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Next-generation sequencing in liquid biopsy: cancer screening and early detection. Hum Genomics 2019; 13:34. [PMID: 31370908 PMCID: PMC6669976 DOI: 10.1186/s40246-019-0220-8] [Citation(s) in RCA: 267] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
In recent years, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost with improved accuracy. In the area of liquid biopsy, NGS has been applied to sequence circulating tumor DNA (ctDNA). Since ctDNA is the DNA fragments released by tumor cells, it can provide a molecular profile of cancer. Liquid biopsy can be applied to all stages of cancer diagnosis and treatment, allowing non-invasive and real-time monitoring of disease development. The most promising aspects of liquid biopsy in cancer applications are cancer screening and early diagnosis because they can lead to better survival results and less disease burden. Although many ctDNA sequencing methods have enough sensitivity to detect extremely low levels of mutation frequency at the early stage of cancer, how to effectively implement them in population screening settings remains challenging. This paper focuses on the application of liquid biopsy in the early screening and diagnosis of cancer, introduces NGS-related methods, reviews recent progress, summarizes challenges, and discusses future research directions.
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Lee J, Park SS, Lee YK, Norton JA, Jeffrey SS. Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor DNA. Mol Oncol 2019; 13:1623-1650. [PMID: 31243883 PMCID: PMC6670020 DOI: 10.1002/1878-0261.12537] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
Reliable biomarkers are required to evaluate and manage pancreatic ductal adenocarcinoma. Circulating tumor cells and circulating tumor DNA are shed into blood and can be relatively easily obtained from minimally invasive liquid biopsies for serial assays and characterization, thereby providing a unique potential for early diagnosis, forecasting disease prognosis, and monitoring of therapeutic response. In this review, we provide an overview of current technologies used to detect circulating tumor cells and circulating tumor DNA and describe recent advances regarding the multiple clinical applications of liquid biopsy in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jee‐Soo Lee
- Department of Laboratory MedicineHallym University Sacred Heart HospitalAnyangKorea
- Department of Laboratory MedicineSeoul National University College of MedicineSeoulKorea
| | - Sung Sup Park
- Department of Laboratory MedicineSeoul National University College of MedicineSeoulKorea
| | - Young Kyung Lee
- Department of Laboratory MedicineHallym University Sacred Heart HospitalAnyangKorea
- Department of Laboratory MedicineHallym University College of MedicineAnyangKorea
| | - Jeffrey A. Norton
- Department of SurgeryStanford University School of MedicineStanfordCAUSA
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PIK3CA mutations early persistence in cell-free tumor DNA as a negative prognostic factor in metastatic breast cancer patients treated with hormonal therapy. Breast Cancer Res Treat 2019; 177:659-667. [PMID: 31297647 DOI: 10.1007/s10549-019-05349-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/04/2019] [Indexed: 10/26/2022]
Abstract
PURPOSE The identification of biomarkers of hormonal therapy (HT) failure would allow tailored monitoring in metastatic breast cancer (mBC) patients. PIK3CA gene mutation is one of the most frequent events in mBC and is associated with HT resistance. We evaluated the early prognostic value of cell-free DNA (cfDNA) PIK3CA detection in first-line HT-treated mBC patients. METHODS Between June 2012 and January 2014, 39 patients were prospectively included in a dedicated clinical trial (NCT01612871). Blood sampling was performed before (M0) and 4 weeks (M1), 3 months (M3) and 6 months (M6) after HT initiation, and at tumor progression. Patients were followed until progression or until the end of the study (2 years). Mutation detection was performed using droplet-based digital PCR (ddPCR). Progression-free survival (PFS) was used as primary endpoint. RESULTS Median age at inclusion was 63 years (range 40-86). Most patients (34/39) received an aromatase inhibitor and presented a non-measurable disease (71.8%). PIK3CA mutations were reported in 10 (27.8%) and 5 (14.3%) cases at M0 and M1, respectively. The persistence of a detectable circulating mutation at M1 was highly correlated with a worse progression-free survival (PFS), rate at 1 year: 40% versus 76.7%; p = 0.0053). CONCLUSIONS Four-week persistence of cfDNA PIK3CA mutation appears highly correlated with PFS. TRIAL REGISTRATION NCT01612871, registered on June 6th, 2012; https://clinicaltrials.gov/ct2/show/NCT01612871 .
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54
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Ma F, Guan Y, Yi Z, Chang L, Li Q, Chen S, Zhu W, Guan X, Li C, Qian H, Xia X, Yang L, Zhang J, Husain H, Liao Z, Futreal A, Huang J, Yi X, Xu B. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2019; 146:1359-1368. [PMID: 31241775 DOI: 10.1002/ijc.32536] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/18/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]
Abstract
Tumor heterogeneity was associated with treatment outcome of metastatic cancers but few studies have examined whether tumor heterogeneity in circulating tumor DNA (ctDNA) can be used to predict treatment outcome. ctDNA analysis was performed in 37 HER2-positive metastatic breast cancer patients treated with pyrotinib. Patients with high tumor heterogeneity had significantly worse PFS outcomes, with a median PFS of 30.0 weeks vs. 60.0 weeks for patients with low tumor heterogeneity (hazard ratio [HR], 2.9; p = 0.02). Patients with trunk resistance mutations receiving pyrotinib monotherapy had worse outcomes (HR, 4.5; p = 0.03), with a median PFS of 7.8 weeks vs. 27.4 weeks for those with branch resistance mutations or without any resistance mutations in baseline ctDNA. Longitudinal monitoring of 21 patients during treatment showed that the molecular tumor burden index ([mTBI] a measure of the percentage of ctDNA in samples) was positively correlated with tumor size as evaluated by computed tomography (p < 0.0001, Pearson r = 0.52) and detected disease progression 8-16 weeks earlier. Our current findings suggested that ctDNA could be used to assess tumor heterogeneity and predict treatment outcomes. Furthermore, the mTBI is better for assessing therapeutic response than single gene mutations and might supplement the current therapeutic response evaluation system.
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Affiliation(s)
- Fei Ma
- 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, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Zongbi Yi
- 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, China
| | - Lianpeng Chang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Qiao Li
- 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, China
| | - Shanshan Chen
- 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, China
| | - Wenjie Zhu
- 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, China
| | - Xiuwen Guan
- 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, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefeng Xia
- Houston Methodist Research Institute, Weill Cornell School of Medicine, Houston, TX
| | - Ling Yang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hatim Husain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Zhongxing Liao
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, 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, China
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Liquid biopsy in hepatocellular carcinoma: circulating tumor cells and circulating tumor DNA. Mol Cancer 2019; 18:114. [PMID: 31269959 PMCID: PMC6607541 DOI: 10.1186/s12943-019-1043-x] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers and a leading cause of death worldwide. Due to latent liver disease, late diagnosis, and nonresponse to systemic treatments, surgical resection and/or biopsy specimens are still generally considered as the gold standard by clinicians for clinical decision-making until now. Since the conventional tissue biopsy is invasive and contains small tissue samples, it is unable to represent tumor heterogeneity or monitor dynamic tumor progression. Therefore, it is imperative to find a new less invasive or noninvasive diagnostic strategy to detect HCC at an early stage and to monitor HCC recurrence. Over the past years, a new diagnostic concept known as “liquid biopsy” has emerged with substantial attention. Liquid biopsy is noninvasive and allows repeated analyses to monitor tumor recurrence, metastasis or treatment responses in real time. With the advanced development of new molecular techniques, HCC circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) detection have achieved interesting and encouraging results. In this review, we focus on the clinical applications of CTCs and ctDNA as key components of liquid biopsy in HCC patients.
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Circulating biomarkers for early detection and clinical management of colorectal cancer. Mol Aspects Med 2019; 69:107-122. [PMID: 31189073 DOI: 10.1016/j.mam.2019.06.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 02/06/2023]
Abstract
New non-invasive approaches that can complement and improve on current strategies for colorectal cancer (CRC) screening and management are urgently needed. A growing number of publications have documented that components of tumors, which are shed into the circulation, can be detected in the form of liquid biopsies and can be used to detect CRC at early stages, to predict response to certain therapies and to detect CRC recurrence in a minimally invasive way. The analysis of circulating tumor DNA (ctDNA), tumor-derived cells (CTC, circulating tumor cells) or circulating microRNA (miRNA) in blood and other body fluids, have a great potential to improve different aspects of CRC management. The challenge now is to find which types of components, biofluids and detection methods would be the most suitable to be applied in the different steps of CRC detection and treatment. This chapter will provide an up to date review on ctDNA, CTCs and circulating miRNAs as new biomarkers for CRC, either for clinical management or early detection, highlighting their advantages and limitations.
