Genomic Characterization of Upper Tract Urothelial Carcinoma

John P. Sfakianos, Eugene K. Cha, Gopa Iyer, Sasinya N. Scott, Emily C. Zabor, Ronak H. Shah, Qinghu Ren, Aditya Bagrodia, Philip H. Kim, A. Ari Hakimi, Irina Ostrovnaya, Ricardo Ramirez, Aphrothiti J. Hanrahan, Neil B. Desai, Arony Sun, Patrizia Pinciroli, Jonathan E. Rosenberg, Guido Dalbagni, Nikolaus Schultz, Dean F. BajorinVictor E. Reuter, Michael F. Berger, Bernard H. Bochner, Hikmat A. Al-Ahmadie, David B. Solit, Jonathan A. Coleman

Research output: Contribution to journalArticle

Abstract

Background Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences. Objective To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity. Design, setting, and participants Tumor and germline DNA from patients with UTUC (n = 83) and UCB (n = 102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes. Outcome measurements and statistical analysis We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n = 59) and high-grade UCB (n = 102). Results and limitations Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6% vs 21.6%; p = 0.065), HRAS (13.6% vs 1.0%; p = 0.001), and CDKN2B (15.3% vs 3.9%; p = 0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4% vs 57.8%; p < 0.001), RB1 (0.0% vs 18.6%; p < 0.001), and ARID1A (13.6% vs 27.5%; p = 0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed. Conclusions High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma. Patient summary Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.

Original languageEnglish
Pages (from-to)970-977
Number of pages8
JournalEuropean Urology
Volume68
Issue number6
DOIs
Publication statusPublished - 2015

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Carcinoma
Urinary Bladder
Mutation
Mutation Rate
Urinary Bladder Neoplasms
Neoplasms
Genes
Neoplasm Genes
Biodiversity
Epigenomics

Keywords

  • Bladder cancer
  • Genomics
  • Targeted therapy
  • Upper tract urothelial carcinoma

ASJC Scopus subject areas

  • Medicine(all)
  • Urology

Cite this

Sfakianos, J. P., Cha, E. K., Iyer, G., Scott, S. N., Zabor, E. C., Shah, R. H., ... Coleman, J. A. (2015). Genomic Characterization of Upper Tract Urothelial Carcinoma. European Urology, 68(6), 970-977. https://doi.org/10.1016/j.eururo.2015.07.039

Genomic Characterization of Upper Tract Urothelial Carcinoma. / Sfakianos, John P.; Cha, Eugene K.; Iyer, Gopa; Scott, Sasinya N.; Zabor, Emily C.; Shah, Ronak H.; Ren, Qinghu; Bagrodia, Aditya; Kim, Philip H.; Hakimi, A. Ari; Ostrovnaya, Irina; Ramirez, Ricardo; Hanrahan, Aphrothiti J.; Desai, Neil B.; Sun, Arony; Pinciroli, Patrizia; Rosenberg, Jonathan E.; Dalbagni, Guido; Schultz, Nikolaus; Bajorin, Dean F.; Reuter, Victor E.; Berger, Michael F.; Bochner, Bernard H.; Al-Ahmadie, Hikmat A.; Solit, David B.; Coleman, Jonathan A.

In: European Urology, Vol. 68, No. 6, 2015, p. 970-977.

