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Abbosh C, Hodgson D, Doherty GJ, Gale D, Black JRM, Horn L, Reis-Filho JS, Swanton C. Implementing circulating tumor DNA as a prognostic biomarker in resectable non-small cell lung cancer. Trends Cancer 2024:S2405-8033(24)00089-X. [PMID: 38839544 DOI: 10.1016/j.trecan.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Systemic treatment of resectable non-small cell lung cancer (NSCLC) is evolving with emerging neoadjuvant, perioperative, and adjuvant immunotherapy approaches. Circulating tumor DNA (ctDNA) detection at clinical diagnosis, during neoadjuvant therapy, or after resection may discern high-risk patients who might benefit from therapy escalation or switch. This Review summarizes translational implications of data supporting ctDNA-based risk determination in NSCLC and outstanding questions regarding ctDNA validity/utility as a prognostic biomarker. We discuss emerging ctDNA capabilities to refine clinical tumor-node-metastasis (TNM) staging in lung adenocarcinoma, ctDNA dynamics during neoadjuvant therapy for identifying patients deriving suboptimal benefit, and postoperative molecular residual disease (MRD) detection to escalate systemic therapy. Considering differential relapse characteristics in landmark MRD-negative/MRD-positive patients, we propose how ctDNA might integrate with pathological response data for optimal postoperative risk stratification.
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Affiliation(s)
- Chris Abbosh
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - Darren Hodgson
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | | | - Davina Gale
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Leora Horn
- Clinical Development, Late Oncology, AstraZeneca, Nashville, TN, USA
| | - Jorge S Reis-Filho
- Cancer Biomarker Development, Early Oncology, AstraZeneca, Gaithersburg, MD, USA
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
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2
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Rodriguez-Quintero JH, Jindani R, Kamel MK, Zhu R, Vimolratana M, Chudgar NP, Stiles BM. Resection of the Primary Tumor and Survival in Patients with Single-Site Synchronous Oligometastatic Non-Small Cell Lung Cancer: Propensity-Matched Analysis of the National Cancer Database. J Am Coll Surg 2024; 238:1122-1136. [PMID: 38334285 PMCID: PMC11096043 DOI: 10.1097/xcs.0000000000001035] [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] [Indexed: 02/10/2024]
Abstract
BACKGROUND Local therapy for the primary tumor is postulated to remove resistant cancer cells as well as immunosuppressive cells from the tumor microenvironment, potentially improving response to systemic therapy (ST). We sought to determine whether resection of the primary tumor was associated with overall survival (OS) in a multicentric cohort of patients with single-site synchronous oligometastatic non-small cell lung cancer. STUDY DESIGN Using the National Cancer Database (2018 to 2020), we evaluated patients with clinical stage IVA disease who received ST and stratified the cohort based on receipt of surgery for the primary tumor (S). We used multivariable and propensity score-matched analysis to study factors associated with S (logistic regression) and OS (Cox regression and Kaplan-Meier), respectively. RESULTS Among 12,215 patients identified, 2.9% (N = 349) underwent S and 97.1% (N = 11,886) ST (chemotherapy or immunotherapy) without surgery. Patients who underwent S were younger, more often White, had higher income levels, were more likely to have private insurance, and were more often treated at an academic facility. Among those who received S, 22.9% (N = 80) also underwent resection of the distant metastatic site. On multivariable analysis, metastasis to bone, N+ disease, and higher T-stages were independently associated with less S. On Cox regression, S and resection of the metastatic site were associated with improved survival (hazard ratio 0.67, 95% CI 0.56 to 0.80 and hazard ratio 0.80, 95% CI 0.72 to 0.88, respectively). After propensity matching, OS was improved in patients undergoing S (median 36.8 vs 20.8 months, log-rank p < 0.001). CONCLUSIONS Advances in ST for non-small cell lung cancer may change the paradigm of eligibility for surgery. This study demonstrates that surgical resection of the primary tumor is associated with improved OS in selected patients with single-site oligometastatic disease.
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Affiliation(s)
- Jorge Humberto Rodriguez-Quintero
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
| | - Rajika Jindani
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
| | - Mohamed K Kamel
- University of Rochester Medical Center, Department of Cardiothoracic Surgery. 601 Elmwood Ave. Rochester, NY 1464
| | - Roger Zhu
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
| | - Marc Vimolratana
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
| | - Neel P Chudgar
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
| | - Brendon M Stiles
- Montefiore Medical Center/ Albert Einstein College of Medicine. Department of Cardiothoracic and Vascular Surgery. 3400 Bainbridge. Bronx, New York. 10467
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Chen K, He Y, Wang W, Yuan X, Carbone DP, Yang F. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing) 2024; 69:1556-1568. [PMID: 38641511 DOI: 10.1016/j.scib.2024.03.062] [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: 09/25/2023] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.
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Affiliation(s)
- Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing 100191, China
| | - David P Carbone
- Thoracic Oncology Center, Ohio State University, Columbus 43026, USA.
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China.
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Nordentoft I, Lindskrog SV, Birkenkamp-Demtröder K, Gonzalez S, Kuzman M, Levatic J, Glavas D, Ptashkin R, Smadbeck J, Afterman D, Lauterman T, Cohen Y, Donenhirsh Z, Tavassoly I, Alon U, Frydendahl A, Rasmussen MH, Andersen CL, Lamy P, Knudsen M, Polak P, Zviran A, Oklander B, Agerbæk M, Jensen JB, Dyrskjøt L. Whole-genome Mutational Analysis for Tumor-informed Detection of Circulating Tumor DNA in Patients with Urothelial Carcinoma. Eur Urol 2024:S0302-2838(24)02384-4. [PMID: 38811314 DOI: 10.1016/j.eururo.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/25/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND AND OBJECTIVE Circulating tumor DNA (ctDNA) can be used for sensitive detection of minimal residual disease (MRD). However, the probability of detecting ctDNA in settings of low tumor burden is limited by the number of mutations analyzed and the plasma volume available. We used a whole-genome sequencing (WGS) approach for ctDNA detection in patients with urothelial carcinoma. METHODS We used a tumor-informed WGS approach for ctDNA-based detection of MRD and evaluation of treatment responses. We analyzed 916 longitudinally collected plasma samples from 112 patients with localized muscle-invasive bladder cancer who received neoadjuvant chemotherapy (NAC) before radical cystectomy. Recurrence-free survival (primary endpoint), overall survival, and ctDNA dynamics during NAC were assessed. KEY FINDINGS AND LIMITATIONS We found that WGS-based ctDNA detection is prognostic for patient outcomes with a median lead time of 131 d over radiographic imaging. WGS-based ctDNA assessment after radical cystectomy identified recurrence with sensitivity of 91% and specificity of 92%. In addition, genomic characterization of post-treatment plasma samples with a high ctDNA level revealed acquisition of platinum therapy-associated mutational signatures and copy number variations not present in the primary tumors. The sequencing depth is a limitation for studying tumor evolution. CONCLUSIONS AND CLINICAL IMPLICATIONS Our results support the use of WGS for ultrasensitive ctDNA detection and highlight the possibility of plasma-based tracking of tumor evolution. WGS-based ctDNA detection represents a promising option for clinical use owing to the low volume of plasma needed and the ease of performing WGS, eliminating the need for personalized assay design. PATIENT SUMMARY Detection of tumor DNA in blood samples from patients with cancer of the urinary tract is associated with poorer outcomes. Disease recurrence after surgery can be identified by the presence of tumor DNA in blood before it can be detected on radiography scans.
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Affiliation(s)
- Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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Fu R, Xiong Y, Cai M, Li F, Chen R, Wu Y, Zhong W. Evaluation of molecular residual disease in operable non-small cell lung cancer with gene fusions, MET exon skipping or de novo MET amplification. Front Med 2024:10.1007/s11684-024-1060-z. [PMID: 38805102 DOI: 10.1007/s11684-024-1060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 05/29/2024]
Abstract
Gene fusions and MET alterations are rare and difficult to detect in plasma samples. The clinical detection efficacy of molecular residual disease (MRD) based on circulating tumor DNA (ctDNA) in patients with non-small cell lung cancer (NSCLC) with these mutations remains unknown. This prospective, non-intervention study recruited 49 patients with operable NSCLC with actionable gene fusions (ALK, ROS1, RET, and FGFR1), MET exon 14 skipping or de novo MET amplification. We analyzed 43 tumor tissues and 111 serial perioperative plasma samples using 1021- and 338-gene panels, respectively. Detectable MRD correlated with a significantly higher recurrence rate (P < 0.001), yielding positive predictive values of 100% and 90.9%, and negative predictive values of 82.4% and 86.4% at landmark and longitudinal time points, respectively. Patients with detectable MRD showed reduced disease-free survival (DFS) compared to those with undetectable MRD (P < 0.001). Patients who harbored tissue-derived fusion/MET alterations in their MRD had reduced DFS compared to those who did not (P = 0.05). To our knowledge, this is the first comprehensive study on ctDNA-MRD clinical detection efficacy in operable NSCLC patients with gene fusions and MET alterations. Patients with detectable tissue-derived fusion/MET alterations in postoperative MRD had worse clinical outcomes.
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Affiliation(s)
- Rui Fu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | | | - Miao Cai
- Geneplus-Beijing, Beijing, 102206, China
| | - Fang Li
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Yilong Wu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Wenzhao Zhong
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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6
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Bossé Y, Dasgupta A, Abadier M, Guthrie V, Song F, Saavedra Armero V, Gaudreault N, Orain M, Lamaze FC, Melton C, Nance T, Hung T, Hodgson D, Abbosh C, Joubert P. Prognostic implication of methylation-based circulating tumor DNA detection prior to surgery in stage I non-small cell lung cancer. Cancer Lett 2024; 594:216984. [PMID: 38797230 DOI: 10.1016/j.canlet.2024.216984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) positivity at diagnosis, which is associated with worse outcomes in multiple solid tumors including stage I-III non-small cell lung cancer (NSCLC), may have utility to guide (neo)adjuvant therapy. METHODS In this retrospective study, 260 patients with clinical stage I NSCLC (180 adenocarcinoma, 80 squamous cell carcinoma) were allocated (2:1) to high- and low-risk groups based on relapse versus disease-free status ≤5 years post-surgery. We evaluated the association of preoperative ctDNA detection by a plasma-only targeted methylation-based multi-cancer early detection (MCED) test with NSCLC relapse ≤5 years post-surgery in the overall population, followed by histology-specific subgroup analyses. RESULTS Across clinical stage I patients, preoperative ctDNA detection did not associate with relapse within 5 years post-surgery. Sub-analyses confined to lung adenocarcinoma suggested a histology-specific association between ctDNA detection and outcome. In this group, ctDNA positivity tended to associate with relapse within 2 years, suggesting prognostic implications of MCED test positivity may be histology- and time-dependent in stage I NSCLC. Preoperative ctDNA detection was associated with upstaging of clinical stage I to pathological stage II-III NSCLC. CONCLUSIONS Our findings suggest preoperative ctDNA detection in patients with resectable clinical stage I NSCLC using MCED, a pan-cancer screening test developed for use in an asymptomatic population, has no detectable prognostic value for relapse ≤5 years post-surgery. MCED detection may be associated with early adenocarcinoma relapse and increased pathological upstaging rates in stage I NSCLC. However, given the exploratory nature of these findings, independent validation is required.
