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Iden CR, Mustafa SM, Øgaard N, Henriksen T, Jensen SØ, Ahlborn LB, Egebjerg K, Baeksgaard L, Garbyal RS, Nedergaard MK, Achiam MP, Andersen CL, Mau-Sørensen M. Circulating tumor DNA predicts recurrence and survival in patients with resectable gastric and gastroesophageal junction cancer. Gastric Cancer 2024:10.1007/s10120-024-01556-9. [PMID: 39369091 DOI: 10.1007/s10120-024-01556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 09/23/2024] [Indexed: 10/07/2024]
Abstract
BACKGROUND Gastric and gastroesophageal junction (GEJ) cancer represents a significant global health challenge, with high recurrence rates and poor survival outcomes. This study investigates circulating tumor DNA (ctDNA) as a biomarker for assessing recurrence risk in patients with resectable gastric and GEJ adenocarcinomas (AC). METHODS Patients with resectable gastric and GEJ AC, undergoing perioperative chemotherapy and surgery, were prospectively enrolled. Serial plasma samples were collected at baseline, after one cycle of chemotherapy, after preoperative chemotherapy, and after surgery. ctDNA was assessed by a ddPCR test (TriMeth), which targets the gastrointestinal cancer-specific methylation patterns of the genes C9orf50, KCNQ5, and CLIP4. RESULTS ctDNA analysis was performed on 229 plasma samples from 86 patients. At baseline, ctDNA was detected in 56% of patients, which decreased to 37% following one cycle of chemotherapy, 25% after preoperative chemotherapy and 15% after surgical resection. The presence of ctDNA after one cycle of chemotherapy was associated with reduced recurrence-free survival (RFS) (HR = 2.54, 95% confidence interval (CI) 1.33-4.85, p = 0.005) and overall survival (OS) (HR = 2.23, 95% CI 1.07-4.62, p = 0.032). Similarly, ctDNA after surgery was associated with significantly shorter RFS (HR = 6.22, 95% CI 2.39-16.2, p < 0.001) and OS (HR = 6.37, 95% CI 2.10-19.3, p = 0.001). Multivariable regression analysis confirmed ctDNA after surgery as an independent prognostic factor (p < 0.001). CONCLUSION ctDNA analysis has the potential to identify patients at elevated risk of recurrence, thus providing personalized treatment strategies for patients with resectable gastric and GEJ cancer. Further validation in larger cohorts and ctDNA-guided interventions are needed for future clinical use.
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Affiliation(s)
- Cecilie Riis Iden
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Salah Mohammad Mustafa
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, 8200, Aarhus N, Denmark
- Institute of Clinical Medicine, Faculty of Health, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, 8200, Aarhus N, Denmark
- Institute of Clinical Medicine, Faculty of Health, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Tenna Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, 8200, Aarhus N, Denmark
- Institute of Clinical Medicine, Faculty of Health, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, 8200, Aarhus N, Denmark
- Institute of Clinical Medicine, Faculty of Health, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Lise Barlebo Ahlborn
- Department of Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Kristian Egebjerg
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Lene Baeksgaard
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Rajendra Singh Garbyal
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Mette Kjølhede Nedergaard
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Michael Patrick Achiam
- Department of Surgery & Transplantation, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, 8200, Aarhus N, Denmark
- Institute of Clinical Medicine, Faculty of Health, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Morten Mau-Sørensen
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark.
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Zheng J, Qin C, Wang Q, Tian D, Chen Z. Circulating tumour DNA-Based molecular residual disease detection in resectable cancers: a systematic review and meta-analysis. EBioMedicine 2024; 103:105109. [PMID: 38614009 PMCID: PMC11021841 DOI: 10.1016/j.ebiom.2024.105109] [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] [Received: 09/23/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA)-based molecular residual disease (MRD) detection technology has been widely used for recurrence evaluation, but there is no agreement on the efficacy of assessing recurrence and overall survival (OS) prognosis, as well as the sensitivity and specificity of landmark detection and longitudinal detection. METHODS We systematically searched Pubmed, Embase, Cochrane, and Scopus for prospective studies or randomized controlled trials that collected blood samples prospectively. The search period was from Jan 1, 2013, to Sept 10, 2023. We excluded retrospective studies. The primary endpoint was to assess the hazard ratio (HR) between circulating tumour DNA positive (ctDNA+) and negative (ctDNA-) for recurrence-free survival incidence (RFS), disease-free survival (DFS), progression-free survival (PFS), event-free survival (EFS), time to recurrence (TTR), distant metastasis-free survival (DMFS) or OS in patients with resectable cancers. We calculated the pooled HR of recurrence and OS and 95% confidence interval (CI) in patients with resected cancers using a random-effects model. Pooled sensitivity and specificity were estimated using the bivariate random effects model. FINDINGS This systematic review and meta-analysis returned 7578 records, yielding 80 included studies after exclusion. We found that the HR of recurrence across all included cancers between patients with ctDNA+ and ctDNA- was 7.48 (95% CI 6.39-8.77), and the OS was 5.58 (95% CI 4.17-7.48). We also found that the sensitivity, area under the summary receiver operating characteristic curve (AUSROC) and diagnostic odds ratio (DOR) of longitudinal tests were higher than that of landmark tests between patients with ctDNA+ and ctDNA- (0.74, 95% CI 0.68-0.80 vs 0.50, 95% CI 0.46-0.55; 0.88 vs. 0.80; 25.70, 95% CI 13.20-45.40 vs. 9.90, 95% CI 7.77-12.40). INTERPRETATION Postoperative ctDNA testing was a significant prognosis factor for recurrence and OS in patients with resectable cancers. However, the overall sensitivity of ctDNA-MRD detection could be better. Longitudinal monitoring can improve the sensitivity, AUSROC, and DOR. FUNDING Special fund project for clinical research of Qingyuan People's Hospital (QYRYCRC2023006), plan on enhancing scientific research in GMU (GZMU-SH-301).