Research output: Contribution to journalArticle

Sfakianos, JP, Cha, EK, Iyer, G, Scott, SN, Zabor, EC, Shah, RH, Ren, Q, Bagrodia, A, Kim, PH, Hakimi, AA, Ostrovnaya, I, Ramirez, R, Hanrahan, AJ, Desai, NB, Sun, A, Pinciroli, P, Rosenberg, JE, Dalbagni, G, Schultz, N, Bajorin, DF, Reuter, VE, Berger, MF, Bochner, BH, Al-Ahmadie, HA, Solit, DB & Coleman, JA 2015, 'Genomic Characterization of Upper Tract Urothelial Carcinoma', European Urology, vol. 68, no. 6, pp. 970-977. https://doi.org/10.1016/j.eururo.2015.07.039
Sfakianos JP, Cha EK, Iyer G, Scott SN, Zabor EC, Shah RH et al. Genomic Characterization of Upper Tract Urothelial Carcinoma. European Urology. 2015;68(6):970-977. https://doi.org/10.1016/j.eururo.2015.07.039
Sfakianos, John P. ; Cha, Eugene K. ; Iyer, Gopa ; Scott, Sasinya N. ; Zabor, Emily C. ; Shah, Ronak H. ; Ren, Qinghu ; Bagrodia, Aditya ; Kim, Philip H. ; Hakimi, A. Ari ; Ostrovnaya, Irina ; Ramirez, Ricardo ; Hanrahan, Aphrothiti J. ; Desai, Neil B. ; Sun, Arony ; Pinciroli, Patrizia ; Rosenberg, Jonathan E. ; Dalbagni, Guido ; Schultz, Nikolaus ; Bajorin, Dean F. ; Reuter, Victor E. ; Berger, Michael F. ; Bochner, Bernard H. ; Al-Ahmadie, Hikmat A. ; Solit, David B. ; Coleman, Jonathan A. / Genomic Characterization of Upper Tract Urothelial Carcinoma. In: European Urology. 2015 ; Vol. 68, No. 6. pp. 970-977.
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title = "Genomic Characterization of Upper Tract Urothelial Carcinoma",
abstract = "Background Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences. Objective To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity. Design, setting, and participants Tumor and germline DNA from patients with UTUC (n = 83) and UCB (n = 102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes. Outcome measurements and statistical analysis We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n = 59) and high-grade UCB (n = 102). Results and limitations Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6{\%} vs 21.6{\%}; p = 0.065), HRAS (13.6{\%} vs 1.0{\%}; p = 0.001), and CDKN2B (15.3{\%} vs 3.9{\%}; p = 0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4{\%} vs 57.8{\%}; p < 0.001), RB1 (0.0{\%} vs 18.6{\%}; p < 0.001), and ARID1A (13.6{\%} vs 27.5{\%}; p = 0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed. Conclusions High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma. Patient summary Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.",
keywords = "Bladder cancer, Genomics, Targeted therapy, Upper tract urothelial carcinoma",
author = "Sfakianos, {John P.} and Cha, {Eugene K.} and Gopa Iyer and Scott, {Sasinya N.} and Zabor, {Emily C.} and Shah, {Ronak H.} and Qinghu Ren and Aditya Bagrodia and Kim, {Philip H.} and Hakimi, {A. Ari} and Irina Ostrovnaya and Ricardo Ramirez and Hanrahan, {Aphrothiti J.} and Desai, {Neil B.} and Arony Sun and Patrizia Pinciroli and Rosenberg, {Jonathan E.} and Guido Dalbagni and Nikolaus Schultz and Bajorin, {Dean F.} and Reuter, {Victor E.} and Berger, {Michael F.} and Bochner, {Bernard H.} and Al-Ahmadie, {Hikmat A.} and Solit, {David B.} and Coleman, {Jonathan A.}",
year = "2015",
doi = "10.1016/j.eururo.2015.07.039",
language = "English",
volume = "68",
pages = "970--977",
journal = "European Urology",
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TY - JOUR

T1 - Genomic Characterization of Upper Tract Urothelial Carcinoma

AU - Sfakianos, John P.

AU - Cha, Eugene K.

AU - Iyer, Gopa

AU - Scott, Sasinya N.

AU - Zabor, Emily C.

AU - Shah, Ronak H.

AU - Ren, Qinghu

AU - Bagrodia, Aditya

AU - Kim, Philip H.

AU - Hakimi, A. Ari

AU - Ostrovnaya, Irina

AU - Ramirez, Ricardo

AU - Hanrahan, Aphrothiti J.

AU - Desai, Neil B.

AU - Sun, Arony

AU - Pinciroli, Patrizia

AU - Rosenberg, Jonathan E.

AU - Dalbagni, Guido

AU - Schultz, Nikolaus

AU - Bajorin, Dean F.

AU - Reuter, Victor E.

AU - Berger, Michael F.

AU - Bochner, Bernard H.

AU - Al-Ahmadie, Hikmat A.

AU - Solit, David B.

AU - Coleman, Jonathan A.

PY - 2015

Y1 - 2015

N2 - Background Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences. Objective To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity. Design, setting, and participants Tumor and germline DNA from patients with UTUC (n = 83) and UCB (n = 102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes. Outcome measurements and statistical analysis We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n = 59) and high-grade UCB (n = 102). Results and limitations Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6% vs 21.6%; p = 0.065), HRAS (13.6% vs 1.0%; p = 0.001), and CDKN2B (15.3% vs 3.9%; p = 0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4% vs 57.8%; p < 0.001), RB1 (0.0% vs 18.6%; p < 0.001), and ARID1A (13.6% vs 27.5%; p = 0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed. Conclusions High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma. Patient summary Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.

AB - Background Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences. Objective To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity. Design, setting, and participants Tumor and germline DNA from patients with UTUC (n = 83) and UCB (n = 102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes. Outcome measurements and statistical analysis We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n = 59) and high-grade UCB (n = 102). Results and limitations Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6% vs 21.6%; p = 0.065), HRAS (13.6% vs 1.0%; p = 0.001), and CDKN2B (15.3% vs 3.9%; p = 0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4% vs 57.8%; p < 0.001), RB1 (0.0% vs 18.6%; p < 0.001), and ARID1A (13.6% vs 27.5%; p = 0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed. Conclusions High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma. Patient summary Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.

KW - Bladder cancer

KW - Genomics

KW - Targeted therapy

KW - Upper tract urothelial carcinoma

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