik, B
dc.contributor.author	Al-Eryani, G
dc.contributor.author	Greenwald, A
dc.contributor.author	Kalavros, N
dc.contributor.author	Dezem, FS
dc.contributor.author	Ma, Y
dc.contributor.author	Pita-Juarez, YH
dc.contributor.author	Wise, K
dc.contributor.author	Degletagne, C
dc.contributor.author	Elz, A
dc.contributor.author	Hadadianpour, A
dc.contributor.author	Johanneson, J
dc.contributor.author	Pakiam, F
dc.contributor.author	Ryu, H
dc.contributor.author	Newell, EW
dc.contributor.author	Tonon, L
dc.contributor.author	Kohlway, A
dc.contributor.author	Drennon, T
dc.contributor.author	Abousoud, J
dc.contributor.author	Stott, R
dc.contributor.author	Lund, P
dc.contributor.author	Durruthy, J
dc.contributor.author	Vallejo, AF
dc.contributor.author	Li, W
dc.contributor.author	Salomon, R https://orcid.org/0000-0003-4504-2901
dc.contributor.author	Kaczorowski, D
dc.contributor.author	Warren, J
dc.contributor.author	Butler, LM
dc.contributor.author	O'Toole, S
dc.contributor.author	Plummer, J
dc.contributor.author	Vlachos, IS
dc.contributor.author	Lundeberg, J
dc.contributor.author	Swarbrick, A
dc.contributor.author	Martelotto, LG
dc.date.accessioned	2024-12-02T01:07:55Z
dc.date.available	2024-10-10
dc.date.available	2024-12-02T01:07:55Z
dc.date.issued	2024-10-16
dc.identifier.citation	Commun Biol, 2024, 7, (1), pp. 1340
dc.identifier.issn	2399-3642
dc.identifier.issn	2399-3642
dc.identifier.uri	http://hdl.handle.net/10453/182207
dc.description.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.
dc.format	Electronic
dc.language	eng
dc.publisher	NATURE PORTFOLIO
dc.relation.ispartof	Commun Biol
dc.relation.isbasedon	10.1038/s42003-024-07043-2
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.classification	31 Biological sciences
dc.subject.classification	32 Biomedical and clinical sciences
dc.subject.mesh	Paraffin Embedding
dc.subject.mesh	Humans
dc.subject.mesh	Sequence Analysis, RNA
dc.subject.mesh	Tissue Fixation
dc.subject.mesh	Single-Cell Analysis
dc.subject.mesh	Formaldehyde
dc.subject.mesh	Transcriptome
dc.subject.mesh	Gene Expression Profiling
dc.subject.mesh	Workflow
dc.subject.mesh	Humans
dc.subject.mesh	Formaldehyde
dc.subject.mesh	Paraffin Embedding
dc.subject.mesh	Tissue Fixation
dc.subject.mesh	Gene Expression Profiling
dc.subject.mesh	Sequence Analysis, RNA
dc.subject.mesh	Workflow
dc.subject.mesh	Single-Cell Analysis
dc.subject.mesh	Transcriptome
dc.subject.mesh	Paraffin Embedding
dc.subject.mesh	Humans
dc.subject.mesh	Sequence Analysis, RNA
dc.subject.mesh	Tissue Fixation
dc.subject.mesh	Single-Cell Analysis
dc.subject.mesh	Formaldehyde
dc.subject.mesh	Transcriptome
dc.subject.mesh	Gene Expression Profiling
dc.subject.mesh	Workflow
dc.title	snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.
dc.type	Journal Article
utslib.citation.volume	7
utslib.location.activity	England
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Science
pubs.organisational-group	University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
utslib.copyright.status	open_access	*
dc.rights.license	This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
dc.date.updated	2024-12-02T01:07:46Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	7
utslib.citation.issue	1

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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/182207