Yu Liu1, Aidan P Noon2, Eduardo Aguiar Cabeza3, Jess Shen3, Cynthia Kuk2, Christine Ilczynski4, Ruoyu Ni4, Balram Sukhu4, Kin Chan3, Nuno L Barbosa-Morais5, Thomas Hermanns2, Benjamin J Blencowe6, Azar Azad4, Theodorus H van der Kwast7, James W F Catto8, Alexandre R Zlotta2, Jeffrey L Wrana9. 1. The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. 2. Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada. 3. The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. 4. Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada. 5. Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. 6. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. 7. Department of Pathology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada. 8. The Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, UK. 9. The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. Electronic address: wrana@lunenfeld.ca.
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.
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.
Authors: Kelli L VanDussen; Aleksandar Stojmirović; Katherine Li; Ta-Chiang Liu; Patrick K Kimes; Brian D Muegge; Katherine F Simpson; Matthew A Ciorba; Jacqueline G Perrigoue; Joshua R Friedman; Jennifer E Towne; Richard D Head; Thaddeus S Stappenbeck Journal: Gastroenterology Date: 2018-05-18 Impact factor: 22.682
Authors: Lawrence N Kwong; Mariana Petaccia De Macedo; Lauren Haydu; Aron Y Joon; Michael T Tetzlaff; Tiffany L Calderone; Chiang-Jun Wu; Man Kam Kwong; Jason Roszik; Kenneth R Hess; Michael A Davies; Alexander J Lazar; Jeffrey E Gershenwald Journal: JCO Precis Oncol Date: 2018-06-14
Authors: Ganna Posternak; Xiaojing Tang; Pierre Maisonneuve; Ting Jin; Hugo Lavoie; Salima Daou; Stephen Orlicky; Theo Goullet de Rugy; Lauren Caldwell; Kin Chan; Ahmed Aman; Michael Prakesch; Gennady Poda; Pavel Mader; Cassandra Wong; Stefan Maier; Julia Kitaygorodsky; Brett Larsen; Karen Colwill; Zhe Yin; Derek F Ceccarelli; Robert A Batey; Mikko Taipale; Igor Kurinov; David Uehling; Jeff Wrana; Daniel Durocher; Anne-Claude Gingras; Rima Al-Awar; Marc Therrien; Frank Sicheri Journal: Nat Chem Biol Date: 2020-08-10 Impact factor: 15.040
Authors: Milica Vukmirovic; Jose D Herazo-Maya; John Blackmon; Vesna Skodric-Trifunovic; Dragana Jovanovic; Sonja Pavlovic; Jelena Stojsic; Vesna Zeljkovic; Xiting Yan; Robert Homer; Branko Stefanovic; Naftali Kaminski Journal: BMC Pulm Med Date: 2017-01-12 Impact factor: 3.317