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Affiliation(s)
- Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Medicine, Université Laval, Quebec City, Canada.
| | - Abhijit Dasgupta
- Oncology Data Science, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Michael Abadier
- Translational Medicine Early Oncology, AstraZeneca, Waltham, MA, USA
| | - Violeta Guthrie
- Oncology Data Science, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Florian Song
- Translational Medicine Early Oncology, AstraZeneca, Munich, Germany
| | - Victoria Saavedra Armero
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Michèle Orain
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Fabien C Lamaze
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | | | | | | | - Darren Hodgson
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Chris Abbosh
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Biology, Pathology and Medical Biochemistry, Université Laval, Quebec City, Canada
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7
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Stetson D, Labrousse P, Russell H, Shera D, Abbosh C, Dougherty B, Barrett JC, Hodgson D, Hadfield J. Next-Generation Molecular Residual Disease Assays: Do We Have the Tools to Evaluate Them Properly? J Clin Oncol 2024:JCO2302301. [PMID: 38754043 DOI: 10.1200/jco.23.02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/27/2024] [Accepted: 03/05/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Dan Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Paul Labrousse
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Hugh Russell
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - David Shera
- Oncology Biometrics, AstraZeneca, Gaithersburg, MD
| | - Chris Abbosh
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Darren Hodgson
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - James Hadfield
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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Liu Y, Zhai Y, Hu H, Liao Y, Liu H, Liu X, He J, Wang L, Wang H, Li L, Zhou X, Xiao X. Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400011. [PMID: 38698560 DOI: 10.1002/advs.202400011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/09/2024] [Indexed: 05/05/2024]
Abstract
DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
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Affiliation(s)
- Yizhou Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuxuan Zhai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuheng Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiachen He
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hongxun Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Longjie Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, China
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Hashimoto T, Nakamura Y, Oki E, Kobayashi S, Yuda J, Shibuki T, Bando H, Yoshino T. Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay. Int J Clin Oncol 2024; 29:495-511. [PMID: 38551727 PMCID: PMC11043144 DOI: 10.1007/s10147-024-02493-4] [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: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.
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Affiliation(s)
- Tadayoshi Hashimoto
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Kobayashi
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taro Shibuki
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
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Payne KFB, Brotherwood P, Suriyanarayanan H, Brooks JM, Batis N, Beggs AD, Gendoo DMA, Mehanna H, Nankivell P. Circulating tumour DNA detects somatic variants contributing to spatial and temporal intra-tumoural heterogeneity in head and neck squamous cell carcinoma. Front Oncol 2024; 14:1374816. [PMID: 38846976 PMCID: PMC11154907 DOI: 10.3389/fonc.2024.1374816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/09/2024] [Indexed: 06/09/2024] Open
Abstract
Background As circulating tumour DNA (ctDNA) liquid biopsy analysis is increasingly incorporated into modern oncological practice, establishing the impact of genomic intra-tumoural heterogeneity (ITH) upon data output is paramount. Despite advances in other cancer types the evidence base in head and neck squamous cell carcinoma (HNSCC) remains poor. We sought to investigate the utility of ctDNA to detect ITH in HNSCC. Methods In a pilot cohort of 9 treatment-naïve HNSCC patients, DNA from two intra-tumoural sites (core and margin) was whole-exome sequenced. A 9-gene panel was designed to perform targeted sequencing on pre-treatment plasma cell-free DNA and selected post-treatment samples. Results Rates of genomic ITH among the 9 patients was high. COSMIC variants from 19 TCGA HNSCC genes demonstrated an 86.9% heterogeneity rate (present in one tumour sub-site only). Across all patients, cell-free DNA (ctDNA) identified 12.9% (range 7.5-19.8%) of tumour-specific variants, of which 55.6% were specific to a single tumour sub-site only. CtDNA identified 79.0% (range: 55.6-90.9%) of high-frequency variants (tumour VAF>5%). Analysis of ctDNA in serial post-treatment blood samples in patients who suffered recurrence demonstrated dynamic changes in both tumour-specific and acquired variants that predicted recurrence ahead of clinical detection. Conclusion We demonstrate that a ctDNA liquid biopsy identified spatial genomic ITH in HNSCC and reliably detected high-frequency driver mutations. Serial sampling allowed post-treatment surveillance and early identification of treatment failure.
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Affiliation(s)
- Karl F. B. Payne
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Brotherwood
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Harini Suriyanarayanan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jill M. Brooks
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nikolaos Batis
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Deena M. A. Gendoo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Interdisciplinary Data Science and AI, University of Birmingham, Birmingham, United Kingdom
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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11
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Nesic M, Rasmussen MH, Henriksen TV, Demuth C, Frydendahl A, Nordentoft I, Dyrskjøt L, Andersen CL. Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection. Int J Cancer 2024. [PMID: 38623608 DOI: 10.1002/ijc.34964] [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: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor-informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1-46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High-CCF mutations were detected more frequently than low-CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72-173, p = 1.73e-12; Cohort I: OR 2.24, 95% CI 1.44-3.52, p = 1.66e-04; and Cohort N: OR 1.78, 95% CI 1.14-2.79, p = 7.86e-03). The detection-likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14-2.11, p = 3.85e-03; Cohort I: OR 1.78, 95% CI 1.23-2.56, p = 1.34e-03; and Cohort N: OR 1.94, 95% CI 1.63-2.31, p = 2.83e-14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection-likelihood, particularly evident when plasma cell-free DNA tumor fractions were below 0.1% (p = 2.1e-07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor-informed ctDNA analysis.
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Affiliation(s)
- Marijana Nesic
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tenna V Henriksen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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12
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Bertolaccini L, Casiraghi M, Uslenghi C, Maiorca S, Spaggiari L. Recent advances in lung cancer research: unravelling the future of treatment. Updates Surg 2024:10.1007/s13304-024-01841-3. [PMID: 38581618 DOI: 10.1007/s13304-024-01841-3] [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: 03/06/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Lung cancer, a multifaceted disease, demands tailored therapeutic approaches due to its diverse subtypes and stages. This comprehensive review explores the intricate landscape of lung cancer research, delving into recent breakthroughs and their implications for diagnosis, therapy, and prevention. Genomic profiling and biomarker identification have ushered in the era of personalised medicine, enabling targeted therapies that minimise harm to healthy tissues while effectively combating cancer cells. The relationship between pulmonary tuberculosis and lung cancer is examined, shedding light on potential mechanisms linking these two conditions. Early detection methods, notably low-dose computed tomography scans, have significantly improved patient outcomes, emphasising the importance of timely interventions. There has been a growing interest in segmentectomy as a surgical intervention for early-stage lung cancer in recent years. Immunotherapy has emerged as a transformative approach, harnessing the body's immune system to recognise and eliminate cancer cells. Combining immunotherapy with traditional treatments, such as chemotherapy and targeted therapies, has shown enhanced efficacy, addressing the disease's heterogeneity and overcoming drug resistance. Precision medicine, guided by genomic profiling, has enabled the development of targeted therapies like tyrosine kinase inhibitors, offering personalised treatments tailored to individual patients. Challenges such as drug resistance and limited accessibility to advanced therapies persist, emphasising the need for collaborative efforts and innovative technologies like artificial intelligence. Despite challenges, ongoing interdisciplinary collaborations and technological advancements offer hope for a future where lung cancer is treatable and preventable, reducing the burden on patients and healthcare systems worldwide.
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Affiliation(s)
- Luca Bertolaccini
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.
| | - Monica Casiraghi
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Clarissa Uslenghi
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - Sebastiano Maiorca
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | - Lorenzo Spaggiari
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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13
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Anagnostou V, Velculescu VE. Pushing the Boundaries of Liquid Biopsies for Early Precision Intervention. Cancer Discov 2024; 14:615-619. [PMID: 38571422 DOI: 10.1158/2159-8290.cd-24-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Liquid biopsies are emerging as powerful minimally invasive approaches that have the potential to solve several long-standing problems spanning the continuum of cancer care: early detection of cancer, minimal residual disease tracking, and refinement of the heterogeneity of clinical responses together with therapeutic response monitoring in the metastatic setting. Existing challenges driven by technical limitations and establishment of the clinical value of liquid biopsies represent fields of active research that call for convergence science approaches to bridge scientific discovery with clinical care.
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Affiliation(s)
- Valsamo Anagnostou
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor E Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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14
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Ren F, Fei Q, Qiu K, Zhang Y, Zhang H, Sun L. Liquid biopsy techniques and lung cancer: diagnosis, monitoring and evaluation. J Exp Clin Cancer Res 2024; 43:96. [PMID: 38561776 PMCID: PMC10985944 DOI: 10.1186/s13046-024-03026-7] [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: 01/12/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer stands as the most prevalent form of cancer globally, posing a significant threat to human well-being. Due to the lack of effective and accurate early diagnostic methods, many patients are diagnosed with advanced lung cancer. Although surgical resection is still a potential means of eradicating lung cancer, patients with advanced lung cancer usually miss the best chance for surgical treatment, and even after surgical resection patients may still experience tumor recurrence. Additionally, chemotherapy, the mainstay of treatment for patients with advanced lung cancer, has the potential to be chemo-resistant, resulting in poor clinical outcomes. The emergence of liquid biopsies has garnered considerable attention owing to their noninvasive nature and the ability for continuous sampling. Technological advancements have propelled circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), tumor metabolites, tumor-educated platelets (TEPs), and tumor-associated antigens (TAA) to the forefront as key liquid biopsy biomarkers, demonstrating intriguing and encouraging results for early diagnosis and prognostic evaluation of lung cancer. This review provides an overview of molecular biomarkers and assays utilized in liquid biopsies for lung cancer, encompassing CTCs, ctDNA, non-coding RNA (ncRNA), EVs, tumor metabolites, TAAs and TEPs. Furthermore, we expound on the practical applications of liquid biopsies, including early diagnosis, treatment response monitoring, prognostic evaluation, and recurrence monitoring in the context of lung cancer.
