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Li JH, Zhang DY, Zhu JM, Dong L. Clinical applications and perspectives of circulating tumor DNA in gastric cancer. Cancer Cell Int 2024; 24:13. [PMID: 38184573 PMCID: PMC10770949 DOI: 10.1186/s12935-024-03209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024] Open
Abstract
Gastric cancer remains a leading cause of cancer-related death worldwide, largely due to inadequate screening methods, late diagnosis, and limited treatment options. Liquid biopsy has emerged as a promising non-invasive approach for cancer screening and prognosis by detecting circulating tumor components like circulating tumor DNA (ctDNA) in the blood. Numerous gastric cancer-specific ctDNA biomarkers have now been identified. CtDNA analysis provides insight into genetic and epigenetic alterations in tumors, holding promise for predicting treatment response and prognosis in gastric cancer patients. This review summarizes current research on ctDNA biology and detection technologies, while highlighting clinical applications of ctDNA for gastric cancer diagnosis, prognosis, and guiding treatment decisions. Current challenges and future perspectives for ctDNA analysis are also discussed.
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Affiliation(s)
- Jing-Han Li
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dan-Ying Zhang
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ji-Min Zhu
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Ling Dong
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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2
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Harrold E, Corrigan L, Barry S, Lowery M. Targeting MET amplification in Gastro-oesophageal (GO) malignancies and overcoming MET inhibitor resistance: challenges and opportunities. Expert Rev Gastroenterol Hepatol 2022; 16:601-624. [PMID: 35757852 DOI: 10.1080/17474124.2022.2093185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION MET, the hepatocyte growth factor receptor is amplified in 8% of gastroesophageal (GO) malignancies and associated with poor prognosis. Therapeutic targeting of MET amplification and MET mutations has the potential to improve outcomes for patients with GO cancers (GOC). AREAS COVERED The efficacy of MET inhibition (METi) in preclinical studies has yet to translate into meaningful improvements in the treatment paradigm for unselected GOC. MET amplification has been proposed as a superior modality for patient selection; however even if confirmed, frequency and duration of response to METi are limited by rapid activation of primary and secondary resistance pathways. These observations illustrate the challenges inherent in the application of precision oncology predicated on the theory of oncogenic addiction. EXPERT OPINION A standardized definition of MET positivity is critical to enhance patient selection. Early successes targeting the METex14 skipping mutation demonstrate the potent therapeutic effects of METi in a clearly molecularly defined cohort. There is robust preclinical rationale and early-phase data supporting exploitation of immune system interaction with MET. Pragmatic investigation of rational therapeutic combinations based on molecular profiling of both primary and metastatic disease sites with sequential circulating tumor DNA analysis can inform successful clinical development of METi agents in GOC.
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Affiliation(s)
- Emily Harrold
- Medical Oncology Department, Mater Private Hospital Dublin, Leinster, Ireland.,Trinity St James Cancer Institute, Trinity College Dublin, Leinster, Ireland
| | - Lynda Corrigan
- Trinity St James Cancer Institute, Trinity College Dublin, Leinster, Ireland.,Medical Oncology Department, Tallaght/AMNCH Hospital Dublin, Leinster, Ireland
| | - Simon Barry
- Medical Oncology Department, St James University Hospital Dublin, Leinster, Ireland
| | - Maeve Lowery
- Trinity St James Cancer Institute, Trinity College Dublin, Leinster, Ireland.,Medical Oncology Department, St James University Hospital Dublin, Leinster, Ireland
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3
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Chivu-Economescu M, Necula L, Matei L, Dragu D, Bleotu C, Diaconu CC. Clinical Applications of Liquid Biopsy in Gastric Cancer. Front Med (Lausanne) 2021; 8:749250. [PMID: 34651002 PMCID: PMC8505538 DOI: 10.3389/fmed.2021.749250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy represents an exciting new area in the field of cancer diagnosis and management, offering a less invasive and more convenient approach to obtain a time-point image of the tumor burden and its genomic profile. Samples collected from several body fluids, mostly blood, can be used to gain access to circulating tumor cells and DNA, non-coding RNAs, microRNAs, and exosomes, at any moment, offering a dynamic picture of the tumor. For patients with GC, the use of blood-based biopsies may be particularly beneficial since tissue biopsies are difficult to obtain and cause real distress to the patient. With advantages such as repeatability and minimal invasion, it is no wonder that the field of liquid biopsy has received tremendous attention. However, the abundance of studies, involving a wide range of assays with different principles, prevented for the moment the reproducibility of the results and therefore the translation into the clinic of liquid biopsy. In this review, we present the latest technical development and data on circulating biomarkers available through liquid biopsy in gastric cancer with an emphasis on their clinical utility in areas such as cancer screening, prognostic stratification, and therapeutic management.
