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Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine

View ORCID ProfileSimeon Springer, Chung-Hsin Chen, Lu Li, View ORCID ProfileChris Douville, View ORCID ProfileYuxuan Wang, Josh Cohen, Bahman Afsari, View ORCID ProfileLudmila Danilova, Natalie Silliman, Joy Schaeffer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Chao-Yuan Huang, Chia-Tung Shun, Rachel Karchin, View ORCID ProfileGeorge J. Netto, Robert J. Turesky, Byeong Hwa Yun, Thomas A. Rosenquist, Ralph H. Hruban, Yeong-Shiau Pu, Arthur P. Grollman, Cristian Tomasetti, Nickolas Papadopoulos, Kenneth W. Kinzler, View ORCID ProfileBert Vogelstein, Kathleen G. Dickman
doi: https://doi.org/10.1101/203968
Simeon Springer
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Chung-Hsin Chen
2Department of Urology, National Taiwan University Hospital, Taipei, Taiwan.
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Lu Li
3Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Chris Douville
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Yuxuan Wang
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Josh Cohen
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Bahman Afsari
3Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Ludmila Danilova
3Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Natalie Silliman
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Joy Schaeffer
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Janine Ptak
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Lisa Dobbyn
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Maria Papoli
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Isaac Kinde
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Chao-Yuan Huang
2Department of Urology, National Taiwan University Hospital, Taipei, Taiwan.
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Chia-Tung Shun
4Department of Forensic Medicine and Pathology, National Taiwan University Hospital, Taipei, Taiwan.
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Rachel Karchin
5Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.
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George J. Netto
6Department of Pathology, University of Alabama at Birmingham, Birmingham, Al, 35233, USA.
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Robert J. Turesky
7Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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Byeong Hwa Yun
7Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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Thomas A. Rosenquist
8Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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Ralph H. Hruban
9Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.
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Yeong-Shiau Pu
2Department of Urology, National Taiwan University Hospital, Taipei, Taiwan.
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Arthur P. Grollman
8Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
10Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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Cristian Tomasetti
3Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
11Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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Nickolas Papadopoulos
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Kenneth W. Kinzler
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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Bert Vogelstein
1The Howard Hughes Medical Institute and Ludwig Center at the Sidney Kimmel Johns Hopkins Cancer Center, Baltimore, MD 21231, USA.
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  • For correspondence: vogelbe@jhmi.edu Kathleen.dickman@stonybrook.edu
Kathleen G. Dickman
8Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
10Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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  • For correspondence: vogelbe@jhmi.edu Kathleen.dickman@stonybrook.edu
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Abstract

Upper tract urothelial carcinomas (UTUC) of the renal pelvis or ureter can be difficult to detect and challenging to diagnose. Here, we report the development and application of a non-invasive test for UTUC based on molecular analyses of DNA recovered from cells shed into the urine. The test, called UroSEEK, incorporates assays for mutations in eleven genes frequently mutated in urologic malignancies and for allelic imbalances on 39 chromosome arms. At least one genetic abnormality was detected in 75% of urinary cell samples from 56 UTUC patients but in only 0.5% of 188 samples from healthy individuals. The assay was considerably more sensitive than urine cytology, the current standard-of-care. UroSEEK therefore has the potential to be used for screening or to aid in diagnosis in patients at increased risk for UTUC, such as those exposed to herbal remedies containing the carcinogen aristolochic acid.

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Posted October 16, 2017.
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Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine
Simeon Springer, Chung-Hsin Chen, Lu Li, Chris Douville, Yuxuan Wang, Josh Cohen, Bahman Afsari, Ludmila Danilova, Natalie Silliman, Joy Schaeffer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Chao-Yuan Huang, Chia-Tung Shun, Rachel Karchin, George J. Netto, Robert J. Turesky, Byeong Hwa Yun, Thomas A. Rosenquist, Ralph H. Hruban, Yeong-Shiau Pu, Arthur P. Grollman, Cristian Tomasetti, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Kathleen G. Dickman
bioRxiv 203968; doi: https://doi.org/10.1101/203968
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Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine
Simeon Springer, Chung-Hsin Chen, Lu Li, Chris Douville, Yuxuan Wang, Josh Cohen, Bahman Afsari, Ludmila Danilova, Natalie Silliman, Joy Schaeffer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Chao-Yuan Huang, Chia-Tung Shun, Rachel Karchin, George J. Netto, Robert J. Turesky, Byeong Hwa Yun, Thomas A. Rosenquist, Ralph H. Hruban, Yeong-Shiau Pu, Arthur P. Grollman, Cristian Tomasetti, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Kathleen G. Dickman
bioRxiv 203968; doi: https://doi.org/10.1101/203968

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