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Affiliation(s)
- Fei Ren
- Department of Geriatrics, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Qian Fei
- Department of Oncology, Shengjing Hospital of China Medical University, Shen Yang, 110000, China
| | - Kun Qiu
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Yuanjie Zhang
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shen Yang, 110000, China.
| | - Lei Sun
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China.
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15
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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16
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Swanton C, Bernard E, Abbosh C, André F, Auwerx J, Balmain A, Bar-Sagi D, Bernards R, Bullman S, DeGregori J, Elliott C, Erez A, Evan G, Febbraio MA, Hidalgo A, Jamal-Hanjani M, Joyce JA, Kaiser M, Lamia K, Locasale JW, Loi S, Malanchi I, Merad M, Musgrave K, Patel KJ, Quezada S, Wargo JA, Weeraratna A, White E, Winkler F, Wood JN, Vousden KH, Hanahan D. Embracing cancer complexity: Hallmarks of systemic disease. Cell 2024; 187:1589-1616. [PMID: 38552609 DOI: 10.1016/j.cell.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
The last 50 years have witnessed extraordinary developments in understanding mechanisms of carcinogenesis, synthesized as the hallmarks of cancer. Despite this logical framework, our understanding of the molecular basis of systemic manifestations and the underlying causes of cancer-related death remains incomplete. Looking forward, elucidating how tumors interact with distant organs and how multifaceted environmental and physiological parameters impinge on tumors and their hosts will be crucial for advances in preventing and more effectively treating human cancers. In this perspective, we discuss complexities of cancer as a systemic disease, including tumor initiation and promotion, tumor micro- and immune macro-environments, aging, metabolism and obesity, cancer cachexia, circadian rhythms, nervous system interactions, tumor-related thrombosis, and the microbiome. Model systems incorporating human genetic variation will be essential to decipher the mechanistic basis of these phenomena and unravel gene-environment interactions, providing a modern synthesis of molecular oncology that is primed to prevent cancers and improve patient quality of life and cancer outcomes.
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Affiliation(s)
- Charles Swanton
- The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Elsa Bernard
- The Francis Crick Institute, London, UK; INSERM U981, Gustave Roussy, Villejuif, France
| | | | - Fabrice André
- INSERM U981, Gustave Roussy, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France; Paris Saclay University, Kremlin-Bicetre, France
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gerard Evan
- The Francis Crick Institute, London, UK; Kings College London, London, UK
| | - Mark A Febbraio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrés Hidalgo
- Department of Immunobiology, Yale University, New Haven, CT 06519, USA; Area of Cardiovascular Regeneration, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Johanna A Joyce
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Katja Lamia
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Department of Medical Oncology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Miriam Merad
- Department of immunology and immunotherapy, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Musgrave
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK; Department of Haematology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Jennifer A Wargo
- Department of Surgical Oncology, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashani Weeraratna
- Sidney Kimmel Cancer Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA; Ludwig Princeton Branch, Ludwig Institute for Cancer Research, Princeton, NJ, USA
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John N Wood
- Molecular Nociception Group, WIBR, University College London, London, UK
| | | | - Douglas Hanahan
- Lausanne Branch, Ludwig Institute for Cancer Research, Lausanne, Switzerland; Swiss institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Agora Translational Cancer Research Center, Lausanne, Switzerland.
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17
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Passaro A, Al Bakir M, Hamilton EG, Diehn M, André F, Roy-Chowdhuri S, Mountzios G, Wistuba II, Swanton C, Peters S. Cancer biomarkers: Emerging trends and clinical implications for personalized treatment. Cell 2024; 187:1617-1635. [PMID: 38552610 PMCID: PMC7616034 DOI: 10.1016/j.cell.2024.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
The integration of cancer biomarkers into oncology has revolutionized cancer treatment, yielding remarkable advancements in cancer therapeutics and the prognosis of cancer patients. The development of personalized medicine represents a turning point and a new paradigm in cancer management, as biomarkers enable oncologists to tailor treatments based on the unique molecular profile of each patient's tumor. In this review, we discuss the scientific milestones of cancer biomarkers and explore future possibilities to improve the management of patients with solid tumors. This progress is primarily attributed to the biological characterization of cancers, advancements in testing methodologies, elucidation of the immune microenvironment, and the ability to profile circulating tumor fractions. Integrating these insights promises to continually advance the precision oncology field, fostering better patient outcomes.
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Affiliation(s)
- Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabrice André
- Gustave-Roussy Cancer Center, Paris Saclay University, Villejuif, France
| | - Sinchita Roy-Chowdhuri
- Department of Anatomic Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, Athens, Greece
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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18
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Fu X, Luo Z, Deng Y, LaFramboise W, Bartlett D, Schwartz R. Marker selection strategies for circulating tumor DNA guided by phylogenetic inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585352. [PMID: 38586041 PMCID: PMC10996527 DOI: 10.1101/2024.03.21.585352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Motivation Blood-based profiling of tumor DNA ("liquid biopsy") has offered great prospects for non-invasive early cancer diagnosis, treatment monitoring, and clinical guidance, but require further advances in computational methods to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific questions: 1) How to apply longitudinal ctDNA data to refine phylogeny models of clonal evolution, and 2) how to quantify changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these questions through a probabilistic framework for optimally identifying maximum likelihood markers and applying them to characterizing clonal evolution. Results We first estimate a distribution over plausible clonal lineage models, using bootstrap samples over pre-treatment tissue-based sequence data. We then refine these lineage models and the clonal frequencies they imply over successive longitudinal samples. We use the resulting framework for modeling and refining tree distributions to pose a set of optimization problems to select ctDNA markers to maximize measures of utility capturing ability to solve the two questions of reducing uncertain in phylogeny models or quantifying clonal frequencies given the models. We tested our methods on synthetic data and showed them to be effective at refining distributions of tree models and clonal frequencies so as to minimize measures of tree distance relative to the ground truth. Application of the tree refinement methods to real tumor data further demonstrated their effectiveness in refining a clonal lineage model and assessing its clonal frequencies. The work shows the power of computational methods to improve marker selection, clonal lineage reconstruction, and clonal dynamics profiling for more precise and quantitative assays of tumor progression. Availability https://github.com/CMUSchwartzLab/Mase-phi.git. Contact russells@andrew.cmu.edu.
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Affiliation(s)
- Xuecong Fu
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Zhicheng Luo
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Yueqian Deng
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - William LaFramboise
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - David Bartlett
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - Russell Schwartz
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
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19
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Northcott J, Bartha G, Harris J, Li C, Navarro FC, Pyke RM, Hong M, Zhang Q, Ma S, Chen TX, Lai J, Udar N, Saldivar JS, Ayash E, Anderson J, Li J, Cui T, Le T, Chow R, Velasco RJ, Mallo C, Santiago R, Bruce RC, Goodman LJ, Chen Y, Norton D, Chen RO, Lyle JM. Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay. Oncotarget 2024; 15:200-218. [PMID: 38484152 PMCID: PMC10939476 DOI: 10.18632/oncotarget.28565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.
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Affiliation(s)
| | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - Qi Zhang
- Personalis, Inc., Fremont, CA 94555, USA
| | - Shuyuan Ma
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Janet Lai
- Personalis, Inc., Fremont, CA 94555, USA
| | - Nitin Udar
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Jiang Li
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tiange Cui
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tu Le
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | - Yi Chen
- Personalis, Inc., Fremont, CA 94555, USA
| | - Dan Norton
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - John M. Lyle
- Personalis, Inc., Fremont, CA 94555, USA
- Co-last authors
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20
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Kunimasa K, Tamiya M, Inoue T, Kawamura T, Miyazaki A, Kojitani Y, Honma K, Nishino K. Clinical application of the Lung Cancer Compact Panel TM using various types of cytological specimens in patients with lung cancer. Lung Cancer 2024; 189:107498. [PMID: 38324922 DOI: 10.1016/j.lungcan.2024.107498] [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: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND The Lung Cancer Compact PanelTM (compact panel) is a gene panel that can detect driver alterations with high sensitivity in liquid samples, including tumor cells. This study examined the ability of a compact panel to detect genetic mutations in liquid specimens used in clinical practice. METHODS Three cohorts, bronchoscopic biopsy forceps washing (washing cohort), pleural effusion (pleural cohort), and spinal fluid (spinal cohort), were analyzed using the compact panel. Liquid samples were added into the GM (Genemetrics) tubes and analyzed. The washing cohort assessed the concordance rate of gene panel analysis outcomes in tissue specimens derived from the primary tumor. Meanwhile, the pleural cohort investigated the impact of storing specimens for 8 weeks and more on nucleic acid and mutation detection rates. RESULTS In the washing cohort (n = 79), the concordance rate with mutations detected in tissues was 75/79 (94.9 %). This rate reached 100 % when focusing solely on driver alterations for treatment. The pleural cohort (n = 8) showed no deterioration in nucleic acid quality or quantity after 8 weeks of storage in GM tubes. Similarly, in the spinal cohort (n = 9), spinal fluid with malignant cells exhibited driver alterations similar to those in the primary tumor. These findings underscore the efficacy of the compact panel in accurately identifying genetic mutations in different liquid specimens. CONCLUSIONS The compact panel is a reliable tool for detecting driver alterations in various cytological specimens. Its consistent performance across diverse sample types emphasizes its potential for guiding targeted therapies for patients with lung cancer and enhancing precision medicine approaches.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan.
