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Du X, Fei X, Wang J, Dong Y, Fan L, Yang B, Chen W, Gong Y, Xia B, Zhu H, Wu F, Wang Y, Dong L, Zhu Y, Pan J, Yao X, Dong B. Early serial circulating tumor DNA sequencing predicts the efficacy of chemohormonal therapy in patients with metastatic hormone-sensitive prostate cancer. Transl Oncol 2023; 34:101701. [PMID: 37247504 DOI: 10.1016/j.tranon.2023.101701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/14/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Chemohormonal therapy is a standard treatment for metastatic hormone-sensitive prostate cancer (mHSPC); however, there are no biomarkers to guide clinical decisions regarding therapeutic options. We aimed to evaluate the clinical utility of serial circulating tumor DNA (ctDNA) sequencing in early prediction of the efficacy of chemohormonal therapy in patients with mHSPC. We conducted a retrospective observational study of 66 patients with mHSPC receiving chemohormonal therapy who underwent serial targeted gene-panel ctDNA sequencing. Peripheral blood samples were collected before treatment and after one cycle of chemotherapy. Kaplan-Meier and log-rank analyses were used to analyze the association between ctDNA status and disease progression-free survival. Serial changes in the ctDNA fraction and genetic alterations were also observed. After one cycle of chemotherapy, 23 (34.8%) patients displayed elevated ctDNA levels, whereas the other patients (65.2%, n = 43) did not. The median time to castration resistance in the group with reduced ctDNA levels was significantly longer than that in the group with increased ctDNA levels (17.70 vs. 8.43 months [mo], p < 0.001). Interestingly, patients with de novo alterations in homologous recombination pathway genes after treatment experienced a shorter time to castration resistance than that experienced by the remaining patients (8.02 vs. 13.20 mo, p = 0.011). The increased ctDNA levels or de novo alterations detected in homologous recombination pathway genes are a harbinger of disease progression. Early serial ctDNA sequencing could aid clinicians in making accurate treatment decisions.
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Affiliation(s)
- Xinxing Du
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaochen Fei
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jialin Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanhao Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liancheng Fan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Yang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiming Gong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Binbin Xia
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hanjing Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanqing Wang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinjie Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Pan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baijun Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Morganti S, Parsons HA, Lin NU, Grinshpun A. Liquid biopsy for brain metastases and leptomeningeal disease in patients with breast cancer. NPJ Breast Cancer 2023; 9:43. [PMID: 37225714 DOI: 10.1038/s41523-023-00550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
A significant subset of patients with metastatic breast cancer develops brain metastasis. As efficacy of systemic therapies has improved and patients live longer with metastatic breast cancer, the incidence of breast cancer brain metastases has increased. Brain metastases pose a clinical challenge in diagnosis, treatment, and monitoring across all breast cancer subtypes, and better tools are needed. Liquid biopsy, which enables minimally invasive sampling of a patient's cancer, has the potential to shed light on intra-cranial tumor biology and to improve patient care by enabling therapy tailoring. Here we review current evidence for the clinical validity of liquid biopsy in patients with breast cancer brain metastases, with a focus on circulating tumor cells and circulating tumor DNA.
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Affiliation(s)
- Stefania Morganti
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Albert Grinshpun
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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Chokr N, Gomez-Arteaga A. Measurable Residual Disease After CAR T-Cell Therapy. Semin Hematol 2023; 60:34-41. [PMID: 37080709 DOI: 10.1053/j.seminhematol.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/21/2023]
Abstract
Testing for measurable residual disease (MRD) provides important prognostic and predictive implications on survival and management of many hematologic diseases. Among the many clinical uses of MRD is post-therapy response assessment and risk stratification. With the integration of precision medicine in routine clinical care and the development of novel and innovative therapies resulting in deeper responses, it is necessary to refine the role of MRD, standardize available methodologies and define its role as a surrogate endpoint for relapse and time-to-next treatment in clinical studies. Chimeric Antigen Receptor (CAR) T-cell therapy is an approved treatment for various hematologic malignancies. Even though it produces high rates of remission, the durability of response is still a consideration as almost 40% to 50% of patients eventually relapse. MRD testing as a prognostic and surrogate marker is being explored in patients after CAR T-cell therapy to predict early relapse. In this chapter, we review the various tools available for MRD detection and monitoring post-CAR T-cell therapy. We later discuss disease-specific MRD assessment and its application in recent studies in the post-CAR T setting.
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Assessment of Tissue Adequacy by EBUS in Conjunction with PET Scan and Operator's Experience. Clin Pract 2022; 12:942-949. [PMID: 36412678 PMCID: PMC9680420 DOI: 10.3390/clinpract12060099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Mediastinal lymph node assessment is a crucial step in non-small cell lung cancer staging. Positron emission tomography (PET) has been the gold standard for the assessment of mediastinal lymphadenopathy, though it has limited specificity. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is quick, accurate, and a less invasive method for obtaining a diagnostic sample in contrast to mediastinoscopy. We performed a retrospective chart analysis of 171 patients to assess the adequacy of tissue obtained by EBUS for diagnosis and molecular profiling as well as the assessment of staging and lymph node (LN) stations diagnostic yield, in correlation to PET scan and the operator’s level of experience. A significantly increased tissue adequacy was observed based on the operators’ experience, with the highest adequacy noted in trained Interventional Pulmonologist (IP) (100%), followed by >5 years of experience (93.33%), and 88.89% adequacy with <5 years of experience (p = 0.0019). PET-CT scan 18F-fluorodeoxyglucose (FDG) uptake in levels 1, 2, and 3 LN had a tissue adequacy of 76.67%, 54.64%, and 35.56%, respectively (p = 0.0009). EBUS bronchoscopy method could be used to achieve an accurate diagnosis, with IP-trained operators yielding the best results. There is no correlation with PET scan positivity, indicating that both PET and EBUS are complementary methods needed for staging.
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Petrylak DP, Watkins SP, Loehr A. What Plasma Can Tell Us When Tissue Cannot: A Case Report of Genomic Testing in mCRPC and Clinical Response to Treatment With the PARP Inhibitor Rucaparib. Front Oncol 2022; 12:951348. [PMID: 35978838 PMCID: PMC9377337 DOI: 10.3389/fonc.2022.951348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background The poly(ADP-ribose) polymerase (PARP) inhibitor rucaparib was approved in the United States based on the phase 2 TRITON2 study of patients with BRCA1 or BRCA2 (BRCA)-mutated metastatic castration-resistant prostate cancer (mCRPC). Although genomic screening is recommended as part of a comprehensive assessment of prostate cancer prognosis and treatment options, the best way to select patients with mCRPC for treatment with a PARP inhibitor depends on individual clinical circumstances. For example, assessment of tumor tissue may not always be feasible. Genomic testing of DNA from plasma has become more readily available, providing a minimally invasive option to evaluate DNA from primary and metastatic lesions simultaneously. Case Presentation A patient from TRITON2 with BRCA-mutated mCRPC had a response to the PARP inhibitor rucaparib and remained on treatment for 32 weeks, which was >2 times longer than the duration of each of his prior therapies (bicalutamide, docetaxel, abiraterone). The patient enrolled in TRITON2 based on results of local genomic testing of an archival biopsy that indicated the presence of a BRCA1 T1399I (allelic fraction, 19%) mutation. Local testing also identified an ATM G1663C mutation, a TP53 P191del mutation, and a BRAF K601E mutation. Analysis of a plasma sample obtained before the patient started rucaparib detected the same alterations as those in the archival biopsy, but it also revealed the presence of a BRCA2 homozygous loss (whole gene, 26 of 26 exons) and several other alterations of unknown functional impact. We hypothesize the response of the patient's tumor to rucaparib was likely driven by DNA damage repair deficiency caused by homozygous loss of all BRCA2 exons. Following discontinuation from rucaparib due to clinical disease progression, the patient received carboplatin and cabazitaxel for ≈3 weeks. The patient died due to progression of his disease. Conclusions A notable aspect of this case is the differences in alterations detected in the archival tumor sample and a more recent plasma sample. This highlights the advantages of plasma testing compared with tissue testing when selecting targeted therapies for treatment of mCRPC; however, physicians must determine which tool presents the best solution for each individual case.
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Affiliation(s)
- Daniel P. Petrylak
- Smilow Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Simon P. Watkins
- Clinical Science, Clovis Oncology UK, Ltd, Cambridge, United Kingdom
| | - Andrea Loehr
- Translational Medicine, Clovis Oncology, Inc., Boulder, CO, United States
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Mizuno Y, Shibata S, Miyagaki T, Ito Y, Taira H, Omori I, Hisamoto T, Oka K, Matsuda KM, Boki H, Takahashi-Shishido N, Sugaya M, Sato S. Serum cell-free DNA as a new biomarker in cutaneous T-cell lymphoma. J Dermatol 2022; 49:1124-1130. [PMID: 35821652 DOI: 10.1111/1346-8138.16520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]
Abstract
In recent years, circulating cell-free DNA (cfDNA) has received a great attention as a biomarker for various cancers. Many reports have shown that serum cfDNA levels are elevated in cancer patients and their levels correlate with prognosis and disease activity. The aim of this study was to measure serum cfDNA levels in patients with cutaneous T-cell lymphoma (CTCL) and to evaluate their correlations with hematological and clinical findings. Serum cfDNA levels in CTCL patients were significantly higher than those in healthy controls, and their levels gradually increased with the progression of the disease stage. Positive correlations were detected between serum cfDNA levels and those of lactate dehydrogenase, thymus and activation-regulated chemokine and soluble IL-2 receptor as well as neutrophil and eosinophil count in peripheral blood and neutrophil-to-lymphocyte ratio. Furthermore, CTCL patients with higher serum cfDNA levels exhibited a significantly worse prognosis. Taken together, these results suggest the potential of cfDNA as a new biomarker reflecting prognosis and disease activity in CTCL. CfDNA levels may serve as an indicator for considering the intensity and timing of subsequent therapeutic intervention.
