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Lin S, Wang S, Xu B. Fragmentation patterns of cell-free DNA and somatic mutations in the urine of metastatic breast cancer patients. J Cancer Res Ther 2024; 20:563-569. [PMID: 38454812 DOI: 10.4103/jcrt.jcrt_1359_23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/08/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Urinary cell-free deoxyribonucleic acid (DNA) (ucfDNA) holds promise as a biomarker; however, its potential remains largely unexplored. We examined the fragmentation pattern of ucfDNA and identified somatic mutations within urine samples from metastatic breast cancer (MBC) patients. METHODS Urine and blood specimens were collected before treatment from 45 MBC patients and posttreatment urine samples from 16 of the 45 patients at the China National Cancer Center. Somatic mutations and tumor mutational burden (TMB) in the urine and plasma of 10 patients were analyzed by next-generation sequencing (NGS). Fragmentation patterns of cfDNA were displayed using electropherograms. Differences in the extracted amount of cfDNA, length of cfDNA fragments, and TMB between urine and plasma were compared using a Wilcoxon test. RESULTS The fragmentation patterns of ucfDNA were categorized as follows: (1) profile A (n = 26) containing a short peak (100-200 bp) and a long peak (>1500 bp); (2) profile B (n = 8) containing only a long peak; and (3) profile C (n = 11) containing flat pattern. For profile A patients, the short-peaked ucfDNA circulating in the bloodstream was much shorter compared with plasma cfDNA (149 vs. 171 bp, Wilcoxon test, P = 0.023). The fragmentation patterns in lung metastasis patients exhibited a higher propensity toward profile C ( P = 0.002). After treatment, 87.5% of the patients exhibited consistent fragmentation patterns. The concordance rate for somatic mutations in the plasma and urine was 30%, and the median TMB of urine and plasma was not significantly different. CONCLUSIONS This study established a fragmentation pattern for ucfDNA and detected somatic mutations in the urine of MBC patients. These results suggest the potential application of ucfDNA as a biomarker for MBC.
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Affiliation(s)
- Shaoyan Lin
- Department of Clinical Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Shusen Wang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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2
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Ruppert T, Roth A, Kollmeier J, Mairinger T, Frost N. Cell-free DNA extraction from urine of lung cancer patients and healthy individuals: Evaluation of a simple method using sample volume up-scaling. J Clin Lab Anal 2023; 37:e24984. [PMID: 37991151 PMCID: PMC10749489 DOI: 10.1002/jcla.24984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Urine holds promise as a source for cell-free DNA (cfDNA) analysis of cancer genetics due to its nature as a self-collectable biospecimen available in large quantities. However, pre-analytical variables such as preservation of cfDNA or efficiency of up-scaling specimen volume need to be better explored to increase analysis sensitivity. PATIENTS AND METHODS Initially effects of pH levels on cfDNA stability of urine preserved with EDTA were investigated in three healthy probands. Furthermore, the efficiency of urine volume up-scaling was examined using a simple DNA extraction method and cfDNA in urine of 32 individuals. Quantification was performed by PCR detection of three relevant targets used for EGFR and KRAS gene mutational analysis. RESULTS Only samples preserved with EDTA at alkaline pH levels showed cfDNA stability of up to 10 days at room temperature. Moreover, it was found that increasing the volume up to 100 mL was highly efficient. A similar amount of copies was detected in three different gene sites in all specimens indicating both a good availability and a non-random distribution pattern across genes. Since the median cfDNA copy number was 1642 copies/mL, abundance of cfDNA in this type of liquid biopsy is low. CONCLUSION Predictable sensitivities with different urine volumes on the ground of detectable cfDNA in our study population revealed that up-scaling (>5 mL) is mandatory if the mutation allele frequency is less than 1%.
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Affiliation(s)
- Tilman Ruppert
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Andreas Roth
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Jens Kollmeier
- Department of PneumologyHelios Klinikum Emil von BehringBerlinGermany
| | - Thomas Mairinger
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Nikolaj Frost
- Department of PneumologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
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3
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Jordaens S, Zwaenepoel K, Tjalma W, Deben C, Beyers K, Vankerckhoven V, Pauwels P, Vorsters A. Urine biomarkers in cancer detection: A systematic review of preanalytical parameters and applied methods. Int J Cancer 2023; 152:2186-2205. [PMID: 36647333 DOI: 10.1002/ijc.34434] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/25/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023]
Abstract
The aim of this review was to explore the status of urine sampling as a liquid biopsy for noninvasive cancer research by reviewing used preanalytical parameters and protocols. We searched two main health sciences databases, PubMed and Web of Science. From all eligible publications (2010-2022), information was extracted regarding: (a) study population characteristics, (b) cancer type, (c) urine preanalytics, (d) analyte class, (e) isolation method, (f) detection method, (g) comparator used, (h) biomarker type, (i) conclusion and (j) sensitivity and specificity. The search query identified 7835 records, of which 924 unique publications remained after screening the title, abstract and full text. Our analysis demonstrated that many publications did not report information about the preanalytical parameters of their urine samples, even though several other studies have shown the importance of standardization of sample handling. Interestingly, it was noted that urine is used for many cancer types and not just cancers originating from the urogenital tract. Many different types of relevant analytes have been shown to be found in urine. Additionally, future considerations and recommendations are discussed: (a) the heterogeneous nature of urine, (b) the need for standardized practice protocols and (c) the road toward the clinic. Urine is an emerging liquid biopsy with broad applicability in different analytes and several cancer types. However, standard practice protocols for sample handling and processing would help to elaborate the clinical utility of urine in cancer research, detection and disease monitoring.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Novosanis NV, Wijnegem, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Wiebren Tjalma
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Multidisciplinary Breast Clinic, Gynecological Oncology Unit, Department of Obstetrics and Gynecology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | | | - Vanessa Vankerckhoven
- Novosanis NV, Wijnegem, Belgium.,Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Alex Vorsters
- Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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Ren XD, Su N, Sun XG, Li WM, Li J, Li BW, Li RX, Lv J, Xu QY, Kong WL, Huang Q. Advances in liquid biopsy-based markers in NSCLC. Adv Clin Chem 2023; 114:109-150. [PMID: 37268331 DOI: 10.1016/bs.acc.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Lung cancer is the second most-frequently occurring cancer and the leading cause of cancer-associated deaths worldwide. Non-small cell lung cancer (NSCLC), the most common type of lung cancer is often diagnosed in middle or advanced stages and have poor prognosis. Diagnosis of disease at an early stage is a key factor for improving prognosis and reducing mortality, whereas, the currently used diagnostic tools are not sufficiently sensitive for early-stage NSCLC. The emergence of liquid biopsy has ushered in a new era of diagnosis and management of cancers, including NSCLC, since analysis of circulating tumor-derived components, such as cell-free DNA (cfDNA), circulating tumor cells (CTCs), cell-free RNAs (cfRNAs), exosomes, tumor-educated platelets (TEPs), proteins, and metabolites in blood or other biofluids can enable early cancer detection, treatment selection, therapy monitoring and prognosis assessment. There have been great advances in liquid biopsy of NSCLC in the past few years. Hence, this chapter introduces the latest advances on the clinical application of cfDNA, CTCs, cfRNAs and exosomes, with a particular focus on their application as early markers in the diagnosis, treatment and prognosis of NSCLC.
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Affiliation(s)
- Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Bo-Wen Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Jing Lv
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Qian-Ying Xu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Wei-Long Kong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, P.R. China.
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Casagrande GMS, Silva MO, Reis RM, Leal LF. Liquid Biopsy for Lung Cancer: Up-to-Date and Perspectives for Screening Programs. Int J Mol Sci 2023; 24. [PMID: 36768828 DOI: 10.3390/ijms24032505] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Lung cancer is the deadliest cancer worldwide. Tissue biopsy is currently employed for the diagnosis and molecular stratification of lung cancer. Liquid biopsy is a minimally invasive approach to determine biomarkers from body fluids, such as blood, urine, sputum, and saliva. Tumor cells release cfDNA, ctDNA, exosomes, miRNAs, circRNAs, CTCs, and DNA methylated fragments, among others, which can be successfully used as biomarkers for diagnosis, prognosis, and prediction of treatment response. Predictive biomarkers are well-established for managing lung cancer, and liquid biopsy options have emerged in the last few years. Currently, detecting EGFR p.(Tyr790Met) mutation in plasma samples from lung cancer patients has been used for predicting response and monitoring tyrosine kinase inhibitors (TKi)-treated patients with lung cancer. In addition, many efforts continue to bring more sensitive technologies to improve the detection of clinically relevant biomarkers for lung cancer. Moreover, liquid biopsy can dramatically decrease the turnaround time for laboratory reports, accelerating the beginning of treatment and improving the overall survival of lung cancer patients. Herein, we summarized all available and emerging approaches of liquid biopsy-techniques, molecules, and sample type-for lung cancer.