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Affiliation(s)
- Jiachun Zheng
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Chuling Qin
- Guangzhou Medical University, Guangzhou, 511436, China
| | - Qianxi Wang
- Guangzhou Medical University, Guangzhou, 511436, China
| | - Dongbo Tian
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
| | - Zisheng Chen
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
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3
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Zhang Y, Du H, Wang N, Wang L, Huang Y. An update of clinical value of circulating tumor DNA in esophageal cancer: a systematic review and meta-analysis. BMC Cancer 2024; 24:129. [PMID: 38267901 PMCID: PMC10809487 DOI: 10.1186/s12885-024-11879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a deadly disease with limited therapeutic options. Although circulating tumor DNA (ctDNA) could be a promising tool in this regard, the availiable evidence is limited. We performed a systematic review and meta-analysis to summarize the clinical applicability of the next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) technology on the ctDNA detection of the EC and listed the current challenges. METHODS We systematically searched MEDLINE (via PubMed), Embase (via OVID), ISI Web of Science database and Cochrane Library from January, 2000 to April, 2023. Progression-free survival (PFS) and overall survival (OS) were set as primary outcome endpoints. Pathologic response was evaluated by tumor regression grade (TRG), according to the eighth edition of the American Joint Committee on Cancer (AJCC). Major pathologic regression (MPR) was defined as TRG 1 and 2. The MPR was set as secondary endpoint. Hazard rate (HR) and associated 95% CI were used as the effect indicators the association between ctDNA and prognosis of EC. MPR rates were also calculated. Fixed-effect model (Inverse Variance) or random-effect model (Mantel-Haenszel method) was performed depending on the statistically heterogeneity. RESULTS Twenty-two studies, containing 1144 patients with EC, were included in this meta-analysis. The results showed that OS (HR = 3.87; 95% CI, 2.86-5.23) and PFS (HR = 4.28; 95% CI, 3.34-5.48) were shorter in ctDNA-positive patients. In the neoadjuvant therapy, the sensitivity analysis showed the clarified HR of ctDNA-positive was 1.13(95% CI, 1.01-1.28). We also found that TP53, NOTCH1, CCND1 and CNKN2A are the most frequent mutation genes. CONCLUSIONS Positive ctDNA is associated with poor prognosis, which demonstrated clinical value of ctDNA. Longitudinal ctDNA monitoring showed potential prognostic value in the neoadjuvant therapy. In an era of precision medicine, ctDNA could be a promising tool to individualize treatment planning and to improve outcomes in EC. PROSPERO REGISTRATION NUMBER CRD42023412465.
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Affiliation(s)
- Yaozhong Zhang
- Department of Infectious diseases, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huazhen Du
- Department of Emergency, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Na Wang
- Department of Molecular Biology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Wang
- Department of Thoracic Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajie Huang
- Department of Medical oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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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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5
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Han HS, Lee KW. Liquid Biopsy: An Emerging Diagnostic, Prognostic, and Predictive Tool in Gastric Cancer. J Gastric Cancer 2024; 24:4-28. [PMID: 38225764 PMCID: PMC10774753 DOI: 10.5230/jgc.2024.24.e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
Liquid biopsy, a minimally invasive procedure that causes minimal pain and complication risks to patients, has been extensively studied for cancer diagnosis and treatment. Moreover, it facilitates comprehensive quantification and serial assessment of the whole-body tumor burden. Several biosources obtained through liquid biopsy have been studied as important biomarkers for establishing early diagnosis, monitoring minimal residual disease, and predicting the prognosis and response to treatment in patients with cancer. Although the clinical application of liquid biopsy in gastric cancer is not as robust as that in other cancers, biomarker studies using liquid biopsy are being actively conducted in patients with gastric cancer. Herein, we aimed to review the role of various biosources that can be obtained from patients with gastric cancer through liquid biopsies, such as blood, saliva, gastric juice, urine, stool, peritoneal lavage fluid, and ascites, by dividing them into cellular and acellular components. In addition, we reviewed previous studies on the diagnostic, prognostic, and predictive biomarkers for gastric cancer using liquid biopsy and discussed the limitations of liquid biopsy and the challenges to overcome these limitations in patients with gastric cancer.
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Affiliation(s)
- Hye Sook Han
- Department of Internal Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Keun-Wook Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea.
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6
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Rulten SL, Grose RP, Gatz SA, Jones JL, Cameron AJM. The Future of Precision Oncology. Int J Mol Sci 2023; 24:12613. [PMID: 37628794 PMCID: PMC10454858 DOI: 10.3390/ijms241612613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Our understanding of the molecular mechanisms underlying cancer development and evolution have evolved rapidly over recent years, and the variation from one patient to another is now widely recognized. Consequently, one-size-fits-all approaches to the treatment of cancer have been superseded by precision medicines that target specific disease characteristics, promising maximum clinical efficacy, minimal safety concerns, and reduced economic burden. While precision oncology has been very successful in the treatment of some tumors with specific characteristics, a large number of patients do not yet have access to precision medicines for their disease. The success of next-generation precision oncology depends on the discovery of new actionable disease characteristics, rapid, accurate, and comprehensive diagnosis of complex phenotypes within each patient, novel clinical trial designs with improved response rates, and worldwide access to novel targeted anticancer therapies for all patients. This review outlines some of the current technological trends, and highlights some of the complex multidisciplinary efforts that are underway to ensure that many more patients with cancer will be able to benefit from precision oncology in the near future.
