Oncotarget

Research Papers:

Genomic characterization of high-risk non-muscle invasive bladder cancer

Joshua J. Meeks _, Benedito A. Carneiro, Sachin G. Pai, Daniel T. Oberlin, Alfred Rademaker, Kyle Fedorchak, Sohail Balasubramanian, Julia Elvin, Nike Beaubier and Francis J. Giles

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Oncotarget. 2016; 7:75176-75184. https://doi.org/10.18632/oncotarget.12661

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Abstract

Joshua J. Meeks1,*, Benedito A. Carneiro2,*, Sachin G. Pai2, Daniel T. Oberlin1, Alfred Rademaker4, Kyle Fedorchak5, Sohail Balasubramanian5, Julia Elvin5, Nike Beaubier3, Francis J. Giles2

1Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

2Developmental Therapeutics Program, Division of Hematology/Oncology, Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA

3Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

4Northwestern University Department of Preventive Medicine, Chicago, IL, USA

5Foundation Medicine Inc, Cambridge, MA, USA

*These authors contributed equally to this work

Correspondence to:

Joshua J. Meeks, email: joshua.meeks@northwestern.edu

Benedito A. Carneiro, email: benedito.carneiro@northwestern.edu

Keywords: bladder cancer, mutation burden, progression, invasion

Received: August 29, 2016     Accepted: October 05, 2016     Published: October 14, 2016

ABSTRACT

The genetic mechanisms associated with progression of high-risk non-muscle-invasive bladder cancer (HR-NMIBC) have not been described. We conducted selective next-generation sequencing (NGS) of HR-NMIBC and compared the genomic profiles of cancers that responded to intravesical therapy and those that progressed to muscle-invasive or advanced disease. DNA was extracted from paraffin-embedded sections from 25 HR-NMIBCs (22 with T1HG; 3 with TaHG with or without carcinoma in situ). Ten patients with HR-NMIBC developed progression (pT2+ or N+) (“progressors”). Fifteen patients had no progression (“non-progressors”). Tissue from 11 patients with metastatic bladder cancer (BC) were analyzed for comparison. We found no difference in frequency of mutations of TP53, PIK3CA, or KMT2D between the primary tumors of progressors compared to non-progressors and metastatic tumors. An increased frequency of deletions of CDKN2A/B was identified in tumors at progression (37%) compared to non-progressors (6%) (p = 0.10). We found a significant decrease in total mutational burden (TMB) that has been associated with immunotherapy response comparing non-progressors, progressors and metastatic tumors at 15, 10.1 and 5.1 mutations/MB respectively (p = 0.02). This association suggests more advanced tumors have decreased neoantigen burden and may explain the mechanism of BCG response in non-progressors. We found no novel genetic drivers in progressors and HR-NMIBC had many genetic features similar to metastatic BC. Loss of CDKN2A/B may occur late during invasion of BC and may represent an important step in progression. Further research is necessary to evaluate TMB and loss of CDKN2A/B locus as a biomarker for progression of NMIBC.


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