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Lapin M, Huang HJ, Chagani S, Javle M, Shroff RT, Pant S, Gouda MA, Raina A, Madwani K, Holley VR, Call SG, Dustin DJ, Lanman RB, Meric-Bernstam F, Raymond VM, Kwong LN, Janku F. Monitoring of Dynamic Changes and Clonal Evolution in Circulating Tumor DNA From Patients With IDH-Mutated Cholangiocarcinoma Treated With Isocitrate Dehydrogenase Inhibitors. JCO Precis Oncol 2022; 6:e2100197. [PMID: 35171660 PMCID: PMC8865526 DOI: 10.1200/po.21.00197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Received: 05/05/2021] [Revised: 09/25/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022] Open
Abstract
PURPOSE IDH mutations occur in about 30% of patients with cholangiocarcinoma. Analysis of mutations in circulating tumor DNA (ctDNA) can be performed by droplet digital polymerase chain reaction (ddPCR). The analysis of ctDNA is a feasible approach to detect IDH mutations. METHODS We isolated ctDNA from the blood of patients with IDH-mutated advanced cholangiocarcinoma collected at baseline, on therapy, and at progression to isocitrate dehydrogenase (IDH) inhibitors. RESULTS Of 31 patients with IDH1R132 (n = 26) or IDH2R172 mutations (n = 5) in the tumor, IDH mutations were detected in 84% of ctDNA samples analyzed by ddPCR and in 83% of ctDNA samples analyzed by next-generation sequencing (NGS). Patients with a low variant allele frequency of ctDNA detected by NGS at baseline had a longer median time to treatment failure compared to patients with high variant allele frequency of ctDNA (3.6 v 1.5 months; P = .008). Patients with a decrease in IDH-mutated ctDNA on therapy by ddPCR compared with no change/increase had a trend to a longer median survival (P = .07). Most frequent emergent alterations in ctDNA by NGS at progression were ARID1A (n = 3) and TP53 mutations (n = 3). CONCLUSION Detection of IDH mutations in ctDNA in patients with advanced cholangiocarcinoma is feasible, and dynamic changes in ctDNA can correspond with the clinical course and clonal evolution.
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Affiliation(s)
- Morten Lapin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Helen J. Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rachna T. Shroff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Hematology/Oncology, University of Arizona Cancer Center, Tucson, AZ
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohamed A. Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anjali Raina
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kiran Madwani
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Veronica R. Holley
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S. Greg Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Derek J. Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Procaccio L, Bergamo F, Daniel F, Rasola C, Munari G, Biason P, Crucitta S, Barsotti G, Zanella G, Angerilli V, Magro C, Paccagnella S, Di Antonio V, Loupakis F, Danesi R, Zagonel V, Del Re M, Lonardi S, Fassan M. A Real-World Application of Liquid Biopsy in Metastatic Colorectal Cancer: The Poseidon Study. Cancers (Basel) 2021; 13:cancers13205128. [PMID: 34680277 PMCID: PMC8533756 DOI: 10.3390/cancers13205128] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND First-line decision making is the key to the successful care of mCRC patients and RAS/BRAF status is crucial to select the best targeted agent. In hub centers, a relevant proportion of patients referred from small volume centers may not have standard tissue-based (STB) molecular results available at the time of the first visit (T0). Liquid biopsy (LB) may help circumvent these hurdles. METHODS A monoinstitutional prospective head-to-head comparison of LB versus (vs.) STB testing was performed in a real-world setting. Selection criteria included: mCRC diagnosis with unknown RAS/BRAF status at T0, tumoral tissue archived in external centers, no previous treatment with anti-EGFR. At T0, patients underwent plasma sampling for LB testing and procedure for tissue recovery. RAS/BRAF genotyping was carried out by droplet digital PCR on circulating-tumoral (ct) DNA. The primary endpoint was the comparison of time to LB (T1) vs. STB (T2) results using the Mann-Whitney U test. Secondary endpoints were the concordance between LB and STB defined as overall percent agreement and the accuracy of LB in terms of specificity, sensitivity, positive and negative predictive value. We also performed an exploratory analysis on urinary (u) ctDNA. RESULTS A total of 33 mCRC patients were included. Mean T1 and T2 was 7 and 22 days (d), respectively (p < 0.00001). T2 included a mean time for archival tissue recovery of 17 d. The overall percent agreement between LB and STB analysis was 83%. Compared to STB testing, LB specificity and sensitivity were 90% and 80%, respectively, with a positive predictive value of 94% and negative one of 69%. In detail, at STB and LB testing, RAS mutation was found in 45% and 42% of patients, respectively; BRAF mutation in 15%. LB results included one false positive and four false negative. False negative cases showed a significantly lower tumor burden at basal CT scan. Concordance between STB and uctDNA testing was 89%. CONCLUSIONS Faster turnaround time, high concordance and accuracy are three key points supporting the adoption of LB in routinary mCRC care, in particular when decision on first-line therapy is urgent and tissue recovery from external centers may require a long time. Results should be interpreted with caution in LB wild-type cases with low tumor burden.
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Affiliation(s)
- Letizia Procaccio
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
- Department of Surgery, Oncology, and Gastroenterology, University of Padova, 35121 Padova, Italy
| | - Francesca Bergamo
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Francesca Daniel
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Cosimo Rasola
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
- Department of Surgery, Oncology, and Gastroenterology, University of Padova, 35121 Padova, Italy
| | - Giada Munari
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padova, 35121 Padova, Italy; (G.M.); (V.A.); (S.P.); (M.F.)
- Veneto Institute of Oncology (IOV-IRCCS), 35128 Padova, Italy
| | - Paola Biason
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Stefania Crucitta
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 56121 Pisa, Italy; (S.C.); (R.D.); (M.D.R.)
| | - Giulia Barsotti
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
- Department of Surgery, Oncology, and Gastroenterology, University of Padova, 35121 Padova, Italy
| | - Giulia Zanella
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Valentina Angerilli
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padova, 35121 Padova, Italy; (G.M.); (V.A.); (S.P.); (M.F.)
| | - Cristina Magro
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Silvia Paccagnella
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padova, 35121 Padova, Italy; (G.M.); (V.A.); (S.P.); (M.F.)
| | - Veronica Di Antonio
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Fotios Loupakis
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Romano Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 56121 Pisa, Italy; (S.C.); (R.D.); (M.D.R.)
| | - Vittorina Zagonel
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy; (L.P.); (F.B.); (F.D.); (C.R.); (P.B.); (G.B.); (G.Z.); (C.M.); (V.D.A.); (F.L.); (V.Z.)
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 56121 Pisa, Italy; (S.C.); (R.D.); (M.D.R.)
| | - Sara Lonardi
- Oncology Unit 3, Department of Oncology, Veneto Institute of Oncology—IRCCS, 35128 Padova, Italy
- Correspondence: ; Tel.: +39-0498215953
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padova, 35121 Padova, Italy; (G.M.); (V.A.); (S.P.); (M.F.)
- Veneto Institute of Oncology (IOV-IRCCS), 35128 Padova, Italy
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8
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Gou Q, Zhang CZ, Sun ZH, Wu LG, Chen Y, Mo ZQ, Mai QC, He J, Zhou ZX, Shi F, Cui W, Zou W, Lv L, Zhuang WH, Xu RD, Li WK, Zhang J, Du HW, Xiang JX, Wang HZ, Hou T, Li ST, Li Y, Chen XM, Zhou ZJ. Cell-free DNA from bile outperformed plasma as a potential alternative to tissue biopsy in biliary tract cancer. ESMO Open 2021; 6:100275. [PMID: 34653800 PMCID: PMC8517551 DOI: 10.1016/j.esmoop.2021.100275] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Biliary tract cancers (BTCs) are rare and highly heterogenous malignant neoplasms. Because obtaining BTC tissues is challenging, the purpose of this study was to explore the potential roles of bile as a liquid biopsy medium in patients with BTC. PATIENTS AND METHODS Sixty-nine consecutive patients with suspected BTC were prospectively enrolled in this study. Capture-based targeted sequencing was performed on tumor tissues, whole blood cells, plasma, and bile samples using a large panel consisting of 520 cancer-related genes. RESULTS Of the 28 patients enrolled in this cohort, tumor tissues were available in eight patients, and plasma and bile were available in 28 patients. Somatic mutations were detected in 100% (8/8), 71.4% (20/28), and 53.6% (15/28) of samples comprising tumor tissue DNA, bile cell-free DNA (cfDNA), and plasma cfDNA, respectively. Bile cfDNA showed a significantly higher maximum allele frequency than plasma cfDNA (P = 0.0032). There were 56.2% of somatic single-nucleotide variant (SNVs)/insertions and deletions (indels) shared between bile and plasma cfDNA. When considering the genetic profiles of tumor tissues as the gold standard, the by-variant sensitivity and positive predictive value for SNVs/indels in bile cfDNA positive for somatic mutations were both 95.5%. The overall concordance for SNVs/indels in bile was significantly higher than that in plasma (99.1% versus 78.3%, P < 0.0001). Moreover, the sensitivity of CA 19-9 combined with bile cfDNA achieved 96.4% in BTC diagnosis. CONCLUSION We demonstrated that bile cfDNA was superior to plasma cfDNA in the detection of tumor-related genomic alterations. Bile cfDNA as a minimally invasive liquid biopsy medium might be a supplemental approach to confirm BTC diagnosis.