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Rossi G, Ignatiadis M. Promises and Pitfalls of Using Liquid Biopsy for Precision Medicine. Cancer Res 2019; 79:2798-2804. [PMID: 31109952 DOI: 10.1158/0008-5472.can-18-3402] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/10/2019] [Accepted: 04/08/2019] [Indexed: 11/16/2022]
Abstract
New sensitive assays are currently available for the detection of circulating tumor DNA (ctDNA) and circulating tumor cells (CTC). However, there remains a need for standardization of preanalytical issues and cross-platform comparison studies. Liquid biopsies are being evaluated for treatment selection, for monitoring disease response and resistance, for tracking minimal residual disease, and for cancer diagnosis. Multiple studies are underway to assess the clinical utility of CTC and ctDNA in different settings (treatment-naïve vs. resistant, adjuvant vs. metastatic) and for different treatment modalities (systemic therapy, surgery, radiation therapy). This review aims to map the challenges that remain to be addressed before liquid biopsies can be widely used for cancer management.
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Affiliation(s)
- Giovanna Rossi
- Department of Medical Oncology, Ospedale dell'Angelo, Mestre (Venice), Italy
| | - Michail Ignatiadis
- Department of Medical Oncology & Academic Trials Promoting Team, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
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Yang X, Zhang K, Zhang C, Peng R, Sun C. Accuracy of analysis of cfDNA for detection of single nucleotide variants and copy number variants in breast cancer. BMC Cancer 2019; 19:465. [PMID: 31101027 PMCID: PMC6525451 DOI: 10.1186/s12885-019-5698-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Gene variants are dependable and sensitive biomarkers for target-specific therapies in breast cancer (BC). However, detection of mutations within tissues has many limitations. Plasma circulating free DNA (cfDNA) has been reported in many studies as an alternative tool for detection of mutations. But the diagnostic accuracy of cfDNA for most mutations in BC needs to be reviewed. This study was designed to perform comparative assessment of the diagnostic performance of cfDNA and DNA extracted from tissues for detection of single nucleotide variants (SNV) and copy number variants (CNV). METHODS True-positive (TP), false-positive (FP), false-negative (FN), and true-negative (TN) values were extracted from each selected study. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were calculated. Subgroup analysis and single study omitted analysis were performed to quantify and explain the study heterogeneity. RESULTS Twenty eligible studies that involved 1055 cases were included in this meta-analysis. SNV studies in early breast cancer (EBC) subgroup are not suitable for meta-analysis owing to high heterogeneity. However, in advanced breast cancer (ABC) subgroup, the pooled sensitivity and specificity of detection of SNVs were 0.78 (0.71-0.84) and 0.92 (0.87-0.95), respectively. The summary receiver operative curve (SROC) exhibited an area under the curve (AUC) of 0.91(0.88-0.93). The pooled results of studies involving subgroups of PIK3CA, TP53, and ESR1 indicate that the diagnostic value of different genes is different, such as AUC for PIK3CA and TP53 were reported to be 0.96 (0.94-0.98) and 0.94 (0.91-0.95), respectively, and ESR1 had the lowest diagnostic value of 0.80 (0.76-0.83). Owing to the low sensitivity and AUC in the cases of CNV, there is no value for cfDNA-based detection of CNV based on insufficient amount of CNV data. CONCLUSION This meta-analysis suggests that the detection of gene mutations in cfDNA have adequate diagnostic accuracy and can be used as an alternative to the tumor tissue for detection of SNV but not for CNV in BC yet.
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Affiliation(s)
- Xin Yang
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China.
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, 100730, People's Republic of China
| | - Caiji Zhang
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, 100730, People's Republic of China
| | - Chengming Sun
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China.
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Abstract
Cell-free circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) can be found in the bloodstream of individuals with cancer and are increasingly being explored as biomarkers in various aspects of cancer management. The application of next-generation sequencing (NGS) technologies to ctDNA and CTC analysis are providing new opportunities to characterize the cancer genome from a simple blood test and can facilitate the ease with which tumor-specific genomic changes can be followed over time. The serial analysis of ctDNA and CTCs has enormous potential to provide insights into intratumor heterogeneity and clonal evolution during disease progression, and may ultimately allow noninvasive molecular disease monitoring to guide therapeutic decisions and improve patient outcomes.
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Affiliation(s)
- Sarah-Jane Dawson
- Divisions of Cancer Medicine and Research, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; Centre for Cancer Research, University of Melbourne, Melbourne 3010, Australia
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60
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Lustberg MB, Stover DG, Chalmers JJ. Implementing Liquid Biopsies in Clinical Trials: State of Affairs, Opportunities, and Challenges. Cancer J 2019; 24:61-64. [PMID: 29601331 PMCID: PMC5880324 DOI: 10.1097/ppo.0000000000000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A primary goal of personalized medicine is to develop tumor-specific biomarkers to aid in treatment selection and to better evaluate response to targeted therapies. The assessment of circulating blood markers as surrogate real-time biopsies of disease status, termed liquid biopsies, has been under investigation. There are many different types of liquid biopsies each with different functionalities and limitations. These include tumor markers, circulating tumor cells, cell-free DNA, and extracellular vesicles including exosomes. Multiple clinical trials have evaluated liquid biopsies as prognostic biomarkers with positive results. Additional studies are underway to evaluate liquid biopsies as predictive biomarkers, pharmacodynamic biomarkers, and surrogate efficacy endpoints for treatment response evaluation. There are several challenges in and barriers to implementation of liquid biopsies into clinical trials and subsequently into routine clinical practice, which are addressed in this review.
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Affiliation(s)
- Maryam B. Lustberg
- Stefanie Spielman Comprehensive Breast Center, The Ohio State University, Columbus, OH, USA
| | - Daniel G Stover
- Stefanie Spielman Comprehensive Breast Center, The Ohio State University, Columbus, OH, USA
| | - Jeff J Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, 151 W. Woodruff Ave., Columbus, OH, 43210, USA
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Abstract
In the context of oncology, liquid biopsies consist of harvesting cancer biomarkers, such as circulating tumor cells, tumor-derived cell-free DNA, and extracellular vesicles, from bodily fluids. These biomarkers provide a source of clinically actionable molecular information that can enable precision medicine. Herein, we review technologies for the molecular profiling of liquid biopsy markers with special emphasis on the analysis of low abundant markers from mixed populations.
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Affiliation(s)
- Camila D. M. Campos
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
| | - Joshua M. Jackson
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
| | - Małgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
- BioEngineering Program, The University of Kansas, Lawrence, KS 66047
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66047
- Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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Ivanov M, Chernenko P, Breder V, Laktionov K, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Utility of cfDNA Fragmentation Patterns in Designing the Liquid Biopsy Profiling Panels to Improve Their Sensitivity. Front Genet 2019; 10:194. [PMID: 30915108 PMCID: PMC6422983 DOI: 10.3389/fgene.2019.00194] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/25/2019] [Indexed: 01/05/2023] Open
Abstract
Genotyping of cell-free DNA (cfDNA) in plasma samples has the potential to allow for a noninvasive assessment of tumor biology, avoiding the inherent shortcomings of tissue biopsy. Next generation sequencing (NGS), a leading technology for liquid biopsy analysis, continues to be hurdled with several major issues with cfDNA samples, including low cfDNA concentration and high fragmentation. In this study, by employing Ion Torrent PGM semiconductor technology, we performed a comparison between two multi-biomarker amplicon-based NGS panels characterized by a substantial difference in average amplicon length. In course of the analysis of the peripheral blood from 13 diagnostic non-small cell lung cancer patients, equivalence of two panels, in terms of overall diagnostic sensitivity and specificity was shown. A pairwise comparison of the allele frequencies for the same somatic variants obtained from the pairs of panel-specific amplicons, demonstrated an identical analytical sensitivity in range of 140 to 170 bp amplicons in size. Further regression analysis between amplicon length and its coverage, illustrated that NGS sequencing of plasma cfDNA equally tolerates amplicons with lengths in the range of 120 to 170 bp. To increase the sensitivity of mutation detection in cfDNA, we performed a computational analysis of the features associated with genome-wide nucleosome maps, evident from the data on the prevalence of cfDNA fragments of certain sizes and their fragmentation patterns. By leveraging the support vector machine-based machine learning approach, we showed that a combination of nucleosome map associated features with GC content, results in the increased accuracy of prediction of high inter-sample sequencing coverage variation (areas under the receiver operating curve: 0.75, 95% CI: 0.750–0.752 vs. 0.65, 95% CI: 0.63–0.67). Thus, nucleosome-guided fragmentation should be utilized as a guide to design amplicon-based NGS panels for the genotyping of cfDNA samples.