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Affiliation(s)
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Susanne A. Gatz
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - J. Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Angus J. M. Cameron
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
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7
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Desai A, Lovly CM. Challenges in the implementation of ultrasensitive liquid biopsy approaches in precision oncology. J Immunother Cancer 2023; 11:e006793. [PMID: 37349128 PMCID: PMC10314676 DOI: 10.1136/jitc-2023-006793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
- Aakash Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Labiano I, Huerta AE, Arrazubi V, Hernandez-Garcia I, Mata E, Gomez D, Arasanz H, Vera R, Alsina M. State of the Art: ctDNA in Upper Gastrointestinal Malignancies. Cancers (Basel) 2023; 15:1379. [PMID: 36900172 PMCID: PMC10000247 DOI: 10.3390/cancers15051379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising non-invasive source to characterize genetic alterations related to the tumor. Upper gastrointestinal cancers, including gastroesophageal adenocarcinoma (GEC), biliary tract cancer (BTC) and pancreatic ductal adenocarcinoma (PADC) are poor prognostic malignancies, usually diagnosed at advanced stages when no longer amenable to surgical resection and show a poor prognosis even for resected patients. In this sense, ctDNA has emerged as a promising non-invasive tool with different applications, from early diagnosis to molecular characterization and follow-up of tumor genomic evolution. In this manuscript, novel advances in the field of ctDNA analysis in upper gastrointestinal tumors are presented and discussed. Overall, ctDNA analyses can help in early diagnosis, outperforming current diagnostic approaches. Detection of ctDNA prior to surgery or active treatment is also a prognostic marker that associates with worse survival, while ctDNA detection after surgery is indicative of minimal residual disease, anticipating in some cases the imaging-based detection of progression. In the advanced setting, ctDNA analyses characterize the genetic landscape of the tumor and identify patients for targeted-therapy approaches, and studies show variable concordance levels with tissue-based genetic testing. In this line, several studies also show that ctDNA serves to follow responses to active therapy, especially in targeted approaches, where it can detect multiple resistance mechanisms. Unfortunately, current studies are still limited and observational. Future prospective multi-center and interventional studies, carefully designed to assess the value of ctDNA to help clinical decision-making, will shed light on the real applicability of ctDNA in upper gastrointestinal tumor management. This manuscript presents a review of the evidence available in this field up to date.
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Affiliation(s)
- Ibone Labiano
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Ana Elsa Huerta
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Virginia Arrazubi
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Irene Hernandez-Garcia
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Elena Mata
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - David Gomez
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Hugo Arasanz
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Ruth Vera
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Maria Alsina
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
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Morimoto Y, Matsuda S, Kawakubo H, Nakamura K, Kobayashi R, Hisaoka K, Okui J, Takeuchi M, Aimono E, Fukuda K, Nakamura R, Saya H, Nishihara H, Kitagawa Y. Tumor Burden Monitoring with Circulating Tumor DNA During Treatment in Patients with Esophageal Squamous Cell Carcinoma. Ann Surg Oncol 2023; 30:3747-3756. [PMID: 36788188 DOI: 10.1245/s10434-023-13194-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND To guide appropriate treatment strategy, an accurate tumor monitoring modality that reflects tumor burden during neoadjuvant treatment is required for esophageal squamous cell carcinoma (ESCC). We aimed to investigate the clinical utility of circulating tumor DNA (ctDNA) in plasma in patients who received neoadjuvant chemotherapy (NAC) followed by esophagectomy. PATIENTS AND METHODS Longitudinally collected plasma samples for ctDNA combined with genomic DNA from primary lesions were obtained from patients with histologically confirmed ESCC who underwent NAC followed by subtotal esophagectomy. Next-generation sequencing was performed to identify mutations from the plasma and the primary tumor. The relationships between changes in ctDNA and the pathological response and recurrence were assessed in patients with locally advanced ESCC. RESULTS In pretreatment samples from 13 patients, multiple concordant mutations in ctDNA and primary tumors were observed in 11 patients (85%), who were classified as ctDNA positive before treatment. The ctDNA positive rate after NAC correlated with the pathological response (responders, 25%; nonresponders, 100%; p = 0.007). The risk of recurrence increased significantly in patients with positive ctDNA after surgery in analysis of 16 patients; the 1-year recurrence-free survival rates were 90 and 0% in ctDNA-negative and ctDNA-positive groups, respectively (p = 0.0008). In two patients with postoperative recurrence, ctDNA was detected approximately 5.5 months earlier than the diagnosis using radiographical imaging. CONCLUSIONS ctDNA is a promising biomarker for predicting pathological response and postoperative recurrence in ESCC. To demonstrate the external validity, we are currently preparing a multicenter prospective study.