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takahisa Kawamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Akito Miyazaki
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yoshiki Kojitani
- Department of Medical Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology & Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
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21
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Desai A, Vázquez TA, Arce KM, Corassa M, Mack PC, Gray JE, Pellini B. ctDNA for the Evaluation and Management of EGFR-Mutant Non-Small Cell Lung Cancer. Cancers (Basel) 2024; 16:940. [PMID: 38473302 DOI: 10.3390/cancers16050940] [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: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating tumor DNA (ctDNA) offers a new paradigm in optimizing treatment strategies for epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC). Its potential spans early-stage disease, influencing adjuvant therapy, to advanced disease, where it aids in identifying genomic markers and resistance mechanisms. This review explores the evolving landscape of utilizing liquid biopsies, specifically circulating tumor DNA (ctDNA), in the management of NSCLC with EGFR mutations. While tissue-based genomic testing remains the cornerstone for clinical decision-making, liquid biopsies offer a well-validated, guideline-recommended alternative approach. Ongoing trials integrating ctDNA for EGFR-mutant NSCLC management are also discussed, shedding light on the potential of ctDNA in early-stage disease, including its applications in prognostication, risk stratification, and minimal residual disease detection post-curative intent treatment. For advanced disease, the role of ctDNA in identifying resistance mechanisms to EGFR tyrosine kinase inhibitors (TKIs) is explored, providing insights into disease progression and guiding treatment decisions. This review also addresses the challenges, including the limitations in sensitivity of current assays for disease recurrence detection, and calls for future studies to refine treatment approaches, standardize reporting, and explore alternative biofluids for enhanced sensitivity. A systematic approach is crucial to address barriers to ctDNA deployment, ensuring equitable access, and facilitating its integration into routine clinical practice.
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Affiliation(s)
- Aakash Desai
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tadana A Vázquez
- School of Medicine, Ponce Health Sciences University, Ponce, PR 00716, USA
| | - Keishla M Arce
- School of Medicine, Ponce Health Sciences University, Ponce, PR 00716, USA
| | - Marcelo Corassa
- Thoracic Oncology Unit, BP-A Beneficência Portuguesa de São Paulo, São Paulo 01323-001, Brazil
| | - Philip C Mack
- Center for Thoracic Oncology, The Tisch Cancer Institute, Mount Sinai Health System, New York, NY 10029, USA
| | - Jhanelle E Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
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22
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Shen X, Dai J, Guo L, Liu Z, Yang L, Gu D, Xie Y, Wang Z, Li Z, Xu H, Shi Q. Single-cell low-pass whole genome sequencing accurately detects circulating tumor cells for liquid biopsy-based multi-cancer diagnosis. NPJ Precis Oncol 2024; 8:30. [PMID: 38321112 PMCID: PMC10847465 DOI: 10.1038/s41698-024-00520-1] [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: 07/06/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Abstract
Accurate detection of circulating tumor cells (CTCs) in blood and non-blood body fluids enables generation of deterministic cancer diagnosis and represent a less invasive and safer liquid biopsy approach. Although genomic alternations have been widely used in circulating tumor DNA (ctDNA) analysis, studies on cell-based genomic alternations profiling for CTC detection are rare due to major technical limitations in single-cell whole genome sequencing (WGS) including low throughput, low accuracy and high cost. We report a single-cell low-pass WGS-based protocol (scMet-Seq) for sensitive and accurate CTC detection by combining a metabolic function-associated marker Hexokinase 2 (HK2) and a Tn5 transposome-based WGS method with improved cell fixation strategy. To explore the clinical use, scMet-Seq has been investigated with blood and non-blood body fluids in diagnosing metastatic diseases, including ascites-based diagnosis of malignant ascites (MA) and blood-based diagnosis of metastatic small-cell lung cancer (SCLC). ScMet-Seq shows high diagnostic sensitivity (MA: 79% in >10 cancer types; metastatic SCLC: 90%) and ~100% of diagnostic specificity and positive predictive value, superior to clinical cytology that exhibits diagnostic sensitivity of 52% in MA diagnosis and could not generate blood-based diagnosis. ScMet-Seq represents a liquid biopsy approach for deterministic cancer diagnosis in different types of cancers and body fluids.
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Affiliation(s)
- Xiaohan Shen
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiao Dai
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Lingchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Zhigang Liu
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Liu Yang
- Shanghai Bone Tumor Institute and Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Dongmei Gu
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Yinghong Xie
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Zhuo Wang
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Haimiao Xu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Qihui Shi
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Engineering Research Center of Biomedical Analysis Reagents, Shanghai, 201203, China.
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23
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Dunne EG, Fick CN, Isbell JM, Chaft JE, Altorki N, Park BJ, Spicer J, Forde PM, Gomez D, Iyengar P, Harpole DH, Stinchcombe TE, Liberman M, Bott MJ, Adusumilli PS, Huang J, Rocco G, Jones DR. The Emerging Role of Immunotherapy in Resectable Non-Small Cell Lung Cancer. Ann Thorac Surg 2024:S0003-4975(24)00080-8. [PMID: 38316378 DOI: 10.1016/j.athoracsur.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Despite surgical resection, long-term survival of patients with resectable non-small cell lung cancer (NSCLC) remains poor. Adjuvant chemotherapy, the standard of care for locally advanced NSCLC, provides a marginal 5.4% benefit in survival. Immune checkpoint inhibitors (ICIs) have shown a significant survival benefit in some patients with advanced NSCLC and are being evaluated for perioperative use in resectable NSCLC. METHODS We conducted a literature search using the PubMed online database to identify clinical trials of immunotherapy in resectable NSCLC and studies analyzing biomarkers and immune priming strategies. RESULTS Building on previous phase I and II trials, randomized phase III trials have shown efficacy of neoadjuvant nivolumab, perioperative pembrolizumab, adjuvant atezolizumab, and adjuvant pembrolizumab in the treatment of NSCLC with improvement of event-free/disease-free survival of 24% to 42%, leading to United States Food and Drug Administration approval of these drugs in the treatment of resectable NSCLC. Three additional phase III trials have also recently reported the use of immunotherapy both before and after surgery, with pathologic complete response rates of 17% to 25%, significantly better than chemotherapy alone. Perioperative ICI therapy has comparable perioperative morbidity to chemotherapy alone and does not impair surgical outcomes. CONCLUSIONS Perioperative immunotherapy, in combination with chemotherapy, is safe and improves outcomes in patients with resectable NSCLC. Questions regarding patient selection, the need for adjuvant ICI therapy after neoadjuvant chemoimmunotherapy, and the duration of perioperative immunotherapy remain to be answered by future trials.
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Affiliation(s)
- Elizabeth G Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cameron N Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James M Isbell
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamie E Chaft
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nasser Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, New York
| | - Bernard J Park
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan Spicer
- Department of Thoracic Surgery, McGill University Health Centre, Montreal, Quebec, Canada
| | - Patrick M Forde
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Daniel Gomez
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Puneeth Iyengar
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H Harpole
- Division of Cardiovascular and Thoracic Surgery, Duke University Medical Center, Durham, North Carolina
| | - Thomas E Stinchcombe
- Division of Medical Oncology, Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Moishe Liberman
- Division of Thoracic Surgery, University of Montreal, Montreal, Quebec, Canada
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Huang
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.
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24
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Dai JY, Zhang J, Braun JV, Simon N, Hubbell E, Zhang N. Clinical performance and utility: A microsimulation model to inform the design of screening trials for a multi-cancer early detection test. J Med Screen 2024:9691413241228041. [PMID: 38304990 DOI: 10.1177/09691413241228041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
OBJECTIVES Designing cancer screening trials for multi-cancer early detection (MCED) tests presents a significant methodology challenge, as natural histories of cell-free DNA-shedding cancers are not yet known. A microsimulation model was developed to project the performance and utility of an MCED test in cancer screening trials. METHODS Individual natural history of preclinical progression through cancer stages for 23 cancer classes was simulated by a stage-transition model under a broad range of cancer latency parameters. Cancer incidences and stage distributions at clinical presentation in simulated trials were set to match the data from Surveillance, Epidemiology, and End Results program. One or multiple rounds of annual screening using a targeted methylation-based MCED test (GalleriⓇ) was conducted to detect preclinical cancers. Mortality benefit of early detection was simulated by a stage-shift model. RESULTS In simulated trials, accounting for healthy volunteer effect and varying test sensitivity, positive predictive value in the prevalence screening round reached 48% to 61% in 6 natural history scenarios. After 3 rounds of annual screening, the cumulative proportions of stage I/II cancers increased by approximately 9% to 14%, the incidence of stage IV cancers was reduced by 37% to 46%, the reduction of stages III and IV cancer incidences was 9% to 24%, and the reduction of mortality reached 13% to 16%. Greater reductions of late-stage cancers and cancer mortality were achieved by five rounds of MCED screening. CONCLUSIONS Simulation results guide trial design and suggest that adding this MCED test to routine screening in the United States may shift cancer detection to earlier stages, and potentially save lives.
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Affiliation(s)
| | | | | | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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25
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Tran HT, Heeke S, Sujit S, Vokes N, Zhang J, Aminu M, Lam VK, Vaporciyan A, Swisher SG, Godoy MCB, Cascone T, Sepesi B, Gibbons DL, Wu J, Heymach JV. Circulating tumor DNA and radiological tumor volume identify patients at risk for relapse with resected, early-stage non-small-cell lung cancer. Ann Oncol 2024; 35:183-189. [PMID: 37992871 DOI: 10.1016/j.annonc.2023.11.008] [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: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Predicting relapse and overall survival (OS) in early-stage non-small-cell lung cancer (NSCLC) patients remains challenging. Therefore, we hypothesized that detection of circulating tumor DNA (ctDNA) can identify patients with increased risk of relapse and that integrating radiological tumor volume measurement along with ctDNA detectability improves prediction of outcome. PATIENTS AND METHODS We analyzed 366 serial plasma samples from 85 patients who underwent surgical resections and assessed ctDNA using a next-generation sequencing liquid biopsy assay, and measured tumor volume using a computed tomography-based three-dimensional annotation. RESULTS Our results showed that patients with detectable ctDNA at baseline or after treatment and patients who did not clear ctDNA after treatment had a significantly worse clinical outcome. Integrating radiological analysis allowed the stratification in risk groups prognostic of clinical outcome as confirmed in an independent cohort of 32 patients. CONCLUSIONS Our findings suggest ctDNA and radiological monitoring could be valuable tools for guiding follow-up care and treatment decisions for early-stage NSCLC patients.