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Affiliation(s)
- Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Valery Breder
- N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | | | - Ekaterina Rozhavskaya
- Atlas Oncology Diagnostics, Ltd., Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Ancha Baranova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Atlas Oncology Diagnostics, Ltd., Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,School of Systems Biology, George Mason University, Fairfax, VA, United States
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Fernandes Marques J, Pereira Reis J, Fernandes G, Hespanhol V, Machado JC, Costa JL. Circulating Tumor DNA: A Step into the Future of Cancer Management. Acta Cytol 2019; 63:456-465. [PMID: 30852572 DOI: 10.1159/000492917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Liquid biopsy was introduced to the oncology field with the promise of revolutionizing the management of cancer patients, minimizing the exposure to invasive procedures such as tissue biopsy, and providing reliable information regarding therapy response and detection of disease relapse. Despite the significant increase in the number of published studies on circulating tumor DNA (ctDNA) in the past years, the emphasis of most studies is on the development of new technologies or on the clinical utility of ctDNA. This leaves a clear gap of knowledge concerning the biology of ctDNA, such as the fundamental mechanisms through which DNA from tumor cells is released into the circulation. Moreover, considering that ctDNA analysis is now currently being applied in clinical practice, the need for rigorous quality control is arising, and with it the necessity to standardize procedures, from sample collection to data analysis. This review focuses on the main aspects of ctDNA, including approaches currently available to evaluate tumor genetics, as well as the points that still require improvement in order to make liquid biopsy a key player in precision medicine.
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Affiliation(s)
- Joana Fernandes Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Joana Pereira Reis
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Gabriela Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Pulmonology, Hospital de São João, Porto, Portugal
| | - Venceslau Hespanhol
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Pulmonology, Hospital de São João, Porto, Portugal
| | - José Carlos Machado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - José Luís Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,
- Faculty of Medicine, University of Porto, Porto, Portugal,
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Cui X, Cao L, Huang Y, Bai D, Huang S, Lin M, Yang Q, Lu TJ, Xu F, Li F. In vitro diagnosis of DNA methylation biomarkers with digital PCR in breast tumors. Analyst 2019; 143:3011-3020. [PMID: 29693662 DOI: 10.1039/c8an00205c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy of cancers using DNA methylation biomarkers has received significant interest, where the quantification of multiple biomarkers is generally needed for improving the sensitivity and specificity of cancer diagnosis. However, the inefficiency of the traditional quantitative polymerase chain reaction (qPCR)-based MethyLight assay for detecting the extremely low concentration of methylated DNA fragments in body fluids limits its clinical applications. Here, we developed an ultrasensitive microwell chip digital polymerase chain reaction (dPCR)-based MethyLight assay. Using the synthesized samples, the developed MethyLight assay can achieve 103-104-fold lower limit of detection and 1-16-fold lower limit of quantification than the traditional MethyLight assay. Four hypermethylated alleles (RARβ2, BRCA1, GSTP1 and RASSF1A) related to breast cancer in twenty-three clinical samples were tested using the microwell chip dPCR-based MethyLight assay. The results showed that the dPCR assay achieves ∼2 times enhancement in the cancer detection rate over the traditional quantitative PCR. Furthermore, the dPCR can detect the healthy and benign samples, which are undetectable using the traditional MethyLight assay. In multiple gene analysis, we achieved the highest detection rate of 93.3% (in the "OR" format of RARβ2 and GSTP1). Lastly, the estimated cut-off values in the dPCR assay were: <1, ∼1 to 100 and >100 (copies per μL) referring to the healthy, benign and malignant breast cancers, respectively. Therefore, the developed microwell chip dPCR-based MethyLight assay could provide a powerful tool for cancer biopsy diagnosis and disease monitoring.
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Affiliation(s)
- Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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Herrera-Martínez AD, Hofland LJ, Gálvez Moreno MA, Castaño JP, de Herder WW, Feelders RA. Neuroendocrine neoplasms: current and potential diagnostic, predictive and prognostic markers. Endocr Relat Cancer 2019; 26:R157-R179. [PMID: 30615596 DOI: 10.1530/erc-18-0354] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022]
Abstract
Some biomarkers for functioning and non-functioning neuroendocrine neoplasms (NENs) are currently available. Despite their application in clinical practice, results should be interpreted cautiously. Considering the variable sensitivity and specificity of these parameters, there is an unmet need for novel biomarkers to improve diagnosis and predict patient outcome. Nowadays, several new biomarkers are being evaluated and may become future tools for the management of NENs. These biomarkers include (1) peptides and growth factors; (2) DNA and RNA markers based on genomics analysis, for example, the so-called NET test, which has been developed for analyzing gene transcripts in circulating blood; (3) circulating tumor/endothelial/progenitor cells or cell-free tumor DNA, which represent minimally invasive methods that would provide additional information for monitoring treatment response and (4) improved imaging techniques with novel radiolabeled somatostatin analogs or peptides. Below we summarize some future directions in the development of novel diagnostic and predictive/prognostic biomarkers in NENs. This review is focused on circulating and selected tissue markers.
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Affiliation(s)
- Aura D Herrera-Martínez
- Division of Endocrinology, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC); Reina Sofia University Hospital, Córdoba, Spain
| | - Leo J Hofland
- Division of Endocrinology, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - María A Gálvez Moreno
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC); Reina Sofia University Hospital, Córdoba, Spain
| | - Justo P Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC); Reina Sofia University Hospital, Córdoba, Spain
| | - Wouter W de Herder
- Division of Endocrinology, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Richard A Feelders
- Division of Endocrinology, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Kaklamani VG, Richardson AL, Arteaga CL. Exploring Biomarkers of Phosphoinositide 3-Kinase Pathway Activation in the Treatment of Hormone Receptor Positive, Human Epidermal Growth Receptor 2 Negative Advanced Breast Cancer. Oncologist 2019; 24:305-312. [PMID: 30651399 PMCID: PMC6519770 DOI: 10.1634/theoncologist.2018-0314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/18/2018] [Indexed: 11/17/2022] Open
Abstract
Resistance to endocrine therapy (ET) is common in patients with hormone receptor positive (HR+) advanced breast cancer (ABC). Consequently, new targeted treatment options are needed in the post-ET setting, with validated biomarkers to inform treatment decisions. Hyperactivation of the phosphoinositide 3-kinase (PI3K) signaling pathway is common in ABC and is implicated in resistance to ET. The most frequent mechanism of PI3K pathway activation is activating mutations or amplification of PIK3CA, which encodes the α-isoform of the catalytic subunit of PI3K. Combining buparlisib, a pan-PI3K-targeted agent, with ET demonstrated modest clinical benefits in patients with aromatase inhibitor-resistant, HR+, human epidermal growth receptor 2 negative (HER2-) ABC in two phase III trials. Importantly, greater efficacy gains were observed in individuals with PIK3CA-mutated disease versus PIK3CA-wild-type tumors. Although the challenging safety profile did not support widespread use of this treatment combination, isoform-selective PI3K inhibitors may improve tolerability. In early clinical trials, promising disease control benefits were demonstrated with the PI3K isoform-selective inhibitors alpelisib and taselisib in patients with PIK3CA-mutated HR+, HER2- ABC. Ongoing biomarker-guided phase II/III studies may provide further opportunities to identify patients most likely to benefit from treatment with PI3K inhibitors and provide insight into optimizing the therapeutic index of PI3K inhibitors. Challenges facing the implementation of routine PIK3CA mutation testing must be addressed promptly so robust and reproducible genotyping can be obtained with liquid and tumor biopsies in a timely and cost-effective manner. IMPLICATIONS FOR PRACTICE: The development of phosphoinositide 3-kinase (PI3K) inhibitors, especially those that selectively target isoforms, may be an effective strategy for overcoming endocrine therapy resistance in hormone receptor positive, human epidermal growth receptor 2 negative advanced breast cancer. Early-phase studies have confirmed that patients with PIK3CA mutations respond best to PI3Kα-isoform inhibition. Ongoing phase III trials will provide further data regarding the efficacy and safety of PI3K inhibitors in patients with different biomarker profiles.
