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Hu Q, Chen L, Li K, Liu R, Sun L, Han T. Circulating tumor DNA: current implementation issues and future challenges for clinical utility. Clin Chem Lab Med 2024; 62:2094-2110. [PMID: 38109307 DOI: 10.1515/cclm-2023-1157] [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: 10/16/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Over the past decades, liquid biopsy, especially circulating tumor DNA (ctDNA), has received tremendous attention as a noninvasive detection approach for clinical applications, including early diagnosis of cancer and relapse, real-time therapeutic efficacy monitoring, potential target selection and investigation of drug resistance mechanisms. In recent years, the application of next-generation sequencing technology combined with AI technology has significantly improved the accuracy and sensitivity of liquid biopsy, enhancing its potential in solid tumors. However, the increasing integration of such promising tests to improve therapy decision making by oncologists still has complexities and challenges. Here, we propose a conceptual framework of ctDNA technologies and clinical utilities based on bibliometrics and highlight current challenges and future directions, especially in clinical applications such as early detection, minimal residual disease detection, targeted therapy, and immunotherapy. We also discuss the necessities of developing a dynamic field of translational cancer research and rigorous clinical studies that may support therapeutic strategy decision making in the near future.
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Affiliation(s)
- Qilin Hu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Lujun Chen
- The General Hospital of Northern Theater Command Training Base for Graduate, China Medical University, Shenyang, P.R. China
| | - Kerui Li
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Ruotong Liu
- Clinical Medicine, Shenyang Medical College, Shenyang, P.R. China
| | - Lei Sun
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Tao Han
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
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2
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Feng Y, Yang J, He Z, Liu X, Ma C. CRISPR-Cas-based biosensors for the detection of cancer biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:6634-6653. [PMID: 39258950 DOI: 10.1039/d4ay01446d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Along with discovering cancer biomarkers, non-invasive detection methods have played a critical role in early cancer diagnosis and prognostic improvement. Some traditional detection methods have been used for detecting cancer biomarkers, but they are time-consuming and involve materials and human costs. With great flexibility, sensitivity and specificity, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated system provides a wide range of application prospects in this field. Herein, we introduce the background of the CRISPR-Cas (CRISPR-associated) system and comprehensively summarize the diagnosis strategies of cancer mediated by the CRISPR-Cas system, including four kinds of biochemical-based markers: nucleic acid, enzyme, tumor-specific protein and exosome. Furthermore, we discuss the challenges in implementing the CRISPR-Cas system in clinical applications.
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Affiliation(s)
- Yuxin Feng
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Jinmeng Yang
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Ziping He
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Xinfa Liu
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
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Saateh A, Ansaryan S, Gao J, de Miranda LO, Zijlstra P, Altug H. Long-Term and Continuous Plasmonic Oligonucleotide Monitoring Enabled by Regeneration Approach. Angew Chem Int Ed Engl 2024:e202410076. [PMID: 39146470 DOI: 10.1002/anie.202410076] [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: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/17/2024]
Abstract
The demand for continuous monitoring of biochemical markers for diagnostic purposes is increasing as it overcomes the limitations of traditional intermittent measurements. This study introduces a method for long-term, continuous plasmonic biosensing of oligonucleotides with high temporal resolution. Our method is based on a regeneration-based reversibility approach that ensures rapid reversibility in less than 1 minute, allowing the sensor to fully reset after each measurement. We investigated label-free and AuNP enhancements for different dynamic ranges and sensitivities, achieving a limit of detection down to pM levels. We developed a regeneration-based reversibility approach for continuous biosensing, optimizing buffer conditions using the Taguchi method to achieve rapid, consistent reversibility, ensuring reliable performance for long-term monitoring. We detected oligonucleotides in buffered and complex solutions, including undiluted and unfiltered human serum, for up to 100 sampling cycles in a day. Moreover, we showed the long-term stability of the sensor for monitoring capabilities in buffered solutions and human serum, with minimal signal value drift and excellent sensor reversibility for up to 9 days. Our method opens the door to new prospects in continuous biosensing by providing insights beyond intermittent measurements for numerous analytical and diagnostic applications.