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Affiliation(s)
- H T Tran
- Department of Thoracic Head & Neck Medical Oncology
| | - S Heeke
- Department of Thoracic Head & Neck Medical Oncology
| | - S Sujit
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - N Vokes
- Department of Thoracic Head & Neck Medical Oncology
| | - J Zhang
- Department of Thoracic Head & Neck Medical Oncology
| | - M Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - V K Lam
- Department of Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore
| | - A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery
| | - S G Swisher
- Department of Thoracic and Cardiovascular Surgery
| | - M C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Cascone
- Department of Thoracic Head & Neck Medical Oncology
| | - B Sepesi
- Department of Thoracic Head & Neck Medical Oncology
| | - D L Gibbons
- Department of Thoracic Head & Neck Medical Oncology
| | - J Wu
- Department of Thoracic Head & Neck Medical Oncology; Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - J V Heymach
- Department of Thoracic Head & Neck Medical Oncology.
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26
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Rolfo C, Russo A. Navigating into a stormy sea: liquid biopsy enters peri-operative management in early-stage non-small cell lung cancer. Ann Oncol 2024; 35:147-149. [PMID: 38331558 DOI: 10.1016/j.annonc.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/21/2023] [Indexed: 02/10/2024] Open
Affiliation(s)
- C Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - A Russo
- Department of Onco-Hematology, Papardo Hospital, Messina, Italy
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27
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Li L, Jiang H, Zeng B, Wang X, Bao Y, Chen C, Ma L, Yuan J. Liquid biopsy in lung cancer. Clin Chim Acta 2024; 554:117757. [PMID: 38184141 DOI: 10.1016/j.cca.2023.117757] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Lung cancer is a highly prevalent malignancy worldwide and the primary cause of mortality. The absence of systematic and standardized diagnostic approaches for identifying potential pulmonary nodules, early-stage cancers, and indeterminate tumors has led clinicians to consider tissue biopsy and pathological sections as the preferred method for clinical diagnosis, often regarded as the gold standard. The conventional tissue biopsy is an invasive procedure that does not adequately capture the diverse characteristics and evolving nature of tumors. Recently, the concept of 'liquid biopsy' has gained considerable attention as a promising solution. Liquid biopsy is a non-invasive approach that facilitates repeated analysis, enabling real-time monitoring of tumor recurrence, metastasis, and response to treatment. Currently, liquid biopsy includes circulating tumor cells, circulating cell-free DNA, circulating tumor DNA, circulating cell-free RNA, extracellular vesicles, and other proteins and metabolites. With rapid progress in molecular technology, liquid biopsy has emerged as a highly promising and intriguing approach, yielding compelling results. This article critically examines the significant role and potential clinical implications of liquid biopsy in the diagnosis, treatment, and prognosis of lung cancer.
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Affiliation(s)
- Lan Li
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Haixia Jiang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Bingjie Zeng
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Xianzhao Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Yunxia Bao
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Changqiang Chen
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Lifang Ma
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Jin Yuan
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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28
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Shin SH, Cha S, Lee HY, Shin SH, Kim YJ, Park D, Han KY, Oh YJ, Park WY, Ahn MJ, Kim H, Won HH, Park HY. Machine learning model for circulating tumor DNA detection in chronic obstructive pulmonary disease patients with lung cancer. Transl Lung Cancer Res 2024; 13:112-125. [PMID: 38404987 PMCID: PMC10891398 DOI: 10.21037/tlcr-23-633] [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: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024]
Abstract
Background Patients with chronic obstructive pulmonary disease (COPD) have a high risk of developing lung cancer. Due to the high rates of complications from invasive diagnostic procedures in this population, detecting circulating tumor DNA (ctDNA) as a non-invasive method might be useful. However, clinical characteristics that are predictive of ctDNA mutation detection remain incompletely understood. This study aimed to investigate factors associated with ctDNA detection in COPD patients with lung cancer. Methods Herein, 177 patients with COPD and lung cancer were prospectively recruited. Plasma ctDNA was genotyped using targeted deep sequencing. Comprehensive clinical variables were collected, including the emphysema index (EI), using chest computed tomography. Machine learning models were constructed to predict ctDNA detection. Results At least one ctDNA mutation was detected in 54 (30.5%) patients. After adjustment for potential confounders, tumor stage, C-reactive protein (CRP) level, and milder emphysema were independently associated with ctDNA detection. An increase of 1% in the EI was associated with a 7% decrease in the odds of ctDNA detection (adjusted odds ratio =0.933; 95% confidence interval: 0.857-0.999; P=0.047). Machine learning models composed of multiple clinical factors predicted individuals with ctDNA mutations at high performance (AUC =0.774). Conclusions ctDNA mutations were likely to be observed in COPD patients with lung cancer who had an advanced clinical stage, high CRP level, or milder emphysema. This was validated in machine learning models with high accuracy. Further prospective studies are required to validate the clinical utility of our findings.
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Affiliation(s)
- Sun Hye Shin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Soojin Cha
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea
| | - Ho Yun Lee
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Department of Radiology, Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Shin
- Geninus Inc., Seoul, Republic of Korea
- Artificial Intelligence Research Center, Hallym University Sacred Heart Hospital, Chuncheon-si, Republic of Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Donghyun Park
- Geninus Inc., Seoul, Republic of Korea
- Planit Healthcare Inc., Seoul, Republic of Korea
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - You Jin Oh
- Department of Radiology, Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Woong-Yang Park
- Geninus Inc., Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Myung-Ju Ahn
- Division of Haematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hong-Hee Won
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hye Yun Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Yang Y, Pei G, Li M, Ma X, Wang S, Min X, Meng S, Qin J, Wang H, Liu J, Huang Y. Case report: Targeted sequencing facilitates the diagnosis and management of rare multifocal pure ground-glass opacities with intrapulmonary metastasis. Front Oncol 2024; 13:1276095. [PMID: 38322291 PMCID: PMC10846301 DOI: 10.3389/fonc.2023.1276095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction Treatments for multiple ground-glass opacities (GGOs) for which the detection rate is increasing are still controversial. Next-generation sequencing (NGS) may provide additional key evidence for differential diagnosis or optimal therapeutic schedules. Case presentation We first reported a rare case in which more than 100 bilateral pulmonary GGOs (91.7% of the GGOs were pure GGOs) were diagnosed as both multiple primary lung cancer and intrapulmonary metastasis. We performed NGS with an 808-gene panel to assess both somatic and germline alterations in tissues and plasma. The patient (male) underwent three successive surgeries and received osimertinib adjuvant therapy due to signs of metastasis and multiple EGFR-mutated tumors. The patient had multiple pure GGOs, and eight tumors of four pathological subtypes were evaluated for the clonal relationship. Metastasis, including pure GGOs and atypical adenomatous hyperplasia, was found between two pairs of tumors. Circulating tumor DNA (ctDNA) monitoring of disease status may impact clinical decision-making. Conclusions Surgery combined with targeted therapies remains a reasonable alternative strategy for treating patients with multifocal GGOs, and NGS is valuable for facilitating diagnostic workup and adjuvant therapy with targeted drugs through tissue and disease monitoring via ctDNA.
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Affiliation(s)
- Yingshun Yang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Guotian Pei
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Mingwei Li
- Department of Medicine, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Xiaoxue Ma
- Department of Medicine, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Shuai Wang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Xianjun Min
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing, China
| | - Shushi Meng
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Jiayue Qin
- Department of Medicine, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Huina Wang
- Department of Medicine, Acornmed Biotechnology Co., Ltd, Beijing, China
| | - Jun Liu
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
| | - Yuqing Huang
- Department of Thoracic Surgery, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, China
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30
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Xu Q, Li J, Zhang Z, Yang Q, Zhang W, Yao J, Zhang Y, Zhang Y, Guo Z, Li C, Li S, Zhang C, Wang C, Du L, Li C, Zhou L. Precise determination of reaction conditions for accurate quantification in digital PCR by real-time fluorescence monitoring within microwells. Biosens Bioelectron 2024; 244:115798. [PMID: 37924656 DOI: 10.1016/j.bios.2023.115798] [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: 07/08/2023] [Revised: 09/27/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Real-time digital polymerase chain reaction (qdPCR) provides enhanced precision in the field of molecular diagnostics by integrating absolute quantification with process information. However, the optimal reaction conditions are traditionally determined through multiple iterative of experiments. Therefore, we proposed a novel approach to precisely determine the optimal reaction conditions for qdPCR using a standard process, employing real-time fluorescence monitoring within microwells. The temperature-sensitive fluorophore intensity presented the real temperature of each microwell. This enabled us to determine the optimal denaturation and annealing time for qdPCR based on the corresponding critical temperatures derived from the melting curves and amplification efficiency, respectively. To confirm this method, we developed an ultrathin laminated chip (UTL chip) and chose a target that need to be absolutely quantitative. The UTL chip was designed using a fluid‒solid‒thermal coupling simulation model and exhibited a faster thermal response than a commercial dPCR chip. By leveraging our precise determination of reaction conditions and utilizing the UTL chip, 40 cycles of amplification were achieved within 18 min. This was accomplished by precisely controlling the denaturation temperature at 2 s and the annealing temperature at 10 s. Furthermore, the absolutely quantitative of DNA showed good correlation (R2 > 0.999) with the concentration gradient detection using the optimal reaction conditions with the UTL chip for qdPCR. Our proposed method can significantly improve the accuracy and efficiency of determining qdPCR conditions, which holds great promise for application in molecular diagnostics.
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Affiliation(s)
- Qi Xu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jinze Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Qi Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China; Ji Hua Laboratory, Foshan, 528000, China
| | - Jia Yao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Yaxin Zhang
- Department of Mechanical and Electric Engineering, Changchun University of Science and Technology, Changchun, 130022, China
| | - Yueye Zhang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Shuli Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Changsong Zhang
- Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, 215153, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan, 250012, China.
| | - Chuanyu Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China.