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Affiliation(s)
- Yuka Mizuno
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Sayaka Shibata
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tomomitsu Miyagaki
- Department of Dermatology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Yukiko Ito
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Haruka Taira
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Issei Omori
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Teruyoshi Hisamoto
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kenta Oka
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kazuki M Matsuda
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hikari Boki
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | | | - Makoto Sugaya
- Department of Dermatology, International University of Health and Welfare, Chiba, Japan
| | - Shinichi Sato
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
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8
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Ding D, Zhang J, Luo Z, Wu H, Lin Z, Liang W, Xue X. Analysis of the lncRNA–miRNA–mRNA Network Reveals a Potential Regulatory Mechanism of EGFR-TKI Resistance in NSCLC. Front Genet 2022; 13:851391. [PMID: 35571024 PMCID: PMC9099042 DOI: 10.3389/fgene.2022.851391] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/17/2022] [Indexed: 12/25/2022] Open
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are widely used for patients with EGFR-mutated lung cancer. Despite its initial therapeutic efficacy, most patients eventually develop drug resistance, which leads to a poor prognosis in lung cancer patients. Previous investigations have proved that non-coding RNAs including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) contribute to drug resistance by various biological functions, whereas how they regulate EGFR-TKI resistance remains unclear. In this study, we examined gene expression using the microarray technology on gefitinib-resistant NSCLC cells to obtain differentially expressed (DE) lncRNAs and mRNAs. A total of 45 DE-lncRNAs associated with overall survival and 1799 target DE-mRNAs were employed to construct a core lncRNA–miRNA–mRNA network to illustrate underlying molecular mechanisms of how EGFR-TKI resistance occurs in NSCLC. We found that target DE-mRNAs were mainly enriched in pathways involved in EGFR-TKI resistance, especially the target DE-mRNAs regulated by LINC01128 were significantly enriched in the PI3K/Akt signaling pathway, where the synergy of these target DE-mRNAs may play a key role in EGFR-TKI resistance. In addition, downregulated LINC01128, acting as a specific miRNA sponge, decreases PTEN via sponging miR-25-3p. Furthermore, signaling reactions caused by the downregulation of PTEN would activate the PI3K/Akt signaling pathway, which may lead to EGFR-TKI resistance. In addition, a survival analysis indicated the low expression of LINC01128, and PTEN is closely related to poor prognosis in lung adenocarcinoma (LUAD). Therefore, the LINC01128/miR-25-3p/PTEN axis may promote EGFR-TKI resistance via the PI3K/Akt signaling pathway, which provides new insights into the underlying molecular mechanisms of drug resistance to EGFR-TKIs in NSCLC. In addition, our study sheds light on developing novel therapeutic approaches to overcome EGFR-TKI resistance in NSCLC.
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Affiliation(s)
- Dandan Ding
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jufeng Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhiming Luo
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Huazhen Wu
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Qingyuan People’s Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Zexiao Lin
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xingyang Xue, ; Weicheng Liang, ; Zexiao Lin,
| | - Weicheng Liang
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xingyang Xue, ; Weicheng Liang, ; Zexiao Lin,
| | - Xingyang Xue
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xingyang Xue, ; Weicheng Liang, ; Zexiao Lin,
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Zhou XC, Chen QP, Yuan JJ, Zhou S, Li M, Zhou WP, Qin Y, Deng H, Zhang L. Kidney-Derived Methylated PAX2 Sequences in the Urine of Healthy Subjects as a Convenient Model for Optimizing Methylation-Based Liquid biopsy. Mol Biotechnol 2022; 64:1088-1094. [PMID: 35412261 DOI: 10.1007/s12033-022-00481-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
Although urine-based liquid biopsy has received considerable attention, there is a lack of a simple model to optimize assay parameters, including cell-free DNA (cfDNA) extraction, bisulfite modification, and bis-DNA recovery after conversion for methylation analysis in urine. The primary aim of this work was to establish a practical model by developing a quantitative methylation-sensitive PCR (qMS-PCR) assay for PAX2 based on hypermethylated PAX2 cfDNA that could be detected in healthy human urine. We first studied the methylation status of PAX2 in kidney tissues and whole blood, followed by an assessment of commercial kits for bisulfite conversion and bis-DNA recovery. Furthermore, we investigated the influence of urine storage and collection conditions on the preservation of methylated PAX2 in urine samples by qMS-PCR. As expected, PAX2 methylation was identified in urine but not in blood. Two commercial kits (CellCook and Zymo Research) had similar conversion efficiency and bis-DNA recovery. Urine storage for up to 5 days did not change PAX2 methylation estimates. Overall, cold storage of urine samples and the CellCook urine container maintained higher levels of methylated PAX2 compared to urine kept at room temperature and the conventional tubes, respectively. These findings highlight the importance of using the correct approaches/kits and optimizing experimental conditions as a diagnostic tool in the clinical setting. Our study provides insights on the development of urine-based liquid biopsy with DNA methylation as a universal biomarker.
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Affiliation(s)
- Xiang-Cheng Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Qiu-Ping Chen
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Jia-Jia Yuan
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Shuai Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Mi Li
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Wei-Ping Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Yan Qin
- Department of Pathology, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Hua Deng
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
| | - Liang Zhang
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
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10
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Kavan S, Kruse TA, Vogsen M, Hildebrandt MG, Thomassen M. Heterogeneity and tumor evolution reflected in liquid biopsy in metastatic breast cancer patients: a review. Cancer Metastasis Rev 2022; 41:433-446. [PMID: 35286542 DOI: 10.1007/s10555-022-10023-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/07/2022] [Indexed: 02/06/2023]
Abstract
Breast cancer is a spatially and temporally dynamic disease in which differently evolving genetic clones are responsible for progression and clinical outcome. We review tumor heterogeneity and clonal evolution from studies comparing primary tumors and metastasis and discuss plasma circulating tumor DNA as a powerful real-time approach for monitoring the clonal landscape of breast cancer during treatment and recurrence. We found only a few early studies exploring clonal evolution and heterogeneity through analysis of multiregional tissue biopsies of different progression steps in comparison with circulating tumor DNA (ctDNA) from blood plasma. The model of linear progression seemed to be more often reported than the model of parallel progression. The results show complex routes to metastasis, however, and plasma most often reflected metastasis more than primary tumor. The described patterns of evolution and the polyclonal nature of breast cancer have clinical consequences and should be considered during patient diagnosis and treatment selection. Current studies focusing on the relevance of clonal evolution in the clinical setting illustrate the role of liquid biopsy as a noninvasive biomarker for monitoring clonal progression and response to treatment. In the clinical setting, circulating tumor DNA may be an ideal support for tumor biopsies to characterize the genetic landscape of the metastatic disease and to improve longitudinal monitoring of disease dynamics and treatment effectiveness through detection of residual tumor after resection, relapse, or metastasis within a particular patient.
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Affiliation(s)
- Stephanie Kavan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. .,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne Vogsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Malene G Hildebrandt
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
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11
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Recent Developments of Circulating Tumor Cell Analysis for Monitoring Cutaneous Melanoma Patients. Cancers (Basel) 2022; 14:cancers14040859. [PMID: 35205608 PMCID: PMC8870206 DOI: 10.3390/cancers14040859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Circulating tumor cells (CTCs) originating from cutaneous melanoma patients have been studied for several decades as surrogates for real-time clinical status and disease outcomes. Here, we will review clinical studies from the last 15 years that assessed CTCs and disease outcomes for melanoma patients. Assessment of multiple molecular melanoma-associated antigen (MAA) markers by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was the most common assay allowing for the improvement of assay sensitivity, to address tumor heterogeneity, and to predict patient outcomes. Multicenter studies demonstrate the utility of CTC assays reducing the bias observed in single-center trials. Recent development of CTC enrichment platforms has provided reproducible methods. CTC assessment enables both multiple mRNAs and DNAs genomic profiling. CTC provides specific important translational information on tumor progression, prediction of treatment response, and survival outcomes for cutaneous melanoma patients. Abstract Circulating tumor cells (CTCs) have been studied using multiple technical approaches for interrogating various cancers, as they allow for the real-time assessment of tumor progression, disease recurrence, treatment response, and tumor molecular profiling without the need for a tumor tissue biopsy. Here, we will review studies from the last 15 years on the assessment of CTCs in cutaneous melanoma patients in relation to different clinical outcomes. The focus will be on CTC detection in blood samples obtained from cutaneous melanoma patients of different clinical stages and treatments utilizing multiple platforms. Assessment of multiple molecular melanoma-associated antigen (MAA) markers by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was the most common assay allowing for the improvement of assay sensitivity, tumor heterogeneity, and to predict patient outcomes. Multicenter studies demonstrate the utility of CTC assays reducing the bias observed in single- center trials. The recent development of CTC enrichment platforms has provided reproducible methods. CTC assessment enables both multiple mRNAs and DNAs genomic aberration profiling. CTC provides specific important translational information on tumor progression, prediction of treatment response, and survival outcomes for cutaneous melanoma patients. The molecular studies on melanoma CTCs have provided and may set standards for other solid tumor CTC analyses.
