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Fujii T, Barzi A, Sartore-Bianchi A, Cassingena A, Siravegna G, Karp DD, Piha-Paul SA, Subbiah V, Tsimberidou AM, Huang HJ, Veronese S, Di Nicolantonio F, Pingle S, Vibat CRT, Hancock S, Berz D, Melnikova VO, Erlander MG, Luthra R, Kopetz ES, Meric-Bernstam F, Siena S, Lenz HJ, Bardelli A, Janku F. Mutation-Enrichment Next-Generation Sequencing for Quantitative Detection of KRAS Mutations in Urine Cell-Free DNA from Patients with Advanced Cancers. Clin Cancer Res 2017; 23:3657-3666. [PMID: 28096270 PMCID: PMC5511562 DOI: 10.1158/1078-0432.ccr-16-2592] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 02/05/2023]
Abstract
Purpose: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers noninvasive biological material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRASExperimental Design: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed, and results were compared with clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer.Results: With 90 to 110 mL of urine, the KRASG12/G13 cfDNA test had an analytical sensitivity of 0.002% to 0.006% mutant copies in wild-type background. In 71 patients, the concordance between urine cfDNA and tumor was 73% (sensitivity, 63%; specificity, 96%) for all patients and 89% (sensitivity, 80%; specificity, 100%) for patients with urine samples of 90 to 110 mL. Patients had significantly fewer KRASG12/G13 copies in urine cfDNA during systemic therapy than at baseline or disease progression (P = 0.002). Compared with no changes or increases in urine cfDNA KRASG12/G13 copies during therapy, decreases in these measures were associated with longer median time to treatment failure (P = 0.03).Conclusions: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA had good concordance with testing of archival tumor tissue. Changes in mutated urine cfDNA were associated with time to treatment failure. Clin Cancer Res; 23(14); 3657-66. ©2017 AACR.
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Affiliation(s)
- Takeo Fujii
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Afsaneh Barzi
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Giulia Siravegna
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Silvio Veronese
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | | | | | | | - David Berz
- Beverly Hills Cancer Center, Beverly Hills, California
- City of Hope, Duarte, California
| | | | | | - Rajyalakshmi Luthra
- Department of Hematopathology, Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - E Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alberto Bardelli
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Kirimli CE, Shih WH, Shih WY. Amplification-free in situ KRAS point mutation detection at 60 copies per mL in urine in a background of 1000-fold wild type. Analyst 2016; 141:1421-33. [PMID: 26783561 PMCID: PMC4747796 DOI: 10.1039/c5an02048d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have examined the in situ detection of a single-nucleotide KRAS mutation in urine using a (Pb(Mg1/3Nb2/3)O3)0.65(PbTiO3)0.35 (PMN-PT) piezoelectric plate sensor (PEPS) coated with a 17-nucleotide (nt) locked nucleic acid (LNA) probe DNA complementary to the KRAS mutation. To enhance the in situ mutant (MT) DNA detection specificity against the wild type (WT), detection was carried out in a flow with a flow rate of 4 mL min(-1) and at 63 °C with the PEPS vertically situated at the center of the flow in which both the temperature and the flow impingement force discriminated the wild type. Under such conditions, PEPS was shown to specifically detect KRAS MT in situ with 60 copies per mL analytical sensitivity in a background of clinically-relevant 1000-fold more WT in 30 min without DNA isolation, amplification, or labeling. For validation, this detection was followed with detection in a mixture of blue MT fluorescent reporter microspheres (FRMs) (MT FRMs) that bound to only the captured MT and orange WT FRMs that bound to only the captured WT. Microscopic examinations showed that the captured blue MT FRMs still outnumbered the orange WT FRMs by a factor of 4 to 1 even though WT was 1000-fold of MT in urine. Finally, multiplexed specific mutation detection was demonstrated using a 6-PEPS array each with a probe DNA targeting one of the 6 codon-12 KRAS mutations.
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Affiliation(s)
- Ceyhun E Kirimli
- Drexel University, School of Biomedical Engineering, Science, and Health Systems, Philadelphia, Pennsylvania 19104, USA.
| | - Wei-Heng Shih
- Drexel University, Department of Materials Science and Engineering, Philadelphia, Pennsylvania, USA
| | - Wan Y Shih
- Drexel University, School of Biomedical Engineering, Science, and Health Systems, Philadelphia, Pennsylvania 19104, USA.
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Su YH, Wang M, Brenner DE, Ng A, Melkonyan H, Umansky S, Syngal S, Block TM. Human urine contains small, 150 to 250 nucleotide-sized, soluble DNA derived from the circulation and may be useful in the detection of colorectal cancer. J Mol Diagn 2004; 6:101-7. [PMID: 15096565 PMCID: PMC1867475 DOI: 10.1016/s1525-1578(10)60497-7] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2003] [Indexed: 11/22/2022] Open
Abstract
Human urine has been shown to possess submicrogram per milliliter amounts of DNA. We show here that DNA isolated from human urine resolves into two size categories: the large species, greater than 1 kb, being predominantly cell associated and heterogeneous in size, and the smaller, between 150 to 250 bp, being mostly non-cell associated. We showed that the low molecular weight class of urine DNA is derived from the circulation, by comparing the mutated K-ras sequences present in DNA isolated from tumor, blood, and urine derived from an individual with a colorectal carcinoma (CRC) containing a mutation in codon 12 of the K-ras proto-oncogene. In the urine, mutated K-ras sequences were abundant in the low molecular weight species, but far less abundant in the large molecular weight-derived DNA. Finally, the possibility that detection of mutant K-ras sequences in DNA derived from the urine correlates with the occurrence of a diagnosis of CRC and polyps that contain mutant K-ras was explored in a blinded study. There was an 83% concurrence of mutated DNA detected in urine and its corresponding disease tissue from the same individuals, when paired urine and tissue sections from 20 subjects with either CRC or adenomatous polyps were analyzed for K-ras mutation. The possibility that the source of the trans renal DNA is apoptotic cells, and the potential use of this finding for cancer detection and monitoring is discussed.
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Affiliation(s)
- Ying-Hsiu Su
- Department of Biochemistry and Molecular Pharmacology, Jefferson Center for Biomedical Research, Thomas Jefferson University, Doylestown, Pennsylvania, USA.
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Scobbie AE, Anderson JB, Horwich A. Measurement of ras p21 in the urine of patients with urological tumours. In Vivo 1994; 8:1067-72. [PMID: 7772739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have measured the product of the ras oncogene, ras p21, in random un-timed urine samples using an immunoblotting method which relies upon enhanced chemiluminescence for visualisation of the nitrocellulose filter. Urine samples were analysed from groups of patients with prostate (n = 10) or bladder (n = 25) cancer and a control group (n = 30) with no apparent urological disease. The mean concentration of urinary ras p21 in the groups with either bladder or prostate cancer was not significantly higher than that of the control group. The most striking difference between the control and clinical groups was the presence of a previously un-reported ras p21 "doublet" in the electrophoretic patterns obtained from 20% of the bladder cancer group and 10% of the prostate cancer group. This doublet was not present in any of the control samples analysed. This doublet is strongly suggestive of a mutation within the ras oncogene.
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Affiliation(s)
- A E Scobbie
- Biomedical Sciences Group, Health and Safety Laboratory, Sheffield, U.K
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