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31
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Cani AK, Hayes DF. Breast Cancer Circulating Tumor Cells: Current Clinical Applications and Future Prospects. Clin Chem 2024; 70:68-80. [PMID: 38175590 DOI: 10.1093/clinchem/hvad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Identification and characterization of circulating tumor markers, designated as "liquid biopsies," have greatly impacted the care of cancer patients. Although more recently referring to circulating tumor DNA (ctDNA), the term liquid biopsy initially was coined to refer to any blood-borne biomarker related to malignancy, including circulating tumor cells (CTCs) in blood. In this manuscript, we review the specific state of the art of CTCs in breast cancer. CONTENT Liquid biopsies might play a clinical role across the entire spectrum of breast cancer, from risk assessment, prevention, screening, and treatment. CTC counts have been shown to carry clear, independent prognostic information in the latter situation. However, the clinical utility of CTCs in breast cancer remains to be determined. Nonetheless, in addition to CTC enumeration, analyses of CTCs provide tumor molecular information representing the entire, often-heterogeneous disease, relatively noninvasively and longitudinally. Technological advances have allowed the interrogation of CTC-derived information, providing renewed hope for a clinical role in disease monitoring and precision oncology. SUMMARY This narrative review examines CTCs, their clinical validity, and current prospects of clinical utility in breast cancer with the goal of improving patient outcomes.
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Affiliation(s)
- Andi K Cani
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Daniel F Hayes
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
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32
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Wang Z, Shen N, Wang Z, Yu L, Yang S, Wang Y, Liu Y, Han G, Zhang Q. TRIM3 facilitates ferroptosis in non-small cell lung cancer through promoting SLC7A11/xCT K11-linked ubiquitination and degradation. Cell Death Differ 2024; 31:53-64. [PMID: 37978273 PMCID: PMC10781973 DOI: 10.1038/s41418-023-01239-5] [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: 06/01/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Ferroptosis, a unique form of regulated necrotic cell death, is caused by excessive iron-dependent lipid peroxidation. However, the underlying mechanisms driving ferroptosis in human cancers remain elusive. In this study, we identified TRIM3, an E3 ubiquitin-protein ligase, as a key regulator of ferroptosis. TRIM3 is downregulated in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), two major types of non-small cell lung cancer (NSCLC). Forced expression of TRIM3 promotes cell death by enhancing the cellular level of ROS and lipid peroxidation. Moreover, our in vivo study determined that TRIM3 overexpression diminishes the tumorigenicity of NSCLC cells, indicating that TRIM3 functions as a tumor suppressor in NSCLC. Mechanistically, TRIM3 directly interacts with SLC7A11/xCT through its NHL domain, leading to SCL7A11 K11-linked ubiquitination at K37, which promotes SLC7A11 proteasome-mediated degradation. Importantly, TRIM3 expression exhibits a negative correlation with SCL7A11 expression in clinical NSCLC samples, and low TRIM3 expression is associated with a worse prognosis. This study reveals that TRIM3 functions as a tumor suppressor that can impede the tumorigenesis of NSCLC by degrading SLC7A11, suggesting a novel therapeutic strategy against NSCLC.
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Affiliation(s)
- Zhangjie Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Na Shen
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Ziao Wang
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
| | - Lei Yu
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Song Yang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Yang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yu Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Gaohua Han
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Qi Zhang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
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33
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Grigoriadis K, Huebner A, Bunkum A, Colliver E, Frankell AM, Hill MS, Thol K, Birkbak NJ, Swanton C, Zaccaria S, McGranahan N. CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction. Nat Protoc 2024; 19:159-183. [PMID: 38017136 DOI: 10.1038/s41596-023-00913-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor cell populations. However, accurate inference of tumor subclonal architecture and reconstruction of tumor evolutionary histories from bulk DNA sequencing data remains challenging. Frequently, sequencing and alignment artifacts are not fully filtered out from cancer somatic mutations, and errors in the identification of copy number alterations or complex evolutionary events (e.g., mutation losses) affect the estimated cellular prevalence of mutations. Together, such errors propagate into the analysis of mutation clustering and phylogenetic reconstruction. In this Protocol, we present a new computational framework, CONIPHER (COrrecting Noise In PHylogenetic Evaluation and Reconstruction), that accurately infers subclonal structure and phylogenetic relationships from multisample tumor sequencing, accounting for both copy number alterations and mutation errors. CONIPHER has been used to reconstruct subclonal architecture and tumor phylogeny from multisample tumors with high-depth whole-exome sequencing from the TRACERx421 dataset, as well as matched primary-metastatic cases. CONIPHER outperforms similar methods on simulated datasets, and in particular scales to a large number of tumor samples and clones, while completing in under 1.5 h on average. CONIPHER enables automated phylogenetic analysis that can be effectively applied to large sequencing datasets generated with different technologies. CONIPHER can be run with a basic knowledge of bioinformatics and R and bash scripting languages.
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Affiliation(s)
- Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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Catarata MJ, Creamer AW, Dias M, Toland S, Chaabouni M, Verbeke K, Vieira Naia J, Hassan M, Naidu SB, Lynch GA, Blyth KG, Rahman NM, Hardavella G. ERS International Congress 2023: highlights from the Thoracic Oncology Assembly. ERJ Open Res 2024; 10:00860-2023. [PMID: 38410708 PMCID: PMC10895436 DOI: 10.1183/23120541.00860-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 02/28/2024] Open
Abstract
Lung cancer is the leading cause of cancer mortality in the world. It greatly affects the patients' quality of life, and is thus a challenge for the daily practice in respiratory medicine. Advances in the genetic knowledge of thoracic tumours' mutational landscape, and the development of targeted therapies and immune checkpoint inhibitors, have led to a paradigm shift in the treatment of lung cancer and pleural mesothelioma. During the 2023 European Respiratory Society Congress in Milan, Italy, experts from all over the world presented their high-quality research and reviewed best clinical practices. Lung cancer screening, management of early stages of lung cancer, application of artificial intelligence and biomarkers were discussed and they will be summarised here.
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Affiliation(s)
- Maria Joana Catarata
- Pulmonology Department, Hospital de Braga, Braga, Portugal
- Tumour and Microenvironment Interactions Group, I3S – Institute for Health Research and Innovation, University of Porto, Porto, Portugal
| | | | - Margarida Dias
- Pulmonology Department, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - Sile Toland
- Department of Medicine, Letterkenny University Hospital, Letterkenny, Ireland
| | - Malek Chaabouni
- Asklepios Klinik Altona, Department of Internal Medicine II, Pulmonology and Thoracic Oncology Section, Hamburg, Germany
| | - Koen Verbeke
- Department of Respiratory Medicine, University Hospital Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Maged Hassan
- Chest Diseases Department, Alexandria University Faculty of Medicine, Alexandria, Egypt
| | | | - Geraldine A. Lynch
- Academic Respiratory Unit, University of Bristol Medical School, Bristol, UK
| | - Kevin G. Blyth
- Queen Elizabeth University Hospital, Glasgow, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Najib M. Rahman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Headington, UK
| | - Georgia Hardavella
- 9th Department of Respiratory Medicine, Sotiria Athens Chest Diseases Hospital, Athens, Greece
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35
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Zhdanov VP. Kinetics of cancer metastasis. Biosystems 2024; 235:105098. [PMID: 38056592 DOI: 10.1016/j.biosystems.2023.105098] [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: 09/03/2023] [Revised: 11/14/2023] [Accepted: 12/02/2023] [Indexed: 12/08/2023]
Abstract
The formation of metastases during cancer is now considered to be induced by migrating metastatic stem cells (MetSCs) in preexisting niches or niches induced by MetSCs or tumor-derived exosomes (TDEs). I propose and compare two simplest generic models describing these two scenarios. The number of tumors is predicted (i) to increase exponentially in the case of preexisting niches and (ii) to diverge during a finite time interval in the case of induced niches. The latter prediction is novel and of interest because rapid collapse in the end of a finite time interval is a well-known feature of the cancer metastasis. Two advanced models describing the two scenarios of cancer metastasis have been scrutinized as well. These models clarify the likely role of various specific factors in the metastasis. In particular, the equations derived in the framework of the advanced model with preexisting niches have been solved analytically allowing (i) to clarify the factors determining the duration of the period from the initiation of the primary tumor to the phase when the metastases start to dominate, (ii) to estimate the number of metastases in the end of this period, and (iii) to explains why the use of chemotherapy typically results in the improvement of the patient state only for a relatively short period. The equations derived in the framework of the advanced model with induced niches have no analytical solution, and their analysis merits additional attention.
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Affiliation(s)
- Vladimir P Zhdanov
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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36
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Melton CA, Freese P, Zhou Y, Shenoy A, Bagaria S, Chang C, Kuo CC, Scott E, Srinivasan S, Cann G, Roychowdhury-Saha M, Chang PY, Singh AH. A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. Cancers (Basel) 2023; 16:82. [PMID: 38201510 PMCID: PMC10777919 DOI: 10.3390/cancers16010082] [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: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.
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37
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Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
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38
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Lindskrog SV, Birkenkamp-Demtröder K, Nordentoft I, Laliotis G, Lamy P, Christensen E, Renner D, Andreasen TG, Lange N, Sharma S, ElNaggar AC, Liu MC, Sethi H, Aleshin A, Agerbæk M, Jensen JB, Dyrskjøt L. Circulating Tumor DNA Analysis in Advanced Urothelial Carcinoma: Insights from Biological Analysis and Extended Clinical Follow-up. Clin Cancer Res 2023; 29:4797-4807. [PMID: 37782315 PMCID: PMC10690087 DOI: 10.1158/1078-0432.ccr-23-1860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/21/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
PURPOSE To investigate whether circulating tumor DNA (ctDNA) assessment in patients with muscle-invasive bladder cancer predicts treatment response and provides early detection of metastatic disease. EXPERIMENTAL DESIGN We present full follow-up results (median follow-up: 68 months) from a previously described cohort of 68 neoadjuvant chemotherapy (NAC)-treated patients who underwent longitudinal ctDNA testing (712 plasma samples). In addition, we performed ctDNA evaluation of 153 plasma samples collected before and after radical cystectomy (RC) in a separate cohort of 102 NAC-naïve patients (median follow-up: 72 months). Total RNA sequencing of tumors was performed to investigate biological characteristics of ctDNA shedding tumors. RESULTS Assessment of ctDNA after RC identified metastatic relapse with a sensitivity of 94% and specificity of 98% using the expanded follow-up data for the NAC-treated patients. ctDNA dynamics during NAC was independently associated with patient outcomes when adjusted for pathologic downstaging (HR = 4.7; P = 0.029). For the NAC-naïve patients, ctDNA was a prognostic predictor before (HR = 3.4; P = 0.0005) and after RC (HR = 17.8; P = 0.0002). No statistically significant difference in recurrence-free survival for patients without detectable ctDNA at diagnosis was observed between the cohorts. Baseline ctDNA positivity was associated with the Basal/Squamous (Ba/Sq) subtype and enrichment of epithelial-to-mesenchymal transition and cell cycle-associated gene sets. CONCLUSIONS ctDNA is prognostic in NAC-treated and NAC-naïve patients with more than 5 years follow-up and outperforms pathologic downstaging in predicting treatment efficacy. Patients without detectable ctDNA at diagnosis may benefit significantly less from NAC, but additional studies are needed.
