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Krell M, Llera B, Brown ZJ. Circulating Tumor DNA and Management of Colorectal Cancer. Cancers (Basel) 2023; 16:21. [PMID: 38201448 PMCID: PMC10778183 DOI: 10.3390/cancers16010021] [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: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Although the incidence of colorectal cancer (CRC) has decreased as a result of increased screening and awareness, it still remains a major cause of cancer-related death. Additionally, early detection of CRC recurrence by conventional means such as CT, endoscopy, and CEA has not translated into an improvement in survival. Liquid biopsies, such as the detection circulating tumor DNA (ctDNA), have been investigated as a biomarker for patients with CRC in terms of prognosis and recurrence, as well as their use to guide therapy. In this manuscript, we provide an overview of ctDNA as well as its utility in providing prognostic information, using it to guide therapy, and monitoring for recurrence in patients with CRC. In addition, we discuss the influence the site of disease may have on the ability to detect ctDNA in patients with metastatic CRC.
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Affiliation(s)
| | | | - Zachary J. Brown
- Department of Surgery, Division of Surgical Oncology, NYU Langone Health, NYU Grossman Long Island School of Medicine, Mineola, NY 11501, USA; (M.K.); (B.L.)
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2
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Faaborg L, Andersen RF, Wen SW, Thomsen CB, Raunkilde L, Hansen TF, Jensen LH, Steffensen KD, Jakobsen A. Prognostic impact of early ctDNA dynamics during chemotherapy of metastatic cancer. Future Oncol 2023; 19:2361-2367. [PMID: 37965794 DOI: 10.2217/fon-2023-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Aim: Clinical utility of the dynamics of ctDNA is sparse. This study aimed at evaluating the prognostic impact of early ctDNA dynamics in patients with metastatic cancer treated with chemotherapy. Materials & methods: The ctDNA dynamics were evaluated in 595 patients with metastatic cancer using droplet digital PCR. Results: Patients with an increase in ctDNA after one treatment cycle (n = 73; 12.2%) had an overall survival of 5.6 months compared with 8.6 months in patients with stable or decreasing ctDNA (n = 328; 55.1%) and 21.0 months in patients with undetectable ctDNA (p < 0.001; hazard ratio: 0.47; 95% CI: 0.41-0.53). Conclusion: Early ctDNA dynamics hold important prognostic information and have great implications for evaluation with the perspective of a more individualized treatment strategy.
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Affiliation(s)
- Louise Faaborg
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Rikke Fredslund Andersen
- Department of Biochemistry & Immunology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Sara Wc Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Caroline B Thomsen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Louise Raunkilde
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Lars Henrik Jensen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Karina Dahl Steffensen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
- Center for Shared Decision Making, Lillebælt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Anders Jakobsen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
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3
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Hai L, Li L, Liu Z, Tong Z, Sun Y. Whole-genome circulating tumor DNA methylation landscape reveals sensitive biomarkers of breast cancer. MedComm (Beijing) 2022; 3:e134. [PMID: 35756163 PMCID: PMC9205580 DOI: 10.1002/mco2.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023] Open
Abstract
The changes in circulating tumor DNA (ctDNA) methylation are believed to be early events in breast cancer initiation, which makes them suitable as promising biomarkers for early diagnosis. However, applying ctDNA in breast cancer early diagnosis remains highly challenging due to the contamination of background DNA from blood and low DNA methylation signals. Here, we report an improved way to extract ctDNA, reduce background contamination, and build a whole-genome bisulfite sequencing (WGBS) library from different stages of breast cancer. We first compared the DNA methylation data of 74 breast cancer patients with those of seven normal controls to screen candidate methylation CpG site biomarkers for breast cancer diagnosis. The obtained 26 candidate ctDNA methylation biomarkers produced high accuracy in breast cancer patients (area under the curve [AUC] = 0.889; sensitivity: 100%; specificity: 75%). Furthermore, we revealed potential ctDNA methylated CpG sites for detecting early-stage breast cancer (AUC = 0.783; sensitivity: 93.44%; specificity: 50%). In addition, different subtypes of breast cancer could be well distinguished by the ctDNA methylome, which was obtained through our improved ctDNA-WGBS method. Overall, we identified high specificity and sensitivity breast cancer-specific methylation CpG site biomarkers, and they will be expected to have the potential to be translated to clinical practice.
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Affiliation(s)
- Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Lingyu Li
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
| | - Zhongsheng Tong
- Department of Breast OncologyTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
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4
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Callesen LB, Hamfjord J, Boysen AK, Pallisgaard N, Guren TK, Kure EH, Spindler KLG. Circulating tumour DNA and its clinical utility in predicting treatment response or survival in patients with metastatic colorectal cancer: a systematic review and meta-analysis. Br J Cancer 2022; 127:500-513. [PMID: 35440666 PMCID: PMC9345951 DOI: 10.1038/s41416-022-01816-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We investigate the current knowledge on circulating tumour DNA (ctDNA) and its clinical utility in predicting outcomes in patients with metastatic colorectal cancer (mCRC). METHODS PubMed, Embase, Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Trials were searched. Last search 16/12/2020. We included studies on patients with mCRC reporting the predictive or prognostic value of ctDNA. We performed separate random-effects meta-analyses to investigate if baseline ctDNA and early changes in ctDNA levels during treatment were associated with survival. The risk of bias was assessed according to the Quality in Prognosis Studies tool. RESULTS Seventy-one studies were included with 6930 patients. Twenty-four studies were included in meta-analyses. High baseline ctDNA level was associated with short progression-free survival (PFS) (HR = 2.2; 95% CI 1.8-2.8; n = 509) and overall survival (OS) (HR = 2.4; 95% CI 1.9-3.1; n = 1336). A small or no early decrease in ctDNA levels during treatment was associated with short PFS (HR = 3.0; 95% CI 2.2-4.2; n = 479) and OS (HR = 2.8; 95% CI 2.1-3.9; n = 583). Results on clonal evolution and lead-time were inconsistent. A majority of included studies (n = 50/71) had high risk of bias in at least one domain. CONCLUSIONS Plasma ctDNA is a strong prognostic biomarker in mCRC. However, true clinical utility is lacking.