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Affiliation(s)
| | | | - Carlos L Arteaga
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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67
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Smith NG, Gyanchandani R, Shah OS, Gurda GT, Lucas PC, Hartmaier RJ, Brufsky AM, Puhalla S, Bahreini A, Kota K, Wald AI, Nikiforov YE, Nikiforova MN, Oesterreich S, Lee AV. Targeted mutation detection in breast cancer using MammaSeq™. Breast Cancer Res 2019; 21:22. [PMID: 30736836 PMCID: PMC6368740 DOI: 10.1186/s13058-019-1102-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 01/16/2019] [Indexed: 01/14/2023] Open
Abstract
Background Breast cancer is the most common invasive cancer among women worldwide. Next-generation sequencing (NGS) has revolutionized the study of cancer across research labs around the globe; however, genomic testing in clinical settings remains limited. Advances in sequencing reliability, pipeline analysis, accumulation of relevant data, and the reduction of costs are rapidly increasing the feasibility of NGS-based clinical decision making. Methods We report the development of MammaSeq, a breast cancer-specific NGS panel, targeting 79 genes and 1369 mutations, optimized for use in primary and metastatic breast cancer. To validate the panel, 46 solid tumors and 14 plasma circulating tumor DNA (ctDNA) samples were sequenced to a mean depth of 2311× and 1820×, respectively. Variants were called using Ion Torrent Suite 4.0 and annotated with cravat CHASM. CNVKit was used to call copy number variants in the solid tumor cohort. The oncoKB Precision Oncology Database was used to identify clinically actionable variants. Droplet digital PCR was used to validate select ctDNA mutations. Results In cohorts of 46 solid tumors and 14 ctDNA samples from patients with advanced breast cancer, we identified 592 and 43 protein-coding mutations. Mutations per sample in the solid tumor cohort ranged from 1 to 128 (median 3), and the ctDNA cohort ranged from 0 to 26 (median 2.5). Copy number analysis in the solid tumor cohort identified 46 amplifications and 35 deletions. We identified 26 clinically actionable variants (levels 1–3) annotated by OncoKB, distributed across 20 out of 46 cases (40%), in the solid tumor cohort. Allele frequencies of ESR1 and FOXA1 mutations correlated with CA.27.29 levels in patient-matched blood draws. Conclusions In solid tumor biopsies and ctDNA, MammaSeq detects clinically actionable mutations (OncoKB levels 1–3) in 22/46 (48%) solid tumors and in 4/14 (29%) of ctDNA samples. MammaSeq is a targeted panel suitable for clinically actionable mutation detection in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13058-019-1102-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas G Smith
- Department of Pharmacology and Chemical Biology, and Human Genetics, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Rekha Gyanchandani
- Department of Pharmacology and Chemical Biology, and Human Genetics, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Osama S Shah
- Graduate Program in Integrated Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - Grzegorz T Gurda
- Department of Pathology, Gundersen Health System, La Crosse, WI, USA
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan J Hartmaier
- Department of Pharmacology and Chemical Biology, and Human Genetics, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Adam M Brufsky
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shannon Puhalla
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amir Bahreini
- Department of Genetics and Molecular Biology, School of Medicine, University of Medical Sciences, Isfahan, Iran
| | - Karthik Kota
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Abigail I Wald
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, and Human Genetics, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, and Human Genetics, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
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Koessler T, Addeo A, Nouspikel T. Implementing circulating tumor DNA analysis in a clinical laboratory: A user manual. Adv Clin Chem 2019; 89:131-188. [PMID: 30797468 DOI: 10.1016/bs.acc.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid biopsy, the analysis of cell-free circulating tumor DNA (ctDNA), is becoming one of the most promising tools in oncology. It has already shown its usefulness in selecting and modulating therapy via remote analysis of the tumor genome and holds important promises in cancer therapy and management, such as assessing the success of key therapeutic steps, monitoring residual disease, early detection of relapses, and establishing prognosis. Yet, ctDNA analysis is technically challenging and its implementation in the laboratory raises multiple strategic and practical issues. As for oncology clinics, integration of this novel test in well-established therapeutic protocols can also pose numerous questions. The current review is intended as a field guide for (1) diagnostic laboratories wishing to implement, validate and possibly accredit ctDNA testing and (2) clinical oncologists interested in integrating the various applications of liquid biopsies in their daily practice. We provide advice and practical recommendations based on our own experience with the technical validations of these methods and on a review of the current literature, with a focus toward gastro-intestinal, lung and breast cancers.
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Affiliation(s)
- Thibaud Koessler
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Alfredo Addeo
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Thierry Nouspikel
- Service of Medical Genetics, Diagnostics Department, Geneva University Hospital, Geneva, Switzerland.
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69
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Gall TMH, Gerrard G, Frampton AE, Castellano L, Ahmad R, Habib N, Spalding D, Pai M, Foroni L, Jiao LR. Can we predict long-term survival in resectable pancreatic ductal adenocarcinoma? Oncotarget 2019; 10:696-706. [PMID: 30774772 PMCID: PMC6366827 DOI: 10.18632/oncotarget.26511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/12/2018] [Indexed: 01/06/2023] Open
Abstract
Objective Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumour associated with poor 5-year survival. We aimed to determine factors which differentiate short and long-term survivors and identify a prognostic biomarker. Methods Over a ten-year period, patients with resected PDAC who developed disease recurrence within 12 months (Group I) and those who had no disease recurrence for 24 months (Group II) were identified. Clinicopathological data was analysed. Ion Torrent high-throughput sequencing on DNA extracted from FFPE tumour samples was used to identify mutations. Additionally, peripheral blood samples were analysed for variants in cell-free DNA, circulating tumour cells (CTCs), and microRNAs. Results Multivariable analysis of clinicopathological factors showed that a positive medial resection margin was significantly associated with short disease-free survival (p = 0.007). Group I patients (n = 21) had a higher frequency of the KRAS mutant mean variant allele (16.93% ± 11.04) compared to those in Group II (n = 13; 7.55% ± 5.76, p = 0.0078). Group I patients also trended towards having a KRAS c.35G>A p.Gly12Asp mutation in addition to variants in other genes, such as TP53, CDKN2A, and SMAD4. Mutational status of cell-free DNA, and number of CTCs, was not found to be useful in this study. A circulating miRNA (hsa-miR-548ah-5p) was found to be significantly differentially expressed. Conclusions Medial resection margin status and the frequency of KRAS mutation in the tumour tissue are independent prognostic indicators for resectable PDAC. Circulating miRNA hsa-miR-548ah-5p has the potential to be used as a prognostic biomarker.
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Affiliation(s)
- Tamara M H Gall
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Gareth Gerrard
- Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom.,Current address: Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London WC1E 6JA, United Kingdom
| | - Adam E Frampton
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Leandro Castellano
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Raida Ahmad
- Department of Histopathology, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Nagy Habib
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Duncan Spalding
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Madhava Pai
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Letizia Foroni
- Department of Histopathology, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Long R Jiao
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
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Zhao ZM, Yost SE, Hutchinson KE, Li SM, Yuan YC, Noorbakhsh J, Liu Z, Warden C, Johnson RM, Wu X, Chuang JH, Yuan Y. CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer. BMC Cancer 2019; 19:96. [PMID: 30665374 PMCID: PMC6341717 DOI: 10.1186/s12885-019-5290-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is aggressive with limited treatment options upon recurrence. Molecular discordance between primary and metastatic TNBC has been observed, but the degree of biological heterogeneity has not been fully explored. Furthermore, genomic evolution through treatment is poorly understood. In this study, we aim to characterize the genomic changes between paired primary and metastatic TNBCs through transcriptomic and genomic profiling, and to identify genomic alterations which may contribute to chemotherapy resistance. METHODS Genomic alterations and mRNA expression of 10 paired primary and metastatic TNBCs were determined through targeted sequencing, microarray analysis, and RNA sequencing. Commonly mutated genes, as well as differentially expressed and co-expressed genes were identified. We further explored the clinical relevance of differentially expressed genes between primary and metastatic tumors to patient survival using large public datasets. RESULTS Through gene expression profiling, we observed a shift in TNBC subtype classifications between primary and metastatic TNBCs. A panel of eight cancer driver genes (CCNE1, TPX2, ELF3, FANCL, JAK2, GSK3B, CEP76, and SYK) were differentially expressed in recurrent TNBCs, and were also overexpressed in TCGA and METABRIC. CCNE1 and TPX2 were co-overexpressed in TNBCs. DNA mutation profiling showed that multiple mutations occurred in genes comprising a number of potentially targetable pathways including PI3K/AKT/mTOR, RAS/MAPK, cell cycle, and growth factor receptor signaling, reaffirming the wide heterogeneity of mechanisms driving TNBC. CCNE1 amplification was associated with poor overall survival in patients with metastatic TNBC. CONCLUSIONS CCNE1 amplification may confer resistance to chemotherapy and is associated with poor overall survival in TNBC.