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Affiliation(s)
- Yosuke Morimoto
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Satoru Matsuda
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan.
| | - Hirofumi Kawakubo
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kohei Nakamura
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Ryota Kobayashi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kazuhiko Hisaoka
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Jun Okui
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan.,Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Masashi Takeuchi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Eriko Aimono
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Kazumasa Fukuda
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Rieko Nakamura
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Saya
- Cancer Center, Fujita Health University, Aichi, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
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Wallander K, Haider Z, Jeggari A, Foroughi-Asl H, Gellerbring A, Lyander A, Chozhan A, Cuba Gyllensten O, Hägglund M, Wirta V, Nordenskjöld M, Lindblad M, Tham E. Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer. Cancers (Basel) 2023; 15:1160. [PMID: 36831507 PMCID: PMC9954085 DOI: 10.3390/cancers15041160] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
In this longitudinal study, cell-free tumour DNA (a liquid biopsy) from plasma was explored as a prognostic biomarker for gastro-oesophageal cancer. Both tumour-informed and tumour-agnostic approaches for plasma variant filtering were evaluated in 47 participants. This was possible through sequencing of DNA from tissue biopsies from all participants and cell-free DNA from plasma sampled before and after surgery (n = 42), as well as DNA from white blood cells (n = 21) using a custom gene panel with and without unique molecular identifiers (UMIs). A subset of the plasma samples (n = 12) was also assayed with targeted droplet digital PCR (ddPCR). In 17/31 (55%) diagnostic plasma samples, tissue-verified cancer-associated variants could be detected by the gene panel. In the tumour-agnostic approach, 26 participants (59%) had cancer-associated variants, and UMIs were necessary to filter the true variants from the technical artefacts. Additionally, clonal haematopoietic variants could be excluded using the matched white blood cells or follow-up plasma samples. ddPCR detected its targets in 10/12 (83%) and provided an ultra-sensitive method for follow-up. Detectable cancer-associated variants in plasma correlated to a shorter overall survival and shorter time to progression, with a significant correlation for the tumour-informed approaches. In summary, liquid biopsy gene panel sequencing using a tumour-agnostic approach can be applied to all patients regardless of the presence of a tissue biopsy, although this requires UMIs and the exclusion of clonal haematopoietic variants. However, if sequencing data from tumour biopsies are available, a tumour-informed approach improves the value of cell-free tumour DNA as a negative prognostic biomarker in gastro-oesophageal cancer patients.
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Affiliation(s)
- Karin Wallander
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Zahra Haider
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Ashwini Jeggari
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Hassan Foroughi-Asl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Anna Gellerbring
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Anna Lyander
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
- Science for Life Laboratory, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Athithyan Chozhan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Ollanta Cuba Gyllensten
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Moa Hägglund
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Stockholm, Sweden
- Science for Life Laboratory, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, 10044 Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Mats Lindblad
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 14152 Huddinge, Sweden
- Department of Upper Abdominal Diseases, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
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11
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Biomarkers for Early Detection, Prognosis, and Therapeutics of Esophageal Cancers. Int J Mol Sci 2023; 24:ijms24043316. [PMID: 36834728 PMCID: PMC9968115 DOI: 10.3390/ijms24043316] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Esophageal cancer (EC) is the deadliest cancer worldwide, with a 92% annual mortality rate per incidence. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two major types of ECs, with EAC having one of the worst prognoses in oncology. Limited screening techniques and a lack of molecular analysis of diseased tissues have led to late-stage presentation and very low survival durations. The five-year survival rate of EC is less than 20%. Thus, early diagnosis of EC may prolong survival and improve clinical outcomes. Cellular and molecular biomarkers are used for diagnosis. At present, esophageal biopsy during upper endoscopy and histopathological analysis is the standard screening modality for both ESCC and EAC. However, this is an invasive method that fails to yield a molecular profile of the diseased compartment. To decrease the invasiveness of the procedures for diagnosis, researchers are proposing non-invasive biomarkers for early diagnosis and point-of-care screening options. Liquid biopsy involves the collection of body fluids (blood, urine, and saliva) non-invasively or with minimal invasiveness. In this review, we have critically discussed various biomarkers and specimen retrieval techniques for ESCC and EAC.