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Affiliation(s)
- Louise B Callesen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Julian Hamfjord
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anders K Boysen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Pallisgaard
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Tormod K Guren
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Elin H Kure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway, Campus Bø, Bø, Norway
| | - Karen-Lise G Spindler
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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5
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Kasi PM, Chakrabarti S, Sawyer S, Krainock M, Poklepovic A, Ansstas G, Maninder M, Malhotra M, Ensor J, Gao L, Eroglu Z, Ellers S, Billings P, Rodriguez A, Aleshin A. BESPOKE IO protocol: a multicentre, prospective observational study evaluating the utility of ctDNA in guiding immunotherapy in patients with advanced solid tumours. BMJ Open 2022; 12:e060342. [PMID: 35636789 PMCID: PMC9152946 DOI: 10.1136/bmjopen-2021-060342] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Immunotherapy (IO) has transformed the treatment paradigm for a wide variety of solid tumours. However, assessment of response can be challenging with conventional radiological imaging (eg, iRECIST), which do not precisely capture the unique response patterns of tumours treated with IO. Emerging data suggest that circulating tumour DNA (ctDNA) can aid in response assessment in patients with solid tumours receiving IO. The short half-life of ctDNA puts it in a unique position for early treatment response monitoring. The BESPOKE IO study is designed to investigate the clinical utility of serial ctDNA testing to assess treatment response using a tumour-informed, bespoke ctDNA assay (Signatera) and to determine its impact on clinical decision-making with respect to continuation/discontinuation, or escalation/de-escalation of immunotherapy in patients with advanced solid tumours. METHODS AND ANALYSIS The BESPOKE IO is a multicentre, prospective, observational study with a goal to enroll over 1500 patients with solid tumours receiving IO in up to 100 US sites. Patients will be followed for up to 2 years with serial ctDNA analysis, timed with every other treatment cycle. The primary endpoint is to determine the percentage of patients who will have their treatment regimen changed as guided by post-treatment bespoke ctDNA results along with standard response assessment tools. The major secondary endpoints include progression-free survival, overall survival and overall response rate based on the ctDNA dynamics. ETHICS AND DISSEMINATION The BESPOKE IO study was approved by the WCG Institutional Review Board (Natera-20-043-NCP BESPOKE Study of ctDNA Guided Immunotherapy (BESPOKE IO)) on 22 February 2021. Data protection and privacy regulations will be strictly observed in the capturing, forwarding, processing and storing patients' data. Natera will approve the publication of any study results in accordance with the site-specific contract. TRIAL REGISTRATION NUMBER NCT04761783.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ling Gao
- VA Long Beach Healthcare, Long Beach, California, USA
- University of California Irvine, Irvine, California, USA
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6
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Faaborg L, Andersen RF, Waldstrøm M, Henriksen JR, Adimi P, Jakobsen A, Steffensen KD. Prognostic Impact of Circulating Methylated Homeobox A9 DNA in Patients Undergoing Treatment for Recurrent Ovarian Cancer. Cancers (Basel) 2022; 14:1766. [PMID: 35406538 PMCID: PMC8997085 DOI: 10.3390/cancers14071766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/23/2023] Open
Abstract
Methylated Homeobox A9 circulating tumor DNA (meth-HOXA9) has been suggested as a blood-based biomarker in epithelial ovarian cancer (EOC), although its prognostic significance remains unproven. The aim of the present study was to investigate the prognostic impact of meth-HOXA9 in patients with recurrent EOC. DNA was purified from 4 mL plasma and, following bilsulfite conversion, meth-HOXA9 was analyzed using a methylation-specific droplet digital PCR. Detection of meth-HOXA9 was reported as a percentage of total DNA and as a binary variable (detectable and undetectable). Meth-HOXA9 status and its dynamics during palliative treatment were correlated with overall survival (OS) as the primary endpoint. At baseline, meth-HOXA9 was detected in 65.9% (83/126) of the patients. The median OS was 8.9 and 17.9 months in patients with detectable and undetectable meth-HOXA9 at baseline (hazard ratio: 2.04, p = 0.002), which remained significant in the multivariate analysis. Median OS in patients with an increase in meth-HOXA9 after one treatment cycle was 5.3 months compared to 33 months in patients with undetectable meth-HOXA9 (p < 0.001). Meth-HOXA9 was significantly related to poor survival and may serve as a prognostic marker in patients with recurrent EOC. The longitudinal monitoring of meth-HOXA9 is clinically feasible with the perspective of aiding clinical decision making.
