Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer

Yu Liu; Aidan P Noon; Eduardo Aguiar Cabeza; Jess Shen; Cynthia Kuk; Christine Ilczynski; Ruoyu Ni; Balram Sukhu; Kin Chan; Nuno L Barbosa-Morais; Thomas Hermanns; Benjamin J Blencowe; Azar Azad; Theodorus H van der Kwast; James W F Catto; Alexandre R Zlotta; Jeffrey L Wrana

doi:10.1016/j.eururo.2014.07.045

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer

Yu Liu, Aidan P Noon, Eduardo Aguiar Cabeza, Jess Shen, Cynthia Kuk, Christine Ilczynski, Ruoyu Ni, Balram Sukhu, Kin Chan, Nuno L Barbosa-Morais, Thomas Hermanns, Benjamin J Blencowe, Azar Azad, Theodorus H van der Kwast, James W F Catto, Alexandre R Zlotta, Jeffrey L Wrana

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

Abstract

UNLABELLED: Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.

PATIENT SUMMARY: In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.

Original language	English
Pages (from-to)	982-986
Number of pages	5
Journal	European Urology
Volume	66
Issue number	6
DOIs	https://doi.org/10.1016/j.eururo.2014.07.045
State	Published - Dec 2014

Keywords

Fixatives
Formaldehyde
Gene Expression Profiling
Humans
Neoplasm Grading
Paraffin Embedding
Sequence Analysis, RNA/methods
Specimen Handling
Urinary Bladder Neoplasms/genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.eururo.2014.07.045

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Liu, Y., Noon, A. P., Aguiar Cabeza, E., Shen, J., Kuk, C., Ilczynski, C., Ni, R., Sukhu, B., Chan, K., Barbosa-Morais, N. L., Hermanns, T., Blencowe, B. J., Azad, A., van der Kwast, T. H., Catto, J. W. F., Zlotta, A. R., & Wrana, J. L. (2014). Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer. European Urology, 66(6), 982-986. https://doi.org/10.1016/j.eururo.2014.07.045

@article{13dd81fe531843feba263fec5f3fe9d7,

title = "Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer",

abstract = "UNLABELLED: Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.PATIENT SUMMARY: In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.",

keywords = "Fixatives, Formaldehyde, Gene Expression Profiling, Humans, Neoplasm Grading, Paraffin Embedding, Sequence Analysis, RNA/methods, Specimen Handling, Urinary Bladder Neoplasms/genetics",

author = "Yu Liu and Noon, {Aidan P} and {Aguiar Cabeza}, Eduardo and Jess Shen and Cynthia Kuk and Christine Ilczynski and Ruoyu Ni and Balram Sukhu and Kin Chan and Barbosa-Morais, {Nuno L} and Thomas Hermanns and Blencowe, {Benjamin J} and Azar Azad and {van der Kwast}, {Theodorus H} and Catto, {James W F} and Zlotta, {Alexandre R} and Wrana, {Jeffrey L}",

note = "Publisher Copyright: {\textcopyright} 2014 Published by Elsevier B.V. on behalf of European Association of Urology.",

year = "2014",

month = dec,

doi = "10.1016/j.eururo.2014.07.045",

language = "English",

volume = "66",

pages = "982--986",

journal = "European Urology",

issn = "0302-2838",

publisher = "Elsevier B.V.",

number = "6",

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Liu, Y, Noon, AP, Aguiar Cabeza, E, Shen, J, Kuk, C, Ilczynski, C, Ni, R, Sukhu, B, Chan, K, Barbosa-Morais, NL, Hermanns, T, Blencowe, BJ, Azad, A, van der Kwast, TH, Catto, JWF, Zlotta, AR & Wrana, JL 2014, 'Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer', European Urology, vol. 66, no. 6, pp. 982-986. https://doi.org/10.1016/j.eururo.2014.07.045

TY - JOUR

T1 - Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer

AU - Liu, Yu

AU - Noon, Aidan P

AU - Aguiar Cabeza, Eduardo

AU - Shen, Jess

AU - Kuk, Cynthia

AU - Ilczynski, Christine

AU - Ni, Ruoyu

AU - Sukhu, Balram

AU - Chan, Kin

AU - Barbosa-Morais, Nuno L

AU - Hermanns, Thomas

AU - Blencowe, Benjamin J

AU - Azad, Azar

AU - van der Kwast, Theodorus H

AU - Catto, James W F

AU - Zlotta, Alexandre R

AU - Wrana, Jeffrey L

PY - 2014/12

Y1 - 2014/12

N2 - UNLABELLED: Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.PATIENT SUMMARY: In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.

AB - UNLABELLED: Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.PATIENT SUMMARY: In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.

KW - Fixatives

KW - Formaldehyde

KW - Gene Expression Profiling

KW - Humans

KW - Neoplasm Grading

KW - Paraffin Embedding

KW - Sequence Analysis, RNA/methods

KW - Specimen Handling

KW - Urinary Bladder Neoplasms/genetics

UR - http://www.scopus.com/inward/record.url?scp=84910076730&partnerID=8YFLogxK

U2 - 10.1016/j.eururo.2014.07.045

DO - 10.1016/j.eururo.2014.07.045

M3 - Article

C2 - 25199720

SN - 0302-2838

VL - 66

SP - 982

EP - 986

JO - European Urology

JF - European Urology

IS - 6

ER -

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer

Abstract

Keywords

UN SDGs

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