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12
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Eyck BM, Jansen MP, Noordman BJ, Atmodimedjo PN, van der Wilk BJ, Martens JW, Helmijr JA, Beaufort CM, Mostert B, Doukas M, Wijnhoven BP, Lagarde SM, van Lanschot JJB, Dinjens WN. Detection of circulating tumour DNA after neoadjuvant chemoradiotherapy in patients with locally advanced oesophageal cancer. J Pathol 2023; 259:35-45. [PMID: 36196486 PMCID: PMC10092085 DOI: 10.1002/path.6016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/05/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Active surveillance instead of standard surgery after neoadjuvant chemoradiotherapy (nCRT) has been proposed for patients with oesophageal cancer. Circulating tumour DNA (ctDNA) may be used to facilitate selection of patients for surgery. We show that detection of ctDNA after nCRT seems highly suggestive of major residual disease. Tumour biopsies and blood samples were taken before, and 6 and 12 weeks after, nCRT. Biopsies were analysed with regular targeted next-generation sequencing (NGS). Circulating cell-free DNA (cfDNA) was analysed using targeted NGS with unique molecular identifiers and digital polymerase chain reaction. cfDNA mutations matching pre-treatment biopsy mutations confirmed the presence of ctDNA. In total, 31 patients were included, of whom 24 had a biopsy mutation that was potentially detectable in cfDNA (77%). Pre-treatment ctDNA was detected in nine of 24 patients (38%), four of whom had incurable disease progression before surgery. Pre-treatment ctDNA detection had a sensitivity of 47% (95% CI 24-71) (8/17), specificity of 85% (95% CI 42-99) (6/7), positive predictive value (PPV) of 89% (95% CI 51-99) (8/9), and negative predictive value (NPV) of 40% (95% CI 17-67) (6/15) for detecting major residual disease (>10% residue in the resection specimen or progression before surgery). After nCRT, ctDNA was detected in three patients, two of whom had disease progression. Post-nCRT ctDNA detection had a sensitivity of 21% (95% CI 6-51) (3/14), specificity of 100% (95% CI 56-100) (7/7), PPV of 100% (95% CI 31-100) (3/3), and NPV of 39% (95% CI 18-64) (7/18) for detecting major residual disease. The addition of ctDNA to the current set of diagnostics did not lead to more patients being clinically identified with residual disease. These results indicate that pre-treatment and post-nCRT ctDNA detection may be useful in identifying patients at high risk of disease progression. The addition of ctDNA analysis to the current set of diagnostic modalities may not improve detection of residual disease after nCRT. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ben M Eyck
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Maurice Phm Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bo Jan Noordman
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Berend J van der Wilk
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - John Wm Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bas Pl Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Sjoerd M Lagarde
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Winand Nm Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
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13
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Zhang Z, Wu H, Chong W, Shang L, Jing C, Li L. Liquid biopsy in gastric cancer: predictive and prognostic biomarkers. Cell Death Dis 2022; 13:903. [PMID: 36302755 PMCID: PMC9613678 DOI: 10.1038/s41419-022-05350-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022]
Abstract
Gastric cancer (GC) is a high-incidence cancer worldwide. Most patients are diagnosed at an advanced stage, by which time they have limited treatment options and poor prognosis. Early diagnosis and precise treatment are important. In the past few years, emerging research has been conducted on the use of non-invasive liquid biopsy, with its advantages of minimal invasiveness and repeated sampling, to monitor tumor occurrence and recurrence in real time and to evaluate prognosis and treatment response. Many studies have demonstrated the potential of liquid biopsy in GC, and the detection of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating free DNA (cfDNA), and exosomes has achieved gratifying results. In this review, we summarize evolving technologies for and information regarding liquid biopsy, the most recently discovered GC liquid biopsy biomarkers, and ongoing clinical trials and discuss the challenges and application prospects of liquid biopsy in GC.
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Affiliation(s)
- Zihao Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Hao Wu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250021, China
- Department of General Surgery, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250021, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong, 250021, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250021, China.
| | - Changqing Jing
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong, 250021, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250021, China.
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, Shandong, 250021, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250021, China.
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14
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Lam RCT, Johnson D, Lam G, Li MLY, Wong JWL, Lam WKJ, Chan KCA, Ma B. Clinical applications of circulating tumor-derived DNA in the management of gastrointestinal cancers - current evidence and future directions. Front Oncol 2022; 12:970242. [PMID: 36248993 PMCID: PMC9556664 DOI: 10.3389/fonc.2022.970242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in Next Generation Sequencing (NGS) technologies have enabled the accurate detection and quantification of circulating tumor-derived (ct)DNA in most gastrointestinal (GI) cancers. The prognostic and predictive utility of ctDNA in patiets with different stages of colorectal (CRC), gastro-esophageal (GEC) and pancreaticobiliary cancers (PBC) are currently under active investigation. The most mature clinical data to date are derived from studies in the prognostic utility of personalized ctDNA-based NGS assays in the detection of minimal residual disease (MRD) and early recurrence after surgery in CRC and other GI cancers. These findings are being validated in several prospective studies which are designed to test if ctDNA could outperform conventional approaches in guiding adjuvant chemotherapy, and in post-operative surveillance in some GI cancers. Several adaptive studies using ctDNA as a screening platform are also being used to identify patients with actionable genomic alterations for clinical trials of targeted therapies. In the palliative setting, ctDNA monitoring during treatment has shown promise in the detection and tracking of clonal variants associated with acquired resistance to targeted therapies and immune-checkpoint inhibitors (ICI). Moreover, ctDNA may help to guide the therapeutic re-challenge of targeted therapies in patients who have prior exposure to such treatment. This review will examine the most updated research findings on ctDNA as a biomarker in CRC, GEC and PBCs. It aims to provide insights into how the unique strengths of this biomarker could be optimally leveraged in improving the management of these GI cancers.
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Affiliation(s)
- Rachel C. T. Lam
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - David Johnson
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir Y. K Pao Centre for Cancer, Hong Kong Cancer Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Gigi Lam
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Michelle L. Y. Li
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Joyce W. L. Wong
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - W. K. Jacky Lam
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - K. C. Allen Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Brigette Ma
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir Y. K Pao Centre for Cancer, Hong Kong Cancer Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
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15
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Fong C, Johnston E, Starling N. Neoadjuvant and Adjuvant Therapy Approaches to Gastric Cancer. Curr Treat Options Oncol 2022; 23:1247-1268. [PMID: 35980522 DOI: 10.1007/s11864-022-01004-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2022] [Indexed: 02/08/2023]
Abstract
OPINION STATEMENT Gastric cancer is an aggressive malignancy, requiring a multimodality approach to achieve optimal curative rates even when the disease is amenable to surgical resection. Neoadjuvant and adjuvant approaches differ across the globe-a preference for peri-operative chemotherapy exists in Europe, in contrast to the adoption of adjuvant chemotherapy in Asia and adjuvant chemoradiotherapy in North America. There are nuances and limitations associated with each therapeutic strategy and an understanding of these distinct approaches is integral to judicious clinical application of the available data. Although a multimodal approach provides a clear survival benefit above a surgical-only approach, data report low completion rates of adjuvant therapy components and strongly suggest a need to refine patient selection particularly for ongoing treatment in the post-operative period. This may be achieved using a risk-stratified strategy. Hence, there is a need to transition from a generalised approach to a multimodality treatment towards one guided by individual patient clinical features and biomarker profiles in order to improve tolerability and patient outcomes irrespective of geographical variation in clinical practice. While the evidences supporting molecular features such as microsatellite instability and predictive gene signatures are provocative, prospective validation is required before these can be confidently used to direct clinical decision-making.