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Affiliation(s)
- Q Gou
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - C Z Zhang
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Z H Sun
- Department of Surgery, The First Affiliated Hospital of Medicine of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - L G Wu
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Y Chen
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, Guangzhou, Guangdong, China
| | - Z Q Mo
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Q C Mai
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - J He
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Z X Zhou
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - F Shi
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - W Cui
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - W Zou
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - L Lv
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - W H Zhuang
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - R D Xu
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - W K Li
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - J Zhang
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - H W Du
- Burning Rock Biotech, Guangzhou, China
| | - J X Xiang
- Burning Rock Biotech, Guangzhou, China
| | - H Z Wang
- Burning Rock Biotech, Guangzhou, China
| | - T Hou
- Burning Rock Biotech, Guangzhou, China
| | - S T Li
- Burning Rock Biotech, Guangzhou, China
| | - Y Li
- Burning Rock Biotech, Guangzhou, China
| | - X M Chen
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Z J Zhou
- Department of Interventional Therapy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
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9
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Dumbrava EE, Call SG, Huang HJ, Stuckett AL, Madwani K, Adat A, Hong DS, Piha-Paul SA, Subbiah V, Karp DD, Fu S, Naing A, Tsimberidou AM, Moulder SL, Koenig KH, Barcenas CH, Kee BK, Fogelman DR, Kopetz ES, Meric-Bernstam F, Janku F. PIK3CA mutations in plasma circulating tumor DNA predict survival and treatment outcomes in patients with advanced cancers. ESMO Open 2021; 6:100230. [PMID: 34479035 PMCID: PMC8414046 DOI: 10.1016/j.esmoop.2021.100230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/08/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background Oncogenic mutations in PIK3CA are prevalent in diverse cancers and can be targeted with inhibitors of the phosphoinositide-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway. Analysis of circulating tumor DNA (ctDNA) provides a minimally invasive approach to detect clinically actionable PIK3CA mutations. Patients and methods We analyzed PIK3CA hotspot mutation frequency by droplet digital PCR (QX 200; BioRad) using 16 ng of unamplified plasma-derived cell-free DNA from 68 patients with advanced solid tumors (breast cancer, n = 41; colorectal cancer, n = 13; other tumor types, n = 14). Results quantified as variant allele frequencies (VAFs) were compared with previous testing of archival tumor tissue and with patient outcomes. Results Of 68 patients, 58 (85%) had PIK3CA mutations in tumor tissue and 43 (74%) PIK3CA mutations in ctDNA with an overall concordance of 72% (49/68, κ = 0.38). In a subset analysis, which excluded samples from 26 patients known not to have disease progression at the time of sample collection, we found an overall concordance of 91% (38/42; κ = 0.74). PIK3CA-mutated ctDNA VAF of ≤8.5% (5% trimmed mean) showed a longer median survival compared with patients with a higher VAF (15.9 versus 9.4 months; 95% confidence interval 6.7-17.1 months; P = 0.014). Longitudinal analysis of ctDNA in 18 patients with serial plasma collections (range 2-22 time points, median 5) showed that those with a decrease in PIK3CA VAF had a longer time to treatment failure (TTF) compared with patients with an increase or no change (10.7 versus 2.6 months; P = 0.048). Conclusions Detection of PIK3CA mutations in ctDNA is concordant with testing of archival tumor tissue. Low quantity of PIK3CA-mutant ctDNA is associated with longer survival and a decrease in PIK3CA-mutant ctDNA on therapy is associated with longer TTF. Testing for PIK3CA mutations in ctDNA is concordant with testing of tumor tissue. High PIK3CA-mutant abundance in ctDNA was associated with shorter survival. Increasing PIK3CA-mutant abundance in serial blood samples was associated with shorter TTF. Longitudinal monitoring of PIK3CA-mutant ctDNA tracked with cancer clinical course.
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Affiliation(s)
- E E Dumbrava
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S G Call
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A L Stuckett
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K Madwani
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Adat
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K H Koenig
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C H Barcenas
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B K Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D R Fogelman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E S Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA.
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10
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Ohta R, Yamada T, Sonoda H, Matsuda A, Shinji S, Takahashi G, Iwai T, Takeda K, Ueda K, Kuriyama S, Miyasaka T, Yokoyama Y, Hara K, Yoshida H. Detection of KRAS mutations in circulating tumour DNA from plasma and urine of patients with colorectal cancer. Eur J Surg Oncol 2021; 47:3151-3156. [PMID: 34315643 DOI: 10.1016/j.ejso.2021.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/12/2021] [Accepted: 07/21/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) is very useful for purposes of cancer genetics; however, it has some limitations. Recently, ctDNA in body fluids, such as urine, sputum, and pleural effusion, has been investigated. The aim of this study was to evaluate the quantity of ctDNA derived from urine (trans-renal ctDNA) and the accuracy of KRAS mutation detection in relation to disease stage in colorectal cancer. METHODS Urine, plasma, and tissue samples were collected from consecutively resected colorectal cancer patients. DNA was extracted from each sample and the quantity was determined. From each DNA sample, KRAS mutations were detected using droplet digital PCR. RESULTS 200 patients participated and KRAS mutations were detected in 84 patients (42.0%) from tumour tissue. The concentration of trans-renal ctDNA (trtDNA) was significantly lower than that of plasma; however, there was no significant difference between the sensitivity using ctDNA and that using trtDNA (29.8% VS 33.3%, p = 0.62). Concordance between these two tests was only 17.5%. Combination analysis (ctDNA + trtDNA) improved the sensitivity to 53.6%, and sensitivity was significantly higher than that of corresponding single assays (p = 0.003). In early cancer stages, trtDNA had greater sensitivity for detecting KRAS mutations than ctDNA (37.7% vs. 21.3%, p = 0.047). Conversely, it was less useful for advanced cancer stages (21.7% vs. 52.2%, p = 0.07). Notably, KRAS mutations were detected using ctDNA or trtDNA in 12 of 116 (10.3%) patients who had no KRAS mutations in their tissue samples. CONCLUSIONS trtDNA and ctDNA have equal potential and combination analysis significantly improved the sensitivity.
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Affiliation(s)
- Ryo Ohta
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan.
| | - Hiromichi Sonoda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Akihisa Matsuda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Seiichi Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Goro Takahashi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Takuma Iwai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Kohki Takeda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Koji Ueda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Sho Kuriyama
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Toshimitsu Miyasaka
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Yasuyuki Yokoyama
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Keisuke Hara
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Hiroshi Yoshida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
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11
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Markus H, Zhao J, Contente-Cuomo T, Stephens MD, Raupach E, Odenheimer-Bergman A, Connor S, McDonald BR, Moore B, Hutchins E, McGilvrey M, de la Maza MC, Van Keuren-Jensen K, Pirrotte P, Goel A, Becerra C, Von Hoff DD, Celinski SA, Hingorani P, Murtaza M. Analysis of recurrently protected genomic regions in cell-free DNA found in urine. Sci Transl Med 2021; 13:13/581/eaaz3088. [PMID: 33597261 DOI: 10.1126/scitranslmed.aaz3088] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 07/16/2020] [Accepted: 01/28/2021] [Indexed: 12/12/2022]
Abstract
Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented. Whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we characterized fragmentation patterns in urine cfDNA using whole-genome sequencing. Size distribution of urine cfDNA fragments showed multiple strong peaks between 40 and 120 base pairs (bp) with a modal size of 81- and sharp 10-bp periodicity, suggesting transient protection from complete degradation. These properties were robust to preanalytical perturbations, such as at-home collection and delay in processing. Genome-wide sequencing coverage of urine cfDNA fragments revealed recurrently protected regions (RPRs) conserved across individuals, with partial overlap with nucleosome positioning maps inferred from plasma cfDNA. The ends of cfDNA fragments clustered upstream and downstream of RPRs, and nucleotide frequencies of fragment ends indicated enzymatic digestion of urine cfDNA. Compared to plasma, fragmentation patterns in urine cfDNA showed greater correlation with gene expression and chromatin accessibility in epithelial cells of the urinary tract. We determined that tumor-derived urine cfDNA exhibits a higher frequency of aberrant fragments that end within RPRs. By comparing the fraction of aberrant fragments and nucleotide frequencies of fragment ends, we identified urine samples from cancer patients with an area under the curve of 0.89. Our results revealed nonrandom genomic positioning of urine cfDNA fragments and suggested that analysis of fragmentation patterns across recurrently protected genomic loci may serve as a cancer diagnostic.
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Affiliation(s)
- Havell Markus
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jun Zhao
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA.,Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | | | | | | | | | - Sydney Connor
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | - Bethine Moore
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | | | | | | | - Patrick Pirrotte
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Ajay Goel
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA.,City of Hope, Duarte, CA 91010, USA
| | - Carlos Becerra
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | | | - Scott A Celinski
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA.,Department of Surgery, Baylor University Medical Center, Dallas, TX 75214, USA
| | | | - Muhammed Murtaza
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
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12
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Oshi M, Murthy V, Takahashi H, Huyser M, Okano M, Tokumaru Y, Rashid OM, Matsuyama R, Endo I, Takabe K. Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:2652. [PMID: 34071230 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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13
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Abstract
Precision medicine is now pivotal to design patients' specific treatment strategies with the aim of prolonging progression and overall survival. In this regard, invasive tumor tissue testing has so far been the golden standard for making cancer diagnosis, but has limitations. Cell-free tumor DNA (ctDNA), a form of liquid biopsy, is a noninvasive biomarker that can be isolated from patients' blood and other biofluids. An increasing body of evidence has demonstrated clinical utility of plasma ctDNA profiling to select patients for genomic-driven therapies. Analyses of mutations in plasma ctDNA have shown high accuracy and more rapid identification of mutations, allowing matching patients for specific therapies with equivalent clinical efficacy to that of the tissue profiling. In the clinical setting, ctDNA has been recently implemented to select patients with specific genomic alterations to targeted treatments, and a few molecular tests have been approved for use in non-small-cell lung, prostate, ovarian, and breast cancers. However, standardization of ctDNA collection, storage, and analysis methods would be critical to facilitate the wide adoption of ctDNA technology in routine clinical practice. This review summarizes how we can exploit ctDNA analysis to treat cancer patients, and explains how the results should be interpreted. In addition, we focus on how ctDNA could be used in the future as a marker of minimal residual disease to guide adjuvant therapy, as an immuno-oncology biomarker in patients treated with immune checkpoint blockade drugs, and as an early cancer detection marker to screen the asymptomatic population.