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12
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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13
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Shohdy KS, Villamar DM, Cao Y, Trieu J, Price KS, Nagy R, Tagawa ST, Molina AM, Sternberg CN, Nanus DM, Mosquera JM, Elemento O, Sonpavde GP, Grivas P, Vogelzang NJ, Faltas BM. Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Br J Cancer 2022; 126:430-439. [PMID: 35046520 PMCID: PMC8810988 DOI: 10.1038/s41416-021-01648-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Targeted sequencing of circulating tumour DNA (ctDNA) is a promising tool to monitor dynamic changes in the variant allele frequencies (VAF) of genomic alterations and predict clinical outcomes in patients with advanced urothelial carcinoma (UC). METHODS We performed targeted sequencing of 182 serial ctDNA samples from 53 patients with advanced UC. RESULTS Serial ctDNA-derived metrics predicted the clinical outcomes in patients with advanced UC. Combining serial ctDNA aggregate VAF (aVAF) values with clinical factors, including age, sex, and liver metastasis, improved the performance of prognostic models. An increase of the ctDNA aVAF by ≥1 in serial ctDNA samples predicted disease progression within 6 months in 90% of patients. The majority of patients with aVAFs ≤0.7 in three consecutive ctDNA samples achieved durable clinical responses (≥6 months). CONCLUSIONS Serial ctDNA analysis predicts disease progression and enables dynamic monitoring to guide precision medicine in patients with advanced UC.
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Affiliation(s)
- Kyrillus S Shohdy
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Clinical Oncology, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
| | - Dario M Villamar
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yen Cao
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA
| | - Janson Trieu
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA
| | | | | | - Scott T Tagawa
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ana M Molina
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cora N Sternberg
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David M Nanus
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Guru P Sonpavde
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Petros Grivas
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Nicholas J Vogelzang
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA.
| | - Bishoy Morris Faltas
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
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14
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NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 2022; 131:19-28. [PMID: 35061087 PMCID: PMC8776978 DOI: 10.1007/s00412-021-00766-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 11/24/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023]
Abstract
Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the “nucleosomics” analysis of cell-free DNA (cfDNA) for the purpose of patient diagnostics in liquid biopsies. The rationale for this is that the apoptotic nucleases that digest chromatin of the dying cells mostly cut DNA between nucleosomes. Thus, the short pieces of DNA in body fluids reflect the positions of nucleosomes in the cells of origin. Here, we report a systematic nucleosomics database — NucPosDB — curating published nucleosome positioning datasets in vivo as well as datasets of sequenced cell-free DNA (cfDNA) that reflect nucleosome positioning in situ in the cells of origin. Users can select subsets of the database by a number of criteria and then obtain raw or processed data. NucPosDB also reports the originally determined regions with stable nucleosome occupancy across several individuals with a given condition. An additional section provides a catalogue of computational tools for the analysis of nucleosome positioning or cfDNA experiments and theoretical algorithms for the prediction of nucleosome positioning preferences from DNA sequence. We provide an overview of the field, describe the structure of the database in this context, and demonstrate data variability using examples of different medical conditions. NucPosDB is useful both for the analysis of fundamental gene regulation processes and the training of computational models for patient diagnostics based on cfDNA. The database currently curates ~ 400 publications on nucleosome positioning in cell lines and in situ as well as cfDNA from > 10,000 patients and healthy volunteers. For open-access cfDNA datasets as well as key MNase-seq datasets in human cells, NucPosDB allows downloading processed mapped data in addition to the regions with stable nucleosome occupancy. NucPosDB is available at https://generegulation.org/nucposdb/.
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15
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Comparison of solid tissue sequencing and liquid biopsy accuracy in identification of clinically relevant gene mutations and rearrangements in lung adenocarcinomas. Mod Pathol 2021; 34:2168-2174. [PMID: 34362997 DOI: 10.1038/s41379-021-00880-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/08/2022]
Abstract
Screening for therapeutic targets is standard of care in the management of advanced non-small cell lung cancer. However, most molecular assays utilize tumor tissue, which may not always be available. "Liquid biopsies" are plasma-based next generation sequencing (NGS) assays that use circulating tumor DNA to identify relevant targets. To compare the sensitivity, specificity, and accuracy of a plasma-based NGS assay to solid-tumor-based NGS we retrospectively analyzed sequencing results of 100 sequential patients with lung adenocarcinoma at our institution who had received concurrent testing with both a solid-tissue-based NGS assay and a commercially available plasma-based NGS assay. Patients represented both new diagnoses (79%) and disease progression on treatment (21%); the majority (83%) had stage IV disease. Tissue-NGS identified 74 clinically relevant mutations, including 52 therapeutic targets, a sensitivity of 94.8%, while plasma-NGS identified 41 clinically relevant mutations, a sensitivity of 52.6% (p < 0.001). Tissue-NGS showed significantly higher sensitivity and accuracy across multiple patient subgroups, both in newly diagnosed and treated patients, as well as in metastatic and nonmetastatic disease. Discrepant cases involved hotspot mutations and actionable fusions including those in EGFR, ALK, and NTRK1. In summary, tissue-NGS detects significantly more clinically relevant alterations and therapeutic targets compared to plasma-NGS, suggesting that tissue-NGS should be the preferred method for molecular testing of lung adenocarcinoma when tissue is available. Plasma-NGS can still play an important role when tissue testing is not possible. However, given its low sensitivity, a negative result should be confirmed with a tissue-based assay.
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16
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Xu E, Su K, Zhou Y, Gong L, Xuan Y, Liao M, Cao J, Li Y, Lu Y, Zhao Y, Chen F. Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. J Cell Mol Med 2021; 25:10279-10290. [PMID: 34658138 PMCID: PMC8572768 DOI: 10.1111/jcmm.16966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 01/18/2023] Open
Abstract
Tumour‐derived DNA found in the plasma of cancer patients provides the probability to detect somatic mutations from circulating cell‐free DNA (cfDNA) in plasma samples. However, clonal hematopoiesis (CH) mutations affect the accuracy of liquid biopsy for cancer diagnosis and treatment. Here, we integrated landscape of CH mutations in 11,725 pan‐cancer patients of Chinese and explored effects of CH on liquid biopsies in real‐world. We first identified 5933 CHs based on panel sequencing of matched DNA of white blood cell and cfDNA on 301 genes for 5100 patients, in which CH number of patients had positive correlation with their diagnosis age. We observed that canonical genes related to CH, including DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2 and SF3B1, were dominant in the Chinese cohort and 13.29% of CH mutations only appeared in the Chinese cohort compared with the Western cohort. Analysis of CH gene distribution bias indicated that CH tended to appear in genes with functions of tyrosine kinase regulation, PI3K‐Akt signalling and TP53 activity, suggesting unfavourable effects of CH mutations in cancer patients. We further confirmed effect of driver genes carried by CH on somatic mutations in liquid biopsy of cancer patients. Forty‐eight actionable somatic mutations in 17 driver genes were considered CH genes in 92 patients (1.80%) of the Chinese cohort, implying potential impacts of CH on clinical decision‐making. Taken together, this study exhibits strong evidence that gene mutations from CH interfere accuracy of liquid biopsies using cfDNA in cancer diagnosis and treatment in real‐world.
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Affiliation(s)
- Enwu Xu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou, China
| | - Kai Su
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou, China
| | - Yang Zhou
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | | | - Yiwen Xuan
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou, China
| | - Ming Liao
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou, China
| | - Jiawang Cao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yaqian Li
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Yujiao Lu
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Yi Zhao
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Fengxia Chen
- Department of Thoracic Surgery, Hainan General Hospital, Haikou, China
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17
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Davidson BA, Croessmann S, Park BH. The breast is yet to come: current and future utility of circulating tumour DNA in breast cancer. Br J Cancer 2021; 125:780-788. [PMID: 34040179 PMCID: PMC8438047 DOI: 10.1038/s41416-021-01422-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic strategies and the development of targeted therapies have enabled precision medicine to revolutionise the field of oncology. Precision medicine uses patient-specific genetic and molecular information, traditionally obtained from tumour biopsy samples, to classify tumours and treat them accordingly. However, biopsy samples often fail to provide complete tumour profiling, and the technique is expensive and, of course, relatively invasive. Advances in genomic techniques have led to improvements in the isolation and detection of circulating tumour DNA (ctDNA), a component of a peripheral blood draw/liquid biopsy. Liquid biopsy offers a minimally invasive method to gather genetic information that is representative of a global snapshot of both primary and metastatic sites and can thereby provide invaluable information for potential targeted therapies and methods for tumour surveillance. However, a lack of prospective clinical trials showing direct patient benefit has limited the implementation of liquid biopsies in standard clinical applications. Here, we review the potential of ctDNA obtained by liquid biopsy to revolutionise personalised medicine and discuss current applications of ctDNA both at the benchtop and bedside.