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Affiliation(s)
- Caroline Fong
- Gastrointestinal/Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London, UK.
| | - Edwina Johnston
- Gastrointestinal/Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Naureen Starling
- Gastrointestinal/Lymphoma Unit, The Royal Marsden NHS Foundation Trust, London, UK
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16
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Fong C, Chau I. HER2 Inhibition in Gastric Cancer-Novel Therapeutic Approaches for an Established Target. Cancers (Basel) 2022; 14:cancers14153824. [PMID: 35954487 PMCID: PMC9367333 DOI: 10.3390/cancers14153824] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer is a leading cause of cancer-related deaths globally. Human epidermal growth receptor 2 (HER2) overexpression of HER2 gene amplification is present in 20% of gastric cancers and defines a subset amenable to HER2-directed therapeutics. The seminal ToGA study led to routine use of the monoclonal antibody trastuzumab in conjunction to platinum-fluoropyridimine first-line chemotherapy for HER2-positive gastric cancers as standard-of-care. Although limited progress was made in the decade following ToGA, there is now an abundance of novel therapeutic approaches undergoing investigation in parallel. Additionally, new data from randomised trials have indicated efficacy of the antibody-drug conjugate trastuzumab deruxtecan in chemorefractory patients and increased responses with the addition of first-line immune checkpoint blockade to trastuzumab and chemotherapy. This review will outline the data supporting HER2 targeting in gastric cancers, discuss mechanisms of response and resistance to HER2-directed therapies and summarise the emerging therapies under clinical evaluation that may evolve the way we manage this subset of gastric cancers in the future.
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17
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Long S. In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform. Methods 2022; 201:82-95. [PMID: 33839286 PMCID: PMC8501152 DOI: 10.1016/j.ymeth.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Sensitive PCR detection of viral nucleic acids plays a critical role in infectious disease research, diagnosis and monitoring. In the context of SARS-CoV-2 detection, recent reports indicate that digital PCR-based tests are significantly more sensitive than traditional qPCR tests. Numerous factors can influence digital PCR reaction sensitivity. In this review, using a model for human HIV infection and the Raindance ddPCR platform as an example, we describe technical aspects that contribute to sensitive viral signal detection in DNA and RNA from tissue samples, which often harbor viral reservoirs and serve as better predictors of disease outcome and indicators of treatment efficacy.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
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18
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Long S, Berkemeier B. Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR). Methods 2022; 201:49-64. [PMID: 33957204 PMCID: PMC8563494 DOI: 10.1016/j.ymeth.2021.04.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Sensitive detection of viral nucleic acids is critically important for diagnosis and monitoring of the progression of infectious diseases such as those caused by SARS-CoV2, HIV-1, and other viruses. In HIV-1 infection cases, assessing the efficacy of treatment interventions that are superimposed on combination antiretroviral therapy (cART) has benefited tremendously from the development of sensitive HIV-1 DNA and RNA quantitation assays. Simian immunodeficiency virus (SIV) infection of Rhesus macaques is similar in many key aspects to human HIV-1 infection and consequently this non-human primate (NHP) model has and continues to prove instrumental in evaluating HIV prevention, treatment and eradication approaches. Cell and tissue associated HIV-1 viral nucleic acids have been found to serve as useful predictors of disease outcome and indicators of treatment efficacy, highlighting the value of and the need for sensitive detection of viruses in cells/tissues from infected individuals or animal models. However, viral nucleic acid detection and quantitation in such sample sources can often be complicated by high nucleic acid input (that is required to detect ultralow level viruses in, for example, cure research) or inhibitors, leading to reduced detection sensitivity and under-quantification, and confounded result interpretation. Here, we present a step-by-step procedure to quantitatively recover cell/tissue associated viral DNA and RNA, using SIV-infected Rhesus macaque cells and tissues as model systems, and subsequently quantify the viral DNA and RNA with an ultrasensitive SIV droplet digital PCR (ddPCR) assay and reverse transcription ddPCR (RT-ddPCR) assay, respectively, on the Raindance ddPCR platform. The procedure can be readily adapted for a broad range of applications where highly sensitive nucleic acid detection and quantitation are required.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
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19
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Jiang M, Zhou H, Jiang S, Yu H. A Review of Circulating Tumor DNA in the Diagnosis and Monitoring of Esophageal Cancer. Med Sci Monit 2022; 28:e934106. [PMID: 35210388 PMCID: PMC8886734 DOI: 10.12659/msm.934106] [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: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is a type of cell-free DNA released by tumor cells after necrosis and apoptosis, and it can be actively secreted by tumor cells. Since ctDNA is derived from various tumor sites, it can provide far more comprehensive genomic and epigenomic information than a single-site biopsy. Therefore, ctDNA can overcome tumor heterogeneity, which is the major limitation of a traditional tissue biopsy approach. Noninvasive ctDNA assays allow continuous real-time monitoring of the molecular status of cancers. Recently, ctDNA assays have been widely used in clinical practice, including cancer diagnosis, evaluation of therapeutic efficacy and prognosis, and monitoring of relapse and metastasis. Although ctDNA shows a high diagnostic performance in advanced esophageal cancer, it is far from satisfactory for early diagnosis of esophageal cancer. Monitoring the dynamic changes of ctDNA is beneficial for the evaluation of therapeutic efficacy and prediction of early recurrence in esophageal cancer. It is necessary to establish standards for individualized ctDNA detection in the evaluation of treatment response and surveillance of esophageal cancer and to develop clinical practice guideline for the systemic treatment of patients with "ctDNA recurrence." This review aims to provide an update on the role of ctDNA in the diagnosis and monitoring of esophageal cancer.