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Affiliation(s)
- Mihaela Chivu-Economescu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Laura Necula
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Lilia Matei
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Denisa Dragu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Carmen C Diaconu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
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4
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Salati M, Venetis K, Fassan M, Malapelle U, Pagni F, Sajjadi E, Fusco N, Ghidini M. ctDNA analysis in the personalized clinical management of gastroesophageal adenocarcinoma: turning hope into reality. Future Oncol 2021; 17:4607-4618. [PMID: 34406032 DOI: 10.2217/fon-2021-0228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gastroesophageal adenocarcinoma (GEA) is a global health issue with a high fatality-to-case ratio and a 5-year overall survival that has only slightly improved. High-throughput molecular profiling has uncovered a profound complexity and heterogeneity in GEA biology, which limits considerably the treatment advances. Liquid biopsy with circulating tumor (ct)DNA analysis could elucidate GEA molecular heterogeneity and provide diagnostic, prognostic and predictive information to guide clinical decision-making. However, only a handful of studies have shown positive results for the application of ctDNA analysis in GEA clinical management. As a result, no comprehensive information is available to date on this continuously evolving topic. Here, we discuss the current state of knowledge, along with promises and challenges related to ctDNA analysis in GEA.
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Affiliation(s)
- Massimiliano Salati
- Division of Oncology, Oncology and Hematology Department, University of Modena and Reggio Emilia, Modena, Italy.,Ph.D. Program Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Konstantinos Venetis
- Department of Oncology and Hemato-Oncology, University of Milan, Milan 20122, Italy.,Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University Milan Bicocca, Milan 20126, Italy
| | - Elham Sajjadi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan 20122, Italy.,Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, Milan 20122, Italy.,Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
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5
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Guo J, Ma K, Bao H, Ma X, Xu Y, Wu X, Shao YW, Jiang M, Huang J. Quantitative characterization of tumor cell-free DNA shortening. BMC Genomics 2020; 21:473. [PMID: 32650715 PMCID: PMC7350596 DOI: 10.1186/s12864-020-06848-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/18/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer diagnosis and treatment monitoring; however, the underlying mechanism of shortened tumor cfDNA was still unknown, which potentially limits its further clinical application. RESULTS Using targeted sequencing of cfDNA in a large cohort of solid tumor patient, sequencing reads harboring tumor-specific somatic mutations were isolated to examine the exact size distribution of tumor cfDNA. For the majority of studied cases, 166 bp remained as the peak size of tumor cfDNA, with tumor cfDNA showing an increased proportion of short fragments (100-150 bp). Less than 1% of cfDNA samples were found to be peaked at 134/144 bp and independent of tumor cfDNA purity. Using whole-genome sequencing of cfDNA, we discovered a positive correlation between cfDNA shortening and the magnitude of chromatin inaccessibility, as measured by transcription, DNase I hypersensitivity, and histone modifications. Tumor cfDNA shortening occurred simultaneously at both 5' and 3' ends of the DNA wrapped around nucleosomes. CONCLUSIONS Tumor cfDNA shortening exhibited two distinctive modes. Tumor cfDNA purity and chromatin inaccessibility were contributing factors but insufficient to trigger a global transition from 166 bp dominant to 134/144 bp dominant phenotype.