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Affiliation(s)
- Louise Faaborg
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
| | - Rikke Fredslund Andersen
- Department of Clinical Biochemistry and Immunology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark;
| | - Marianne Waldstrøm
- Department of Pathology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark;
| | - Jon Røikjær Henriksen
- Department of Oncology, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark;
| | - Parvin Adimi
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
| | - Anders Jakobsen
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
| | - Karina Dahl Steffensen
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
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7
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Brenner Thomsen C, Dandanell Juul A, Lefèvre AC, Glismand Truelsen C, Dizdarevic E, Ryssel H, Mathilde Kjaer I, Lycke Wind K, Callesen LB, Faaborg Larsen L, Støchkel Frank M, Fredslund Andersen R, Garm Spindler KL, Jakobsen A. Reporting on circulating tumor DNA monitoring in metastatic cancer-From clinical validity to clinical utility. Cancer 2022; 128:2052-2057. [PMID: 35302663 PMCID: PMC9543969 DOI: 10.1002/cncr.34168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Caroline Brenner Thomsen
- Danish Colorectal Cancer Center South, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark.,Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | | | - Anna Cecilie Lefèvre
- Experimental Clinical Oncology, Department of Oncology, Arhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Glismand Truelsen
- Experimental Clinical Oncology, Department of Oncology, Arhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Edina Dizdarevic
- Danish Colorectal Cancer Center South, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark.,Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Heidi Ryssel
- Department of Clinical Physiology, PET and Nuclear Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Ina Mathilde Kjaer
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark.,Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Karen Lycke Wind
- Experimental Clinical Oncology, Department of Oncology, Arhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Louise Bach Callesen
- Experimental Clinical Oncology, Department of Oncology, Arhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Louise Faaborg Larsen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Malene Støchkel Frank
- Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Fredslund Andersen
- Danish Colorectal Cancer Center South, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Karen-Lise Garm Spindler
- Experimental Clinical Oncology, Department of Oncology, Arhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anders Jakobsen
- Danish Colorectal Cancer Center South, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark.,Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
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8
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Shi M, Yuan H, Ji J, Zhang S, Li Q, Chen Y, Gong X, Zhu Z, Zhang J. Mutational landscape of circulating tumor DNA identifies distinct molecular features associated with therapeutic response in patients with metastatic colorectal cancer. Ther Adv Med Oncol 2022; 14:17588359211070643. [PMID: 35096147 PMCID: PMC8793119 DOI: 10.1177/17588359211070643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
Background: We investigated the mutational landscape of circulating tumor DNA (ctDNA) in predicting tumor response to first-line treatment in patients with metastatic colorectal cancer (mCRC). Methods: We included 41 patients with initially unresectable mCRC, treated with 5-fluorouracil/leucovorin/oxaliplatin (FOLFOX)/5-fluorouracil/leucovorin/irinotecan (FOLFIRI) with/without bevacizumab (Bev)/cetuximab (Cet). Blood samples were prospectively collected at two timepoints: at baseline and after four cycles of first-line treatment. Mutational status of 1086 genes were studied in ctDNA by targeted next-generation sequencing (NGS). Molecular mutational burden (MMB) was defined as mean mutation frequency among obtained mutations for each gene. To evaluate the association between molecular characteristics of cfDNA and therapeutic response better, we divided these patients into MMB-high and MMB-low group according to the median value of MMB (0.3). Results: Among the 41 enrolled patients, alterations of six genes ( TRIM24, SPEN, RNF43, PRKAR1A, KRAS, and KDM5 C) were found at baseline. Baseline MMB of six genes was significantly lower in partial response (PR)/stable disease (SD) patients than progression disease (PD) patients ( p = 0.0012). Further analysis demonstrated that genomic profiling of ctDNA from pretreatment blood samples was significantly different between PR/SD (non-PD) group and PD group. By comparing the baseline levels of KRAS MMB in the two subgroups, we found that PD cases were all MMB-high, whereas non-PD cases were mainly in MMB-low subgroup. Furthermore, patients with low-KRAS MMB had superior response rate, significantly longer progression-free survival (PFS) and longer overall survival (OS) than high-KRAS MMB group. Conclusions: This prospective and serial genomic profiling study revealed the utility of ctDNA in predicting clinical outcomes in mCRC patients under first-line treatment. Levels of KRAS MMB might aid in monitoring therapeutic efficacy in mCRC patients at pretreatment/after four cycles of first-line treatment.
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Affiliation(s)
- Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Yuan
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ji
- Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shouwei Zhang
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Qingyuan Li
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Yawei Chen
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Xiaoli Gong
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Zhenggang Zhu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, ChinaDepartment of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Oncology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
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9
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Angeles AK, Christopoulos P, Yuan Z, Bauer S, Janke F, Ogrodnik SJ, Reck M, Schlesner M, Meister M, Schneider MA, Dietz S, Stenzinger A, Thomas M, Sültmann H. Early identification of disease progression in ALK-rearranged lung cancer using circulating tumor DNA analysis. NPJ Precis Oncol 2021; 5:100. [PMID: 34876698 PMCID: PMC8651695 DOI: 10.1038/s41698-021-00239-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022] Open
Abstract
Targeted kinase inhibitors improve the prognosis of lung cancer patients with ALK alterations (ALK+). However, due to the emergence of acquired resistance and varied clinical trajectories, early detection of disease progression is warranted to guide patient management and therapy decisions. We utilized 343 longitudinal plasma DNA samples from 43 ALK+ NSCLC patients receiving ALK-directed therapies to determine molecular progression based on matched panel-based targeted next-generation sequencing (tNGS), and shallow whole-genome sequencing (sWGS). ALK-related alterations were detected in 22 out of 43 (51%) patients. Among 343 longitudinal plasma samples analyzed, 174 (51%) were ctDNA-positive. ALK variant and fusion kinetics generally reflected the disease course. Evidence for early molecular progression was observed in 19 patients (44%). Detection of ctDNA at therapy baseline indicated shorter times to progression compared to cases without mutations at baseline. In patients who succumbed to the disease, ctDNA levels were highly elevated towards the end of life. Our results demonstrate the potential utility of these NGS assays in the clinical management of ALK+ NSCLC.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Petros Christopoulos
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Zhao Yuan
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Simon John Ogrodnik
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | - Matthias Schlesner
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Faculty for Applied Informatics, Augsburg University, Augsburg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Dietz
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- AstraZeneca GmbH, Wedel, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany.
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Clinical Applications of Minimal Residual Disease Assessments by Tumor-Informed and Tumor-Uninformed Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13184547. [PMID: 34572774 PMCID: PMC8471730 DOI: 10.3390/cancers13184547] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Circulating tumor DNA, or ctDNA, are fragments of tumor DNA that can be detected in the blood of patients with colorectal cancer. Measuring ctDNA levels in the blood has shown the potential to provide important information that can be helpful in the clinical care of patients with colorectal cancer. For example, in patients with colon cancer that has been removed by surgery, measuring ctDNA in the blood can predict the likelihood of cancer recurrence, while in those with metastatic colorectal cancer, measuring ctDNA can inform the clinician whether chemotherapy is effective at earlier timepoints than currently available tests. In this review, we discuss the results from ongoing studies describing the utility of ctDNA measurements across all stages of colorectal cancer. We also discuss the various clinical scenarios that ctDNA may have the most immediate impact in colorectal cancer management. Abstract Emerging data suggest that circulating tumor DNA (ctDNA) can detect colorectal cancer (CRC)-specific signals across both non-metastatic and metastatic settings. With the development of multiple platforms, including tumor-informed and tumor-agnostic ctDNA assays and demonstration of their provocative analytic performance to detect minimal residual disease, there are now ongoing, phase III randomized clinical trials to evaluate their role in the management paradigm of CRC. In this review, we highlight landmark studies that have formed the basis for ongoing studies on the clinically applicability of plasma ctDNA assays in resected, stage I–III CRC and metastatic CRC. We discuss clinical settings by which ctDNA may have the most immediate impact in routine clinical practice. These include the potential for ctDNA to (1) guide surveillance and intensification or de-intensification strategies of adjuvant therapy in resected, stage I–III CRC, (2) predict treatment response to neoadjuvant therapy in locally advanced rectal cancer inclusive of total neoadjuvant therapy (TNT), and (3) predict response to systemic and surgical therapies in metastatic disease. We end by considering clinical variables that can influence our ability to reliably interpret ctDNA dynamics in the clinic.