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Affiliation(s)
- L De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - G Siravegna
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
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14
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Bach S, Paulis I, Sluiter NR, Tibbesma M, Martin I, van de Wiel MA, Tuynman JB, Bahce I, Kazemier G, Steenbergen RDM. Detection of colorectal cancer in urine using DNA methylation analysis. Sci Rep 2021; 11:2363. [PMID: 33504902 PMCID: PMC7840909 DOI: 10.1038/s41598-021-81900-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause for cancer-related death globally. Clinically, there is an urgent need for non-invasive CRC detection. This study assessed the feasibility of CRC detection by analysis of tumor-derived methylated DNA fragments in urine. Urine samples, including both unfractioned and supernatant urine fractions, of 92 CRC patients and 63 healthy volunteers were analyzed for DNA methylation levels of 6 CRC-associated markers (SEPT9, TMEFF2, SDC2, NDRG4, VIM and ALX4). Optimal marker panels were determined by two statistical approaches. Methylation levels of SEPT9 were significantly increased in urine supernatant of CRC patients compared to controls (p < 0.0001). Methylation analysis in unfractioned urine appeared inaccurate. Following multivariate logistic regression and classification and regression tree analysis, a marker panel consisting of SEPT9 and SDC2 was able to detect up to 70% of CRC cases in urine supernatant at 86% specificity. First evidence is provided for CRC detection in urine by SEPT9 methylation analysis, which combined with SDC2 allows for an optimal differentiation between CRC patients and controls. Urine therefore provides a promising liquid biopsy for non-invasive CRC detection.
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Affiliation(s)
- S Bach
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Paulis
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - N R Sluiter
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - M Tibbesma
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Martin
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1089a, Amsterdam, The Netherlands
| | - M A van de Wiel
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1089a, Amsterdam, The Netherlands
| | - J B Tuynman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Bahce
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - G Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - R D M Steenbergen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
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15
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Abstract
Urinary cell-free DNA offers an important noninvasive source of material for genomic testing also for nonurological tumors. Its clinical utility in monitoring tumor evolution and treatment failure is promising. Here we describe a method to detect cancer mutations into urine from patients affected by colorectal cancer.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" - IRST S.r.l., Meldola, Italy.
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" - IRST S.r.l., Meldola, Italy
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16
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Zhang J, Liu Y, Xu B, Li F, Wang Y, Li M, Du R, Zhou Y, Salgia M, Yang L, Jones JO. Circulating tumor DNA analysis of metastatic renal cell carcinoma. Mol Clin Oncol 2020; 14:16. [PMID: 33312563 PMCID: PMC7726308 DOI: 10.3892/mco.2020.2178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022] Open
Abstract
The genomic landscape of metastatic renal cell carcinoma (RCC) is not well understood, and currently available data suggest that it is functionally distinct from that of localized tumors. Additionally, the large number of approved and trial agents used to treat metastatic RCC likely cause selective adaptations in the tumors. Circulating tumor DNA (ctDNA) is a platform to non-invasively determine the genomic profiles of these tumors. The objectives of the present study were to corroborate previous ctDNA studies in metastatic RCC, to identify novel mutations in metastatic RCC, and to compare ctDNA profiles obtained from plasma and urine in patients with metastatic RCC. ctDNA sequencing using the plasma and urine of 50 patients with metastatic RCC who received ctDNA profiling as part of routine clinical care at a single institution was performed using an investigational 120-gene panel. Genomic alterations (GAs) were identified in all 50 patients. The genes with the most GAs were GNAS, PTEN, MYC, MET and HNF1A and novel mutations in additional genes were identified. A significant correlation between the number of GAs detected in matched urine and plasma samples was also identified, but only 28.1% of GAs detected in plasma samples were also detected in matched urine samples. The results of the present study were consistent with those of the largest previous study of ctDNA from patients with metastatic RCC and may help identify additional potential targets for the treatment of such patients.
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Affiliation(s)
- Jingbo Zhang
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Yunchao Liu
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Bing Xu
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Fuwei Li
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Yan Wang
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Mengjian Li
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Rong Du
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Ye Zhou
- Beijing USCI Medical Laboratory, Beijing 100049, P.R. China
| | - Meghan Salgia
- Department of Medical Oncology, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Lixin Yang
- Department of Medical Oncology, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Jeremy O Jones
- Department of Medical Oncology, City of Hope Medical Center, Duarte, CA 91010, USA
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17
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Abstract
Because cancer is caused by an accumulation of genetic mutations, mutant DNA released by tumors can be used as a highly specific biomarker for cancer. Although this principle was described decades ago, the advent and falling costs of next-generation sequencing have made the use of tumor DNA as a biomarker increasingly practical. This review surveys the use of cellular and cell-free DNA for the detection of cancer, with a focus on recent technological developments and applications to solid tumors. It covers (a) key principles and technology enabling the highly sensitive detection of tumor DNA; (b) assessment of tumor DNA in plasma, including for genotyping, minimal residual disease detection, and early detection of localized cancer; (c) detection of tumor DNA in body cavity fluids, such as urine or cerebrospinal fluid; and (d) challenges posed to the use of tumor DNA as a biomarker by the phenomenon of benign clonal expansions.
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Affiliation(s)
- Jonathan C Dudley
- Ludwig Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA;
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18
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Janku F, Sakamuri D, Kato S, Huang HJ, Call SG, Naing A, Holley VR, Patel SP, Amaria RN, Falchook GS, Piha-Paul SA, Zinner RG, Tsimberidou AM, Hong DS, Meric-Bernstam F. Dose-escalation study of vemurafenib with sorafenib or crizotinib in patients with BRAF-mutated advanced cancers. Cancer 2020; 127:391-402. [PMID: 33119140 DOI: 10.1002/cncr.33242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/09/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND BRAF inhibitors are effective in melanoma and other cancers with BRAF mutations; however, patients ultimately develop therapeutic resistance through the activation of alternative signaling pathways such as RAF/RAS or MET. The authors hypothesized that combining the BRAF inhibitor vemurafenib with either the multikinase inhibitor sorafenib or the MET inhibitor crizotinib could overcome therapeutic resistance. METHODS Patients with advanced cancers and BRAF mutations were enrolled in a dose-escalation study (3 + 3 design) to determine the maximum tolerated dose (MTD) and the dose-limiting toxicities (DLTs) of vemurafenib with sorafenib (VS) or vemurafenib with crizotinib (VC). RESULTS In total, 38 patients (VS, n = 24; VC, n = 14) were enrolled, and melanoma was the most represented tumor type (VS, 38%; VC, 64%). In the VS arm, vemurafenib 720 mg twice daily and sorafenib 400 mg am/200 mg pm were identified as the MTDs, DLTs included grade 3 rash (n = 2) and grade 3 hypertension, and partial responses were reported in 5 patients (21%), including 2 with ovarian cancer who had received previous treatment with BRAF, MEK, or ERK inhibitors. In the VC arm, vemurafenib 720 mg twice daily and crizotinib 250 mg daily were identified as the MTDs, DLTs included grade 3 rash (n = 2), and partial responses were reported in 4 patients (29%; melanoma, n = 3; lung adenocarcinoma, n = 1) who had received previous treatment with BRAF, MEK, and/or ERK inhibitors. Optional longitudinal collection of plasma to assess dynamic changes in circulating tumor DNA demonstrated the elimination of BRAF-mutant DNA from plasma during therapy (P = .005). CONCLUSIONS Vemurafenib combined with sorafenib or crizotinib was well tolerated with encouraging activity, including among patients who previously received treatment with BRAF, MEK, or ERK inhibitors.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Divya Sakamuri
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shumei Kato
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - S Greg Call
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aung Naing
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Veronica R Holley
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gerald S Falchook
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Sarah Cannon Research Institute at HealthONE, Presbyterian/St Luke's Medical Center, Denver, Colorado
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ralph G Zinner
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,University of Kentucky Markey Cancer Center, Lexington, Kentucky
| | - Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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19
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Chen N, Zhang W, Tang X, Ming Z, Xiao X. Branch migration-based polymerase chain reaction combined with endonuclease IV-assisted target recycling probe/blocker system for detection of low-abundance point mutations. Analyst 2020; 145:1355-1361. [PMID: 31970369 DOI: 10.1039/c9an02209k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sensitive detection of low-abundance point mutations in blood or tissue may provide a great opportunity for the minimally invasive diagnosis of cancer and other related diseases. We demonstrate a novel method for ultra-sensitive detection of point mutations at low abundance by combination of branch migration-based PCR with endonuclease IV-assisted target recycling probe/blocker system. The method is able to identify the point mutations at abundances down to 0.01-0.02%. We anticipate this method to be widely adopted in clinical diagnosis and molecular research.