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Affiliation(s)
- Juntang Guo
- Department of Thoracic Surgery, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
| | - Kefeng Ma
- Department of Thoracic Surgery, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
| | - Hua Bao
- Translational Medicine Research Institution, Geneseeq Technology Inc., Suite 200, South Tower, MaRS Discovery District, 101 College St, Toronto, ON, M5G 1L7, Canada
| | - Xiangyuan Ma
- Translational Medicine Research Institution, Geneseeq Technology Inc., Suite 200, South Tower, MaRS Discovery District, 101 College St, Toronto, ON, M5G 1L7, Canada
| | - Yang Xu
- Translational Medicine Research Institution, Geneseeq Technology Inc., Suite 200, South Tower, MaRS Discovery District, 101 College St, Toronto, ON, M5G 1L7, Canada
| | - Xue Wu
- Translational Medicine Research Institution, Geneseeq Technology Inc., Suite 200, South Tower, MaRS Discovery District, 101 College St, Toronto, ON, M5G 1L7, Canada
| | - Yang W Shao
- Translational Medicine Research Institution, Geneseeq Technology Inc., Suite 200, South Tower, MaRS Discovery District, 101 College St, Toronto, ON, M5G 1L7, Canada
- Department of Public Health, Nanjing Medical University, 140 Hanzhong Rd, Nanjing, 210029, Jiangsu Province, China
| | - Mei Jiang
- Oncology Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, 16 Jichang Rd, Guangzhou, 510405, Guangdong Province, China.
| | - Jin Huang
- Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, 410008, Hunan Province, China.
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6
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Gastric Cancer with Radiographically Occult Metastatic Disease: Biology, Challenges, and Diagnostic Approaches. Cancers (Basel) 2020; 12:cancers12030592. [PMID: 32150838 PMCID: PMC7139817 DOI: 10.3390/cancers12030592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/13/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
Gastric adenocarcinoma is an aggressive cancer that demonstrates heterogeneous biology depending on patient ethnicity, tumor location, tumor type, and genetic profile. It remains the third leading cause of cancer deaths worldwide and was estimated to result in 782,000 deaths in 2018. Challenges exist in accurately assessing the disease burden, as available radiological staging often underestimates metastatic disease. This diagnostic handicap, along with the poor understanding of the heterogeneous biology of gastric cancer, has hindered the development of effective therapeutic solutions and thus halted improvement in patient outcomes over the last few decades. The management of occult peritoneal disease is complicated, as most patients are understaged by standard imaging studies and therefore thought to have local diseases. In this article, we systematically review recent literature on the limitations that are associated with standard radiographic staging, discuss recent molecular biology advances to better identify and diagnose occult peritoneal disease, and propose possible management strategies to approach this complicated clinical problem.
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7
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MET targeting: time for a rematch. Oncogene 2020; 39:2845-2862. [PMID: 32034310 DOI: 10.1038/s41388-020-1193-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/16/2020] [Accepted: 01/24/2020] [Indexed: 12/21/2022]
Abstract
MET, the receptor tyrosine kinase (RTK) for hepatocyte growth factor, is a proto-oncogene involved in embryonic development and throughout life in homeostasis and tissue regeneration. Deregulation of MET signaling has been reported in numerous malignancies, prompting great interest in MET targeting for cancer therapy. The present review offers a summary of the biology of MET and its known functions in normal physiology and carcinogenesis, followed by an overview of the most relevant MET-targeting strategies and corresponding clinical trials, highlighting both past setbacks and promising future prospects. By placing their efforts on a more precise stratification strategy through the genetic analysis of tumors, modern trials such as the NCI-MATCH trial could revive the past enthusiasm for MET-targeted therapy.
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8
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Matsuoka T, Yashiro M. Precision medicine for gastrointestinal cancer: Recent progress and future perspective. World J Gastrointest Oncol 2020; 12:1-20. [PMID: 31966910 PMCID: PMC6960076 DOI: 10.4251/wjgo.v12.i1.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/12/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
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9
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Xu C, Cao H, Shi C, Feng J. The Role Of Circulating Tumor DNA In Therapeutic Resistance. Onco Targets Ther 2019; 12:9459-9471. [PMID: 31807023 PMCID: PMC6850686 DOI: 10.2147/ott.s226202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
The application of precision medicine in cancer treatment has partly succeeded in reducing the side effects of unnecessary chemotherapeutics and in improving the survival rate of patients. However, with the long-term use of therapy, the dynamically changing intratumoral and intertumoral heterogeneity eventually gives rise to therapeutic resistance. In recent years, a novel testing technology (termed liquid biopsy) using circulating tumor DNAs (ctDNAs) extracted from peripheral blood samples from patients with cancer has brought about new expectations to the medical community. Using ctDNAs, clinicians can trace the heterogeneity pattern to duly adjust individual therapy and prolong overall survival for patients with cancer. Technological advances in detecting and characterizing ctDNAs (eg, development of next-generation sequencing) have provided clinicians with a valuable tool for genotyping tumors individually and identifying genetic and epigenetic alterations of the entire tumor to capture mutations associated with therapeutic resistance.
