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

doi:10.1038/s42003-024-07043-2

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 TononAndrew 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

College of Science and Engineering

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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.

Original language	English
Article number	1340
Number of pages	12
Journal	Communications Biology
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s42003-024-07043-2
Publication status	Published - Dec 2024

Keywords

Formalin-fixed paraffin-embedded (FFPE)
FFPE
Single-cell multimodal genomics
RNA sequencing
snPATHO-seq

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10.1038/s42003-024-07043-2Licence: CC BY

Published versionFinal published version, 8.91 MBLicence: CC BY

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Wang, T., Roach, M. J., Harvey, K., Morlanes, J. E., Kiedik, B., Al-Eryani, G., Greenwald, A., Kalavros, N., Dezem, F. S., Ma, Y., Pita-Juarez, Y. H., Wise, K., Degletagne, C., Elz, A., Hadadianpour, A., Johanneson, J., Pakiam, F., Ryu, H., Newell, E. W., ... Martelotto, L. G. (2024). snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives. Communications Biology, 7(1), Article 1340. https://doi.org/10.1038/s42003-024-07043-2

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

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{\textquoteright} 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.",

keywords = "Formalin-fixed paraffin-embedded (FFPE), FFPE, Single-cell multimodal genomics, RNA sequencing, snPATHO-seq",

author = "Taopeng Wang and Roach, {Michael J.} and Kate Harvey and Morlanes, {Javier Escudero} and Beata Kiedik and Ghamdan Al-Eryani and Alissa Greenwald and Nikolaos Kalavros and Dezem, {Felipe Segato} and Yuling Ma and Pita-Juarez, {Yered H.} and Kellie Wise and Cyril Degletagne and Anna Elz and Azi Hadadianpour and Jack Johanneson and Fiona Pakiam and Heeju Ryu and Newell, {Evan W.} and Laurie Tonon and Andrew Kohlway and Tingsheng Drennon and Jawad Abousoud and Ryan Stott and Paul Lund and Jens Durruthy and Vallejo, {Andres F.} and Wenyan Li and Robert Salomon and Dominik Kaczorowski and Joanna Warren and Butler, {Lisa M.} and Sandra O{\textquoteright}Toole and Jasmine Plummer and Vlachos, {Ioannis S.} and Joakim Lundeberg and Alexander Swarbrick and Martelotto, {Luciano G.}",

year = "2024",

month = dec,

doi = "10.1038/s42003-024-07043-2",

language = "English",

volume = "7",

journal = "Communications Biology",

issn = "2399-3642",

publisher = "Springer Nature",

number = "1",

}

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 2024, 'snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives', Communications Biology, vol. 7, no. 1, 1340. https://doi.org/10.1038/s42003-024-07043-2

TY - JOUR

T1 - snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives

AU - Wang, Taopeng

AU - Roach, Michael J.

AU - Harvey, Kate

AU - Morlanes, Javier Escudero

AU - Kiedik, Beata

AU - Al-Eryani, Ghamdan

AU - Greenwald, Alissa

AU - Kalavros, Nikolaos

AU - Dezem, Felipe Segato

AU - Ma, Yuling

AU - Pita-Juarez, Yered H.

AU - Wise, Kellie

AU - Degletagne, Cyril

AU - Elz, Anna

AU - Hadadianpour, Azi

AU - Johanneson, Jack

AU - Pakiam, Fiona

AU - Ryu, Heeju

AU - Newell, Evan W.

AU - Tonon, Laurie

AU - Kohlway, Andrew

AU - Drennon, Tingsheng

AU - Abousoud, Jawad

AU - Stott, Ryan

AU - Lund, Paul

AU - Durruthy, Jens

AU - Vallejo, Andres F.

AU - Li, Wenyan

AU - Salomon, Robert

AU - Kaczorowski, Dominik

AU - Warren, Joanna

AU - Butler, Lisa M.

AU - O’Toole, Sandra

AU - Plummer, Jasmine

AU - Vlachos, Ioannis S.

AU - Lundeberg, Joakim

AU - Swarbrick, Alexander

AU - Martelotto, Luciano G.

PY - 2024/12

Y1 - 2024/12

N2 - 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.

AB - 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.

KW - Formalin-fixed paraffin-embedded (FFPE)

KW - FFPE

KW - Single-cell multimodal genomics

KW - RNA sequencing

KW - snPATHO-seq

UR - http://www.scopus.com/inward/record.url?scp=85206670031&partnerID=8YFLogxK

UR - http://purl.org/au-research/grants/NHMRC/2004774

U2 - 10.1038/s42003-024-07043-2

DO - 10.1038/s42003-024-07043-2

M3 - Article

C2 - 39414943

AN - SCOPUS:85206670031

SN - 2399-3642

VL - 7

JO - Communications Biology

JF - Communications Biology

IS - 1

M1 - 1340

ER -

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

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