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Affiliation(s)
- Abtin Saateh
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Saeid Ansaryan
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Jiarui Gao
- Department of Chemical Engineering, Tsinghua University, 100084, Beijing, P. R. China
| | - Livio Oliveira de Miranda
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Peter Zijlstra
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Hatice Altug
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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Gray JE, Markovets A, Reungwetwattana T, Majem M, Nogami N, Peled N, Lee JS, Cho BC, Chewaskulyong B, John T, Han JY, Sebastian M, Todd A, Rukazenkov Y, Barrett C, Chmielecki J, Lee SM, Ramalingam SS, Hartmaier R. Longitudinal Analyses of Circulating Tumor DNA for the Detection of EGFR Mutation-Positive Advanced NSCLC Progression During Treatment: Data From FLAURA and AURA3. J Thorac Oncol 2024:S1556-0864(24)00676-2. [PMID: 39029876 DOI: 10.1016/j.jtho.2024.07.008] [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: 06/29/2023] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
INTRODUCTION EGFR tyrosine kinase inhibitor (EGFR-TKI)-sensitizing and -resistance mutations may be detected in plasma through circulating tumor DNA (ctDNA). Circulating tumor DNA level changes reflect alterations in tumor burden and could be a dynamic indicator of treatment effect. This analysis aimed to determine whether longitudinal EGFR-mutation ctDNA testing could detect progressive disease (PD) before radiologic detection. METHODS This was a retrospective, exploratory ctDNA analysis in two phase 3 trials (FLAURA, NCT02296125; AURA3, NCT02151981). Patients had treatment-naïve (FLAURA) or EGFR-TKI pre-treated (AURA3) advanced NSCLC with EGFR mutations and on-study PD (RECIST [Response Evaluation Criteria in Solid Tumors]), with a baseline ctDNA result and EGFR-mutation ctDNA monitoring beyond Cycle 3 Day 1. Patients received osimertinib versus comparator EGFR-TKIs (FLAURA) or chemotherapy (AURA3). Outcomes included time from ctDNA PD to RECIST PD and the first subsequent treatment (FLAURA only). RESULTS Circulating tumor DNA PD preceded or co-occurred with RECIST-defined PD in 93 out of 146 patients (64%) in FLAURA and 82 out of 146 patients (56%) in AURA3. Median time from ctDNA PD to RECIST-defined PD (mo) was 3.4 and 2.6 in the osimertinib and comparator EGFR-TKI arms (FLAURA) and 2.8 and 1.5 in the osimertinib and chemotherapy arms (AURA3). In FLAURA, the median time from ctDNA PD to the first subsequent treatment (mo) was 6.0 and 4.7 in the osimertinib (n = 51) and comparator EGFR-TKI arms (n = 70). CONCLUSIONS Among patients with EGFR mutation-positive advanced NSCLC receiving EGFR-TKI or chemotherapy with ctDNA data and RECIST-defined PD, ctDNA PD preceded/co-occurred with RECIST-defined PD in approximately 60% of cases. Longitudinal ctDNA monitoring may detect PD before radiologic PD.
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Affiliation(s)
- Jhanelle E Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Aleksandra Markovets
- Oncology Data Science, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Margarita Majem
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Naoyuki Nogami
- Department of Thoracic Oncology, National Hospital Organization Shikoku Cancer Center, Minamiumemoto-machi, Matsuyama, Japan
| | - Nir Peled
- Department of Oncology, The Institute of Oncology, Shaare Zedek Cancer Center & Ben-Gurion University, Jerusalem, Israel
| | - Jong-Seok Lee
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Tom John
- Department of Medical Oncology, Austin Health, Melbourne, Australia
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Martin Sebastian
- Goethe University Frankfurt, University Hospital, Hematology/Medical Oncology, Frankfurt, Germany
| | - Alexander Todd
- Oncology Biometrics, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Carl Barrett
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Juliann Chmielecki
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Siow Ming Lee
- Department of Oncology, University College London Hospitals and UCL Cancer Institute, Paul O'Gorman Building, London, United Kingdom
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Winship Cancer Institute, Atlanta, Georgia, USA
| | - Ryan Hartmaier
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
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Afzal MZ, Vahdat LT. Evolving Management of Breast Cancer in the Era of Predictive Biomarkers and Precision Medicine. J Pers Med 2024; 14:719. [PMID: 39063972 PMCID: PMC11278458 DOI: 10.3390/jpm14070719] [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: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer is the most common cancer among women in the world as well as in the United States. Molecular and histological differentiation have helped clinicians optimize treatments with various therapeutics, including hormonal therapy, chemotherapy, immunotherapy, and radiation therapy. Recently, immunotherapy has become the standard of care in locally advanced triple-negative breast cancer and an option across molecular subtypes for tumors with a high tumor mutation burden. Despite the advancements in personalized medicine directing the management of localized and advanced breast cancers, the emergence of resistance to these therapies is the leading cause of death among breast cancer patients. Therefore, there is a critical need to identify and validate predictive biomarkers to direct treatment selection, identify potential responders, and detect emerging resistance to standard therapies. Areas of active scientific and clinical research include novel personalized and predictive biomarkers incorporating tumor microenvironment, tumor immune profiling, molecular characterization, and histopathological differentiation to predict response and the potential emergence of resistance.