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Wang Y, Yang L, Bao H, Fan X, Xia F, Wan J, Shen L, Guan Y, Bao H, Wu X, Xu Y, Shao Y, Sun Y, Tong T, Li X, Xu Y, Cai S, Zhu J, Zhang Z. Utility of ctDNA in predicting response to neoadjuvant chemoradiotherapy and prognosis assessment in locally advanced rectal cancer: A prospective cohort study. PLoS Med 2021; 18:e1003741. [PMID: 34464382 PMCID: PMC8407540 DOI: 10.1371/journal.pmed.1003741] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND For locally advanced rectal cancer (LARC) patients who receive neoadjuvant chemoradiotherapy (nCRT), there are no reliable indicators to accurately predict pathological complete response (pCR) before surgery. For patients with clinical complete response (cCR), a "Watch and Wait" (W&W) approach can be adopted to improve quality of life. However, W&W approach may increase the recurrence risk in patients who are judged to be cCR but have minimal residual disease (MRD). Magnetic resonance imaging (MRI) is a major tool to evaluate response to nCRT; however, its ability to predict pCR needs to be improved. In this prospective cohort study, we explored the value of circulating tumor DNA (ctDNA) in combination with MRI in the prediction of pCR before surgery and investigated the utility of ctDNA in risk stratification and prognostic prediction for patients undergoing nCRT and total mesorectal excision (TME). METHODS AND FINDINGS We recruited 119 Chinese LARC patients (cT3-4/N0-2/M0; median age of 57; 85 males) who were treated with nCRT plus TME at Fudan University Shanghai Cancer Center (China) from February 7, 2016 to October 31, 2017. Plasma samples at baseline, during nCRT, and after surgery were collected. A total of 531 plasma samples were collected and subjected to deep targeted panel sequencing of 422 cancer-related genes. The association among ctDNA status, treatment response, and prognosis was analyzed. The performance of ctDNA alone, MRI alone, and combining ctDNA with MRI was evaluated for their ability to predict pCR/non-pCR. Ranging from complete tumor regression (pathological tumor regression grade 0; pTRG0) to poor regression (pTRG3), the ctDNA clearance rate during nCRT showed a significant decreasing trend (95.7%, 77.8%, 71.1%, and 66.7% in pTRG 0, 1, 2, and 3 groups, respectively, P = 0.008), while the detection rate of acquired mutations in ctDNA showed an increasing trend (3.8%, 8.3%, 19.2%, and 23.1% in pTRG 0, 1, 2, and 3 groups, respectively, P = 0.02). Univariable logistic regression showed that ctDNA clearance was associated with a low probability of non-pCR (odds ratio = 0.11, 95% confidence interval [95% CI] = 0.01 to 0.6, P = 0.04). A risk score predictive model, which incorporated both ctDNA (i.e., features of baseline ctDNA, ctDNA clearance, and acquired mutation status) and MRI tumor regression grade (mrTRG), was developed and demonstrated improved performance in predicting pCR/non-pCR (area under the curve [AUC] = 0.886, 95% CI = 0.810 to 0.962) compared with models derived from only ctDNA (AUC = 0.818, 95% CI = 0.725 to 0.912) or only mrTRG (AUC = 0.729, 95% CI = 0.641 to 0.816). The detection of potential colorectal cancer (CRC) driver genes in ctDNA after nCRT indicated a significantly worse recurrence-free survival (RFS) (hazard ratio [HR] = 9.29, 95% CI = 3.74 to 23.10, P < 0.001). Patients with detectable driver mutations and positive high-risk feature (HR_feature) after surgery had the highest recurrence risk (HR = 90.29, 95% CI = 17.01 to 479.26, P < 0.001). Limitations include relatively small sample size, lack of independent external validation, no serial ctDNA testing after surgery, and a relatively short follow-up period. CONCLUSIONS The model combining ctDNA and MRI improved the predictive performance compared with the models derived from individual information, and combining ctDNA with HR_feature can stratify patients with a high risk of recurrence. Therefore, ctDNA can supplement MRI to better predict nCRT response, and it could potentially help patient selection for nonoperative management and guide the treatment strategy for those with different recurrence risks.