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Affiliation(s)
- Zi-Ming Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Susan E Yost
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | | | - Sierra Min Li
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Yate-Ching Yuan
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Javad Noorbakhsh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Zheng Liu
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Charles Warden
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Radia M Johnson
- Genentech, Inc., Oncology Biomarker Development, South San Francisco, CA, USA
| | - Xiwei Wu
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yuan Yuan
- City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA.
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Eigeliene N, Saarenheimo J, Jekunen A. Potential of Liquid Biopsies for Breast Cancer Screening, Diagnosis, and Response to Treatment. Oncology 2019; 96:115-124. [PMID: 30654364 DOI: 10.1159/000495615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022]
Abstract
Cancer therapy decisions are often made according to the histopathological-molecular profile of tumor tissue obtained from surgery or biopsy. It has been shown that tumor profiles change with time and treatment, and that tumor tissue is heterogeneous. Thus, other approaches that are easily accessible and less invasive than surgery or biopsy to monitor responses to treatment and predict relapses are urgently needed. In the last few years, the term "liquid biopsies" has been introduced to represent multifunctional circulating biomarkers in the peripheral blood and other physiological fluids of patients with cancer. Liquid biopsies are a noninvasive alternative to tissue biopsies, but they have not been implemented in routine clinical practice for breast cancer. In addition, liquid biopsies seem to be a promising approach for personalized medicine, which enables the prediction, monitoring, and rational selection of appropriate therapy for individual patients. In this review, we outline recent progress and current challenges with liquid biopsies in clinical practice for breast cancer diagnosis, treatment choices, and responses to therapy from a clinician's perspective.
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Affiliation(s)
- Natalja Eigeliene
- Department of Oncology, Vaasa Central Hospital, Vaasa, Finland, .,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland,
| | - Jatta Saarenheimo
- Department of Pathology, Vaasa Central Hospital, Vaasa, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Antti Jekunen
- Department of Oncology, Vaasa Central Hospital, Vaasa, Finland.,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland
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Mittendorf EA, Bartlett JMS, Lichtensztajn DL, Chandarlapaty S. Incorporating Biology Into Breast Cancer Staging: American Joint Committee on Cancer, Eighth Edition, Revisions and Beyond. Am Soc Clin Oncol Educ Book 2018; 38:38-46. [PMID: 30231409 DOI: 10.1200/edbk_200981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Higher-quality imaging, refined surgical procedures, enhanced pathologic evaluation, and improved understanding of the impact of tumor biology on treatment and prognosis have necessitated revisions of the AJCC breast cancer staging system. The eighth edition includes clinical and pathologic prognostic stages that incorporate biologic variables-grade, estrogen and progesterone receptor status, HER2 status, and multigene panels-with the anatomic extent of disease defined by tumor, node, and metastasis categories. The prognostic staging systems facilitate more refined stratification with respect to survival than anatomic stage alone. Because the prognostic staging systems are dependent on biologic factors, accuracy is dependent on rigorous pathologic evaluation of tumors and on administration of treatment dictated by tumor biology. It is anticipated that technological advances will facilitate even more refined determination of underlying biology within tumors and in the peripheral blood, which increasingly is being evaluated as a compartment that reflects the primary tumor and sites of distant metastases. Diseases should be staged according to the eighth edition staging system to accurately reflect prognosis and to allow standardized data collection. Such standardization will facilitate assessment of the impact of advances in diagnosis and treatment of patients with breast cancer.
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Affiliation(s)
- Elizabeth A Mittendorf
- From the Dana-Farber Cancer Institute and Brigham and Women's Cancer Center, Boston, MA; Ontario Institute for Cancer Research, Ontario, Canada; Cancer Prevention Institute of California, Fremont, CA; Memorial Sloan Kettering Cancer Center, New York, NY
| | - John M S Bartlett
- From the Dana-Farber Cancer Institute and Brigham and Women's Cancer Center, Boston, MA; Ontario Institute for Cancer Research, Ontario, Canada; Cancer Prevention Institute of California, Fremont, CA; Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daphne L Lichtensztajn
- From the Dana-Farber Cancer Institute and Brigham and Women's Cancer Center, Boston, MA; Ontario Institute for Cancer Research, Ontario, Canada; Cancer Prevention Institute of California, Fremont, CA; Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarat Chandarlapaty
- From the Dana-Farber Cancer Institute and Brigham and Women's Cancer Center, Boston, MA; Ontario Institute for Cancer Research, Ontario, Canada; Cancer Prevention Institute of California, Fremont, CA; Memorial Sloan Kettering Cancer Center, New York, NY
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Shang M, Chang C, Pei Y, Guan Y, Chang J, Li H. Potential Management of Circulating Tumor DNA as a Biomarker in Triple-Negative Breast Cancer. J Cancer 2018; 9:4627-4634. [PMID: 30588246 PMCID: PMC6299380 DOI: 10.7150/jca.28458] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 12/18/2022] Open
Abstract
As a specific subtype of breast cancer, Triple-negative breast cancer (TNBC) is associated with worse prognosis and higher tumor aggressiveness than HER2-amplified or hormone receptor positive breast cancers. Circulating tumor DNA (ctDNA), as a non-invasive “liquid biopsy”, is an emerging original blood-based biomarker for early breast cancer diagnosis, monitoring treatment response, and determining prognosis. In TNBC patients, ctDNA has an inherent tendency to characterize tumor heterogeneity and metastasis-specific mutations providing a key alternative to tumor tissue profiling. Several studies have already demonstrated the potential of ctDNA in TNBC patients from early to advanced stages of the disease including diagnosis, therapy decisions and assessment of prognosis. This review provides a critical brief summary of the evidence that gives credence to the utility of ctDNA as a biomarker for its role into clinical management in TNBC.
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Affiliation(s)
- Mao Shang
- School of Medicine and Life Sciences, University of Jinan Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong Province, China. 250117
| | - Chunxiao Chang
- Department of Medical Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong Province, China. 250117
| | - Yanqing Pei
- Department of Quality Management Office, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong Province, China. 250117
| | - Yin Guan
- Department of Medical Oncology, Beijing Chao-Yang Hospital, Beijing, China
| | - Jin Chang
- Oncology department, Affiliated Hospital of Taishan Medical university
| | - HuiHui Li
- Department of Medical Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong Province, China. 250117
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Fettke H, Kwan EM, Azad AA. Cell-free DNA in cancer: current insights. Cell Oncol (Dordr) 2018; 42:13-28. [PMID: 30367445 DOI: 10.1007/s13402-018-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The field of liquid biopsies in oncology is rapidly expanding, with the application of cell-free circulating tumour DNA (ctDNA) showing promise in this era of precision medicine. Compared with traditional clinical and radiographic tumour monitoring methods, the analysis of ctDNA provides a minimally-invasive and technically feasible approach to assess temporal and spatial molecular evolutions of the tumour landscape. The constantly advancing technological platforms available for ctDNA extraction and analysis allow greater analytical sensitivities than ever before. The potential translational impact of ctDNA as a blood-based biomarker for the identification, characterization and monitoring of cancer has been demonstrated in numerous proof-of-concept studies, with ctDNA analysis beginning to be applied clinically across multiple facets of oncology. CONCLUSIONS In this review we discuss the biology, recent advancements, technical considerations and clinical implications of ctDNA in the context of cancer, and highlight important challenges and future directions for the integration of ctDNA into standardised patient care.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
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Lee JH, Jeong H, Choi JW, Oh HE, Kim YS. Liquid biopsy prediction of axillary lymph node metastasis, cancer recurrence, and patient survival in breast cancer: A meta-analysis. Medicine (Baltimore) 2018; 97:e12862. [PMID: 30334995 PMCID: PMC6211877 DOI: 10.1097/md.0000000000012862] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Liquid biopsies using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) have been developed for early cancer detection and patient monitoring. To investigate the clinical usefulness of ctDNA aberrations and cfDNA levels in patients with breast cancer (BC), we conducted a meta-analysis of 69 published studies on 5736 patients with BC. METHODS The relevant publications were identified by searching PubMed and Embase databases. The effect sizes of outcome parameters were pooled using a random-effects model. RESULTS The ctDNA mutation rates of TP53, PIK3CA, and ESR1 were approximately 38%, 27%, and 32%, respectively. High levels of cfDNA were associated with BCs rather than with healthy controls. However, these detection rates were not satisfactory for BC screening. Although the precise mechanisms have been unknown, high cfDNA levels were significantly associated with axillary lymph node metastasis (odds ratio [OR] = 2.148, P = .030). The ctDNA mutations were significantly associated with cancer recurrence (OR = 3.793, P < .001), short disease-free survival (univariate hazard ratio [HR] = 5.180, P = .026; multivariate HR = 3.605, P = .001), and progression-free survival (HR = 1.311, P = .013) rates, and poor overall survival outcomes (HR = 2.425, P = .007). CONCLUSION This meta-analysis demonstrates that ctDNA mutation status predicts disease recurrence and unfavorable survival outcomes, while cfDNA levels can be predictive of axillary lymph node metastasis in patients with BC.
