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Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications.
Eur Urol 2018; 74(6):741-753EU

Abstract

BACKGROUND

Integrated molecular profiling has identified intrinsic expression-based bladder cancer molecular subtypes. Despite frequent histological diversity, robustness of subtypes in paired conventional (urothelial) and squamous components of the same bladder tumor has not been reported.

OBJECTIVE

To assess the impact of histological heterogeneity on expression-based bladder cancer subtypes.

DESIGN, SETTING, AND PARTICIPANTS

We performed clinically applicable, targeted DNA and/or RNA sequencing (multiplexed DNA and RNA sequencing [mxDNAseq and mxRNAseq, respectively]) on 112 formalin-fixed paraffin-embedded (FFPE) bladder cancer samples, including 12 cases with paired urothelial/squamous components and 21 bladder cancer cell lines.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Unsupervised hierarchical and consensus clustering of target gene expression enabled derivation of basal/luminal molecular subtyping.

RESULTS AND LIMITATION

Across 21 bladder cancer cell lines, our custom mxRNAseq panel was highly concordant with whole transcriptome sequencing, and assessed targets robustly determined expression-based basal/luminal subtypes from The Cancer Genome Atlas data (in silico) and internally sequenced FFPE tissues. Frequent deleterious TP53 (56%) and activating hotspot PIK3CA (30%) somatic mutations were seen across 69 high-quality tissue samples. Potentially targetable focal ERBB2 (6%) or EGFR (6%) amplifications were also identified, and a novel subgene copy-number detection approach is described. Combined DNA/RNA analysis showed that focally amplified samples exhibit outlier EGFR and ERBB2 expression distinct from subtype-intrinsic profiles. Critically, paired urothelial and squamous components showed divergent basal/luminal status in three of 12 cases (25%), despite identical putatively clonal prioritized somatic genomic alterations. Limitations include lack of profiled paired normal tissues for formal somatic alteration determination, and the need for formal analytical and clinical validation.

CONCLUSIONS

Our results support the feasibility of clinically relevant integrative bladder cancer profiling and challenge the intrinsic nature of expression subtypes in histologically diverse bladder cancers.

PATIENT SUMMARY

A targeted RNA sequencing assay is capable of assessing gene expression-based subtypes in individual components of clinical bladder cancer tissue specimens. Different histological components of the same tumor may yield divergent expression profiles, suggesting that expression-based subtypes should be interpreted with caution in heterogeneous cancers.

Authors+Show Affiliations

Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA.Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA.Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Internal Medicine (Hematology/Oncology), Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Internal Medicine (Hematology/Oncology), Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA.Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Medical University of Vienna, Vienna, Austria.Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.ThermoFisher Scientific, Ann Arbor, MI, USA.Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA.Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, Michigan Medicine, Ann Arbor, MI, USA. Electronic address: tomlinss@umich.edu.

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30033047

Citation

Hovelson, Daniel H., et al. "Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications." European Urology, vol. 74, no. 6, 2018, pp. 741-753.
Hovelson DH, Udager AM, McDaniel AS, et al. Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. Eur Urol. 2018;74(6):741-753.
Hovelson, D. H., Udager, A. M., McDaniel, A. S., Grivas, P., Palmbos, P., Tamura, S., ... Tomlins, S. A. (2018). Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. European Urology, 74(6), pp. 741-753. doi:10.1016/j.eururo.2018.06.047.
Hovelson DH, et al. Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. Eur Urol. 2018;74(6):741-753. PubMed PMID: 30033047.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. AU - Hovelson,Daniel H, AU - Udager,Aaron M, AU - McDaniel,Andrew S, AU - Grivas,Petros, AU - Palmbos,Phillip, AU - Tamura,Shuzo, AU - Lazo de la Vega,Lorena, AU - Palapattu,Ganesh, AU - Veeneman,Brendan, AU - El-Sawy,Layla, AU - Sadis,Seth E, AU - Morgan,Todd M, AU - Montgomery,Jeffrey S, AU - Weizer,Alon Z, AU - Day,Kathleen C, AU - Neamati,Nouri, AU - Liebert,Monica, AU - Keller,Evan T, AU - Day,Mark L, AU - Mehra,Rohit, AU - Tomlins,Scott A, Y1 - 2018/07/20/ PY - 2018/04/21/received PY - 2018/06/28/accepted PY - 2018/7/24/pubmed PY - 2019/6/14/medline PY - 2018/7/24/entrez KW - Molecular subtypes KW - Muscle-invasive bladder cancer KW - Next-generation sequencing KW - Squamous cell carcinoma KW - Urinary bladder SP - 741 EP - 753 JF - European urology JO - Eur. Urol. VL - 74 IS - 6 N2 - BACKGROUND: Integrated molecular profiling has identified intrinsic expression-based bladder cancer molecular subtypes. Despite frequent histological diversity, robustness of subtypes in paired conventional (urothelial) and squamous components of the same bladder tumor has not been reported. OBJECTIVE: To assess the impact of histological heterogeneity on expression-based bladder cancer subtypes. DESIGN, SETTING, AND PARTICIPANTS: We performed clinically applicable, targeted DNA and/or RNA sequencing (multiplexed DNA and RNA sequencing [mxDNAseq and mxRNAseq, respectively]) on 112 formalin-fixed paraffin-embedded (FFPE) bladder cancer samples, including 12 cases with paired urothelial/squamous components and 21 bladder cancer cell lines. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Unsupervised hierarchical and consensus clustering of target gene expression enabled derivation of basal/luminal molecular subtyping. RESULTS AND LIMITATION: Across 21 bladder cancer cell lines, our custom mxRNAseq panel was highly concordant with whole transcriptome sequencing, and assessed targets robustly determined expression-based basal/luminal subtypes from The Cancer Genome Atlas data (in silico) and internally sequenced FFPE tissues. Frequent deleterious TP53 (56%) and activating hotspot PIK3CA (30%) somatic mutations were seen across 69 high-quality tissue samples. Potentially targetable focal ERBB2 (6%) or EGFR (6%) amplifications were also identified, and a novel subgene copy-number detection approach is described. Combined DNA/RNA analysis showed that focally amplified samples exhibit outlier EGFR and ERBB2 expression distinct from subtype-intrinsic profiles. Critically, paired urothelial and squamous components showed divergent basal/luminal status in three of 12 cases (25%), despite identical putatively clonal prioritized somatic genomic alterations. Limitations include lack of profiled paired normal tissues for formal somatic alteration determination, and the need for formal analytical and clinical validation. CONCLUSIONS: Our results support the feasibility of clinically relevant integrative bladder cancer profiling and challenge the intrinsic nature of expression subtypes in histologically diverse bladder cancers. PATIENT SUMMARY: A targeted RNA sequencing assay is capable of assessing gene expression-based subtypes in individual components of clinical bladder cancer tissue specimens. Different histological components of the same tumor may yield divergent expression profiles, suggesting that expression-based subtypes should be interpreted with caution in heterogeneous cancers. SN - 1873-7560 UR - https://www.unboundmedicine.com/medline/citation/30033047/Targeted_DNA_and_RNA_Sequencing_of_Paired_Urothelial_and_Squamous_Bladder_Cancers_Reveals_Discordant_Genomic_and_Transcriptomic_Events_and_Unique_Therapeutic_Implications_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0302-2838(18)30475-5 DB - PRIME DP - Unbound Medicine ER -