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Affiliation(s)
- Yaqi Wang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Lifeng Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Hua Bao
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Xiaojun Fan
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Fan Xia
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Juefeng Wan
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Lijun Shen
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Yun Guan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Cyberknife Center, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Hairong Bao
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Yang Xu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yiqun Sun
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Tong Tong
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xinxiang Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ye Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Sanjun Cai
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ji Zhu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China
- * E-mail: (JZ); (ZZ)
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- * E-mail: (JZ); (ZZ)
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12
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Jia N, Chang L, Gao X, Shi X, Dou X, Guan M, Shao Y, Li N, Cheng Y, Ying H, Sun Z, Zhou Y, Zhao L, Zhou J, Bai C. Association of emergence of new mutations in circulating tumuor DNA during chemotherapy with clinical outcome in metastatic colorectal cancer. BMC Cancer 2021; 21:845. [PMID: 34294055 PMCID: PMC8296534 DOI: 10.1186/s12885-021-08309-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The understanding of molecular changes in mCRC during treatment could be used to personalise therapeutic strategies. The aim of our study was to explore the association of circulating tumour DNA (ctDNA) with clinical outcome in metastatic colorectal cancer (mCRC). METHODS Sequential patients with mCRC receiving standard first-line chemotherapy were included prospectively. Both plasma ctDNA and serum CEA were assessed in samples obtained before treatment and after 4 cycles of chemotherapy (C4). Computed tomography (CT) scans were carried out at baseline and post-C4 (8-10 weeks) and were assessed using Response Evaluation Criteria In Solid Tumours version 1.1 (RECIST v1.1). Target-capture deep sequencing with a panel covering 1021 genes was performed to detected somatic mutations in ctDNA. RESULTS A total of 20 patients were prospectively included and treated with either leucovorin, fluorouracil, and oxaliplatin (FOLFOX) (15/20) or leucovorin, fluorouracil, and irinotecan (FOLFIRI) (5/20). Median follow-up was 6.9 months (range 1.6-26.6). Somatic mutations for baseline ctDNA analysis were identified in 85% (17/20) of the patients. Mutation variations of ctDNA after chemotherapy were tested in 16/20 (80.0%) of the patients. In multivariate analyses, a high baseline molecular tumour burden index (mTBI) in ctDNA was associated with a higher risk of disease progression, as well as emergence of new mutations in ctDNA during chemotherapy. Patients with newly detected mutations had shorter progression-free survival (PFS) compared to those without (median 3.0 versus 7.3 months; hazard ratio (HR), 5.97; 95% confidence interval (CI), 0.70-50.69; P = 0.0003). Fold changes in mTBI from baseline to post-C4 were obtained in 80.0% (16/20) of the patients, which were also related to PFS. Patients with fold reduction in mTBI above 0.8-fold had longer PFS compared to those below (median 9.3 versus 4.1 months; HR, 4.51; 95% CI, 1.29-15.70; P = 0.0008). CONCLUSIONS Newly detected mutations in ctDNA during treatment might potentially be associated with clinical outcome in mCRC and may provide important clinical information.
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Affiliation(s)
- Ning Jia
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | | | - Xin Gao
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohua Shi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuelin Dou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Mei Guan
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yajuan Shao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Ningning Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yuejuan Cheng
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Hongyan Ying
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Zhao Sun
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yanping Zhou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Lin Zhao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Jianfeng Zhou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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Cervena K, Pardini B, Urbanova M, Vodenkova S, Eva P, Veskrnova V, Levy M, Buchler T, Mokrejs M, Naccarati A, Vodicka P, Vymetalkova V. Mutational landscape of plasma cell-free DNA identifies molecular features associated with therapeutic response in patients with colon cancer. A pilot study. Mutagenesis 2021; 36:358-368. [PMID: 34214148 DOI: 10.1093/mutage/geab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Cell-free DNA (cfDNA) has recently been used as a non-invasive diagnostic tool for detecting tumor-specific mutations. cfDNA may also be used for monitoring disease progression and treatment response, but so far researchers focused on one or few genes only. A genomic profile may provide better information on patient prognosis compared to single specific mutations. In this hypothesis-generating study, we profiled by whole exome sequencing serial plasma samples from 10 colon cancer (CC) patients collected before and after 5-fluorouracil-based therapy, and one year after diagnosis to determine alterations associated with treatment response. In parallel, genome profiling was also performed in patients' corresponding tumor tissue to ascertain the molecular landscape of resistant tumors. The mutation concordance between cfDNA and tumor tissue DNA was higher in more advanced tumor stages than in the early stages of the disease. In non-responders, a specific mutation profile was observed in tumor tissues (TPSD1 p.Ala92Thr, CPAMD8 p.Arg341Gln, OBP2A p.ArgTyr123CysHis). A pathogenic APC mutation (p.Ser1315Ter) was detected only in cfDNA of one poor responder one year after the diagnosis and after therapy termination. Another poor responder presented a likely pathogenic TP53 mutation (p.Arg110Pro) in cfDNA of all plasma samplings and in tumor tissue. In conclusion, cfDNA could be used for genetic characterization of CC patients and might be clinically useful for non-invasive therapy response monitoring.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Pazourkova Eva
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Department of Nephrology, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Czech Republic
| | - Veronika Veskrnova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, Thomayer University Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Martin Mokrejs
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Alessio Naccarati
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
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14
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Content of circulating tumor DNA depends on the tumor type and the dynamics of tumor size, but is not influenced significantly by physical exercise, time of the day or recent meal. Cancer Genet 2021; 256-257:165-178. [PMID: 34186498 DOI: 10.1016/j.cancergen.2021.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 01/20/2023]
Abstract
PURPOSE This study aimed to investigate factors, which influence the content of circulating tumor DNA (ctDNA). METHODS 398 serial plasma samples were collected within 1-7 consecutive days from patients with EGFR-mutated lung cancer (n = 13), RAS/RAF-mutated colorectal cancer (n = 54) and BRAF-mutated melanoma (n = 17), who presented with measurable tumor disease. The amount of ctDNA was determined by ddPCR. RESULTS Among 82 patients, who donated 2-6 serial plasma samples, 42 subjects were classified as ctDNA-positive; only 22% cases were mutation-positive across all consecutive tests, while 24/82 (29%) patients showed presence of mutated ctDNA in some but not all blood draws. Subjects with progressing tumors had higher probability of being detected ctDNA-positive as compared to patients, who responded to therapy or had stable disease (39/55 (71%) vs. 4/24 (17%); p = 0.0001). Our study failed to reveal the impact of the time of the day, recent meal or prior physical exercise on the results of ctDNA testing. CONCLUSIONS Presence of ctDNA in plasma is particularly characteristic for patients, who experience clinical progression of tumor disease. Consecutive plasma tests may occasionally provide discordant data; thus, the repetition of analysis may be advised in certain cases in order to ensure the validity of negative ctDNA result.