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Affiliation(s)
- Sia V. Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Tine G. Andreasen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Naja Lange
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen B. Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [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: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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Lee H, Liao JD, Wong TW, Wu CW, Huang BY, Wu SC, Shao PL, Wei YH, Cheng MH. Detection of micro-plasma-induced exosomes secretion in a fibroblast-melanoma co-culture model. Anal Chim Acta 2023; 1281:341910. [PMID: 38783745 DOI: 10.1016/j.aca.2023.341910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 05/25/2024]
Abstract
BACKGROUND Melanoma is a highly aggressive tumor and a significant cause of skin cancer-related death. Timely diagnosis and treatment require identification of specific biomarkers in exosomes secreted by melanoma cells. In this study, label-free surface-enhanced Raman spectroscopy (SERS) method with size-matched selectivity was used to detect membrane proteins in exosomes released from a stimulated environment of fibroblasts (L929) co-cultured with melanoma cells (B16-F10). To promote normal secretion of exosomes, micro-plasma treatment was used to gently induce the co-cultured cells and slightly increase the stress level around the cells for subsequent detection using the SERS method. RESULTS AND DISCUSSION Firstly, changes in reactive oxygen species/reactive nitrogen species (ROS/RNS) concentrations in the cellular microenvironment and the viability and proliferation of healthy cells are assessed. Results showed that micro-plasma treatment increased extracellular ROS/RNS levels while modestly reducing cell proliferation without significantly affecting cell survival. Secondly, the particle size of secreted exosomes isolated from the culture medium of L929, B16-F10, and co-cultured cells with different micro-plasma treatment time did not increase significantly under single-cell conditions at short treatment time but might be changed under co-culture condition or longer treatment time. Third, for SERS signals related to membrane protein biomarkers, exosome markers CD9, CD63, and CD81 can be assigned to significant Raman shifts in the range of 943-1030 and 1304-1561 cm-1, while the characteristics SERS peaks of L929 and B16-F10 cells are most likely located at 1394/1404, 1271 and 1592 cm-1 respectively. SIGNIFICANCE AND NOVELTY Therefore, this micro-plasma-induced co-culture model provides a promising preclinical approach to understand the diagnostic potential of exosomes secreted by cutaneous melanoma/fibroblasts. Furthermore, the label-free SERS method with size-matched selectivity provides a novel approach to screen biomarkers in exosomes secreted by melanoma cells, aiming to reduce the use of labeling reagents and the processing time traditionally required.
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Affiliation(s)
- Han Lee
- Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Jiunn-Der Liao
- Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Tak-Wah Wong
- Department of Dermatology, National Cheng Kung University Hospital, Department of Biochemistry and Molecular Biology, College of Medicine, Center of Applied Nanomedicine, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Che-Wei Wu
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80701, Taiwan; Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung, 80701, Taiwan.
| | - Bo-Yao Huang
- Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Shun-Cheng Wu
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80701, Taiwan; Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung, 80701, Taiwan.
| | - Pei-Lin Shao
- Department of Nursing, Asia University, 500 Liou Feng Road, Taichung, 413, Taiwan.
| | - Yu-Han Wei
- Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Ming-Hsien Cheng
- Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
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Pu Y, Li L, Peng H, Liu L, Heymann D, Robert C, Vallette F, Shen S. Drug-tolerant persister cells in cancer: the cutting edges and future directions. Nat Rev Clin Oncol 2023; 20:799-813. [PMID: 37749382 DOI: 10.1038/s41571-023-00815-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.
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Affiliation(s)
- Yi Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Haoning Peng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Nantes, France
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
- Nantes Université, INSERM, U1307, CRCI2NA, Nantes, France.
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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Zhao J, Reuther J, Scozzaro K, Hawley M, Metzger E, Emery M, Chen I, Barbosa M, Johnson L, O'Connor A, Washburn M, Hartje L, Reckase E, Johnson V, Zhang Y, Westheimer E, O'Callaghan W, Malani N, Chesh A, Moreau M, Daber R. Personalized Cancer Monitoring Assay for the Detection of ctDNA in Patients with Solid Tumors. Mol Diagn Ther 2023; 27:753-768. [PMID: 37632661 PMCID: PMC10590345 DOI: 10.1007/s40291-023-00670-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Highly sensitive molecular assays have been developed to detect plasma-based circulating tumor DNA (ctDNA), and emerging evidence suggests their clinical utility for monitoring minimal residual disease and recurrent disease, providing prognostic information, and monitoring therapy responses in patients with solid tumors. The Invitae Personalized Cancer Monitoring™ assay uses a patient-specific, tumor-informed variant signature identified through whole exome sequencing to detect ctDNA in peripheral blood of patients with solid tumors. METHODS The assay's tumor whole exome sequencing and ctDNA detection components were analytically validated using 250 unique human specimens and nine commercial reference samples that generated 1349 whole exome sequencing and cell-free DNA (cfDNA)-derived libraries. A comparison of tumor and germline whole exome sequencing was used to identify patient-specific tumor variant signatures and generate patient-specific panels, followed by targeted next-generation sequencing of plasma-derived cfDNA using the patient-specific panels with anchored multiplex polymerase chain reaction chemistry leveraging unique molecular identifiers. RESULTS Whole exome sequencing resulted in overall sensitivity of 99.8% and specificity of > 99.9%. Patient-specific panels were successfully designed for all 63 samples (100%) with ≥ 20% tumor content and 24 (80%) of 30 samples with ≥ 10% tumor content. Limit of blank studies using 30 histologically normal, formalin-fixed paraffin-embedded specimens resulted in 100% expected panel design failure. The ctDNA detection component demonstrated specificity of > 99.9% and sensitivity of 96.3% for a combination of 10 ng of cfDNA input, 0.008% allele frequency, 50 variants on the patient-specific panels, and a baseline threshold. Limit of detection ranged from 0.008% allele frequency when utilizing 60 ng of cfDNA input with 18-50 variants in the patient-specific panels (> 99.9% sensitivity) with a baseline threshold, to 0.05% allele frequency when using 10 ng of cfDNA input with an 18-variant panel with a monitoring threshold (> 99.9% sensitivity). CONCLUSIONS The Invitae Personalized Cancer Monitoring assay, featuring a flexible patient-specific panel design with 18-50 variants, demonstrated high sensitivity and specificity for detecting ctDNA at variant allele frequencies as low as 0.008%. This assay may support patient prognostic stratification, provide real-time data on therapy responses, and enable early detection of residual/recurrent disease.
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Affiliation(s)
- Jianhua Zhao
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA.
| | | | - Kaylee Scozzaro
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Megan Hawley
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Emily Metzger
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Matthew Emery
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Ingrid Chen
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | - Laura Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Alijah O'Connor
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Mike Washburn
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Luke Hartje
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Erik Reckase
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Verity Johnson
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
- Affiliated with Invitae Corp. at the time of the study, currently employees at Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Yuhua Zhang
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | | | | | - Nirav Malani
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Adrian Chesh
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Michael Moreau
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
| | - Robert Daber
- Invitae Corp., 1400 16th Street, San Francisco, CA, 94103, USA
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Osoegawa A, Karashima T, Takumi Y, Sato T, Abe M, Hashimoto T, Sugio K. Osimertinib as first-line treatment for recurrent lung cancer patients with EGFR mutation. J Thorac Dis 2023; 15:5566-5573. [PMID: 37969303 PMCID: PMC10636461 DOI: 10.21037/jtd-23-537] [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: 04/01/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023]
Abstract
Background Although osimertinib was approved as adjuvant therapy for lung cancer patients with EGFR mutation in various countries, there is still some ongoing debate as osimertinib has been approved based on disease-free survival (DFS) rather than overall survival (OS). We curated a case series in which we documented patterns of recurrence and efficacy and safety of osimertinib after recurrence. Methods Patients who received osimertinib as first-line treatment for postoperative recurrence between September 2018 and January 2023 were included. Clinicopathological factors, duration of osimertinib treatment (DoT), and adverse events were collected and analyzed. Results Twenty patients received osimertinib [male, n=6; median age, 75 years (range, 55-85 years)]. The EGFR mutation type was L858R in 11 patients and exon 19 deletion in eight patients. The performance status (PS) was 0 or 1 in all but two patients, who had symptomatic brain metastasis and were therefore PS 3. The first site of postoperative recurrence was locoregional in five patients and distant in 15 patients, including seven with brain metastasis. As of February 2023, 10 patients were still on osimertinib, including three with brain metastasis. Patients with brain metastasis or poor PS had a considerably shorter DoT than their counterparts. Three patients with symptomatic brain metastasis or leptomeningeal metastasis initially responded to osimertinib, but all died of disease progression. Five patients discontinued osimertinib due to serious adverse effects (pneumonitis, drug eruption, and heart failure). Conclusions Although osimertinib exerts great disease control, even in patients with brain metastasis or poor PS, their presence was associated with a poor prognosis, even with osimertinib treatment. Therefore, adjuvant osimertinib is recommended unless contraindicated.