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Circulating tumor DNA, liquid biopsy, and next generation sequencing: A comprehensive technical and clinical applications review. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Palmirotta R, Lovero D, Cafforio P, Felici C, Mannavola F, Pellè E, Quaresmini D, Tucci M, Silvestris F. Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology. Ther Adv Med Oncol 2018; 10:1758835918794630. [PMID: 30181785 PMCID: PMC6116068 DOI: 10.1177/1758835918794630] [Citation(s) in RCA: 268] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Over the last decades, the concept of precision medicine has dramatically renewed
the field of medical oncology; the introduction of patient-tailored therapies
has significantly improved all measurable outcomes. Liquid biopsy is a
revolutionary technique that is opening previously unexpected perspectives. It
consists of the detection and isolation of circulating tumor cells, circulating
tumor DNA and exosomes, as a source of genomic and proteomic information in
patients with cancer. Many technical hurdles have been resolved thanks to newly
developed techniques and next-generation sequencing analyses, allowing a broad
application of liquid biopsy in a wide range of settings. Initially correlated
to prognosis, liquid biopsy data are now being studied for cancer diagnosis,
hopefully including screenings, and most importantly for the prediction of
response or resistance to given treatments. In particular, the identification of
specific mutations in target genes can aid in therapeutic decisions, both in the
appropriateness of treatment and in the advanced identification of secondary
resistance, aiming to early diagnose disease progression. Still application is
far from reality but ongoing research is leading the way to a new era in
oncology. This review summarizes the main techniques and applications of liquid
biopsy in cancer.
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Affiliation(s)
- Raffaele Palmirotta
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Domenica Lovero
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Paola Cafforio
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Felici
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Mannavola
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Eleonora Pellè
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Davide Quaresmini
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Tucci
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Franco Silvestris
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, 70124, Italy
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78
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Mathé E, Hays JL, Stover DG, Chen JL. The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources. Yearb Med Inform 2018; 27:211-222. [PMID: 30157526 PMCID: PMC6115204 DOI: 10.1055/s-0038-1667085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The aim is to provide a comprehensive review of state-of-the art omics approaches, including proteomics, metabolomics, cell-free DNA, and patient cohort matching algorithms in precision oncology. METHODS In the past several years, the cancer informatics revolution has been the beneficiary of a data explosion. Different complementary omics technologies have begun coming into their own to provide a more nuanced view of the patient-tumor interaction beyond that of DNA alterations. A combined approach is beneficial to the patient as nearly all new cancer therapeutics are designed with an omics biomarker in mind. Proteomics and metabolomics provide us with a means of assaying in real-time the response of the tumor to treatment. Circulating cell-free DNA may allow us to better understand tumor heterogeneity and interactions with the host genome. RESULTS Integration of increasingly available omics data increases our ability to segment patients into smaller and smaller cohorts, thereby prompting a shift in our thinking about how to use these omics data. With large repositories of patient omics-outcomes data being generated, patient cohort matching algorithms have become a dominant player. CONCLUSIONS The continued promise of precision oncology is to select patients who are most likely to benefit from treatment and to avoid toxicity for those who will not. The increased public availability of omics and outcomes data in patients, along with improved computational methods and resources, are making precision oncology a reality.
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Affiliation(s)
- Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - John L. Hays
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, USA
| | - Daniel G. Stover
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James L. Chen
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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79
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Gorgannezhad L, Umer M, Islam MN, Nguyen NT, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. LAB ON A CHIP 2018; 18:1174-1196. [PMID: 29569666 DOI: 10.1039/c8lc00100f] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.
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Affiliation(s)
- Lena Gorgannezhad
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
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80
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Chen X, Guan Z, Lu J, Wang H, Zuo Z, Ye F, Huang J, Teng L. Synergistic antitumor effects of cMet inhibitor in combination with anti-VEGF in colorectal cancer patient-derived xenograft models. J Cancer 2018; 9:1207-1217. [PMID: 29675102 PMCID: PMC5907669 DOI: 10.7150/jca.20964] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 02/27/2018] [Indexed: 12/19/2022] Open
Abstract
cMet signaling pathway is involved in the resistance to anti-VEGF therapy and cMet overexpression is associated with tumor progression and poor prognosis. In this study, the expression of cMet in 146 Chinese colorectal cancer (CRC) patients was examined by immunohistochemistry staining. Our data demonstrated that cMet overexpression rate was 42.5% (62/146) and cMet overexpression was closely correlated with distant metastasis of CRC. Using CRC patient-derived xenograft (PDX) mouse models we investigated antitumor activity of a novel selective cMet inhibitor volitinib alone or in combination with anti-VEGF inhibitor apatinib in vivo. Our results showed that combination treatment significantly inhibited tumor growth in two PDX models. While volitinib treatment alone induced moderate improvement in tumor growth inhibition, combination treatment synergistically reduced microvessel density, suppressed proliferation, and increased apoptosis in PDX models. Further analysis showed synergistic inhibition of MAPK and PI3K/Akt pathways by volitinib and apatinib. Taken together, our data provide a rationale to targeting both cMet and VEGF in the treatment of cMet overexpressing CRC in clinical trials.
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Affiliation(s)
- Xiangheng Chen
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital of University of South China, Hengyang, Hunan, P. R. China
| | - Zhonghai Guan
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Haohao Wang
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Zhongkun Zuo
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China
| | - Fei Ye
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China
| | - Jiangsheng Huang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
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Ma F, Zhu W, Guan Y, Yang L, Xia X, Chen S, Li Q, Guan X, Yi Z, Qian H, Yi X, Xu B. ctDNA dynamics: a novel indicator to track resistance in metastatic breast cancer treated with anti-HER2 therapy. Oncotarget 2018; 7:66020-66031. [PMID: 27602761 PMCID: PMC5323211 DOI: 10.18632/oncotarget.11791] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Most studies utilizing circulating tumor DNA (ctDNA) to monitor disease interrogated only one or a few genes and failed to develop workable criteria to inform clinical practice. We evaluated the feasibility of detecting resistance to anti-HER2 therapy by serial gene-panel ctDNA sequencing. RESULTS Primary therapeutic resistance was identified in 6 out of 14 patients with events of progressive disease. For this subset comparison of pre- and post-treatment ctDNA assay results revealed that HER2 amplification concurred with disease progression (4/6, 66.7%). Mutations in TP53 (3/6, 50.0%) and genes implicated in the PI3K/mTOR pathway (3/6, 50.0%) were also dominant markers of resistance. Together, resistance to HER2 blockade should be indicated during treatment if any of the following situations applies: 1) recurrence or persistence of HER2 amplification in the blood; 2) emergence or ≥20% increase in the fraction of mutations in any of these resistance-related genes including TP53/PIK3CA/MTOR/PTEN. Compared with CT scans, dynamic ctDNA profiling utilizing pre-defined criteria was sensitive in identifying drug resistance (sensitivity 85.7%, specificity 55.0%), with a concordance rate up to 82.1%. Besides, the ctDNA criteria had a discriminating role in the prognosis of HER2-positive metastatic breast cancer. METHODS 52 plasma samples were prospectively collected from 18 patients with HER2-positive metastatic breast cancer who were treated with an oral anti-HER1/HER2 tyrosine kinase inhibitor (ClinicalTrials.gov NCT01937689). ctDNA was assayed by gene-panel target-capture next-generation sequencing. CONCLUSIONS Longitudinal gene-panel ctDNA sequencing could be exploited to determine resistance and guide the precise administration of anti-HER2 targeted therapy in the metastatic setting.
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Affiliation(s)
- Fei Ma
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Zhu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | - Xuefeng Xia
- Houston Methodist Research Institute, Weill Cornell School of Medicine, Houston, TX, USA
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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82
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Fontanilles M, Duran-Peña A, Idbaih A. Liquid Biopsy in Primary Brain Tumors: Looking for Stardust! Curr Neurol Neurosci Rep 2018. [PMID: 29520561 DOI: 10.1007/s11910-018-0820-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW Personalized medicine is a challenge to improve survival and quality of life of patients suffering from primary malignant brain tumor. Molecular biology is integrated in initial diagnosis and relapse, and, in the nearest future, over treatment schedule and monitoring. Liquid biopsy is a minimally invasive way to obtain tumor material. RECENT FINDINGS Over the past years, three fluids have been explored to provide tumor information in primary malignant brain tumor: blood, cerebrospinal fluid, and vitreous liquid. Different tumor components were identified: (1) circulating tumor cells, (2) circulating tumor DNA, (3) RNA and non-coding miRNA, and (4) extracellular vesicles. The performance of the liquid biopsy depends on the tumor type and on the method of detection. Liquid biopsy could be a valuable tool to improve patient care in primary malignant brain tumor. Improvement of its sensitivity is the major challenge to generalize its use in daily practice.