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15
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Zou D, Day R, Cocadiz JA, Parackal S, Mitchell W, Black MA, Lawrence B, Fitzgerald S, Print C, Jackson C, Guilford P. Circulating tumor DNA is a sensitive marker for routine monitoring of treatment response in advanced colorectal cancer. Carcinogenesis 2021; 41:1507-1517. [PMID: 32955091 DOI: 10.1093/carcin/bgaa102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
Accurate assessment of chemotherapy response provides the means to terminate ineffective treatment, trial alternative drug regimens or schedules and reduce dose to minimize toxicity. Here, we have compared circulating tumor DNA (ctDNA) with carcinoembryonic antigen (CEA) for the cycle by cycle assessment of chemotherapy response in 30 patients with metastatic colorectal cancer. CtDNA (quantified using individualized digital droplet PCR (ddPCR) assays) and CEA levels were determined immediately prior to each chemotherapy cycle over time periods ranging from 42-548 days (average of 10 time points/patient). Twenty-nine/thirty (97%) patients had detectable ctDNA compared with 83% whose tumors were CEA-positive (>5 ng/ml) during the monitoring course. Over the course of treatment, 20 disease progression events were detected by computed tomography; ctDNA predicted significantly more of these events than CEA (16 (80%) versus 6 (30%), respectively; P-value = 0.004). When progression was detected by both ctDNA and CEA, the rise in ctDNA occurred significantly earlier than CEA (P-value = 0.046). Partial responses to chemotherapy were also detected more frequently by ctDNA, although this was not significant (P-value = 0.07). In addition, another 28 colorectal cancer patients who underwent potentially curative surgery and showed no evidence of residual disease were monitored with ctDNA for up to 2 years. Clinical relapse was observed in 6/28 (21%) patients. Four out of 6 of these patients showed a significant increase in ctDNA at or prior to relapse. Overall, ctDNA analyses were able to be performed in a clinically relevant timeline and were a more sensitive and responsive measure of tumor burden than CEA.
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Affiliation(s)
- Donghui Zou
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Robert Day
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Judy A Cocadiz
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Sarah Parackal
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Wilson Mitchell
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
| | - Ben Lawrence
- Discipline of Oncology, The University of Auckland, Auckland, New Zealand
| | - Sandra Fitzgerald
- Department of Molecular Medicine and Pathology, Faculty of Medicine, The University of Auckland, Auckland, New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology, Faculty of Medicine, The University of Auckland, Auckland, New Zealand
| | - Christopher Jackson
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Parry Guilford
- Department of Biochemistry, Cancer Genetics Laboratory, Te Aho Matatū, University of Otago, Dunedin, New Zealand
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16
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Jones RP, Pugh SA, Graham J, Primrose JN, Barriuso J. Circulating tumour DNA as a biomarker in resectable and irresectable stage IV colorectal cancer; a systematic review and meta-analysis. Eur J Cancer 2021; 144:368-381. [PMID: 33422803 DOI: 10.1016/j.ejca.2020.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/01/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND For patients with metastatic colorectal cancer, stratification for treatment (surgery or chemotherapy) is often based on crude clinicopathological characteristics like tumour size and number of lesions. Circulating tumour DNA (ctDNA) acts as a potential biomarker of disease trajectory and biology, allowing better stratification. This study aims to systematically review ctDNA in stage IV colorectal cancer to assess its potential role as a prospective biomarker to guide management decisions. METHODS A literature search was performed to identify studies where the measurement of ctDNA in stage IV colorectal cancer was correlated with a clinical outcome (radiological response, secondary resection rate, PFS, DFS or OS). RESULTS Twenty-eight studies were included, reporting on 2823 patients. Circulating tumour DNA was detectable in between 80% and 90% of patients prior to treatment. Meta-analysis identified a strong correlation between detectable ctDNA after treatment (surgery or chemotherapy) and overall survival (HR 2.2, 95% CI 1.79-2.69, p < 0.00001), as well as progression-free survival (HR 3.15, 95% CI 2.10-4.73, p < 0.00001). ctDNA consistently offered an early marker of long-term prognosis in irresectable disease, with changes after one cycle of systemic therapy demonstrating prognostic value. In resectable disease treated with curative intent, detection of ctDNA offered a lead time over radiological recurrence of 10 months. CONCLUSION Circulating tumour DNA is detectable in the majority of resectable and irresectable patients. The presence of ctDNA is clearly associated with shorter overall survival, with changes in ctDNA an early biomarker of adverse disease behaviour. Prospective trials are essential to test its clinical efficacy.
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Affiliation(s)
- Robert P Jones
- School of Cancer Studies, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Hepatobiliary Surgery, Liverpool University Teaching Hospitals NHS Foundation Trust, Liverpool, UK.
| | | | - Janet Graham
- Beatson West of Scotland Cancer Centre, Glasgow, UK; University of Glasgow, UK
| | | | - Jorge Barriuso
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
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Wojas-Krawczyk K, Kubiatowski T. Imperfect Predictors for Lung Cancer Immunotherapy-A Field for Further Research. Front Oncol 2020; 10:568174. [PMID: 33330041 PMCID: PMC7734866 DOI: 10.3389/fonc.2020.568174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
The armamentarium for lung cancer immunotherapy has been strengthened using two groups of monoclonal antibodies: 1) anti-PD-1 antibodies, including pembrolizumab and nivolumab, which block the programmed death 1 receptor on the lymphocyte surface, resulting in increasing activity of these cells, and 2) anti-PD-L1 antibodies, including atezolizumab, durvalumab, and avelumab, which block the ligand for the PD-1 molecule on tumor cells and on tumor-infiltrating immune cells. The effectiveness of both groups of antibodies has been proven in many clinical trials, which translates into positive immunotherapeutic registrations for cancer patients. Regarding the predictive factor, PD-L1 expression on cancer cells is the only biomarker validated in prospective clinical trials used for qualification to immunotherapy in advanced non-small cell lung cancer (NSCLC) patients. However, it is not an ideal one. Unfortunately, no clinical benefits could be noted in patients with high PD-L1 expression on tumor cells against the effectiveness of immunotherapy that may be observed in patients without PD-L1 expression. Furthermore, the mechanism of antitumor immune response is extremely complex, multistage, and depends on many factors. Cancer cells could be recognized by the immune system, provided tumor-specific antigen presentation, and these arise as a result of somatic mutations in tumor cells. Based on novel immunotherapy registration, high tumor mutation burden (TMB) has become an important predictive factor. The intensity of lymphocyte infiltration in tumor tissue may be another predictive factor. The effectiveness of anti-PD-L1 immunotherapy is observed in patients with high expression of genes associated with the effector function of T lymphocytes (i.e., their ability to produce IFN-gamma). This does not end the list of potential factors that become useful in qualification of cancer patients for immunotherapy. There remains a need to search for new and perfect predictive factors for immunotherapy.