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Affiliation(s)
- Chenxin Xu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
| | - Haixia Cao
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Chen Shi
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
| | - Jifeng Feng
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
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10
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Shen B, Wu F, Ye J, Liang R, Wang R, Yu R, Wu X, Shao YW, Feng J. Crizotinib-resistant MET mutations in gastric cancer patients are sensitive to type II tyrosine kinase inhibitors. Future Oncol 2019; 15:2585-2593. [PMID: 31339066 DOI: 10.2217/fon-2019-0140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: Crizotinib has been used to counter MET amplification in different human malignancies. However, transient responses were observed in some patients with rapid acquisition of resistant mutations in MET. Materials & methods: MET mutations stably expressed Ba/F3 cell lines were used for IC50 detection. Signaling pathway analysis was done using 293T cell line. Results: Four MET mutations conferred resistance to crizotinib with sustained activation of downstream signaling pathways of MET. On the other hand, the four MET mutations displayed different response to type II tyrosine kinase inhibitors with variable deterioration of the downstream signals. Conclusion: This study suggested that patients carrying MET V1092L, D1228G or Y1230H mutations could benefit from type II tyrosine kinase inhibitor treatment, but not patients with G1163R or D1228Y/N mutations.
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Affiliation(s)
- Bo Shen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, PR China
| | - Feixiang Wu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, PR China.,Guangxi Liver Cancer Diagnosis & Treatment Engineering & Technology Research Center, PR China.,Key Laboratory of Early Prevention & Treatment for Regional High Frequency Tumor, Ministry of Education, PR China
| | - Jiazhou Ye
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, PR China
| | - Rong Liang
- Department of Digestive Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, PR China
| | - Ruping Wang
- Department of Research & Development, Nanjing Geneseeq Technology, Inc., Nanjing, Jiangsu, PR China
| | - Ruoying Yu
- Translational Medicine Research Institute, Geneseeq Technology, Inc., Toronto, Ontario, M5G1L7, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology, Inc., Toronto, Ontario, M5G1L7, Canada
| | - Yang W Shao
- Translational Medicine Research Institute, Geneseeq Technology, Inc., Toronto, Ontario, M5G1L7, Canada
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, PR China
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11
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Koldby KM, Mortensen MB, Detlefsen S, Pfeiffer P, Thomassen M, Kruse TA. Tumor-specific genetic aberrations in cell-free DNA of gastroesophageal cancer patients. J Gastroenterol 2019; 54:108-121. [PMID: 30242476 DOI: 10.1007/s00535-018-1508-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/04/2018] [Indexed: 02/04/2023]
Abstract
The applicability of liquid biopsies is studied intensively in all types of cancer and analysis of circulating tumor DNA (ctDNA) has recently been implemented clinically for mutation detection in lung cancer. ctDNA may provide information about tumor quantity and mutations present in the tumor, and as such have many potential applications in diagnosis and treatment of cancer. It has been suggested that ctDNA analysis may overcome the issue of intra-tumor heterogeneity faced by tissue biopsies and serve as an additional diagnostic tool. Furthermore, liquid biopsies are potentially helpful for monitoring of treatment response as well as detection of minimal residual disease and relapse. Gastroesophageal cancers (GEC) have high mortality rates and the majority of patients present with advanced stage at diagnosis or succumb due to disease recurrence even after radical resection of the primary tumor. Biomarkers that can help optimize treatment strategy are thus highly desirable. The present study is a review of published data on ctDNA in GEC patients. We identified 25 studies in which tumor-specific genetic aberrations were investigated in plasma or serum and discuss these in relation to the methods applied for ctDNA analysis. The methods used for ctDNA detection greatly influence the sensitivity of the analysis and, therefore, the potential clinical applications. We found that studies of ctDNA in GEC, although limited in number, are promising for several applications such as genetic profiling of tumors and monitoring of disease progression. However, more studies are needed to establish if and how this analysis can be clinically implemented.