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Affiliation(s)
- Na Chen
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
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20
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Crisafulli G, Mussolin B, Cassingena A, Montone M, Bartolini A, Barault L, Martinetti A, Morano F, Pietrantonio F, Sartore-Bianchi A, Siena S, Di Nicolantonio F, Marsoni S, Bardelli A, Siravegna G. Whole exome sequencing analysis of urine trans-renal tumour DNA in metastatic colorectal cancer patients. ESMO Open 2020; 4:S2059-7029(20)30089-2. [PMID: 32149725 PMCID: PMC7001107 DOI: 10.1136/esmoopen-2019-000572] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 12/22/2022] Open
Abstract
Background The analysis of circulating free tumour DNA (ctDNA) in blood, commonly referred as liquid biopsy, is being used to characterise patients with solid cancers. Tumour-specific genetic variants can also be present in DNA isolated from other body fluids, such as urine. Unlike blood, urine sampling is non-invasive, can be self-performed, and allows recurrent longitudinal monitoring. The features of tumour DNA that clears from the glomerular filtration barrier, named trans-renal tumour DNA (trtDNA), are largely unexplored. Patients and methods Specimens were collected from 24 patients with KRAS or BRAF mutant metastatic colorectal cancer (mCRC). Driver mutations were assessed by droplet digital PCR (ddPCR) in ctDNA from plasma and trtDNA from urine. Whole exome sequencing (WES) was performed in DNA isolated from tissue, plasma and urine. Results Out of the 24 CRC cases, only four had sufficient DNA to allow WES analyses in urine and plasma. We found that tumour alterations primarily reside in low molecular weight fragments (less than 112 bp). In patients whose trtDNA was more than 2.69% of the urine derived DNA, cancer-specific molecular alterations, mutational signatures and copy number profiles identified in urine DNA are comparable with those detected in plasma ctDNA. Conclusions With current technologies, WES analysis of trtDNA is feasible in a small fraction of mCRC patients. Tumour-related genetic information is mainly present in low molecular weight DNA fragments. Although the limited amounts of trtDNA poses analytical challenges, enrichment of low molecular weight DNAs and optimised computational tools can improve the detection of tumour-specific genetic information in urine.
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Affiliation(s)
- Giovanni Crisafulli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Andrea Cassingena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Monica Montone
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Ludovic Barault
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Federica Morano
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Salvatore Siena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Di Nicolantonio
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Silvia Marsoni
- IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Alberto Bardelli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Giulia Siravegna
- University of Turin, Department of Oncology, Candiolo (TO), Italy .,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
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21
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Parikh AR, Mojtahed A, Schneider JL, Kanter K, Van Seventer EE, Fetter IJ, Thabet A, Fish MG, Teshome B, Fosbenner K, Nadres B, Shahzade HA, Allen JN, Blaszkowsky LS, Ryan DP, Giantonio B, Goyal L, Nipp RD, Roeland E, Weekes CD, Wo JY, Zhu AX, Dias-Santagata D, Iafrate AJ, Lennerz JK, Hong TS, Siravegna G, Horick N, Clark JW, Corcoran RB. Serial ctDNA Monitoring to Predict Response to Systemic Therapy in Metastatic Gastrointestinal Cancers. Clin Cancer Res 2020; 26:1877-1885. [PMID: 31941831 PMCID: PMC7165022 DOI: 10.1158/1078-0432.ccr-19-3467] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [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] [Received: 10/25/2019] [Revised: 12/09/2019] [Accepted: 01/10/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE ctDNA offers a promising, noninvasive approach to monitor therapeutic efficacy in real-time. We explored whether the quantitative percent change in ctDNA early after therapy initiation can predict treatment response and progression-free survival (PFS) in patients with metastatic gastrointestinal cancer. EXPERIMENTAL DESIGN A total of 138 patients with metastatic gastrointestinal cancers and tumor profiling by next-generation sequencing had serial blood draws pretreatment and at scheduled intervals during therapy. ctDNA was assessed using individualized droplet digital PCR measuring the mutant allele fraction in plasma of mutations identified in tumor biopsies. ctDNA changes were correlated with tumor markers and radiographic response. RESULTS A total of 138 patients enrolled. A total of 101 patients were evaluable for ctDNA and 68 for tumor markers at 4 weeks. Percent change of ctDNA by 4 weeks predicted partial response (PR, P < 0.0001) and clinical benefit [CB: PR and stable disease (SD), P < 0.0001]. ctDNA decreased by 98% (median) and >30% for all PR patients. ctDNA change at 8 weeks, but not 2 weeks, also predicted CB (P < 0.0001). Four-week change in tumor markers also predicted response (P = 0.0026) and CB (P = 0.022). However, at a clinically relevant specificity threshold of 90%, 4-week ctDNA change more effectively predicted CB versus tumor markers, with a sensitivity of 60% versus 24%, respectively (P = 0.0109). Patients whose 4-week ctDNA decreased beyond this threshold (≥30% decrease) had a median PFS of 175 days versus 59.5 days (HR, 3.29; 95% CI, 1.55-7.00; P < 0.0001). CONCLUSIONS Serial ctDNA monitoring may provide early indication of response to systemic therapy in patients with metastatic gastrointestinal cancer prior to radiographic assessments and may outperform standard tumor markers, warranting further evaluation.
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Affiliation(s)
- Aparna R Parikh
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amikasra Mojtahed
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jaime L Schneider
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Katie Kanter
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Isobel J Fetter
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ashraf Thabet
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Madeleine G Fish
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bezaye Teshome
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kathryn Fosbenner
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brandon Nadres
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heather A Shahzade
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jill N Allen
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lawrence S Blaszkowsky
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - David P Ryan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bruce Giantonio
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan D Nipp
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric Roeland
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Colin D Weekes
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew X Zhu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Giulia Siravegna
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nora Horick
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeffrey W Clark
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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22
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Calandri M, Siravegna G, Yevich SM, Stranieri G, Gazzera C, Kopetz S, Fonio P, Gupta S, Bardelli A, Veltri A, Odisio BC. Liquid biopsy, a paradigm shift in oncology: what interventional radiologists should know. Eur Radiol 2020; 30:4496-4503. [PMID: 32193642 DOI: 10.1007/s00330-020-06700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/21/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
Abstract
The acquisition of adequate tumor sample is required to verify primary tumor type and specific biomarkers and to assess response to therapy. Historically, invasive surgical procedures were the standard methods to acquire tumor samples until advancements in imaging and minimally invasive equipment facilitated the paradigm shift image-guided biopsy. Image-guided biopsy has improved sampling yield and minimized risk to the patient; however, there are still limitations, such as its invasive nature and its consequent limitations to longitudinal tumor monitoring. The next paradigm shift in sampling technique will need to address these issues to provide a more reliable and less invasive technique. Recently, liquid biopsy (LB) has emerged as a non-invasive alternative to tissue sampling. This technique relies on direct sampling of blood or other bodily fluids in contact with the tumor in order to collect circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating RNAs-in particular microRNA (miRNAs). Clinical applications of LB involve different steps of cancer patient management including screening, detection of disease recurrence, and evaluation of acquired resistance. With any paradigm shift, old techniques are often relegated to a secondary option. Although image-guided biopsies may appear as a passive spectator on the rapid advancement of LB, the two techniques may well be codependent. Interventional radiology may be integral to directly sample the liquid surrounding or draining from the tumor. In addition, LB may help to correctly select the patients for image-guided loco-regional treatments, to determine its treatment endpoint, and to early detect recurrence. KEY POINTS: • Liquid biopsy is a novel technology with potential high impact in the management of patients undergoing image-guided procedures. • Interventional radiology procedures may increase liquid biopsy sensitivity through direct fluid sampling. • Liquid biopsy techniques may provide a venue for improving patients' selection and enhance outcomes of interventional loco-regional therapies performed by interventional radiologists.
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Affiliation(s)
- Marco Calandri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy.,Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Steven M Yevich
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Giuseppe Stranieri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy
| | - Carlo Gazzera
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Paolo Fonio
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Sanjay Gupta
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Turin, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy
| | - Andrea Veltri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Bruno C Odisio
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
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23
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Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
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Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
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24
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Oreskovic A, Brault ND, Panpradist N, Lai JJ, Lutz BR. Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine. J Mol Diagn 2019; 21:1067-1078. [PMID: 31442674 DOI: 10.1016/j.jmoldx.2019.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 11/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Norman D Brault
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington.
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25
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Bhatty M, Kato S, Piha-Paul SA, Naing A, Subbiah V, Huang HJ, Karp DD, Tsimberidou AM, Zinner RG, Hwu WJ, Javle M, Patel SP, Hu MI, Varadhachary GR, Conley AP, Ramzanali NM, Holley VR, Kurzrock R, Meric-Bernstam F, Chae YK, Kim KB, Falchook GS, Janku F. Phase 1 study of the combination of vemurafenib, carboplatin, and paclitaxel in patients with BRAF-mutated melanoma and other advanced malignancies. Cancer 2019; 125:463-472. [PMID: 30383888 PMCID: PMC6340722 DOI: 10.1002/cncr.31812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/12/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 11/11/2022]
Abstract
BACKGROUND BRAF inhibitors are effective against selected BRAFV600 -mutated tumors. Preclinical data suggest that BRAF inhibition in conjunction with chemotherapy has increased therapeutic activity. METHODS Patients with advanced cancers and BRAF mutations were enrolled into a dose-escalation study (3+3 design) to determine the maximum tolerated dose (MTD) and dose-limiting toxicities (DLTs). RESULTS Nineteen patients with advanced cancers and BRAF mutations were enrolled and received vemurafenib (480-720 mg orally twice a day), carboplatin (area under the curve [AUC] 5-6 intravenously every 3 weeks), and paclitaxel (100-135 mg/m2 intravenously every 3 weeks). The MTD was not reached, and vemurafenib at 720 mg twice a day, carboplatin at AUC 5, and paclitaxel at 135 mg/m2 were the last safe dose levels. DLTs included a persistent grade 2 creatinine elevation (n = 1), grade 3 transaminitis (n = 1), and grade 4 thrombocytopenia (n = 1). Non-dose-limiting toxicities that were grade 3 or higher and occurred in more than 2 patients included grade 3/4 neutropenia (n = 5), grade 3/4 thrombocytopenia (n = 5), grade 3 fatigue (n = 4), and grade 3 anemia (n = 3). Of the 19 patients, 5 (26%; all with melanoma) had a partial response (PR; n = 4) or complete response (CR; n = 1); these responses were mostly durable and lasted 3.1 to 54.1 months. Of the 13 patients previously treated with BRAF and/or mitogen-activated protein kinase kinase (MEK) inhibitors, 4 (31%) had a CR (n = 1) or PR (n = 3). Patients not treated with prior platinum therapy had a higher response rate than those who did (45% vs 0%; P = .045). CONCLUSIONS The combination of vemurafenib, carboplatin, and paclitaxel is well tolerated and demonstrates encouraging activity, predominantly in patients with advanced melanoma and BRAFV600 mutations, regardless of prior treatment with BRAF and/or MEK inhibitors.