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Affiliation(s)
- Kamila Wojas-Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, Lublin, Poland
| | - Tomasz Kubiatowski
- Department of Clinical Oncology, Saint John of Dukla Oncology Centre of the Lublin Region, Lublin, Poland
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18
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Lueong SS, Herbst A, Liffers ST, Bielefeld N, Horn PA, Tannapfel A, Reinacher-Schick A, Hinke A, Hegewisch-Becker S, Kolligs FT, Siveke JT. Serial Circulating Tumor DNA Mutational Status in Patients with KRAS-Mutant Metastatic Colorectal Cancer from the Phase 3 AIO KRK0207 Trial. Clin Chem 2020; 66:1510-1520. [PMID: 33257977 DOI: 10.1093/clinchem/hvaa223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND We assessed the usefulness of circulating tumor DNA (ctDNA) pre- or post-treatment initiation for outcome prediction and treatment monitoring in metastatic colorectal cancer (mCRC). METHODS Droplet digital PCR was used to measure absolute mutant V-Ki-ras2 Kirsten rat sarcoma viral oncogene ((mut)KRAS) ctDNA concentrations in 214 healthy controls (plasma and sera) and in 151 tissue-based mutKRAS positive patients with mCRC from the prospective multicenter phase 3 trial AIO KRK0207. Serial mutKRAS ctDNA was analyzed prior to and 2-3 weeks after first-line chemotherapy initiation with fluoropyrimidine, oxaliplatin, and bevacizumab in patients with mCRC and correlated with clinical parameters. RESULTS mut KRAS ctDNA was detected in 74.8% (113/151) of patients at baseline and in 59.6% (90/151) at follow-up. mutKRAS ctDNA at baseline and follow-up was associated with poor overall survival (OS) (hazard ratio [HR] =1.88, 95% confidence interval [CI] 1.20-2.95; HR = 2.15, 95% CI 1.47-3.15) and progression-free survival (PFS) (HR = 2.53, 95% CI 1.44-4.46; HR = 1.90, 95% CI 1.23-2.95), respectively. mutKRAS ctDNA clearance at follow-up conferred better disease control (P = 0.0075), better OS (log-rank P = 0.0018), and PFS (log-rank P = 0.0018). Measurable positive mutKRAS ctDNA at follow-up was the strongest and most significant independent prognostic factor on OS in multivariable analysis (HR = 2.31, 95% CI 1.40-3.25). CONCLUSIONS Serial analysis of circulating mutKRAS concentrations in mCRC has prognostic value. Post treatment mutKRAS concentrations 2 weeks after treatment initiation were associated with therapeutic response in multivariable analysis and may be an early response predictor in patients receiving first-line combination chemotherapy. CLINICALTRIALSGOV IDENTIFIER NCT00973609.
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Affiliation(s)
- Smiths S Lueong
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Andreas Herbst
- Institute of Laboratory Medicine, University of Munich, Munich, Germany.,German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Sven-Thorsten Liffers
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Nicola Bielefeld
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Peter A Horn
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | | | - Anke Reinacher-Schick
- Department of Hematology, Oncology and Palliative Care, St. Josef-Hospital, Ruhr-University Bochum
| | - Axel Hinke
- CCRC: Cancer Clinical Research Consulting, Düsseldorf, Germany
| | | | - Frank T Kolligs
- German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Department of Medicine, Division of- Gastroenterology, Hepatology & Infectiology, Helios Clinic Berlin-Buch, Berlin, Germany.,Department of Medicine II, University of Munich, Munich, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
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19
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Li J, Jiang W, Wei J, Zhang J, Cai L, Luo M, Wang Z, Sun W, Wang S, Wang C, Dai C, Liu J, Wang G, Wang J, Xu Q, Deng Y. Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors. J Transl Med 2020; 18:293. [PMID: 32738923 PMCID: PMC7395971 DOI: 10.1186/s12967-020-02449-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) offers a convenient way to monitor tumor progression and treatment response. Because tumor mutational profiles are highly variable from person to person, a fixed content panel may be insufficient to track treatment response in all patients. METHODS We design ctDNA fingerprint panels specific to individual patients which are based on whole exome sequencing and target to high frequency clonal population clusters in patients. We test the fingerprint panels in 313 patients who together have eight tumor types (colorectal, hepatocellular, gastric, breast, pancreatic, and esophageal carcinomas and lung cancer and cholangiocarcinoma) and exposed to multiple treatment methods (surgery, chemotherapy, radiotherapy, targeted-drug therapy, immunotherapy, and combinations of them). We also monitor drug-related mutations in the patients using a pre-designed panel with eight hotspot genes. RESULTS 291 (93.0%) designed fingerprint panels harbor less than ten previously known tumor genes. We detected 7475 ctDNA mutations in 238 (76%) patients and 6196 (96.0%) of the mutations are detected in only one test. Both the level of ctDNA content fraction (CCF) and fold change of CCF (between the definitive and proceeding tests) are highly correlated with clinical outcomes (p-values 1.36e-6 for level and 5.64e-10 for fold change, Kruskal-Wallis test). The CCFs of PD patients are an order of magnitude higher than the CCFs of SD and OR patients (median/mean 2.22%/8.96% for SD, 0.18/0.21% for PD, and 0.31/0.54% for OR; pairwise p-values 7.8e-6 for SD ~ PD, 2.7e-4 for OR ~ PD, and 7.0e-3 for SD ~ OR, Wilcoxon rank sum test). The fold change of CCF distinguishes the patient groups even better, which increases for PD, remains stable for SD, and decreases for OR patients (p-values 0.002, ~ 1, and 0.0001 respectively, Wilcoxon signed-rank test). Eleven drug-related mutations are identified from nine out of the 313 patients. CONCLUSIONS The ctDNA fingerprint method improves both specificity and sensitivity of monitoring treatment response across several tumor types. It can identify tumor relapse/recurrence potentially earlier than imaging-based diagnosis. When augmented with tumor hotspot genes, it can track acquired drug-related mutations in patients.