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Affiliation(s)
- Brad A Davidson
- The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sarah Croessmann
- The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ben H Park
- The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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18
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Zhou L, Zhao H, Shao Y, Chen X, Hong R, Wang L, Ni F, Nagler A, Hu Y, Huang H. Serial surveillance by circulating tumor DNA profiling after chimeric antigen receptor T therapy for the guidance of r/r diffuse large B cell lymphoma precise treatment. J Cancer 2021; 12:5423-5431. [PMID: 34405005 PMCID: PMC8364638 DOI: 10.7150/jca.60390] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Circulating tumor DNA (ctDNA) released from tumor cells carries the tumor-associated genetic and epigenetic characteristics of cancer patients. Next-generation sequencing (NGS) facilitates the application of ctDNA profiling for identification and monitoring of minimal residual disease (MRD) in cancer, and can serve as the guidance for precise treatment. Methods: In this study, we profiled genomic alterations in the baseline, relapsed, and progressive tumor samples of eight diffuse large B cell lymphoma (DLBCL) patients (NCT03118180) after chimeric antigen receptor T (CAR-T) cell therapy. Results: The median follow-up was 41 months. 4 (50%) patients achieved complete remission (CR), 1 (12.5%) patient achieved partial remission (PR), and the other 3 (37.5%) patients showed no response. 3 of 5 patients who achieved remission relapsed within 4 months after CAR-T therapy, while the rest 2 patients remained CR for more than 3 years. Based on the positron emission tomography-computed tomography (PET-CT) scan, the current gold standard for evaluating response to therapy in lymphoma, the sensitivity and specificity of our ctDNA profiling in detecting tumor-related ctDNA mutations were 94.7% and 83.3%, respectively. The median numbers of baseline plasma ctDNA mutations in patients who remained long-term CR and patients who relapsed or became refractory to CAR-T therapy were 3 and 14.3, respectively. GNA13, SOCS1, TNFAIP3 and XPO1 mutations appeared to be associated with poor prognosis after CAR-T cell therapy. Our results also suggested that lenalidomide might relieve relapsed lymphoma with mutations in NFKBIA 202C>T (p.Q68*) and NFKBIE 433A>T (p.K145*) by targeting NF-Kappa B signaling. In addition, the inhibitor selinexor may be another choice for refractory or relapse (r/r) DLBCL patients after CAR-T cell treatment. Conclusion: Serial ctDNA monitoring is an emerging technology for the surveillance of disease status and prognosis prediction. In this work, we demonstrated the use of serial ctDNA monitoring in r/r DLBCL patients after CD19-targeted CAR-T cell therapy. Our longitudinal NGS profiling revealed the changes of ctDNA mutation in accordance with prognosis, and shed some light on exploring more targeted treatment options together with CAR-T cell therapy.
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Affiliation(s)
- Linghui Zhou
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Houli Zhao
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Xin Chen
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Ruimin Hong
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Linqin Wang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Fang Ni
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Arnon Nagler
- Chaim Sheba Medical Center, Tel Hashomer, Israel, Tel Hashomer, Israel
| | - Yongxian Hu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - He Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine.,Institute of Hematology, Zhejiang University.,Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
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19
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Lim Y, Kim S, Kang JK, Kim HP, Jang H, Han H, Kim H, Kim MJ, Lee KH, Ryoo SB, Park JW, Jeong SY, Park KJ, Kang GH, Han SW, Kim TY. Circulating tumor DNA sequencing in colorectal cancer patients treated with first-line chemotherapy with anti-EGFR. Sci Rep 2021; 11:16333. [PMID: 34381078 PMCID: PMC8358023 DOI: 10.1038/s41598-021-95345-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/19/2021] [Indexed: 01/03/2023] Open
Abstract
Circulating tumor DNA (ctDNA) may reveal dynamic tumor status during therapy. We conducted serial ctDNA analysis to investigate potential association with clinical outcome in metastatic colorectal cancer (mCRC) patients receiving chemotherapy. Tissue KRAS/NRAS wild-type mCRC patients were enrolled and treated with first-line cetuximab-containing chemotherapy. ctDNA isolated from plasma were analyzed by next generation sequencing (NGS) with 16 targeted gene panel. Among 93 patients, 84 (90.3%) had at least 1 somatic mutation in baseline ctDNA samples (average 2.74). Five patients with KRAS or NRAS hotspot mutation in the ctDNA showed significantly worse progression-free survival (PFS) (p = 0.029). Changes in average variant allele frequency (VAF) in ctDNA showed significant correlation with tumor size change at the time of first response evaluation (p = 0.020) and progressive disease (PD) (p = 0.042). Patients whose average VAF decreased below cutoff (< 1%) at the first evaluation showed significantly better PFS (p < 0.001), and the average VAF change further discriminated the PFS in the patients in partial response (p = 0.018). At the time of PD, 54 new mutations including KRAS and MAP2K1 emerged in ctDNA. ctDNA sequencing can provide mutation profile that could better reflect tumor mutation status and predict treatment outcome.
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Affiliation(s)
- Yoojoo Lim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sheehyun Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jun-Kyu Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Hwang-Phill Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | | | | | | | - Min Jung Kim
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Seung-Bum Ryoo
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Ji Won Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Seung-Yong Jeong
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Kyu Joo Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
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20
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Attili I, Del Re M, Guerini-Rocco E, Crucitta S, Pisapia P, Pepe F, Barberis M, Troncone G, Danesi R, de Marinis F, Malapelle U, Passaro A. The role of molecular heterogeneity targeting resistance mechanisms to lung cancer therapies. Expert Rev Mol Diagn 2021; 21:757-766. [PMID: 34278933 DOI: 10.1080/14737159.2021.1943365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: The treatment scenario of lung cancer is rapidly evolving through time. In parallel, growing evidence is accumulating on different mechanisms of treatment resistance. Inter- and intra-tumor heterogeneity define the spatial and temporal tumor clonal evolution, that is at the basis of tumor progression and resistance to anticancer treatments.Areas covered: This review summarizes the available evidence on molecular heterogeneity in lung cancer, from diagnosis to the occurrence of treatment resistance. The application of novel molecular diagnostic methods to detect molecular heterogeneity, and the implications of understanding heterogeneity for drug development strategies are discussed, with focus on clinical relevance and impact on patients' survival.Expert opinion: The current knowledge of molecular heterogeneity allows to identify different molecular subgroups of patients within the same conventional tumor type. Deeper understanding of heterogeneity determinants and the possibility to comprehensively investigate tumor molecular patterns will lead to the development of personalized treatment approaches, with the final goal to overcome resistance and prolong survival in lung cancer patients.
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Affiliation(s)
- Ilaria Attili
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine,IEO, European Institute of Oncology, IRCCS, Milano, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Massimo Barberis
- Division of Pathology and Laboratory Medicine,IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
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21
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Li S, Zhang G, Li X, Li X, Chen X, Xu Y, Ren H. Role of the preoperative circulating tumor DNA KRAS mutation in patients with resectable pancreatic cancer. Pharmacogenomics 2021; 22:657-667. [PMID: 34120460 DOI: 10.2217/pgs-2020-0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The prognosis of resectable pancreatic cancer patients with the same stage of disease is highly variable. The purpose of this study is to establish a scoring system for preoperative screening of resectable patients. Materials & methods: The clinical information and laboratory tests of 105 resectable patients with pancreatic cancer were enrolled and analyzed. Results: The consistency of clinical stage and pathological stage was poor (κ = 0.193; p < 0.003). We performed a comprehensive scoring system with KRAS mutations in circulating tumor DNA (mutKRAS ctDNA) for the resectable patients. Patients with higher scores were more prone to early postoperative recurrence and poorer prognosis. Conclusion: The scoring system can help preoperatively screen out resectable patients who are prone to early postoperative recurrence.
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Affiliation(s)
- Shengnan Li
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Gengpu Zhang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xin Li
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xiaojie Li
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - XiaoBing Chen
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Yu Xu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.,Department of Oncology, Tianjin Huanghe Hospital, Tianjin, 300060, China
| | - He Ren
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.,Department of Gastroenterology, Center of Tumor Immunology & Cytotherapy, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
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22
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Circulating tumor DNA in lung cancer: real-time monitoring of disease evolution and treatment response. Chin Med J (Engl) 2021; 133:2476-2485. [PMID: 32960843 PMCID: PMC7575184 DOI: 10.1097/cm9.0000000000001097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.
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23
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A Systematic Review of the Use of Circulating Cell-Free DNA Dynamics to Monitor Response to Treatment in Metastatic Breast Cancer Patients. Cancers (Basel) 2021; 13:cancers13081811. [PMID: 33920135 PMCID: PMC8069506 DOI: 10.3390/cancers13081811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/24/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
Monitoring treatment response in metastatic breast cancer currently consists mainly of radiological and clinical assessments. These methods have high inter-observer variation, suboptimal sensitivity to determine response to treatment and give little insight into the biological characteristics of the tumor. Assessing circulating tumor DNA (ctDNA) over time could be employed to address these limitations. Several ways to quantify and characterize ctDNA exist, based on somatic mutations, copy number variations, methylation, and global circulating cell-free DNA (cfDNA) fragment sizes and concentrations. These methods are being explored and technically validated, but to date none of these methods are applied clinically. We systematically reviewed the literature on the use of quantitative ctDNA measurements over time to monitor response to systemic therapy in patients with metastatic breast cancer. Cochrane, Embase, PubMed and Google Scholar databases were searched to find studies focusing on the use of cfDNA to longitudinally monitor treatment response in advanced breast cancer patients until October 2020. This resulted in a total of 33 studies which met the inclusion criteria. These studies were heterogeneous in (pre-)processing procedures, applied techniques and design. An association between ctDNA and treatment response was found in most of the included studies, independent of the applied assay. To implement ctDNA-based response monitoring into daily clinical practice for metastatic breast cancer patients, sample (pre-) processing procedures need to be standardized and large prospectively collected sample cohorts with well annotated clinical follow-up are required to establish its clinical validity.