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Affiliation(s)
- Minny Bhatty
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shumei Kato
- Division of Hematology & Oncology and Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| | - Sarina A. Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aung Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Helen J. Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel D. Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Apostolia M. Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sapna P. Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mimi I. Hu
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gauri R. Varadhachary
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anthony P. Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nishma M. Ramzanali
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Veronica R. Holley
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Razelle Kurzrock
- Division of Hematology & Oncology and Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, San Diego, California
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Young Kwang Chae
- Developmental Therapeutics Lurie Cancer Center and Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kevin B. Kim
- California Pacific Medical Center Research Institute, San Francisco, California
| | | | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Abstract
The range of potential applications of liquid biopsies for non-small cell lung cancer management is expanded by the use of circulating tumor deoxyribonucleic acid and circulating tumor cells. Principal studies have demonstrated the predictive accuracy of droplet digital polymerase chain reaction detection, next-generation sequencing, and circulating tumor cells detection in patients with non-small cell lung cancer. The translational potential of these liquid biopsy technologies promotes the improvement of sensitivity and specificity in genomic and molecular methods. Here, we highlight the realities and challenges associated with the use of liquid biopsies for the detection of non-small cell lung cancer in patients. However, liquid biopsy technologies including circulating tumor cells detection, droplet digital polymerase chain reaction detection, and next-generation sequencing detection for precision therapy in non-small cell lung cancer will show substantive clinical applications in the future.
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Affiliation(s)
- Jun Lu
- 1 Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Baohui Han
- 1 Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
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Abstract
Urine could be a convenient source of biomarkers for different diseases and clinical applications, mostly for cancer diagnosis, prognosis, treatment monitoring, and prenatal diagnosis. The ultra-noninvasive sampling and the possibility to analyze large volume are the main undisputed advantages of urine-based protocols. Recent and comprehensive studies showed that urinary cell-free DNA (ucfDNA) is informative to identify the genomic signature of patients, resulting in a huge tool to track the tumor evolution and for personalized medicine in urological and non-urological cancer.In this chapter, we reported the main published evidences on ucfDNA, with the aim at discussing its promising and translatable role in clinical practices.
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Affiliation(s)
- Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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Vymetalkova V, Cervena K, Bartu L, Vodicka P. Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review. Int J Mol Sci 2018; 19:ijms19113356. [PMID: 30373199 PMCID: PMC6274807 DOI: 10.3390/ijms19113356] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/06/2023] Open
Abstract
There is a strong demand for the identification of new biomarkers in colorectal cancer (CRC) diagnosis. Among all liquid biopsy analysts, cell-free circulating DNA (cfDNA) is probably the most promising tool with respect to the identification of minimal residual diseases, assessment of treatment response and prognosis, and identification of resistance mechanisms. Circulating cell-free tumor DNA (ctDNA) maintains the same genomic signatures that are present in the matching tumor tissue allowing for the quantitative and qualitative evaluation of mutation burdens in body fluids. Thus, ctDNA-based research represents a non-invasive method for cancer detection. Among the numerous possible applications, the diagnostic, predictive, and/or prognostic utility of ctDNA in CRC has attracted intense research during the last few years. In the present review, we will describe the different aspects related to cfDNA research and evidence from studies supporting its potential use in CRC diagnoses and the improvement of therapy efficacy. We believe that ctDNA-based research should be considered as key towards the introduction of personalized medicine and patient benefits.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
| | - Klara Cervena
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Linda Bartu
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
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Li P, Ning J, Luo X, Du H, Zhang Q, Zhou G, Du Q, Ou Z, Wang L, Wang Y. New method to preserve the original proportion and integrity of urinary cell-free DNA. J Clin Lab Anal 2018; 33:e22668. [PMID: 30175467 DOI: 10.1002/jcla.22668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Due to high nuclease activity and complex contents in urine, urinary cell-free DNA (ucfDNA) was prone to degrade. So, we developed standardized urine collection tube (UCT) to prevent ucfDNA degradation and simultaneously maintain urinary cells in their original form during the sample collection process, ensuring stabilization of the original proportion and integrity of ucfDNA. METHODS Urine samples were collected from bladder cancer patients and divided into 10-mL normal tubes and 10-mL UCTs, respectively, and kept at ambient temperature. Urine supernatant was separated by centrifuging, and ucfDNA was extracted. Then ucfDNA was quantified by quantitative real-time polymerase chain reaction. UcfDNA fragments distribution was analyzed by Agilent 2200, and the frequency of specific mutations of urinary system disease was detected by next-generation sequencing method. RESULTS Urine collected into UCTs showed no statistically significant changes in their original proportion and integrity of ucfDNA up to 7 days at ambient temperature and also ucfDNA fragments were maintained well. Conversely, urine collected into normal tubes was observed an obviously decline in their original proportion of ucfDNA and ucfDNA fragments changed greatly. The △% of allele fraction (AF) for specific genes of ucfDNA from UCTs was lower than from normal tubes by 3.7-fold. CONCLUSION Using UCTs, they can maximally keep the original proportion and integrity of ucfDNA and stabilize urinary cells and minimize the background noise caused by urinary cellular DNA releasing, it will be help to open the door of next-generation noninvasive liquid biopsy applications utilizing urine.
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Affiliation(s)
- Pei Li
- XiangYa Hospital of Central South University, Changsha, Hunan, China.,Hunan UPSBio, Inc., Hunan University National Science Park, Changsha, Hunan, China
| | - Jun Ning
- XiangYa Hospital of Central South University, Changsha, Hunan, China
| | - Xipeng Luo
- Hunan UPSBio, Inc., Hunan University National Science Park, Changsha, Hunan, China
| | - Hongli Du
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Qing Zhang
- Hunan UPSBio, Inc., Hunan University National Science Park, Changsha, Hunan, China
| | - Ganlin Zhou
- Hunan UPSBio, Inc., Hunan University National Science Park, Changsha, Hunan, China
| | - Qiu Du
- XiangYa Hospital of Central South University, Changsha, Hunan, China
| | - Zhenyu Ou
- XiangYa Hospital of Central South University, Changsha, Hunan, China
| | - Long Wang
- XiangYa Hospital of Central South University, Changsha, Hunan, China
| | - Yu Wang
- Hunan UPSBio, Inc., Hunan University National Science Park, Changsha, Hunan, China
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30
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Adir Y, Tirman S, Abramovitch S, Botbol C, Lutaty A, Scheinmann T, Davidovits E, Arbel I, Davidovits G, Schneer S, Shteinberg M, Peretz Soroka H, Tirosh R, Patolsky F. Novel non-invasive early detection of lung cancer using liquid immunobiopsy metabolic activity profiles. Cancer Immunol Immunother 2018; 67:1135-1146. [PMID: 29785657 PMCID: PMC11028225 DOI: 10.1007/s00262-018-2173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/13/2017] [Accepted: 05/14/2018] [Indexed: 12/19/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide. Survival is largely dependent on the stage of diagnosis: the localized disease has a 5-year survival greater than 55%, whereas, for spread tumors, this rate is only 4%. Therefore, the early detection of lung cancer is key for improving prognosis. In this study, we present an innovative, non-invasive, cancer detection approach based on measurements of the metabolic activity profiles of immune system cells. For each Liquid ImmunoBiopsy test, a 384 multi-well plate is loaded with freshly separated PBMCs, and each well contains 1 of the 16 selected stimulants in several increasing concentrations. The extracellular acidity is measured in both air-open and hermetically-sealed states, using a commercial fluorescence plate reader, for approximately 1.5 h. Both states enable the measurement of real-time accumulation of 'soluble' versus 'volatile' metabolic products, thereby differentiating between oxidative phosphorylation and aerobic glycolysis. The metabolic activity profiles are analyzed for cancer diagnosis by machine-learning tools. We present a diagnostic accuracy study, using a multivariable prediction model to differentiate between lung cancer and control blood samples. The model was developed and tested using a cohort of 200 subjects (100 lung cancer and 100 control subjects), yielding 91% sensitivity and 80% specificity in a 20-fold cross-validation. Our results clearly indicate that the proposed clinical model is suitable for non-invasive early lung cancer diagnosis, and is indifferent to lung cancer stage and histological type.