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Affiliation(s)
- Jiaping Li
- Department of Interventional Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangdong, China
| | - Wei Jiang
- Department of Radiation Oncology, Huanhu Hospital, Tianjin, China
| | - Jinwang Wei
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Jianwei Zhang
- Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, No. 26 Erheng Road, Tianhe District, Guangzhou, 510655, China
| | - Linbo Cai
- Department of Oncology, Guangdong 999 Brain Hospital, Guangdong, China
| | - Minjie Luo
- Department of Pediatric Neurosurgery, Zhujiang Hospital of Southern Medical University, Guangdong, China
| | - Zhan Wang
- Department of Medical Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Wending Sun
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | | | - Chen Wang
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Jun Liu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Guan Wang
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Jiping Wang
- Division of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Qiang Xu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China.
| | - Yanhong Deng
- Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, No. 26 Erheng Road, Tianhe District, Guangzhou, 510655, China.
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20
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Target-based genomic profiling of ctDNA from Chinese non-small cell lung cancer patients: a result of real-world data. J Cancer Res Clin Oncol 2020; 146:1867-1876. [PMID: 32221744 DOI: 10.1007/s00432-020-03192-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/20/2020] [Indexed: 01/01/2023]
Abstract
PURPOSE Approximately 30% of NSCLC patients cannot obtain tissue sample or sufficient tissue sample for molecular subtyping. Cell-free circulating tumor DNA (ctDNA) in plasma is a potential alternative specimen type to assess genomic variants in patients with non-small cell lung cancer (NSCLC). The purpose of this study was to identify the genomic alteration profile of ctDNA in real-world Chinese NSCLC patients. METHODS A total of 325 subjects with pathological diagnosis of NSCLC were enrolled. 10 ml Peripheral blood was collected in streck tube, and ctDNA NGS analysis was carried out using an Ampliseq-based 11-gene panel. RESULTS 295 out of 325 patients (90.8%) had detected ctDNA results. In 62.1% (183/295) of these cases, at least one genomic alterations was detected. Frequency altered genes were EGFR (27.8%), TP53 (22.7%), KRAS (21.36%), and PIK3CA (4.75%). EGFR mutation was associated with female, younger age (< 65 years), and adenocarcinoma. The most common mutations in EGFR were L858R (39.4%), exon19 deletions (31.73%), and T790M (18.3%); G13S was the most common alterations in KRAS. TP53 mutation was most occurred in exon7 and exon8. TP53 mutation was significantly more common in patients with history of radiochemotherapy/chemotherapy therapy, and T790M was mainly found in patients with TKIs treatments. Co-existence EGFR mutation with KRAS and different multiple gene co-mutation panels were detected. CONCLUSION In Chinese NSCLC patients, EGFR mutation was significantly associated with female, younger age (< 65 years), and adenocarcinoma. Genomic profiles of NSCLC were associated with the treatment history; TP53 mutation was significantly more frequent in the patients with history of radiochemotherapy/chemotherapy therapy. Various multiple genes co-mutation panels, especially EGFR and KRAS co-mutation, were observed in the ctDNA of Chinese NSCLC patients.
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21
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Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
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Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
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22
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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23
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Zhao Y, Li J, Li D, Wang Z, Zhao J, Wu X, Sun Q, Lin PP, Plum P, Damanakis A, Gebauer F, Zhou M, Zhang Z, Schlösser H, Jauch KW, Nelson PJ, Bruns CJ. Tumor biology and multidisciplinary strategies of oligometastasis in gastrointestinal cancers. Semin Cancer Biol 2019; 60:334-343. [PMID: 31445220 DOI: 10.1016/j.semcancer.2019.08.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/20/2019] [Indexed: 12/11/2022]
Abstract
More than 70% of gastrointestinal (GI) cancers are diagnosed with metastases, leading to poor prognosis. For some cancer patients with limited sites of metastatic tumors, the term oligometastatic disease (OMD) has been coined as opposed to systemic polymetastasis (PMD) disease. Stephan Paget first described an organ-specific pattern of metastasis in 1889, now known as the "seed and soil" theory where distinct cancer types are found to metastasize to different tumor-specific sites. Our understanding of the biology of tumor metastasis and specifically the molecular mechanisms driving their formation are still limited, in particular, as it relates to the genesis of oligometastasis. In the following review, we discuss recent advances in general understanding of this metastatic behavior including the role of specific signaling pathways, various molecular features and biomarkers, as well as the interaction of carcinoma cells with their tissue microenvironments (both primary and metastatic niches). The unique features that underlie OMD provide potential targets for localized therapy. As it relates to clinical practice, OMD is emerging as treatable with surgical resection and/or other local therapy options. Strategies currently being applied in the clinical management of OMD will be discussed including surgical, radiation-based therapy, ablation procedures, and the results of emerging clinical trials involving immunotherapy.
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Affiliation(s)
- Yue Zhao
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Department of General, Visceral und Vascular Surgery, Otto von Guericke University, Magdeburg, Germany.
| | - Jiahui Li
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Dai Li
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Department of Anethesiology, Changhai Hospital, Naval Medical University, Shanghai, PR China
| | - Zhefang Wang
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Jiangang Zhao
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Department of General, Visceral und Vascular Surgery, Ludwig-Maximilian-University (LMU), Munich, Germany
| | - Xiaolin Wu
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Qiye Sun
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | | | - Patrick Plum
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Alexander Damanakis
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Florian Gebauer
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Menglong Zhou
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hans Schlösser
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Center for Integrated Oncology (CIO) Achen, Bonn, Cologne and Düsseldorf, Cologne, Germany
| | - Karl-Walter Jauch
- Department of General, Visceral und Vascular Surgery, Ludwig-Maximilian-University (LMU), Munich, Germany
| | - Peter J Nelson
- Department of Internal Medicine IV, University Hospital of Munich, Ludwig-Maximilians-University Munich, Germany
| | - Christiane J Bruns
- Department of General, Visceral und Tumor Surgery, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany; Center for Integrated Oncology (CIO) Achen, Bonn, Cologne and Düsseldorf, Cologne, Germany.
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