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24
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Chiou CC, Wang CL, Luo JD, Liu CY, Ko HW, Yang CT. Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients. Cancer Genomics Proteomics 2021; 17:417-423. [PMID: 32576586 DOI: 10.21873/cgp.20200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Circulating tumor DNA (ctDNA) bears specific mutations derived from tumor cells. The amount of mutant ctDNA may reflect tumor burden. In this study, we detected epidermal growth factor receptor (EGFR) mutations in ctDNA as a monitoring marker for the response of non-small cell lung cancer (NSCLC) patients to tyrosine kinase inhibitors (TKIs). PATIENTS AND METHODS Serial plasma samples from eight NSCLC patients during TKI treatment were collected. Libraries with barcoded adapters were constructed from ctDNA of these plasma samples using a PCR-based targeted DNA panel. The libraries were then sequenced for measuring EGFR mutations. In addition, carcinoembryonic antigen (CEA) was also measured in these patients. RESULTS In six patients who suffered disease progression (PD), five had elevated EGFR mutation reads before PD. In the two patients who did not develop PD, EGFR mutations remained undetectable in their plasma. The CEA levels were higher than the cutoff value in most samples and had a poor correlation with disease status. CONCLUSION The mutation count of tumor-specific mutations can be a monitoring marker of TKI treatment in NSCLC patients.
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Affiliation(s)
- Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Chih-Liang Wang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, U.S.A
| | - Chien-Ying Liu
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - How-Wen Ko
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. .,Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
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25
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Smyth LM, Reichel JB, Tang J, Patel JAA, Meng F, Selcuklu DS, Houck-Loomis B, You D, Samoila A, Schiavon G, Li BT, Razavi P, Piscuoglio S, Reis-Filho JS, Taylor BS, Baselga J, Solit DB, Hyman DM, Berger MF, Chandarlapaty S. Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study. JCO Precis Oncol 2021; 5:PO.20.00184. [PMID: 34250397 DOI: 10.1200/po.20.00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/18/2020] [Accepted: 10/28/2020] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1-mutant solid tumor basket study. METHODS Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens. RESULTS Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy. CONCLUSION Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations.
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Affiliation(s)
| | | | - Jiabin Tang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Fanli Meng
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Daoqi You
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Gaia Schiavon
- R&D Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - José Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY
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26
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Garrido-Navas MC, García-Díaz A, Molina-Vallejo MP, González-Martínez C, Alcaide Lucena M, Cañas-García I, Bayarri C, Delgado JR, González E, Lorente JA, Serrano MJ. The Polemic Diagnostic Role of TP53 Mutations in Liquid Biopsies from Breast, Colon and Lung Cancers. Cancers (Basel) 2020; 12:E3343. [PMID: 33198130 PMCID: PMC7696715 DOI: 10.3390/cancers12113343] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Being minimally invasive and thus allowing repeated measures over time, liquid biopsies are taking over traditional solid biopsies in certain circumstances such as those for unreachable tumors, very early stages or treatment monitoring. However, regarding TP53 mutation status analysis, liquid biopsies have not yet substituted tissue samples, mainly due to the lack of concordance between the two types of biopsies. This needs to be examined in a study-dependent manner, taking into account the particular type of liquid biopsy analyzed, that is, circulating tumor cells (CTCs) or cell-free DNA (cfDNA), its involvement in the tumor biology and evolution and, finally, the technology used to analyze each biopsy type. Here, we review the main studies analyzing TP53 mutations in either CTCs or cfDNA in the three more prevalent solid tumors: breast, colon and lung cancers. We evaluate the correlation for mutation status between liquid biopsies and tumor tissue, suggesting possible sources of discrepancies, as well as evaluating the clinical utility of using liquid biopsies for the analysis of TP53 mutation status and the future actions that need to be undertaken to make liquid biopsy analysis a reality for the evaluation of TP53 mutations.
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Affiliation(s)
- M. Carmen Garrido-Navas
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Universidad Internacional de la Rioja, Avenida de la Paz, 137, 26006 Logroño, Spain
| | - Abel García-Díaz
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Departamento de Medicina, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain
| | - Maria Pilar Molina-Vallejo
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Coral González-Martínez
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Miriam Alcaide Lucena
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Inés Cañas-García
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Clara Bayarri
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Department of Thoracic Surgery, Virgen de las Nieves University Hospital, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Juan Ramón Delgado
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Encarna González
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Jose Antonio Lorente
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071 Granada, Spain
| | - M. Jose Serrano
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
- Department of Pathological Anatomy, Faculty of Medicine, Campus de Ciencias de la Salud, University of Granada, 18016 Granada, Spain
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27
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Sharbatoghli M, Vafaei S, Aboulkheyr Es H, Asadi-Lari M, Totonchi M, Madjd Z. Prediction of the treatment response in ovarian cancer: a ctDNA approach. J Ovarian Res 2020; 13:124. [PMID: 33076944 PMCID: PMC7574472 DOI: 10.1186/s13048-020-00729-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is the eighth most commonly occurring cancer in women. Clinically, the limitation of conventional screening and monitoring approaches inhibits high throughput analysis of the tumor molecular markers toward prediction of treatment response. Recently, analysis of liquid biopsies including circulating tumor DNA (ctDNA) open new way toward cancer diagnosis and treatment in a personalized manner in various types of solid tumors. In the case of ovarian carcinoma, growing pre-clinical and clinical studies underscored promising application of ctDNA in diagnosis, prognosis, and prediction of treatment response. In this review, we accumulate and highlight recent molecular findings of ctDNA analysis and its associations with treatment response and patient outcome. Additionally, we discussed the potential application of ctDNA in the personalized treatment of ovarian carcinoma. ctDNA-monitoring usage during the ovarian cancer treatments procedures.
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Affiliation(s)
- Mina Sharbatoghli
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Somayeh Vafaei
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Asadi-Lari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
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28
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Hrebien S, Citi V, Garcia-Murillas I, Cutts R, Fenwick K, Kozarewa I, McEwen R, Ratnayake J, Maudsley R, Carr TH, de Bruin EC, Schiavon G, Oliveira M, Turner N. Early ctDNA dynamics as a surrogate for progression-free survival in advanced breast cancer in the BEECH trial. Ann Oncol 2020; 30:945-952. [PMID: 30860573 PMCID: PMC6594458 DOI: 10.1093/annonc/mdz085] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Dynamic changes in circulating tumour DNA (ctDNA) levels may predict long-term outcome. We utilised samples from a phase I/II randomised trial (BEECH) to assess ctDNA dynamics as a surrogate for progression-free survival (PFS) and early predictor of drug efficacy. Patients and methods Patients with estrogen receptor-positive advanced metastatic breast cancer (ER+ mBC) in the BEECH study, paclitaxel plus placebo versus paclitaxel plus AKT inhibitor capivasertib, had plasma samples collected for ctDNA analysis at baseline and at multiple time points in the development cohort (safety run-in, part A) and validation cohort (randomised, part B). Baseline sample ctDNA sequencing identified mutations for longitudinal analysis and mutation-specific digital droplet PCR (ddPCR) assays were utilised to assess change in ctDNA abundance (allele fraction) between baseline and 872 on-treatment samples. Primary objective was to assess whether early suppression of ctDNA, based on pre-defined criteria from the development cohort, independently predicted outcome in the validation cohort. Results In the development cohort, suppression of ctDNA was apparent after 8 days of treatment (P = 0.014), with cycle 2 day 1 (4 weeks) identified as the optimal time point to predict PFS from early ctDNA dynamics. In the validation cohort, median PFS was 11.1 months in patients with suppressed ctDNA at 4 weeks and 6.4 months in patients with high ctDNA (hazard ratio = 0.20, 95% confidence interval 0.083–0.50, P < 0.0001). There was no difference in the level of ctDNA suppression between patients randomised to capivasertib or placebo overall (P = 0.904) nor in the PIK3CA mutant subpopulation (P = 0.071). Clonal haematopoiesis of indeterminate potential (CHIP) was evident in 30% (18/59) baseline samples, although CHIP had no effect on tolerance of chemotherapy nor on PFS. Conclusion Early on-treatment ctDNA dynamics are a surrogate for PFS. Dynamic ctDNA assessment has the potential to substantially enhance early drug development. Clinical registration number NCT01625286.
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Affiliation(s)
- S Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - V Citi
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK; Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - I Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - R Cutts
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - K Fenwick
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - I Kozarewa
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - R McEwen
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - J Ratnayake
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - R Maudsley
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - T H Carr
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - E C de Bruin
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - G Schiavon
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - M Oliveira
- Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - N Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK; Breast Unit, Royal Marsden Hospital, London, UK.
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29
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Filip S, Vymetalkova V, Petera J, Vodickova L, Kubecek O, John S, Cecka F, Krupova M, Manethova M, Cervena K, Vodicka P. Distant Metastasis in Colorectal Cancer Patients-Do We Have New Predicting Clinicopathological and Molecular Biomarkers? A Comprehensive Review. Int J Mol Sci 2020; 21:E5255. [PMID: 32722130 PMCID: PMC7432613 DOI: 10.3390/ijms21155255] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) remains a serious health problem worldwide. Approximately half of patients will develop distant metastasis after CRC resection, usually with very poor prognosis afterwards. Because patient performance after distant metastasis surgery remains very heterogeneous, ranging from death within 2 years to a long-term cure, there is a clinical need for a precise risk stratification of patients to aid pre- and post-operative decisions. Furthermore, around 20% of identified CRC cases are at IV stage disease, known as a metastatic CRC (mCRC). In this review, we overview possible molecular and clinicopathological biomarkers that may provide prognostic and predictive information for patients with distant metastasis. These may comprise sidedness of the tumor, molecular profile and epigenetic characteristics of the primary tumor and arising metastatic CRC, and early markers reflecting cancer cell resistance in mCRC and biomarkers identified from transcriptome. This review discusses current stage in employment of these biomarkers in clinical practice as well as summarizes current experience in identifying predictive biomarkers in mCRC treatment.
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Affiliation(s)
- Stanislav Filip
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Jiri Petera
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Ondrej Kubecek
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Stanislav John
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Filip Cecka
- Department of Surgery, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic;
| | - Marketa Krupova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic; (M.K.); (M.M.)
| | - Monika Manethova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic; (M.K.); (M.M.)