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Affiliation(s)
- Min Jiang
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Huilin Zhou
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Su Jiang
- Department of Rehabilitation, Taizhou People’s Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Hong Yu
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
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20
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Paschold L, Binder M. Circulating Tumor DNA in Gastric and Gastroesophageal Junction Cancer. Curr Oncol 2022; 29:1430-1441. [PMID: 35323320 PMCID: PMC8947276 DOI: 10.3390/curroncol29030120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Tumor cells shed DNA into the plasma. “Liquid biopsy” analysis of mutations or other genomic alterations in circulating cell-free DNA (cfDNA) may provide us with a tool to detect minimal residual cancer, comprehensively profile the genomic tumor landscape in search of druggable targets, and monitor cancers non-invasively over time for treatment failure or emerging treatment-resistant tumor subclones. While liquid biopsies have not yet entered routine clinical management in patients with gastric and gastroesophageal junction cancers, this group of diseases may benefit from such advanced diagnostic tools due to their pronounced genetic spatiotemporal heterogeneity and limitations in imaging sensitivity. Moreover, as the armamentarium of targeted treatment approaches and immunotherapies expands, cfDNA analyses may reveal their utility not only as a biomarker of response but also for precision monitoring. In this review, we discuss the different applications of cfDNA analyses in patients with gastric and gastroesophageal junction cancer and the technical challenges that such liquid biopsies have yet to overcome.
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Affiliation(s)
| | - Mascha Binder
- Correspondence: ; Tel.: +49-345-557-4972; Fax: +49-345-557-2950
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21
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Chidambaram S, Markar SR. Clinical utility and applicability of circulating tumor DNA testing in esophageal cancer: a systematic review and meta-analysis. Dis Esophagus 2022; 35:doab046. [PMID: 34286823 PMCID: PMC8832526 DOI: 10.1093/dote/doab046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022]
Abstract
Esophageal cancer is an aggressive malignancy with a relatively poor prognosis even after multimodality therapy. Currently, patients undergo a series of investigations that can be invasive and costly or pose secondary risks to their health. In other malignancies, liquid biopsies of circulating tumor DNA (ctDNA) are used in clinical practice for diagnostic and surveillance purposes. This systematic review summarizes the latest evidence for the clinical applicability of ctDNA technology in esophageal cancer. A systematic review of the literature was performed using MEDLINE, EMBASE, the Cochrane Review and Scopus databases. Articles were evaluated for the use of ctDNA for diagnosis and monitoring of patients with esophageal cancer. Quality assessment of studies was performed using the QUADAS-2 tool. A meta-analysis was performed to assess the diagnostic accuracy of sequencing methodologies. We included 15 studies that described the use of ctDNA technology in the qualitative synthesis and eight studies involving 414 patients in the quantitative analysis. Of these, four studies assessed its utility in cancer diagnosis, while four studies evaluated its use for prognosis and monitoring. The pooled sensitivity and specificity for diagnostic studies were 71.0% (55.7-82.6%) and 98.6% (33.9-99.9%), while the pooled sensitivity and specificity for surveillance purposes were 48.9% (29.4-68.8%) and 95.5% (90.6-97.9%). ctDNA technology is an acceptable method for diagnosis and monitoring with a moderate sensitivity and high specificity that is enhanced in combination with current imaging methods. Further work should demonstrate the practical integration of ctDNA in the diagnostic and surveillance clinical pathway.
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Affiliation(s)
| | - Sheraz R Markar
- Department of Surgery and Cancer, Imperial College London, London, UK
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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22
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Flach S, Howarth K, Hackinger S, Pipinikas C, Ellis P, McLay K, Marsico G, Forshew T, Walz C, Reichel CA, Gires O, Canis M, Baumeister P. Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)-a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma. Br J Cancer 2022; 126:1186-1195. [PMID: 35132238 PMCID: PMC9023460 DOI: 10.1038/s41416-022-01716-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/11/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) remain a substantial burden to global health. Cell-free circulating tumour DNA (ctDNA) is an emerging biomarker but has not been studied sufficiently in HNSCC. METHODS We conducted a single-centre prospective cohort study to investigate ctDNA in patients with p16-negative HNSCC who received curative-intent primary surgical treatment. Whole-exome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) tumour tissue. We utilised RaDaRTM, a highly sensitive personalised assay using deep sequencing for tumour-specific variants, to analyse serial pre- and post-operative plasma samples for evidence of minimal residual disease and recurrence. RESULTS In 17 patients analysed, personalised panels were designed to detect 34 to 52 somatic variants. Data show ctDNA detection in baseline samples taken prior to surgery in 17 of 17 patients. In post-surgery samples, ctDNA could be detected at levels as low as 0.0006% variant allele frequency. In all cases with clinical recurrence to date, ctDNA was detected prior to progression, with lead times ranging from 108 to 253 days. CONCLUSIONS This study illustrates the potential of ctDNA as a biomarker for detecting minimal residual disease and recurrence in HNSCC and demonstrates the feasibility of personalised ctDNA assays for the detection of disease prior to clinical recurrence.