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Affiliation(s)
- Kristina Magaard Koldby
- Department of Clinical Genetics, Odense University Hospital, J.B. Winsløws Vej 4, Odense, Denmark. .,Human Genetics, Department of Clinical Research, University of Southern Denmark, Sdr. Boulevard 29, Odense, Denmark.
| | - Michael Bau Mortensen
- Department of Surgery, Odense University Hospital, J.B. Winsløws Vej 4, Odense, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, J.B. Winsløws Vej 15, Odense, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, J.B. Winsløws Vej 4, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, J.B. Winsløws Vej 4, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Sdr. Boulevard 29, Odense, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, J.B. Winsløws Vej 4, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Sdr. Boulevard 29, Odense, Denmark
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12
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Abstract
Genetic material derived from tumours is constantly shed into the circulation of cancer patients both in the form of circulating free nucleic acids and within circulating cells or extracellular vesicles. Monitoring cancer-specific genomic alterations, particularly mutant allele frequencies, in circulating nucleic acids allows for a non-invasive liquid biopsy for detecting residual disease and response to therapy. The advent of molecular targeted treatments and immunotherapies with increasing effectiveness requires corresponding effective molecular biology methods for the detection of biomarkers such as circulating nucleic acid to monitor and ultimately personalise therapy. The use of polymerase chain reaction (PCR)-based methods, such as droplet digital PCR, allows for a very sensitive analysis of circulating tumour DNA, but typically only a limited number of gene mutations can be detected in parallel. In contrast, next-generation sequencing allows for parallel analysis of multiple mutations in many genes. The development of targeted next-generation sequencing cancer gene panels optimised for the detection of circulating free DNA now provides both the flexibility of multiple mutation analysis coupled with a sensitivity that approaches or even matches droplet digital PCR. In this review, we discuss the advantages and disadvantages of these current molecular technologies in conjunction with how this field is evolving in the context of melanoma diagnosis, prognosis, and monitoring of response to therapy.
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13
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Diefenbach RJ, Lee JH, Kefford RF, Rizos H. Evaluation of commercial kits for purification of circulating free DNA. Cancer Genet 2018; 228-229:21-27. [DOI: 10.1016/j.cancergen.2018.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/27/2018] [Accepted: 08/19/2018] [Indexed: 12/11/2022]
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14
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Katoh M. Fibroblast growth factor receptors as treatment targets in clinical oncology. Nat Rev Clin Oncol 2018; 16:105-122. [DOI: 10.1038/s41571-018-0115-y] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Zhou S, Xu B, Qi L, Zhu D, Liu B, Wei J. Next-generation sequencing reveals mutational accordance between cell-free DNA from plasma, malignant pleural effusion and ascites and directs targeted therapy in a gastric cancer patient. Cancer Biol Ther 2018; 20:15-20. [PMID: 30118648 PMCID: PMC6343684 DOI: 10.1080/15384047.2018.1504720] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cell-free DNA (cfDNA) has been a research hotspot in molecular tumor profiling. In advanced gastric cancer patients, malignant pleural effusion (MPE) and ascites provide a wealth of tumor cells that can be investigated. Here we conducted next-generation sequencing (NGS) on matched cfDNA from plasma, MPE and ascites from a stage-IV gastric cancer patient to identify potential therapeutic targets. In all three samples, we detected an amplification in the cellular-mesenchymal to epithelial transition factor (MET) gene, a truncation mutation in SMAD3 (p.R368X), and four ataxia telangiectasia-mutated gene (ATM) variants, including a missense mutation (p.E2351A), an in-frame deletion (p.NPAVIM2353delinsK), a frame-shift deletion (p.D1758fs) and an ATM- BPI fold containing family B member 1 (BPIFB1) gene fusion. In contrast, we detected amplification of TEK only in malignant ascites. The patient was subjected to Crizotinib to counter MET amplification. Our study demonstrates high accordance in mutational spectra of matched cfDNA from plasma, MPE and ascites, and suggests that it is feasible to utilize these tumor sources in clinical decision-making.