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
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Crippa A, De Laere B, Discacciati A, Larsson B, Connor JT, Gabriel EE, Thellenberg C, Jänes E, Enblad G, Ullen A, Hjälm-Eriksson M, Oldenburg J, Ost P, Lindberg J, Eklund M, Grönberg H. The ProBio trial: molecular biomarkers for advancing personalized treatment decision in patients with metastatic castration-resistant prostate cancer. Trials 2020; 21:579. [PMID: 32586393 PMCID: PMC7318749 DOI: 10.1186/s13063-020-04515-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Multiple therapies exist for patients with metastatic castration-resistant prostate cancer (mCRPC). However, their improvement on progression-free survival (PFS) remains modest, potentially explained by tumor molecular heterogeneity. Several prognostic molecular biomarkers have been identified for mCRPC that may have predictive potential to guide treatment selection and prolong PFS. We designed a platform trial to test this hypothesis. METHODS The Prostate-Biomarker (ProBio) study is a multi-center, outcome-adaptive, multi-arm, biomarker-driven platform trial for tailoring treatment decisions for men with mCRPC. Treatment decisions in the experimental arms are based on biomarker signatures defined as mutations in certain genes/pathways suggested in the scientific literature to be important for treatment response in mCRPC. The biomarker signatures are determined by targeted sequencing of circulating tumor and germline DNA using a panel specifically designed for mCRPC. DISCUSSION Patients are stratified based on the sequencing results and randomized to either current clinical practice (control), where the treating physician decides treatment, or to molecularly driven treatment selection based on the biomarker profile. Outcome-adaptive randomization is implemented to early identify promising treatments for a biomarker signature. Biomarker signature-treatment combinations graduate from the platform when they demonstrate 85% probability of improving PFS compared to the control arm. Graduated combinations are further evaluated in a seamless confirmatory trial with fixed randomization. The platform design allows for new drugs and biomarkers to be introduced in the study. CONCLUSIONS The ProBio design allows promising treatment-biomarker combinations to quickly graduate from the platform and be confirmed for rapid implementation in clinical care. TRIAL REGISTRATION ClinicalTrials.gov Identifier NCT03903835. Date of registration: April 4, 2019. Status: Recruiting.
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Affiliation(s)
- Alessio Crippa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Andrea Discacciati
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Berit Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jason T Connor
- University of Central Florida College of Medicine, Orlando, FL, USA
- Confluence Stat LLC, Orlando, FL, USA
| | - Erin E Gabriel
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Thellenberg
- Department of Radiation Sciences and Oncology, Umeå University, Umeå, Sweden
| | - Elin Jänes
- Länssjukhuset Sundsvall Härnösand, Sundsvall, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Uppsala, Sweden
| | - Anders Ullen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Jan Oldenburg
- Division of Medicine, University of Oslo, Oslo, Norway
| | - Piet Ost
- Department of Radiotherapy and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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31
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Plasma DNA as a "liquid biopsy" incompletely complements tumor biopsy for identification of mutations in a case series of four patients with oligometastatic breast cancer. Breast Cancer Res Treat 2020; 182:665-677. [PMID: 32562118 DOI: 10.1007/s10549-020-05714-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Circulating tumor DNA in plasma may present a minimally invasive opportunity to identify tumor-derived mutations to inform selection of targeted therapies for individual patients, particularly in cases of oligometastatic disease where biopsy of multiple tumors is impractical. To assess the utility of plasma DNA as a "liquid biopsy" for precision oncology, we tested whether sequencing of plasma DNA is a reliable surrogate for sequencing of tumor DNA to identify targetable genetic alterations. METHODS Blood and biopsies of 1-3 tumors were obtained from 4 evaluable patients with advanced breast cancer. One patient provided samples from an additional 7 tumors post-mortem. DNA extracted from plasma, tumor tissues, and buffy coat of blood were used for probe-directed capture of all exons in 149 cancer-related genes and massively parallel sequencing. Somatic mutations in DNA from plasma and tumors were identified by comparison to buffy coat DNA. RESULTS Sequencing of plasma DNA identified 27.94 ± 11.81% (mean ± SD) of mutations detected in a tumor(s) from the same patient; such mutations tended to be present at high allelic frequency. The majority of mutations found in plasma DNA were not found in tumor samples. Mutations were also found in plasma that matched clinically undetectable tumors found post-mortem. CONCLUSIONS The incomplete overlap of genetic alteration profiles of plasma and tumors warrants caution in the sole reliance of plasma DNA to identify therapeutically targetable alterations in patients and indicates that analysis of plasma DNA complements, but does not replace, tumor DNA profiling. TRIAL REGISTRATION Subjects were prospectively enrolled in trial NCT01836640 (registered April 22, 2013).
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32
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Wu C, Zhang J, Li H, Xu W, Zhang X. The potential of liquid biopsies in gastrointestinal cancer. Clin Biochem 2020; 84:1-12. [PMID: 32540214 DOI: 10.1016/j.clinbiochem.2020.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/09/2020] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid biopsy is a novel approach for cancer diagnosis, the value of which in human gastrointestinal (GI) cancer has been confirmed by the previous studies. This article summarized the recent advances in liquid biopsy with a focus on novel technologies and the use of it in the screening, monitoring, and treatment of human GI cancer. CONTENT The concept of liquid biopsy was first used to define the detection of circulating tumor cells (CTCs) in cancer patients, and has been expanded to other biomarkers in blood and body fluids, such as circulating tumor DNA (ctDNA), extracellular vesicles (EVs) and circulating tumor RNA. If analyzed with proper and advanced techniques like next generation sequencing (NGS) or proteomics, liquid biopsies can open an enormous array of potential biomarkers. The amount changes of target biomarkers and the mutation of genetic materials provide quantitative and qualitative information, which can be utilized clinically for cancer diagnosis and disease monitoring. SUMMARY As a highly efficient, minimally invasive, and cost-effective approach to diagnose and evaluate prognosis of GI cancer, liquid biopsy has lots of advantages over traditional biopsy and is promising in future clinical utility. If the challenges are overcome in the near future, liquid biopsy will become a widely available and dependable option.
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Affiliation(s)
- Chenxi Wu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Jiayin Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Haibo Li
- Department of Clinical Laboratory, Nantong Maternal and Child Health Care Hospital, Nantong, Jiangsu 226000, China
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
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Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
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Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
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34
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Chu LY, Peng YH, Weng XF, Xie JJ, Xu YW. Blood-based biomarkers for early detection of esophageal squamous cell carcinoma. World J Gastroenterol 2020; 26:1708-1725. [PMID: 32351288 PMCID: PMC7183865 DOI: 10.3748/wjg.v26.i15.1708] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignant tumor of the digestive system worldwide, especially in China. Due to the lack of effective early detection methods, ESCC patients often present at an advanced stage at the time of diagnosis, which seriously affects the prognosis of patients. At present, early detection of ESCC mainly depends on invasive and expensive endoscopy and histopathological biopsy. Therefore, there is an unmet need for a non-invasive method to detect ESCC in the early stages. With the emergence of a large class of non-invasive diagnostic tools, serum tumor markers have attracted much attention because of their potential for detection of early tumors. Therefore, the identification of serum tumor markers for early detection of ESCC is undoubtedly one of the most effective ways to achieve early diagnosis and treatment of ESCC. This article reviews the recent advances in the discovery of blood-based ESCC biomarkers, and discusses the origins, clinical applications, and technical challenges of clinical validation of various types of biomarkers.
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Affiliation(s)
- Ling-Yu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yu-Hui Peng
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Xue-Fen Weng
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yi-Wei Xu
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, Guangdong Province, China
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35
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Parikh AR, Mojtahed A, Schneider JL, Kanter K, Van Seventer EE, Fetter IJ, Thabet A, Fish MG, Teshome B, Fosbenner K, Nadres B, Shahzade HA, Allen JN, Blaszkowsky LS, Ryan DP, Giantonio B, Goyal L, Nipp RD, Roeland E, Weekes CD, Wo JY, Zhu AX, Dias-Santagata D, Iafrate AJ, Lennerz JK, Hong TS, Siravegna G, Horick N, Clark JW, Corcoran RB. Serial ctDNA Monitoring to Predict Response to Systemic Therapy in Metastatic Gastrointestinal Cancers. Clin Cancer Res 2020; 26:1877-1885. [PMID: 31941831 PMCID: PMC7165022 DOI: 10.1158/1078-0432.ccr-19-3467] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/09/2019] [Accepted: 01/10/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE ctDNA offers a promising, noninvasive approach to monitor therapeutic efficacy in real-time. We explored whether the quantitative percent change in ctDNA early after therapy initiation can predict treatment response and progression-free survival (PFS) in patients with metastatic gastrointestinal cancer. EXPERIMENTAL DESIGN A total of 138 patients with metastatic gastrointestinal cancers and tumor profiling by next-generation sequencing had serial blood draws pretreatment and at scheduled intervals during therapy. ctDNA was assessed using individualized droplet digital PCR measuring the mutant allele fraction in plasma of mutations identified in tumor biopsies. ctDNA changes were correlated with tumor markers and radiographic response. RESULTS A total of 138 patients enrolled. A total of 101 patients were evaluable for ctDNA and 68 for tumor markers at 4 weeks. Percent change of ctDNA by 4 weeks predicted partial response (PR, P < 0.0001) and clinical benefit [CB: PR and stable disease (SD), P < 0.0001]. ctDNA decreased by 98% (median) and >30% for all PR patients. ctDNA change at 8 weeks, but not 2 weeks, also predicted CB (P < 0.0001). Four-week change in tumor markers also predicted response (P = 0.0026) and CB (P = 0.022). However, at a clinically relevant specificity threshold of 90%, 4-week ctDNA change more effectively predicted CB versus tumor markers, with a sensitivity of 60% versus 24%, respectively (P = 0.0109). Patients whose 4-week ctDNA decreased beyond this threshold (≥30% decrease) had a median PFS of 175 days versus 59.5 days (HR, 3.29; 95% CI, 1.55-7.00; P < 0.0001). CONCLUSIONS Serial ctDNA monitoring may provide early indication of response to systemic therapy in patients with metastatic gastrointestinal cancer prior to radiographic assessments and may outperform standard tumor markers, warranting further evaluation.