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Affiliation(s)
- Atsushi Osoegawa
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Takashi Karashima
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Yohei Takumi
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Takahiro Sato
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Miyuki Abe
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Takafumi Hashimoto
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
| | - Kenji Sugio
- Department of Thoracic and Breast Surgery, Oita University Faculty of Medicine, Yufu, Japan
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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Wu H, Weng GZ, Sun LN, Pan ZC, Zhang L, Chen Q, Shi CM. T Cell Invigoration is Associated with the Clinical Response to Anti-PD-1-Based Immunotherapy in Non-Small Cell Lung Cancer. Cancer Manag Res 2023; 15:1141-1153. [PMID: 37842130 PMCID: PMC10576507 DOI: 10.2147/cmar.s415629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/02/2023] [Indexed: 10/17/2023] Open
Abstract
Purpose Immune checkpoint inhibitors (ICIs) have been developed for clinical application and proven effective for non-small cell lung cancer (NSCLC). Blockade of the programmed cell death 1 (PD-1) protein can partially reinvigorate circulating exhausted-phenotype CD8+ T cells (Tex cells) in preclinical models, however the clinical implication in anti-PD-1-based immunotherapy in NSCLC is unknown. Methods Serum specimens were obtained before and during treatment from 145 patients with NSCLC patients who received anti-PD-1 treatment and their prognoses were followed-up. Indicators such as cell subpopulations, T cell invigoration were detected by clinical laboratory testing. Survival curves were estimated by the Kaplan-Meier method, Cox regression analysis was used to identify factors associated with prognoses of NSCLC patients. Results The expressions of Ki-67 in PD-1+/CD8+ T cells in most NSCLC patients (97 of 145 cases) increased after treatment. The responding Ki-67+/CD8+ T cell population was mainly CD45RAlo CD27hi, containing cells with high expression of CTLA-4, PD-1, and 2B4 and low expression of NKG2-D (P < 0.0001). The maximum fold change of Ki-67+/PD-1+/CD8+T cells in treatment cycles and the tumor burden determined by imaging may be associated with survival. Patients with higher Ki-67 expression on PD-1+CD8+ T-cells (pretreatment) had statistically significant increased progression-free survival (PFS). A Ki-67 expression to tumor burden ratio greater than 0.6 at the 1st cycle of anti-PD-1 immunotherapy was associated with improvement of PFS and overall survival (P < 0.05). Conclusion Activation of circulating Tex cells before or during therapy related to tumor burden may be associated with clinical efficacy of anti-PD-1 immune therapy in NSCLC.
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Affiliation(s)
- Hui Wu
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, People’s Republic of China
- Department of Oncology, Lishui Central Hospital and Fifth Affiliated Hospital of Wenzhou Medical College, Lishui, Zhejiang, 323000, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350001, People’s Republic of China
| | - Gui Zhen Weng
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, People’s Republic of China
| | - Li Na Sun
- Department of Oncology, Lishui Central Hospital and Fifth Affiliated Hospital of Wenzhou Medical College, Lishui, Zhejiang, 323000, People’s Republic of China
| | - Zhang Chi Pan
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, People’s Republic of China
| | - Lu Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, People’s Republic of China
| | - Qiang Chen
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350001, People’s Republic of China
| | - Chun Mei Shi
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, People’s Republic of China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350001, People’s Republic of China
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Li Z, Lu S. Integrating minimal residual disease monitoring into clinical practice for NSCLC: Is the era upon us? Cancer Cell 2023; 41:1699-1701. [PMID: 37816330 DOI: 10.1016/j.ccell.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023]
Abstract
In this issue of Cancer Cell, Chen et al. and Pan et al. employ personalized, tumor-informed technology to detect minimal residual disease in non-small-cell lung cancer and demonstrate the clinical promise of integrating liquid biopsy techniques to improve the assessment of cancer progression and metastasis risk.
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Affiliation(s)
- Ziming Li
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Shun Lu
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
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Chen K, Yang F, Shen H, Wang C, Li X, Chervova O, Wu S, Qiu F, Peng D, Zhu X, Chuai S, Beck S, Kanu N, Carbone D, Zhang Z, Wang J. Individualized tumor-informed circulating tumor DNA analysis for postoperative monitoring of non-small cell lung cancer. Cancer Cell 2023; 41:1749-1762.e6. [PMID: 37683638 DOI: 10.1016/j.ccell.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
We report a personalized tumor-informed technology, Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) using deep sequencing of 50 patient-specific variants to detect molecular residual disease (MRD) with a limit of detection of 0.004%. PROPHET and state-of-the-art fixed-panel assays were applied to 760 plasma samples from 181 prospectively enrolled early stage non-small cell lung cancer patients. PROPHET shows higher sensitivity of 45% at baseline with circulating tumor DNA (ctDNA). It outperforms fixed-panel assays in prognostic analysis and demonstrates a median lead-time of 299 days to radiologically confirmed recurrence. Personalized non-canonical variants account for 98.2% with prognostic effects similar to canonical variants. The proposed tumor-node-metastasis-blood (TNMB) classification surpasses TNM staging for prognostic prediction at the decision point of adjuvant treatment. PROPHET shows potential to evaluate the effect of adjuvant therapy and serve as an arbiter of the equivocal radiological diagnosis. These findings highlight the potential advantages of personalized cancer techniques in MRD detection.
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Fan Yang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Haifeng Shen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | | | - Xi Li
- Burning Rock Biotech, Guangzhou 510300, China
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Shuailai Wu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Fujun Qiu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Di Peng
- Burning Rock Biotech, Guangzhou 510300, China
| | - Xin Zhu
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Nnennaya Kanu
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - David Carbone
- James Thoracic Oncology Center, Ohio State University, Columbus, OH 43026, USA
| | | | - Jun Wang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
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48
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Kisistók J, Christensen DS, Rasmussen MH, Duval L, Aggerholm-Pedersen N, Luczak AA, Sorensen BS, Jakobsen MR, Oellegaard TH, Birkbak NJ. Analysis of circulating tumor DNA during checkpoint inhibition in metastatic melanoma using a tumor-agnostic panel. Melanoma Res 2023; 33:364-374. [PMID: 37294123 PMCID: PMC10470440 DOI: 10.1097/cmr.0000000000000903] [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: 12/15/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Immunotherapy has revolutionized treatment of patients diagnosed with metastatic melanoma, where nearly half of patients receive clinical benefit. However, immunotherapy is also associated with immune-related adverse events, which may be severe and persistent. It is therefore important to identify patients that do not benefit from therapy early. Currently, regularly scheduled CT scans are used to investigate size changes in target lesions to evaluate progression and therapy response. This study aims to explore if panel-based analysis of circulating tumor DNA (ctDNA) taken at 3-week intervals may provide a window into the growing cancer, can be used to identify nonresponding patients early, and determine genomic alterations associated with acquired resistance to checkpoint immunotherapy without analysis of tumor tissue biopsies. We designed a gene panel for ctDNA analysis and sequenced 4-6 serial plasma samples from 24 patients with unresectable stage III or IV melanoma and treated with first-line checkpoint inhibitors enrolled at the Department of Oncology at Aarhus University Hospital, Denmark. TERT was the most mutated gene found in ctDNA and associated with a poor prognosis. We detected more ctDNA in patients with high metastatic load, which indicates that more aggressive tumors release more ctDNA into the bloodstream. Although we did not find evidence of specific mutations associated with acquired resistance, we did demonstrate in this limited cohort of 24 patients that untargeted, panel-based ctDNA analysis has the potential to be used as a minimally invasive tool in clinical practice to identify patients where the benefits of immunotherapy outweigh the drawbacks.
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Affiliation(s)
- Judit Kisistók
- Department of Molecular Medicine, Aarhus University Hospital
- Department of Clinical Medicine, Aarhus University
- Bioinformatics Research Center, Aarhus University
| | - Ditte Sigaard Christensen
- Department of Molecular Medicine, Aarhus University Hospital
- Department of Clinical Medicine, Aarhus University
- Department of Oncology, Aarhus University Hospital, Aarhus
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital
- Department of Clinical Medicine, Aarhus University
| | - Lone Duval
- Department of Oncology, Goedstrup Hospital, Herning
| | | | | | | | | | - Trine Heide Oellegaard
- Department of Clinical Medicine, Aarhus University
- Department of Oncology, Goedstrup Hospital, Herning
| | - Nicolai Juul Birkbak
- Department of Molecular Medicine, Aarhus University Hospital
- Department of Clinical Medicine, Aarhus University
- Bioinformatics Research Center, Aarhus University
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49
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Fukuda S, Suda K, Hamada A, Tsutani Y. Recent Advances in Perioperative Immunotherapies in Lung Cancer. Biomolecules 2023; 13:1377. [PMID: 37759777 PMCID: PMC10526295 DOI: 10.3390/biom13091377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Several clinical trials have been revolutionizing the perioperative treatment of early-stage non-small cell lung cancer (NSCLC). Many of these clinical trials involve cancer immunotherapies with antibody drugs that block the inhibitory immune checkpoints programmed death 1 (PD-1) and its ligand PD-L1. While these new treatments are expected to improve the treatment outcome of NSCLC patients after pulmonary resection, several major clinical questions remain, including the appropriate timing of immunotherapy (neoadjuvant, adjuvant, or both) and the identification of patients who should be treated with neoadjuvant and/or adjuvant immunotherapies, because some early-stage NSCLC patients are cured by surgical resection alone. In addition, immunotherapy may induce immune-related adverse events that will require permanent treatment in some patients. Based on this fact as well, it is desirable to select appropriate patients for neoadjuvant/adjuvant immunotherapies. So far, data from several important trials have been published, with findings demonstrating the efficacy of adjuvant atezolizumab (IMpower010 trial), neoadjuvant nivolumab plus platinum-doublet chemotherapy (CheckMate816 trial), and several perioperative (neoadjuvant plus adjuvant) immunotherapies (AEGEAN, KEYNOTE-671, NADIM II, and Neotorch trials). In addition to these key trials, numerous clinical trials have reported a wealth of data, although most of the above clinical questions have not been completely answered yet. Because there are so many ongoing clinical trials in this field, a comprehensive understanding of the results and/or contents of these trials is necessary to explore answers to the clinical questions above as well as to plan a new clinical trial. In this review, we comprehensively summarize the recent data obtained from clinical trials addressing such questions.
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Affiliation(s)
| | - Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama 589-8511, Japan; (S.F.); (A.H.); (Y.T.)
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50
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Lorenz C, Hillmer AM, Brägelmann J. Predicting the next move: tracking the complexity of lung cancer evolution and metastasis. Signal Transduct Target Ther 2023; 8:291. [PMID: 37553337 PMCID: PMC10409755 DOI: 10.1038/s41392-023-01567-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Carina Lorenz
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
| | - Axel M Hillmer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology Cologne, Cologne, Germany.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany.
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