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Affiliation(s)
- Susanne Flach
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.
| | | | | | | | - Pete Ellis
- Inivata Ltd, Babraham Research Park, Cambridge, UK
| | | | | | - Tim Forshew
- Inivata Ltd, Babraham Research Park, Cambridge, UK
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Christoph A Reichel
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
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23
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van Velzen MJM, Creemers A, van den Ende T, Schokker S, Krausz S, Reinten RJ, Dijk F, van Noesel CJM, Halfwerk H, Meijer SL, Mearadji B, Derks S, Bijlsma MF, van Laarhoven HWM. Circulating tumor DNA predicts outcome in metastatic gastroesophageal cancer. Gastric Cancer 2022; 25:906-915. [PMID: 35763187 PMCID: PMC9365750 DOI: 10.1007/s10120-022-01313-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/25/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has predictive and prognostic value in localized and metastatic cancer. This study analyzed the prognostic value of baseline and on-treatment ctDNA in metastatic gastroesophageal cancer (mGEC) using a region-specific next generation sequencing (NGS) panel. METHODS Cell free DNA was isolated from plasma of patients before start of first-line palliative systemic treatment and after 9 and 18 weeks. Two NGS panels were designed comprising the most frequently mutated genes and targetable mutations in GEC. Tumor-derived mutations in matched metastatic biopsies were used to validate that the sequencing panels assessed true tumor-derived variants. Tumor volumes were calculated from baseline CT scans and correlated to variant allele frequency (VAF). Survival analyses were performed using univariable and multivariable Cox-regression analyses. RESULTS ctDNA was detected in pretreatment plasma in 75% of 72 patients and correlated well with mutations in metastatic biopsies (86% accordance). The VAF correlated with baseline tumor volume (Pearson's R 0.53, p < 0.0001). Detection of multiple gene mutations at baseline in plasma was associated with worse overall survival (OS, HR 2.16, 95% CI 1.10-4.28; p = 0.027) and progression free survival (PFS, HR 2.71, 95% CI 1.28-5.73; p = 0.009). OS and PFS were inferior in patients with residual detectable ctDNA after 9 weeks of treatment (OS: HR 4.95, 95% CI 1.53-16.04; p = 0.008; PFS: HR 4.08, 95% CI 1.31-12.75; p = 0.016). CONCLUSION Based on our NGS panel, the number of ctDNA mutations before start of first-line chemotherapy has prognostic value. Moreover, residual ctDNA after three cycles of systemic treatment is associated with inferior survival.
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Affiliation(s)
- Merel J. M. van Velzen
- grid.7177.60000000084992262Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Aafke Creemers
- grid.7177.60000000084992262Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.7177.60000000084992262Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Tom van den Ende
- grid.7177.60000000084992262Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Sandor Schokker
- grid.7177.60000000084992262Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Krausz
- grid.7177.60000000084992262Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Roy J. Reinten
- grid.7177.60000000084992262Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Frederike Dijk
- grid.7177.60000000084992262Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Carel J. M. van Noesel
- grid.7177.60000000084992262Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Hans Halfwerk
- grid.7177.60000000084992262Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Sybren L. Meijer
- grid.7177.60000000084992262Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Banafsche Mearadji
- grid.7177.60000000084992262Department of Radiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Sarah Derks
- grid.12380.380000 0004 1754 9227Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, Amsterdam, The Netherlands
| | - Maarten F. Bijlsma
- grid.7177.60000000084992262Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Hanneke W. M. van Laarhoven
- grid.7177.60000000084992262Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.12380.380000 0004 1754 9227Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, Amsterdam, The Netherlands
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Underhill HR. Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology? Mol Diagn Ther 2021; 25:389-408. [PMID: 34018157 PMCID: PMC8249304 DOI: 10.1007/s40291-021-00534-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy’s molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.
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Affiliation(s)
- Hunter R Underhill
- Division of Medical Genetics, Department of Pediatrics, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA. .,Department of Radiology, University of Utah, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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25
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Long S, Berkemeier B. Development of a reverse transcription droplet digital PCR (RT-ddPCR) assay for sensitive detection of simian immunodeficiency virus (SIV). Virol J 2021; 18:35. [PMID: 33588884 PMCID: PMC7883996 DOI: 10.1186/s12985-021-01503-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Simian immunodeficiency virus (SIV)-infected rhesus macaques constitute an excellent model of human HIV infection. Sensitive detection of SIV RNA in cell and tissue samples from infected animals subjected to treatment regimens becomes especially critical in determining which therapeutic attempts are successful, and consequently, which interventions should be prioritized in HIV cure research. RESULTS In this report, we describe the design and testing of a Raindance ddPCR platform-based, sensitive SIV reverse transcription droplet digital PCR (RT-ddPCR) assay by exploring the combinations of various priming conditions and reverse transcriptases, and testing one-step vs. two-step procedures, to eliminate background signal(s) and enable detection and quantification of low level target signals. CONCLUSIONS Similar reaction conditions and assay validation procedures can be explored for potential development of additional assays for other applications that require sensitive detection of low-level targets in RNA samples.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
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