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Affiliation(s)
- Aparna R Parikh
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amikasra Mojtahed
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jaime L Schneider
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Katie Kanter
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Isobel J Fetter
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ashraf Thabet
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Madeleine G Fish
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bezaye Teshome
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kathryn Fosbenner
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brandon Nadres
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heather A Shahzade
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jill N Allen
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lawrence S Blaszkowsky
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - David P Ryan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bruce Giantonio
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan D Nipp
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric Roeland
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Colin D Weekes
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew X Zhu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Giulia Siravegna
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nora Horick
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeffrey W Clark
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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Pappas-Gogos G, Baltagiannis EG, Kyrochristos ID, Ziogas DE, Goussia A, Mitsis M, Roukos DH. Predictive and patient-monitoring biomarkers: precision in the management of colorectal cancer. Biomark Med 2020; 14:335-339. [PMID: 32250157 DOI: 10.2217/bmm-2020-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Georgios Pappas-Gogos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Demosthenes E Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, 'G Hatzikosta' General Hospital, Ioannina, Greece
| | - Anna Goussia
- Department of Pathology, University Hospital of Ioannina, Ioannina, Greece
| | - Michail Mitsis
- Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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37
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Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors. ACTA ACUST UNITED AC 2020; 1:382-393. [PMID: 32864625 DOI: 10.1038/s43018-020-0047-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alpelisib is a selective inhibitor of PI3Kα, shown to improve outcomes for PIK3CA mutant, hormone receptor positive (HR+) metastatic breast cancers (MBC) when combined with antiestrogen therapy. To uncover mechanisms of resistance, we conducted a detailed, longitudinal analysis of tumor and plasma circulating tumor DNA among such patients from a phase I/II trial combining alpelisib with an aromatase inhibitor (AI) (NCT01870505). The trial's primary objective was to establish safety with maculopapular rash emerging as the most common grade 3 adverse event (33%). Among 44 evaluable patients, the observed clinical benefit rate was 52%. Correlating genetic alterations with outcome, we identified loss-of-function PTEN mutations in 25% of patients with resistance. ESR1 activating mutations also expanded in number and allele fraction during treatment and were associated with resistance. These data indicate that genomic alterations that mediate resistance to alpelisib or antiestrogen may promote disease progression and highlight PTEN loss as a recurrent mechanism of resistance to PI3Kα inhibition.
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38
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Perspectives of the Application of Liquid Biopsy in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6843180. [PMID: 32258135 PMCID: PMC7085834 DOI: 10.1155/2020/6843180] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal tumors and the second leading cause of cancer death worldwide. Since traditional biopsies are invasive and do not reflect tumor heterogeneity or monitor the dynamic progression of tumors, there is an urgent need for new noninvasive methods that can supplement and improve the current management strategies of CRC. Blood-based liquid biopsies are a promising noninvasive biomarker that can detect disease early, assist in staging, monitor treatment responses, and predict relapse and metastasis. Over time, an increasing number of experiments have indicated the clinical utility of liquid biopsies in CRC. In this review, we mainly focus on the development of circulating tumor cells and circulating tumor DNA as key components of liquid biopsies in CRC and introduce the potential of exosomal microRNAs as emerging liquid biopsy markers in clinical application for CRC.
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39
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Liu X, Lang J, Li S, Wang Y, Peng L, Wang W, Han Y, Qi C, Song L, Yang S, Zhang K, Zang G, Pei H, Lu Q, Peng Y, Xi S, Wang W, Yuan D, Bing P, Zhou L, Tian G. Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations. Front Genet 2020; 11:147. [PMID: 32180799 PMCID: PMC7059766 DOI: 10.3389/fgene.2020.00147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/07/2020] [Indexed: 02/03/2023] Open
Abstract
Human blood contains cell-free DNA (cfDNA), with circulating tumor-derived DNAs (ctDNAs) widely used in cancer diagnosis and treatment. However, it is still difficult to efficiently and accurately identify and distinguish specific ctDNAs from normal cfDNA in cancer patient blood samples. In this study, ctDNA fragment length distribution analysis showed that ctDNA fragments are frequently shorter than the normal cfDNAs, which is consistent with previous findings. Interestingly, the ctDNA fragment length was found to be partially associated with the mutant allele frequency, with a low mutant allele frequency (< ~0.6%) associated with a longer ctDNA fragment length when compared to normal cfDNAs. The findings of this study contribute to improving the detection of low-frequency tumor mutations.
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Affiliation(s)
- Xiaojun Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Jidong Lang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Shijun Li
- Department of Pathology, Chifeng Municipal Hospital, Chifeng, China
| | - Yuehua Wang
- Department of Pathology, Chifeng Municipal Hospital, Chifeng, China
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Weitao Wang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Yingmin Han
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Cuixiao Qi
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Lei Song
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Shuangshuang Yang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Kaixin Zhang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Guoliang Zang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Hong Pei
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Qingqing Lu
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Yonggang Peng
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Shuxue Xi
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Weiwei Wang
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Dawei Yuan
- Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Pingping Bing
- Academics Working Station, Changsha Medical University, Changsha, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Geng Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, China.,Bioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, China
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40
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Oliveira KC, Ramos IB, Silva JM, Barra WF, Riggins GJ, Palande V, Pinho CT, Frenkel-Morgenstern M, Santos SE, Assumpcao PP, Burbano RR, Calcagno DQ. Current Perspectives on Circulating Tumor DNA, Precision Medicine, and Personalized Clinical Management of Cancer. Mol Cancer Res 2020; 18:517-528. [DOI: 10.1158/1541-7786.mcr-19-0768] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/13/2019] [Accepted: 01/23/2020] [Indexed: 11/16/2022]
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41
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Circulating cell-free DNA: Translating prostate cancer genomics into clinical care. Mol Aspects Med 2020; 72:100837. [PMID: 31954523 DOI: 10.1016/j.mam.2019.100837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/12/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
Abstract
Only in the past decade tremendous advances have been made in understanding prostate cancer genomics and consequently in applying new treatment strategies. As options regarding treatments are increasing so are the challenges in selecting the right treatment option for each patient and not the least, understanding the optimal time-point and sequence of applying available treatments. Critically, without reliable methods that enable sequential monitoring of evolving genotypes in individual patients, we will never reach effective personalised driven treatment approaches. This review focuses on the clinical implications of prostate cancer genomics and the potential of cfDNA in facilitating treatment management.
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42
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Said R, Guibert N, Oxnard GR, Tsimberidou AM. Circulating tumor DNA analysis in the era of precision oncology. Oncotarget 2020; 11:188-211. [PMID: 32010431 PMCID: PMC6968778 DOI: 10.18632/oncotarget.27418] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal genomic heterogeneity of various tumor types and advances in technology have stimulated the development of circulating tumor DNA (ctDNA) genotyping. ctDNA was developed as a non-invasive, cost-effective alternative to tumor biopsy when such biopsy is associated with significant risk, when tumor tissue is insufficient or inaccessible, and/or when repeated assessment of tumor molecular abnormalities is needed to optimize treatment. The role of ctDNA is now well established in the clinical decision in certain alterations and tumors, such as the epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer and the v-Ki-ras2 kirsten rat sarcoma viral oncogene homolog (KRAS) mutation in colorectal cancer. The role of ctDNA analysis in other tumor types remains to be validated. Evolving data indicate the association of ctDNA level with tumor burden, and the usefulness of ctDNA analysis in assessing minimal residual disease, in understanding mechanisms of resistance to treatment, and in dynamically guiding therapy. ctDNA analysis is increasingly used to select therapy. Carefully designed clinical trials that use ctDNA analysis will increase the rate of patients who receive targeted therapy, will elucidate our understanding of evolution of tumor biology and will accelerate drug development and implementation of precision medicine. In this article we provide a critical overview of clinical trials and evolving data of ctDNA analysis in specific tumors and across tumor types.