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Affiliation(s)
- Maxime Fontanilles
- Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, F-76031, Rouen, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, F-75013, Paris, France
| | - Alberto Duran-Peña
- AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, F-75013, Paris, France
| | - Ahmed Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, F-75013, Paris, France.
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83
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Kumar M, Choudhury Y, Ghosh SK, Mondal R. Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics. Tumour Biol 2018; 40:1010428318760342. [PMID: 29484962 DOI: 10.1177/1010428318760342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.
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Affiliation(s)
- Manish Kumar
- 1 Department of Biotechnology, Assam University, Silchar, India
| | | | - Sankar Kumar Ghosh
- 1 Department of Biotechnology, Assam University, Silchar, India.,2 University of Kalyani, Kalyani, India
| | - Rosy Mondal
- 3 Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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84
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Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:543-553. [PMID: 29298117 PMCID: PMC5815405 DOI: 10.1200/jco.2017.76.0033] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.
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Affiliation(s)
- Daniel G. Stover
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Heather A. Parsons
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gavin Ha
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Samuel S. Freeman
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - William T. Barry
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Hao Guo
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Atish D. Choudhury
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gregory Gydush
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah C. Reed
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Justin Rhoades
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Denisse Rotem
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Melissa E. Hughes
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Deborah A. Dillon
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ann H. Partridge
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nikhil Wagle
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ian E. Krop
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gad Getz
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Todd R. Golub
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Christopher Love
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Eric P. Winer
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sara M. Tolaney
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nancy U. Lin
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Viktor A. Adalsteinsson
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
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85
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A novel high-sensitivity assay to detect a small fraction of mutant IDH1 using droplet digital PCR. Brain Tumor Pathol 2018; 35:97-105. [DOI: 10.1007/s10014-018-0310-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
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86
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Rossi G, Mu Z, Rademaker AW, Austin LK, Strickland KS, Costa RLB, Nagy RJ, Zagonel V, Taxter TJ, Behdad A, Wehbe FH, Platanias LC, Gradishar WJ, Cristofanilli M. Cell-Free DNA and Circulating Tumor Cells: Comprehensive Liquid Biopsy Analysis in Advanced Breast Cancer. Clin Cancer Res 2018; 24:560-568. [PMID: 29180605 DOI: 10.1158/1078-0432.ccr-17-2092] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/01/2017] [Accepted: 11/20/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Liquid biopsy provides a real-time assessment of metastatic breast cancer (MBC). We evaluated the utility of combining circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) to predict prognosis in MBC.Experimental Design: We conducted a retrospective study of 91 patients with locally advanced breast cancer and MBC. CTCs were enumerated by CellSearch; the plasma-based assay was performed utilizing Guardant360 and the survival analysis using Kaplan-Meier curves.Results: Eighty-four patients had stage IV cancer, and 7 patients had no metastases. Eighty patients had CTC analysis: median number 2 (0-5,612). Blood samples [232 of 277 (84%)] had mutations. The average ctDNA fraction was 4.5% (0-88.2%) and number of alterations 3 (0-27); the most commonly mutated genes were TP53 (52%), PIK3CA (40%), and ERBB2 (20%). At the time of analysis, 36 patients (39.6%) were dead. The median follow-up for CTCs was 9 months; for ctDNA, it was 9.9 months. For CTCs and ctDNA, respectively, progression-free survival (PFS) was 4.2 and 5.2 months and overall survival (OS) was 18.7 and 21.5 months. There was a statistically significant difference in PFS and OS for baseline CTCs < 5 versus CTCs ≥ 5 (P = 0.021 and P = 0.0004, respectively); %ctDNA < 0.5 versus ≥ 0.5 (P = 0.003 and P = 0.012); number of alterations < 2 versus ≥ 2 (P = 0.059 borderline and P = 0.0015). A significant association by Fisher exact test was found between the number of alterations and the %ctDNA in the baseline sample (P < 0.0001).Conclusions: The study demonstrated that liquid biopsy is an effective prognostic tool. Clin Cancer Res; 24(3); 560-8. ©2017 AACR.
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Affiliation(s)
- Giovanna Rossi
- Division of Thoracic Oncology, European Institute of Oncology, Milan, Italy
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Zhaomei Mu
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - Laura K Austin
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Kimberly S Strickland
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | | | | | - Vittorina Zagonel
- U.O.C. Oncologia Medica 1, Istituto Oncologico Veneto, IRCCS, Padova, Italy
| | - Timothy J Taxter
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Amir Behdad
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Firas H Wehbe
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
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87
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Moon DH, Lindsay DP, Hong S, Wang AZ. Clinical indications for, and the future of, circulating tumor cells. Adv Drug Deliv Rev 2018; 125:143-150. [PMID: 29626548 DOI: 10.1016/j.addr.2018.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 03/14/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022]
Abstract
Circulating tumor cells (CTCs) are cells that have detached from the primary tumor and entered circulation with potential to initiate a site of metastasis. Currently, CTC detection using CellSearch is cleared by the Food and Drug Administration for monitoring metastatic breast, prostate, and colorectal cancers as a prognostic biomarker for progression-free and overall survival. Accumulating evidence suggests CTCs have similar prognostic value in other metastatic and non-metastatic settings. Current research efforts are focused on extending the utility of CTCs beyond a prognostic biomarker to help guide clinical decision-making. These include using CTCs as a screening tool for diagnosis, liquid biopsy for molecular profiling, predictive biomarker to specific therapies, and monitoring tool to assess response and guide changes to treatment. CTCs have unique advantages vs circulating tumor DNA in this endeavor. Indications for CTCs in daily practice will expand as isolation techniques improve and clinical studies validating their utility continue to grow.
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Affiliation(s)
- Dominic H Moon
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA
| | - Daniel P Lindsay
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA
| | - Seungpyo Hong
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA; Yonsei Frontier Lab, Yonsei University, Seoul 03722, Republic of Korea
| | - Andrew Z Wang
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599, USA.
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88
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Nikolaev S, Lemmens L, Koessler T, Blouin JL, Nouspikel T. Circulating tumoral DNA: Preanalytical validation and quality control in a diagnostic laboratory. Anal Biochem 2018; 542:34-39. [DOI: 10.1016/j.ab.2017.11.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/09/2017] [Indexed: 01/08/2023]
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89
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Genetic profiling of cancer with circulating tumor DNA analysis. J Genet Genomics 2018; 45:79-85. [DOI: 10.1016/j.jgg.2017.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 12/21/2022]
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90
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Takeshita T, Yamamoto Y, Yamamoto-Ibusuki M, Inao T, Sueta A, Fujiwara S, Omoto Y, Iwase H. Clinical significance of monitoring ESR1 mutations in circulating cell-free DNA in estrogen receptor positive breast cancer patients. Oncotarget 2018; 7:32504-18. [PMID: 27102299 PMCID: PMC5078029 DOI: 10.18632/oncotarget.8839] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/14/2016] [Indexed: 01/23/2023] Open
Abstract
Background The measurement of circulating cell-free DNA (cfDNA) may transform the management of breast cancer patients. We aimed to investigate the clinical significance of sequential measurements of ESR1 mutations in primary breast cancer (PBC) and metastatic breast cancer (MBC) patients. Results ESR1 mutations ratio in the PBC groups was used as the minimum cutoff for determining increases in cfDNA ESR1 mutation ratio. An increase in cfDNA ESR1 mutations was found in 13 samples of cfDNA from 12 (28.6%) out of 42 MBC patients. A total of 10 (83.3%) out of 12 MBC patients with increase cfDNA ESR1 mutations showed a poor response to treatment. In survival analysis, increase cfDNA ESR1 mutations may predict a shorter duration of post-endocrine-therapy effectiveness (P = 0.0033). Methods A total of 119 patients (253 plasma samples) with breast carcinoma were enrolled in this study. Cases were selected if archival plasma samples were available from PBC before and after treatment and from MBC gathered more than twice at the time of progression. cfDNA was isolated from the 77 PBC patients (154 plasma samples) and from the 42 MBC patients (99 plasma samples). To investigate any changes in each cfDNA ESR1 mutation before and after treatment, we analyzed the difference with cfDNA ESR1 mutations ratio in the first blood sample using droplet digital polymerase chain reaction (ddPCR). Conclusions We demonstrate that ddPCR monitoring of the recurrent ESR1 mutation in cfDNA of MBC patients is a feasible and useful method of providing relevant predictive information.