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Affiliation(s)
- Muhammad Zubair Afzal
- Medical Oncology, Comprehensive Breast Program, Dartmouth Cancer Center, Lebanon, NH 03755, USA
| | - Linda T. Vahdat
- Medical Oncology and Hematology (Interim), Dartmouth Cancer Center, Lebanon, NH 03755, USA;
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Chen W, Yan YH, Young B, Pinto A, Jiang Q, Song N, Yaseen A, Yao W, Zhang DY, Zhang JX. Microsatellite Instability Detection in Cancer: A Multiplex qPCR Approach that Obviates the Need for Matching Normal Samples. Clin Chem 2024; 70:830-840. [PMID: 38581343 DOI: 10.1093/clinchem/hvae045] [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: 11/14/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Microsatellite instability (MSI) indicates DNA mismatch repair deficiency in certain types of cancer, such as colorectal cancer. The current gold standard technique, PCR-capillary electrophoresis (CE), requires matching normal samples and specialized instrumentation. We developed VarTrace, a rapid and low-cost quantitative PCR (qPCR) assay, to evaluate MSI using solely the tumor sample DNA, obviating the requirement for matching normal samples. METHODS One hundred and one formalin-fixed paraffin-embedded (FFPE) tumor samples were tested using VarTrace and compared with the Promega OncoMate assay utilizing PCR-CE. Tumor percentage limit of detection was evaluated on contrived samples derived from clinical high MSI (MSI-H) samples. Analytical sensitivity, specificity, limit of detection, and input requirements were assessed using synthetic commercial reference standards. RESULTS VarTrace successfully analyzed all 101 clinical FFPE samples, demonstrating 100% sensitivity and 98% specificity compared to OncoMate. It detected MSI-H with 97% accuracy down to 10% tumor. Analytical studies using synthetic samples showed a limit of detection of 5% variant allele frequency and a limit of input of 0.5 ng. CONCLUSIONS This study validates VarTrace as a swift, accurate, and economical assay for MSI detection in samples with low tumor percentages without the need for matching normal DNA. VarTrace's capacity for highly sensitive MSI analysis holds potential for enhancing the efficiency of clinical work flows and broadening the availability of this test.
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Affiliation(s)
- Wei Chen
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Yan Helen Yan
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Blake Young
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Alessandro Pinto
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Qi Jiang
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Nanjia Song
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Adam Yaseen
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - Weijie Yao
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
| | - David Yu Zhang
- NuProbe USA, R&D and Innovation Department, Houston, TX, United States
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Park BC, Soh JO, Choi HJ, Park HS, Lee SM, Fu HE, Kim MS, Ko MJ, Koo TM, Lee JY, Kim YK, Lee JH. Ultrasensitive and Rapid Circulating Tumor DNA Liquid Biopsy Using Surface-Confined Gene Amplification on Dispersible Magnetic Nano-Electrodes. ACS NANO 2024; 18:12781-12794. [PMID: 38733343 DOI: 10.1021/acsnano.3c12266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Circulating tumor DNA (ctDNA) detection has been acknowledged as a promising liquid biopsy approach for cancer diagnosis, with various ctDNA assays used for early detection and treatment monitoring. Dispersible magnetic nanoparticle-based electrochemical detection methods have been proposed as promising candidates for ctDNA detection based on the detection performance and features of the platform material. This study proposes a nanoparticle surface-localized genetic amplification approach by integrating Fe3O4-Au core-shell nanoparticles into polymerase chain reactions (PCR). These highly dispersible and magnetically responsive superparamagnetic nanoparticles act as nano-electrodes that amplify and accumulate target ctDNA in situ on the nanoparticle surface upon PCR amplification. These nanoparticles are subsequently captured and subjected to repetitive electrochemical measurements to induce reconfiguration-mediated signal amplification for ultrasensitive (∼3 aM) and rapid (∼7 min) metastatic breast cancer ctDNA detection in vitro. The detection platform can also detect metastatic biomarkers from in vivo samples, highlighting the potential for clinical applications and further expansion to rapid and ultrasensitive multiplex detection of various cancers.