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Affiliation(s)
- Rabih Said
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Oncology, St. George Hospital University Medical Center, University of Balamand, Beirut, Lebanon
- Co-authorship
| | - Nicolas Guibert
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Thoracic Oncology, Toulouse University Hospital, Toulouse, France
- Co-authorship
| | - Geoffrey R. Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Apostolia M. Tsimberidou
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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43
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Contreras AL, Andal JJL, Lo RM, Ang DC. Pre-analytics, Current Testing Technologies, and Limitations of Testing. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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44
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Iwama E, Sakai K, Hidaka N, Inoue K, Fujii A, Nakagaki N, Ota K, Toyozawa R, Azuma K, Nakatomi K, Harada T, Hisasue J, Sakata S, Shimose T, Kishimoto J, Nakanishi Y, Nishio K, Okamoto I. Longitudinal monitoring of somatic genetic alterations in circulating cell‐free DNA during treatment with epidermal growth factor receptor–tyrosine kinase inhibitors. Cancer 2020; 126:219-227. [DOI: 10.1002/cncr.32481] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/30/2019] [Indexed: 08/30/2023]
Affiliation(s)
- Eiji Iwama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Kazuko Sakai
- Department of Genome Biology Kindai University Faculty of Medicine Osaka‐Sayama Japan
| | - Noriko Hidaka
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Koji Inoue
- Department of Respiratory Medicine Kitakyushu Municipal Medical Center Kita‐Kyushu Japan
| | - Akiko Fujii
- Department of Respiratory Medicine Koga Hospital 21 Kurume Japan
| | - Noriaki Nakagaki
- Department of Respiratory Medicine Steel Memorial Yawata Hospital Kita‐Kyushu Japan
| | - Keiichi Ota
- Department of Respiratory Medicine National Hospital Organization Fukuoka‐higashi Medical Center Fukuoka‐Koga Japan
| | - Ryo Toyozawa
- Department of Thoracic Oncology National Kyushu Cancer Center Fukuoka Japan
| | - Koichi Azuma
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine Kurume University School of Medicine Kurume Japan
| | - Keita Nakatomi
- Department of Respiratory Medicine Kyushu Chuo Hospital Fukuoka Japan
| | - Taishi Harada
- Department of Respiratory Medicine Japan Community Healthcare Organization Kyushu Hospital Kita‐Kyushu Japan
| | - Junko Hisasue
- Department of Respiratory Medicine Hara Sanshin Hospital Fukuoka Japan
| | - Shinya Sakata
- Department of Respiratory Medicine, Faculty of Life Sciences Kumamoto University Kumamoto Japan
| | | | - Junji Kishimoto
- Department of Research and Development of Next Generation Medicine Kyushu University Fukuoka Japan
| | - Yoichi Nakanishi
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Kazuto Nishio
- Department of Genome Biology Kindai University Faculty of Medicine Osaka‐Sayama Japan
| | - Isamu Okamoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
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45
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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46
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Bos MK, Angus L, Nasserinejad K, Jager A, Jansen MPHM, Martens JWM, Sleijfer S. Whole exome sequencing of cell-free DNA - A systematic review and Bayesian individual patient data meta-analysis. Cancer Treat Rev 2019; 83:101951. [PMID: 31874446 DOI: 10.1016/j.ctrv.2019.101951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/21/2022]
Abstract
Molecular profiling of tumor derived cell free DNA (cfDNA) is gaining ground as a prognostic and predictive biomarker. However to what extent cfDNA reflects the full metastatic landscape as currently determined by tumor tissue analysis remains controversial. Though technically challenging, whole exome sequencing (WES) of cfDNA enables thorough evaluation of somatic alterations. Here, we review the feasibility of WES of cfDNA and determine the sensitivity of WES-detected single nucleotide variants (SNVs) in cfDNA on individual patient data level using paired tumor tissue as reference (sharedSNVsAlltissueSNVs×100%). The pooled sensitivity was 50% (95% credible interval (CI): 29-72%). The tissue mutant allele frequency (MAF) of variants exclusively identified in tissue was significantly lower (12.5%, range: 0.5-18%) than the tissue MAF of variants identified in both tissue and cfDNA (23.9%, range: 17-38%), p = 0.004. The overall agreement (sharedSNVsAllSNVs×100%)between SNVs in cfDNA and tumor tissue was 31% (95% CI: 15-49%). The number of detected SNVs was positively correlated with circulating tumor DNA (ctDNA) fraction (p = 0.016). A sub analysis of samples with ctDNA fractions ≥ 25% improved the sensitivity to 69% (95% CI: 46-89%) and agreement to 46% (95% CI: 36-59%), suggesting that WES is mainly feasible for patients with high ctDNA fractions. Pre- and post-analytical procedures were highly variable between studies rendering comparisons problematic. In conclusion, various aspects of WES of cfDNA are largely in its investigative phase, standardization of methodologies is highly needed to bring this promising technique to its clinical potential.
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Affiliation(s)
- Manouk K Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Kazem Nasserinejad
- HOVON Data Center, Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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47
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Kyrochristos ID, Ziogas DE, Goussia A, Glantzounis GK, Roukos DH. Bulk and Single-Cell Next-Generation Sequencing: Individualizing Treatment for Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11111809. [PMID: 31752125 PMCID: PMC6895993 DOI: 10.3390/cancers11111809] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
The increasing incidence combined with constant rates of early diagnosis and mortality of colorectal cancer (CRC) over the past decade worldwide, as well as minor overall survival improvements in the industrialized world, suggest the need to shift from conventional research and clinical practice to the innovative development of screening, predictive and therapeutic tools. Explosive integration of next-generation sequencing (NGS) systems into basic, translational and, more recently, basket trials is transforming biomedical and cancer research, aiming for substantial clinical implementation as well. Shifting from inter-patient tumor variability to the precise characterization of intra-tumor genetic, genomic and transcriptional heterogeneity (ITH) via multi-regional bulk tissue NGS and emerging single-cell transcriptomics, coupled with NGS of circulating cell-free DNA (cfDNA), unravels novel strategies for therapeutic response prediction and drug development. Remarkably, underway and future genomic/transcriptomic studies and trials exploring spatiotemporal clonal evolution represent most rational expectations to discover novel prognostic, predictive and therapeutic tools. This review describes latest advancements and future perspectives of integrated sequencing systems for genome and transcriptome exploration to overcome unmet research and clinical challenges towards Precision Oncology.
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Affiliation(s)
- Ioannis D. Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, Ioannina University Hospital, 45500 Ioannina, Greece;
| | - Demosthenes E. Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, ‘G. Hatzikosta’ General Hospital, 45001 Ioannina, Greece
| | - Anna Goussia
- Department of Pathology, Ioannina University Hospital, 45500 Ioannina, Greece;
| | | | - Dimitrios H. Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, Ioannina University Hospital, 45500 Ioannina, Greece;
- Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece
- Correspondence: ; Tel.: +302651005572
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Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
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Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
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49
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Dekaliuk M, Qiu X, Troalen F, Busson P, Hildebrandt N. Discrimination of the V600E Mutation in BRAF by Rolling Circle Amplification and Förster Resonance Energy Transfer. ACS Sens 2019; 4:2786-2793. [PMID: 31577130 DOI: 10.1021/acssensors.9b01420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantification of very low concentrations of circulating tumor DNA (ctDNA) biomarkers from liquid biopsies has become an important requirement for clinical diagnostics and personalized medicine. In particular, the simultaneous detection of wild-type (WT) dsDNA and their cancer-related counterparts presenting single-point mutations with simple, sensitive, specific, and reproducible technologies is paramount for ctDNA assays in clinical practice. Here, we present the development and evaluation of an amplified dsDNA assay based on a combination of isothermal rolling circle amplification (RCA) and time-gated Förster resonance energy transfer (TG-FRET) between a Tb donor and two dye (Cy3.5 and Cy5.5) acceptors. The RCA-FRET assay is free of washing and separation steps and can quantify both WT and mutated (MT) (V600E) dsDNA in the BRAF gene from a single sample in the 75 fM to 4.5 pM (4.5 × 105 to 2.7 × 107 copies) concentration range. This assay includes all steps from denaturation of the dsDNA targets to the final duplexed quantification of WT and MT targets. High assay performance at different dsDNA sequence lengths and high target specificity even in the presence of a large excess of nonspecific cell-free DNA from human plasma samples demonstrated the applicability to clinical samples. The RCA-FRET single-point mutation sensor has the potential to become an important complementary technique for analyzing liquid biopsies in advanced cancer diagnostics.
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Affiliation(s)
- Mariia Dekaliuk
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Department of Neurochemistry, O. V. Palladin Institute of Biochemistry, Kyiv, 01030, Ukraine
| | - Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Frédéric Troalen
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
| | - Pierre Busson
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont Saint-Aignan, France
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50
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Mizuno K, Akamatsu S, Sumiyoshi T, Wong JH, Fujita M, Maejima K, Nakano K, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Inoue T, Ogawa O, Nakagawa H, Fujimoto A. eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA. Sci Rep 2019; 9:15017. [PMID: 31641155 PMCID: PMC6805874 DOI: 10.1038/s41598-019-51459-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/28/2019] [Indexed: 01/06/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) testing plays an increasingly important role in precision medicine for cancer. However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, complicating ctDNA detection and analysis. To identify low-frequency variants, we developed a program, eVIDENCE, which is a workflow for filtering candidate variants detected by using the ThruPLEX tag-seq (Takara Bio), a commercially-available molecular barcoding kit. We analyzed 27 cfDNA samples from hepatocellular carcinoma patients. Sequencing libraries were constructed and hybridized to our custom panel targeting about 80 genes. An initial variant calling identified 36,500 single nucleotide variants (SNVs) and 9,300 insertions and deletions (indels) across the 27 samples, but the number was much greater than expected when compared with previous cancer genome studies. eVIDENCE was applied to the candidate variants and finally 70 SNVs and 7 indels remained. Of the 77 variants, 49 (63.6%) showed VAF of < 1% (0.20–0.98%). Twenty-five variants were selected in an unbiased manner and all were successfully validated, suggesting that eVIDENCE can identify variants with VAF of ≥ 0.2%. Additionally, this study is the first to detect hepatitis B virus integration sites and genomic rearrangements in the TERT region from cfDNA of HCC patients. We consider that our method can be applied in the examination of cfDNA from other types of malignancies using specific custom gene panels and will contribute to comprehensive ctDNA analysis.
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Affiliation(s)
- Kei Mizuno
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shusuke Akamatsu
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Sumiyoshi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jing Hao Wong
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuaki Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takahiro Inoue
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. .,Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan.
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