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Affiliation(s)
- Shujuan Zhou
- a Department of Oncology, The Comprehensive Cancer Centre of Drum Tower Hospital , Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University , Nanjing , China
| | - Bo Xu
- a Department of Oncology, The Comprehensive Cancer Centre of Drum Tower Hospital , Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University , Nanjing , China
| | - Liang Qi
- a Department of Oncology, The Comprehensive Cancer Centre of Drum Tower Hospital , Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University , Nanjing , China
| | - Dongqin Zhu
- b Nanjing Geneseeq Technology Inc ., Nanjing , Jiangsu , China
| | - Baorui Liu
- a Department of Oncology, The Comprehensive Cancer Centre of Drum Tower Hospital , Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University , Nanjing , China
| | - Jia Wei
- a Department of Oncology, The Comprehensive Cancer Centre of Drum Tower Hospital , Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University , Nanjing , China
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Saluja H, Karapetis CS, Pedersen SK, Young GP, Symonds EL. The Use of Circulating Tumor DNA for Prognosis of Gastrointestinal Cancers. Front Oncol 2018; 8:275. [PMID: 30087854 PMCID: PMC6066577 DOI: 10.3389/fonc.2018.00275] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/02/2018] [Indexed: 01/10/2023] Open
Abstract
Gastrointestinal cancers, including oesophageal, gastric and colorectal cancers (CRC) have high rates of disease recurrence despite curative resection. There are a number of recent studies that have investigated the use of circulating tumor DNA (ctDNA) for prognostic value in these cancers. We reviewed studies that had been published prior to March 2018 that assessed the prognostic values of ctDNA in patients with oesophageal and gastric cancers, gastrointestinal stromal tumors (GIST) and CRC. We identified 63 eligible clinical studies that focussed on recurrence and survival. Studies assessed investigated various ctDNA biomarkers in patients with different stages of cancer undergoing surgical resection, chemotherapy and no treatment. For oesophageal squamous cell carcinoma and oesophageal adenocarcinoma, methylation of certain genes such as APC and DAPK have been highlighted as promising biomarkers for prognostication, but these studies are limited and more comprehensive research is needed. Studies focusing on gastric cancer patients showed that methylation of ctDNA in SOX17 and APC were independently associated with poor survival. Two studies demonstrated an association between ctDNA and recurrence and survival in GIST patients, but more studies are needed for this type of gastrointestinal cancer. A large proportion of the literature was on CRC which identified both somatic mutations and DNA methylation biomarkers to determine prognosis. ctDNA biomarkers that identified somatic mutations were more effective if they were personalized based on mutations found in the primary tumor tissue, but ctDNA methylation studies identified various biomarkers that predicted increased risk of recurrence, poor disease free survival and overall survival. While the use of non-invasive ctDNA biomarkers for prognosis is promising, larger studies are needed to validate the clinical utility for optimizing treatment and surveillance strategies to reduce mortality from gastrointestinal cancers.
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Affiliation(s)
- Hariti Saluja
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Department of Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | | | - Graeme P Young
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
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Uchôa Guimarães CT, Ferreira Martins NN, Cristina da Silva Oliveira K, Almeida CM, Pinheiro TM, Gigek CO, Roberto de Araújo Cavallero S, Assumpção PP, Cardoso Smith MA, Burbano RR, Calcagno DQ. Liquid biopsy provides new insights into gastric cancer. Oncotarget 2018; 9:15144-15156. [PMID: 29599934 PMCID: PMC5871105 DOI: 10.18632/oncotarget.24540] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/01/2017] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsies have great promise for precision medicine as they provide information about primary and metastatic tumors via a minimally invasive method. In gastric cancer patients, a large number of blood-based biomarkers have been reported for their potential role in clinical practice for screening, early diagnosis, prognostic evaluation, recurrence monitoring and therapeutic efficiency follow-up. This current review focuses on blood liquid biopsies' role and their clinical implications in gastric cancer patients, with an emphasis on circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) and circulating non-coding RNAs (ncRNAs). We also provide a brief discussion of the potential and limitations of liquid biopsies use and their future use in the routine clinical care of gastric cancer.
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Affiliation(s)
- Camila Tavares Uchôa Guimarães
- Residência Multiprofissional em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
| | | | | | - Caroline Martins Almeida
- Residência Multiprofissional em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Carolina Oliveira Gigek
- Disciplina de Genética, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Disciplina de Gastroenterologia Cirurgica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Rommel Rodríguez Burbano
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
- Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, PA, Brazil
| | - Danielle Queiroz Calcagno
- Residência Multiprofissional em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
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