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Affiliation(s)
- Yochai Adir
- Pulmonary Division, Faculty of Medicine, Lady Davis Carmel Medical Center, The Technion, Institute of Technology, 32000, Haifa, Israel
| | - Shoval Tirman
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Shirley Abramovitch
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Cynthia Botbol
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Aviv Lutaty
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Tali Scheinmann
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Eyal Davidovits
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Irit Arbel
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Giora Davidovits
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, Haifa, 3190501, Israel
| | - Sonia Schneer
- Pulmonary Division, Faculty of Medicine, Lady Davis Carmel Medical Center, The Technion, Institute of Technology, 32000, Haifa, Israel
| | - Michal Shteinberg
- Pulmonary Division, Faculty of Medicine, Lady Davis Carmel Medical Center, The Technion, Institute of Technology, 32000, Haifa, Israel
| | - Hagit Peretz Soroka
- School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ruven Tirosh
- School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Fernando Patolsky
- School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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31
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Liu L, Toung JM, Jassowicz AF, Vijayaraghavan R, Kang H, Zhang R, Kruglyak KM, Huang HJ, Hinoue T, Shen H, Salathia NS, Hong DS, Naing A, Subbiah V, Piha-Paul SA, Bibikova M, Granger G, Barnes B, Shen R, Gutekunst K, Fu S, Tsimberidou AM, Lu C, Eng C, Moulder SL, Kopetz ES, Amaria RN, Meric-Bernstam F, Laird PW, Fan JB, Janku F. Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification. Ann Oncol 2018; 29:1445-1453. [PMID: 29635542 PMCID: PMC6005020 DOI: 10.1093/annonc/mdy119] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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] [Indexed: 12/18/2022] Open
Abstract
Background Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis. Patients and methods We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes. Results Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016). Conclusions Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.
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Affiliation(s)
- L Liu
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - J M Toung
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Jassowicz
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Vijayaraghavan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Kang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Zhang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K M Kruglyak
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Hinoue
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Shen
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - N S Salathia
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M Bibikova
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Granger
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Barnes
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Shen
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K Gutekunst
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E S Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P W Laird
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J-B Fan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
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Abstract
In recent years, there has been a revolutionary expansion in technologic advances and therapeutic innovations in cancer medicine. Cancer diagnostics has begun to move away from a sole dependence on direct tumor tissue biopsy for cancer detection, diagnosis, and treatment monitoring. The need for improvement in molecular cancer diagnostics has never been more important, with not only the advent of cancer genomics and genomics-guided precision medicine but also the recent arrival of cancer immunotherapies. Owing to the practical limitations and risks associated with tissue-based biopsy diagnostics, novel noninvasive cancer diagnostics platforms have continued to evolve and expand in recent years. Examples of these platforms include the liquid biopsy, which is used to interrogate ctDNA or circulating tumor cells, proteomics, metabolomics, and exosomes; the urine biopsy, which is used to assay ctDNAs; saliva and stool biopsies, which are used for molecular genomics assays; and the breath biopsy, which measures volatile organic compounds. These next-generation noninvasive molecular diagnostics assays beyond tissues fundamentally transform the potential utilities of cancer diagnostics to enable repeat, prospective, and serial longitudinal "biopsies" to monitor disease response resistance and progression on therapies. Moreover, they allow continual interrogation and molecular in-depth analysis of the evolving tumor's pan-canceromics under therapeutic stress. These technological and diagnostic advances have already brought about paradigm-changing next-generation cancer therapeutic strategies to enhance overall treatment efficacies. This article reviews the key noninvasive next-generation molecular diagnostics platforms beyond tissues, with emphasis on clinical utilities and applications.
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Affiliation(s)
- Xiaoliang Wu
- From the West Virginia University Cancer Institute, West Virginia University Medicine, West Virginia University, Morgantown, WA; West Virginia Clinical and Translational Institute, Morgantown, WV
| | - Lin Zhu
- From the West Virginia University Cancer Institute, West Virginia University Medicine, West Virginia University, Morgantown, WA; West Virginia Clinical and Translational Institute, Morgantown, WV
| | - Patrick C Ma
- From the West Virginia University Cancer Institute, West Virginia University Medicine, West Virginia University, Morgantown, WA; West Virginia Clinical and Translational Institute, Morgantown, WV
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Abstract
Mutations, the fuel of evolution, are first manifested as rare DNA changes within a population of cells. Although next-generation sequencing (NGS) technologies have revolutionized the study of genomic variation between species and individual organisms, most have limited ability to accurately detect and quantify rare variants among the different genome copies in heterogeneous mixtures of cells or molecules. We describe the technical challenges in characterizing subclonal variants using conventional NGS protocols and the recent development of error correction strategies, both computational and experimental, including consensus sequencing of single DNA molecules. We also highlight major applications for low-frequency mutation detection in science and medicine, describe emerging methodologies and provide our vision for the future of DNA sequencing.
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Affiliation(s)
- Jesse J Salk
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, Divisions of Hematology and Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Michael W Schmitt
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, Divisions of Hematology and Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Lawrence A Loeb
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
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34
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Khakoo S, Georgiou A, Gerlinger M, Cunningham D, Starling N. Circulating tumour DNA, a promising biomarker for the management of colorectal cancer. Crit Rev Oncol Hematol 2018; 122:72-82. [PMID: 29458792 DOI: 10.1016/j.critrevonc.2017.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 07/27/2017] [Revised: 11/18/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023] Open
Abstract
Circulating cell free tumour DNA (ctDNA) maintains the same genomic alterations that are present in the corresponding tumour, thereby allowing for quantitative and qualitative real-time evaluation in body fluids as an alternative to onerous repeat biopsies. Improvements in the sensitivity of techniques used to identify ctDNA has led to a surge of research investigating its role in the detection of: early disease, relapse, response to therapy and emerging drug resistance mechanisms. Following curative surgery, ctDNA detection is a promising marker of minimal residual disease and could better select patients for adjuvant chemotherapy. Longitudinal monitoring could help identify early relapse. In metastatic disease, ctDNA can predict response to chemotherapy prior to evidence of disease progression on imaging and investigate novel primary and acquired resistance mechanisms to targeted therapies. More experience in detecting, analysing and interpreting ctDNA within prospective trials, will better define its role for implementation into routine clinical practice.
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Affiliation(s)
- Shelize Khakoo
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
| | - Alexandros Georgiou
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom; Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Marco Gerlinger
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom; Centre of Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - David Cunningham
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
| | - Naureen Starling
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom.
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35
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Kim MK, Woo SM, Park B, Yoon KA, Kim YH, Joo J, Lee WJ, Han SS, Park SJ, Kong SY. Prognostic Implications of Multiplex Detection of KRAS Mutations in Cell-Free DNA from Patients with Pancreatic Ductal Adenocarcinoma. Clin Chem 2018; 64:726-734. [PMID: 29352043 DOI: 10.1373/clinchem.2017.283721] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is known to provide potential biomarkers for predicting clinical outcome, but its value in pancreatic ductal adenocarcinoma (PDAC) has not been fully evaluated. The aim of this study was to evaluate the clinical applicability of quantitative analysis of multiplex KRAS mutations in cell-free DNA from patients with PDAC. METHODS A total of 106 patients with PDAC were enrolled in this prospective study. The concentration and fraction of KRAS mutations were determined through multiplex detection of KRAS mutations in plasma samples by use of a droplet digital PCR kit (Bio-Rad). RESULTS KRAS mutations were detected in 96.1% of tissue samples. Eighty patients (80.5%) harbored KRAS mutations in cfDNA, with a median KRAS mutation concentration of 0.165 copies/μL and a median fractional abundance of 0.415%. Multivariable analyses demonstrated that the KRAS mutation concentration [hazard ratio (HR), 2.08; 95% CI, 1.20-3.63] and KRAS fraction (HR, 1.73; 95% CI, 1.02-2.95) were significant factors for progression-free survival. KRAS mutation concentration (HR, 1.97; 95% CI, 1.05-3.67) also had prognostic implications for overall survival. Subgroup analyses showed that KRAS mutation concentration and fractional abundance significantly affected progression-free survival in resectable PDAC (P = 0.016). Moreover, when combined with the cancer biomarker CA19-9, the KRAS mutation concentration in cfDNA showed additive benefits for the prediction of overall survival. CONCLUSIONS This study demonstrates that multiplex detection of KRAS mutations in plasma cfDNA is clinically relevant, providing a potential candidate biomarker for prognosis of PDAC.
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Affiliation(s)
- Min Kyeong Kim
- Translational Cancer Research Branch, Division of Translational Science, National Cancer Center, Goyang, Korea
| | - Sang Myung Woo
- Center for Liver Cancer, National Cancer Center, Goyang, Korea
| | - Boram Park
- Biometrics Research Branch, Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Yun-Hee Kim
- Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Molecular Imaging Branch, Division of Convergence Technology, National Cancer Center, Goyang, Korea
| | - Jungnam Joo
- Biometrics Research Branch, Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Woo Jin Lee
- Center for Liver Cancer, National Cancer Center, Goyang, Korea
| | - Sung-Sik Han
- Center for Liver Cancer, National Cancer Center, Goyang, Korea
| | - Sang-Jae Park
- Center for Liver Cancer, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- Translational Cancer Research Branch, Division of Translational Science, National Cancer Center, Goyang, Korea; .,Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Department of Laboratory Medicine, Center for Diagnostic Oncology, National Cancer Center, Goyang, Korea
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36
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Mahesh PA. Molecular biology tools for precision medicine in managing lung cancer. Lung India 2018; 35:1-3. [PMID: 29319025 PMCID: PMC5760860 DOI: 10.4103/lungindia.lungindia_470_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- P A Mahesh
- Department of Pulmonary Medicine, JSS Medical College, JSS University, Mysore, Karnataka, India
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37
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Chen I, Raymond VM, Geis JA, Collisson EA, Jensen BV, Hermann KL, Erlander MG, Tempero M, Johansen JS. Ultrasensitive plasma ctDNA KRAS assay for detection, prognosis, and assessment of therapeutic response in patients with unresectable pancreatic ductal adenocarcinoma. Oncotarget 2017; 8:97769-97786. [PMID: 29228650 PMCID: PMC5716690 DOI: 10.18632/oncotarget.22080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 10/11/2017] [Indexed: 12/18/2022] Open
Abstract
Precision oncology requires sensitive and specific clinical biomarkers. Carbohydrate Antigen 19-9 (CA19-9) is widely used in pancreatic ductal adenocarcinoma (PDA) but lacks sensitivity and specificity. Nearly all PDAs harbor somatic KRAS mutations, nominating circulating tumor DNA (ctDNA) KRAS as an alternative disease biomarker, however, variable clinical performance has limited its clinical utility. We applied an ultrasensitive, PCR mutation enrichment, next generation sequencing ctDNA KRAS assay in a large cohort of patients with unresectable PDA (N = 189) recruited to the BIOPAC study between 2008-2015. Baseline and longitudinal serum CA19-9 and plasma ctDNA KRAS were correlated with time to progression (TTP) and overall survival (OS). Baseline ctDNA KRAS detection rate was 93.7% (86.4% in patients with non-elevated CA19-9). ctDNA KRAS and CA19-9 were positively correlated yet independently associated with TTP and OS (ctDNA KRAS p = 0.0018 and 0.0014; CA19-9 p = 0.0294 and 0.0007, respectively). A generated model quantitating longitudinal ctDNA KRAS correctly assessed greater than 80% of patient responses. Quantitative detection of KRAS ctDNA is an informative prognostic biomarker, complementary to CA19-9 in patients with unresectable PDA. Longitudinal ctDNA KRAS may inform therapeutic decision making and provides a kinetically dynamic and quantitative metric of patient response.