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Affiliation(s)
- Takashi Takeshita
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Toko Inao
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Saori Fujiwara
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yoko Omoto
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan.,Department of Endocrine and Breast Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Hirokoji Agaru, Kawaramachi-dori, Kamigyo-ku, Kyoto, 602-0841, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Graduate School of Medical Science, Kumamoto University, Chuo-ku, Kumamoto, 860-8556, Japan
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91
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Hahn AW, Nussenzveig RH, Pal SK, Agarwal N. Blood- and tissue-based tumor genomics: a battle royale or match made in heaven? Ann Oncol 2018; 28:2333-2335. [PMID: 28945831 DOI: 10.1093/annonc/mdx418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A W Hahn
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, USA
| | - R H Nussenzveig
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, USA
| | - S K Pal
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, USA
| | - N Agarwal
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, USA.
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92
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Cell-free DNA mutations as biomarkers in breast cancer patients receiving tamoxifen. Oncotarget 2017; 7:43412-43418. [PMID: 27270325 PMCID: PMC5190033 DOI: 10.18632/oncotarget.9727] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/08/2016] [Indexed: 12/21/2022] Open
Abstract
The aim was to identify mutations in serum cell-free DNA (cfDNA) associated with disease progression on tamoxifen treatment in metastatic breast cancer (MBC). Sera available at start of therapy, during therapy and at disease progression were selected from 10 estrogen receptor (ER)-positive breast cancer patients. DNA from primary tumor and normal tissue and cfDNA from minute amounts of sera were analyzed by targeted next generation sequencing (NGS) of 45 genes (1,242 exons). At disease progression, stop-gain single nucleotide variants (SNVs) for CREBBP (1 patient) and SMAD4 (1 patient) and non-synonymous SNVs for AKAP9 (1 patient), PIK3CA (2 patients) and TP53 (2 patients) were found. Mutations in CREBBP and SMAD4 have only been occasionally reported in breast cancer. All mutations, except for AKAP9, were also present in the primary tumor but not detected in all blood specimens preceding progression. More sensitive detection by deeper re-sequencing and digital PCR confirmed the occurrence of circulating tumor DNA (ctDNA) and these biomarkers in blood specimens.
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93
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Henry NL, Bedard PL, DeMichele A. Standard and Genomic Tools for Decision Support in Breast Cancer Treatment. Am Soc Clin Oncol Educ Book 2017; 37:106-115. [PMID: 28561710 DOI: 10.1200/edbk_175617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the past few decades, comprehensive characterization of the cancer genome has elucidated pathways that drive cancer and mechanisms of resistance to therapy and provided important insights for development of new therapies. These advances have resulted in the development of prognostic and predictive tools for use in clinical settings, which can assist clinicians and patients in making informed decisions about the benefits of established therapies. In early-stage breast cancer, multiparameter genomic assays are now available for decision making about the duration of adjuvant endocrine therapy and the use of adjuvant chemotherapy. Similarly, in metastatic disease, there are multiple commercially available next-generation sequencing options for identifying genetic alterations in tumors that may be targeted with a drug. Although these tools hold great promise for providing precision medicine, it can be difficult for the treating physician to evaluate their clinical utility and appropriately select tools for individual clinical situations. This review summarizes the currently available genomic tools in breast cancer, the data underlying their clinical validity and utility, and how they can be used in conjunction with standard clinicopathologic data for making adjuvant and metastatic treatment decisions.
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Affiliation(s)
- N Lynn Henry
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Philippe L Bedard
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Angela DeMichele
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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94
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Burgener JM, Rostami A, De Carvalho DD, Bratman SV. Cell-free DNA as a post-treatment surveillance strategy: current status. Semin Oncol 2017; 44:330-346. [DOI: 10.1053/j.seminoncol.2018.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/18/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023]
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95
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Kumar G, Chaudhary KK, Misra K, Tripathi A. Next-Generation Sequencing for Drug Designing and Development: An Omics Approach for Cancer Treatment. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.709.723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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96
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Masunaga N, Kagara N, Motooka D, Nakamura S, Miyake T, Tanei T, Naoi Y, Shimoda M, Shimazu K, Kim SJ, Noguchi S. Highly sensitive detection of ESR1 mutations in cell-free DNA from patients with metastatic breast cancer using molecular barcode sequencing. Breast Cancer Res Treat 2017; 167:49-58. [PMID: 28905136 DOI: 10.1007/s10549-017-4487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/28/2017] [Indexed: 12/18/2022]
Abstract
PURPOSE We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR). RESULTS MB-NGS showed a higher sensitivity (0.1%) than NGS without barcode (1%) by reducing background errors. Of the cfDNA samples from 34 patients with metastatic breast cancer, NGS without barcode revealed seven mutations in six patients (17.6%) and MB-NGS revealed six additional mutations including three mutations not reported in the COSMIC database of breast cancer, resulting in total 13 ESR1 mutations in ten patients (29.4%). Regarding the three hotspot mutations, all the patients with mutations detected by MB-NGS had identical mutations detected by droplet digital PCR (ddPCR), and mutant allele frequency correlated very well between both (r = 0.850, p < 0.01). Moreover, all the patients without these mutations by MB-NGS were found to have no mutations by ddPCR. CONCLUSION In conclusion, MB-NGS could successfully detect ESR1 mutations in cfDNA with a higher sensitivity of 0.1% than conventional NGS and was considered as clinically useful as ddPCR.
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Affiliation(s)
- Nanae Masunaga
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Beddowes E, Sammut SJ, Gao M, Caldas C. Predicting treatment resistance and relapse through circulating DNA. Breast 2017; 34 Suppl 1:S31-S35. [PMID: 28694015 DOI: 10.1016/j.breast.2017.06.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The use of circulating DNA(ctDNA) to provide a non-invasive, personalised genomic snapshot of a patients' tumour has huge potential. Over the past five years this area of research has gained huge momentum. A number of studies in metastatic breast cancer have shown the potential of ctDNA to predict prognosis and treatment response using ctDNA. Further developments have included deeper sequencing using whole exome and shallow whole genome approaches which has the potential to identify new mutations and chromosomal copy number changes which appear upon resistance to treatment. In early breast cancer, recent work utilising personalised digital PCR probes has shown huge potential in predicting disease relapse and the detection of micrometastatic disease which could lead to improved treatment and outcome for these patients. Specific pathways of resistance can also be monitored and liquid biopsy approaches for the detection of ESR1 mutations have been used which could identify patients who have become resistant to particular endocrine therapies. The identification of PIK3CA mutations in plasma has also been shown to predict a higher response rate to specific PI3K inhibitors and could be used as a non-invasive screening tool prior to treatment. Further work on the detection of exosomal miRNA and hypermethylated DNA in plasma have shown promise in terms of specificity for early breast cancer detection and could be used to monitor treatment response. This review will focus on technological advances in the field, early detection of relapse and the detection of tumour-specific genomic alterations which could predict treatment response and resistance in patients with breast cancer.
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Affiliation(s)
- Emma Beddowes
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Stephen J Sammut
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Meiling Gao
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Carlos Caldas
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom.
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Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer. Clin Cancer Res 2017; 23:6487-6497. [DOI: 10.1158/1078-0432.ccr-17-1140] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/12/2017] [Accepted: 07/26/2017] [Indexed: 11/16/2022]
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99
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Parimi S, Ko JJ. Recent advances in circulating tumor cells and cell-free DNA in metastatic prostate cancer: a review. Expert Rev Anticancer Ther 2017; 17:939-949. [DOI: 10.1080/14737140.2017.1359544] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sunil Parimi
- Department of Medical Oncology, BC Cancer Agency, Victoria, Canada
| | - Jenny J. Ko
- Department of Medical Oncology, BC Cancer Agency, Abbotsford, Canada
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100
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Technical Validation of a Next-Generation Sequencing Assay for Detecting Clinically Relevant Levels of Breast Cancer–Related Single-Nucleotide Variants and Copy Number Variants Using Simulated Cell-Free DNA. J Mol Diagn 2017; 19:525-536. [DOI: 10.1016/j.jmoldx.2017.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/02/2017] [Accepted: 04/05/2017] [Indexed: 12/28/2022] Open
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