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Affiliation(s)
- Inna Chen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Eric A Collisson
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Benny V Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kirstine L Hermann
- Department of Radiology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Margaret Tempero
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Julia S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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38
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Lu T, Li J. Clinical applications of urinary cell-free DNA in cancer: current insights and promising future. Am J Cancer Res 2017; 7:2318-2332. [PMID: 29218253 PMCID: PMC5714758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023] Open
Abstract
Liquid biopsy is gaining significant attention as a tool for unveiling the molecular landscape of tumor and holds great promise for individualized medicine for cancer. Cell-free DNA serves as an extremely important component of liquid biopsy for cancer, and cell-free DNA in urine is even promising due to the remarkable advantage of urine as an ultra-noninvasive sample source over tissue and blood. Compared with the widely studied cell-free DNA in blood, less is known about the role of urinary cell-free DNA. Urinary cell-free DNA has the ability to give comprehensive and crucial information on cancer as it carries genetic messages from cells shedding directly into urine as well as transporting from circulation. As an indispensable component of liquid biopsy, urinary cell-free DNA is believed to have the potential of being a useful and ultra-noninvasive tool for cancer screening, diagnosis, prognosis, and monitoring of cancer progression and therapeutic effect. In this review, we provide the current insights into the clinical applications of urinary cell-free DNA in cancer. We also introduce the basic biological significance and some technical issues in the detection of urinary cell-free DNA.
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Affiliation(s)
- Tian Lu
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijing, People’s Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijing, People’s Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijing, People’s Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijing, People’s Republic of China
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39
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Möhrmann L, Huang HJ, Hong DS, Tsimberidou AM, Fu S, Piha-Paul SA, Subbiah V, Karp DD, Naing A, Krug A, Enderle D, Priewasser T, Noerholm M, Eitan E, Coticchia C, Stoll G, Jordan LM, Eng C, Kopetz ES, Skog J, Meric-Bernstam F, Janku F. Liquid Biopsies Using Plasma Exosomal Nucleic Acids and Plasma Cell-Free DNA Compared with Clinical Outcomes of Patients with Advanced Cancers. Clin Cancer Res 2017; 24:181-188. [PMID: 29051321 DOI: 10.1158/1078-0432.ccr-17-2007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 10/10/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Blood-based liquid biopsies offer easy access to genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. Exosomal nucleic acids (exoNAs) originate from living cells, which can better reflect underlying cancer biology.Experimental Design: Next-generation sequencing (NGS) was used to test exoNA, and droplet digital PCR (ddPCR) and BEAMing PCR were used to test cfDNA for BRAFV600, KRASG12/G13, and EGFRexon19del/L858R mutations in 43 patients with progressing advanced cancers. Results were compared with clinical testing of archival tumor tissue and clinical outcomes.Results: Forty-one patients had BRAF, KRAS, or EGFR mutations in tumor tissue. These mutations were detected by NGS in 95% of plasma exoNA samples, by ddPCR in 92% of cfDNA samples, and by BEAMing in 97% cfDNA samples. NGS of exoNA did not detect any mutations not present in tumor, whereas ddPCR and BEAMing detected one and two such mutations, respectively. Compared with patients with high exoNA mutation allelic frequency (MAF), patients with low MAF had longer median survival (11.8 vs. 5.9 months; P = 0.006) and time to treatment failure (7.4 vs. 2.3 months; P = 0.009). A low amount of exoNA was associated with partial response and stable disease ≥6 months (P = 0.006).Conclusions: NGS of plasma exoNA for common BRAF, KRAS, and EGFR mutations has high sensitivity compared with clinical testing of archival tumor and testing of plasma cfDNA. Low exoNA MAF is an independent prognostic factor for longer survival. Clin Cancer Res; 24(1); 181-8. ©2017 AACR.
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Affiliation(s)
- Lino Möhrmann
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- 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
| | - Siqing Fu
- 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
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aung Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne Krug
- Exosome Diagnostics, Waltham, Massachusetts
| | | | | | | | - Erez Eitan
- Exosome Diagnostics, Waltham, Massachusetts
| | | | | | | | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, 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
| | - Johan Skog
- Exosome Diagnostics, Waltham, Massachusetts
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - 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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Abstract
Precision medicine approaches in oncology are reliant on the accurate genomic characterization of tumors. While tissue remains the mainstay specimen for molecular testing, tumor biopsies are riddled with challenges and limitations due to their invasive and site-specific nature. Tumor inaccessibility and intratumoral heterogeneity, in particular, represent significant obstacles to the identification of actionable genetic alterations and hence effective mono- and combination therapy strategies. Proof-of-concept studies indicate that circulating tumor DNA (ctDNA) released from multiple tumor regions and anatomical locations is more reflective of intra- and intertumoral heterogeneity. Non-invasive liquid biopsy approaches that allow for the analysis of ctDNA are thus being increasingly implemented in routine patient care for the detection and monitoring of cancer-associated mutations. Indeed, the use of plasma testing to screen for epidermal growth factor receptor (EGFR) T790M mutant positive non-small cell lung cancer (NSCLC) patients eligible for treatment with third-generation EGFR inhibitors was recently approved by the U.S. Food and Drug Administration and is incorporated into the most recent version of the National Comprehensive Cancer Center guidelines as an alternative to tissue biopsy. Urine represents another liquid biopsy specimen that is distinguished by its ease of collection, option for home collection, and lack of temporal and volumetric collection restrictions. Importantly, there is an accumulating body of evidence supporting the clinical validity of urinary EGFR mutant testing for the identification and stratification of patients likely to benefit from EGFR-directed therapies and as a means to assess patient response, the presence of residual disease, and emergence of resistant tumor cell populations.
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Karachaliou N, Sosa AE, Molina MA, Centelles Ruiz M, Rosell R. Possible application of circulating free tumor DNA in non-small cell lung cancer patients. J Thorac Dis 2017; 9:S1364-S1372. [PMID: 29184675 DOI: 10.21037/jtd.2017.09.59] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsies have been heralded as a game changer in cancer management. Blood tests offer a minimally invasive, safe and sensitive complementary (or even alternative) approach for tissue biopsies. With lung cancer being the second most commonly diagnosed cancer and the leading cause of cancer deaths worldwide, due to the limitations of tissue sampling, liquid biopsies must urgently materialize in the clinic. In this short review, we will present the current applications of cell-free DNA (cfDNA) in lung cancer management, emphasizing on our own experience and previous work. We will also shortly comment on the challenges and need for a coordinated collaboration combining disciplines and sectors (from academia to health economies) in order to accelerate liquid biopsy development in lung cancer and other cancers.
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Affiliation(s)
- Niki Karachaliou
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain.,Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain
| | - Aaron E Sosa
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain
| | - Miguel Angel Molina
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain
| | | | - Rafael Rosell
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain.,Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain.,Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain.,Institut Català d'Oncologia, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Siravegna G, Sartore-Bianchi A, Mussolin B, Cassingena A, Amatu A, Novara L, Buscarino M, Corti G, Crisafulli G, Bartolini A, Tosi F, Erlander M, Di Nicolantonio F, Siena S, Bardelli A. Tracking aCAD-ALK gene rearrangement in urine and blood of a colorectal cancer patient treated with an ALK inhibitor. Ann Oncol 2017; 28:1302-1308. [DOI: 10.1093/annonc/mdx095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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43
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Abstract
In the era of personalized medicine, tumor sampling is paramount to enable the assessment of actionable molecular aberrations to help rationalize and guide treatment decisions. Longitudinal tracking of such aberrations may also be helpful to detect emerging drug resistance and to allow for timely modifications to ongoing therapies to improve patient outcomes. Nevertheless, tumor tissue sampling involves an invasive procedure with potential risks to patients and involves logistical challenges. As such, other less invasive and safer methods such as blood sampling for molecular profiling has been gaining traction. In this article, we discuss the concept of circulating tumor DNA, the technology platforms available for its interrogation, and its current applications in the clinic. We also envision how circulating tumor DNA may be applied at multiple time points along a patient's cancer journey to guide diagnosis, prognostication, and therapeutic decisions.
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