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Affiliation(s)
- Bum Chul Park
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Jeong Ook Soh
- Department of Bionano Engineering, Hanyang University, Ansan 15588, Republic of Korea
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Hee-Joo Choi
- Department of Pathology, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology (HY-IBB), Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Biomedical Research Institute (HBRI), Hanyang University, Seoul 04763, Republic of Korea
| | - Hyeon Su Park
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Sang Min Lee
- Department of Bionano Engineering, Hanyang University, Ansan 15588, Republic of Korea
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Hong En Fu
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Myeong Soo Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Min Jun Ko
- Department of Radiology, Northwestern University, Chicago, Illinois 60611, United States
| | - Thomas Myeongseok Koo
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jeong-Yeon Lee
- Department of Pathology, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology (HY-IBB), Hanyang University, Seoul 04763, Republic of Korea
| | - Young Keun Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Brain Korea Center for Smart Materials and Devices, Korea University, Seoul 02841, Republic of Korea
| | - Ju Hun Lee
- Department of Bionano Engineering, Hanyang University, Ansan 15588, Republic of Korea
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, Republic of Korea
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Dubey AK, Kaur I, Madaan R, Raheja S, Bala R, Garg M, Kumar S, Lather V, Mittal V, Pandita D, Gundamaraju R, Singla RK, Sharma R. Unlocking the potential of oncology biomarkers: advancements in clinical theranostics. Drug Metab Pers Ther 2024; 39:5-20. [PMID: 38469723 DOI: 10.1515/dmpt-2023-0056] [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: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Cancer biomarkers have revolutionized the field of oncology by providing valuable insights into tumor changes and aiding in screening, diagnosis, prognosis, treatment prediction, and risk assessment. The emergence of "omic" technologies has enabled biomarkers to become reliable and accurate predictors of outcomes during cancer treatment. CONTENT In this review, we highlight the clinical utility of biomarkers in cancer identification and motivate researchers to establish a personalized/precision approach in oncology. By extending a multidisciplinary technology-based approach, biomarkers offer an alternative to traditional techniques, fulfilling the goal of cancer therapeutics to find a needle in a haystack. SUMMARY AND OUTLOOK We target different forms of cancer to establish a dynamic role of biomarkers in understanding the spectrum of malignancies and their biochemical and molecular characterization, emphasizing their prospective contribution to cancer screening. Biomarkers offer a promising avenue for the early detection of human cancers and the exploration of novel technologies to predict disease severity, facilitating maximum survival and minimum mortality rates. This review provides a comprehensive overview of the potential of biomarkers in oncology and highlights their prospects in advancing cancer diagnosis and treatment.
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Affiliation(s)
- Ankit Kumar Dubey
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Reecha Madaan
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Shikha Raheja
- Jan Nayak Ch. Devi Lal Memorial College of Pharmacy, Sirsa, Haryana, India
| | - Rajni Bala
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, 77282 Amity University, Sector-125 , Noida, India
| | - Suresh Kumar
- Department of Pharmaceutical Sciences and Drug Research, 429174 Punjabi University Patiala , Patiala, India
| | - Viney Lather
- Amity Institute of Pharmacy, 77282 Amity University , Noida, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, 29062 Maharshi Dayanand University , Rohtak, Haryana, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, PushpVihar, 633274 Govt. of NCT of Delhi , New Delhi, India
- Centre for Advanced Formulation and Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, PushpVihar, Govt. of NCT of Delhi, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, 8785 University of Tasmania , Launceston, Tasmania, Australia
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- School of Pharmaceutical Sciences, 34753 Lovely Professional University , Phagwara, Punjab, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, 80095 Banaras Hindu University , Varanasi, Uttar Pradesh, India
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van der Leest P, Schuuring E. Critical Factors in the Analytical Work Flow of Circulating Tumor DNA-Based Molecular Profiling. Clin Chem 2024; 70:220-233. [PMID: 38175597 DOI: 10.1093/clinchem/hvad194] [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: 07/29/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Liquid biopsy testing, especially molecular tumor profiling of circulating tumor DNA (ctDNA) in cell-free plasma, has received increasing interest in recent years as it serves as a reliable alternative for the detection of tumor-specific aberrations to guide treatment decision-making in oncology. Many (commercially available) applications have been developed, however, broad divergences in (pre)analytical work flows and lack of universally applied guidelines impede routine clinical implementation. In this review, critical factors in the blood-based ctDNA liquid biopsy work flow are evaluated. CONTENT In the preanalytical phase, several aspects (e.g., blood collection tubes [BCTs], plasma processing, and extraction method) affect the quantity and quality of the circulating cell-free DNA (ccfDNA) applicable for subsequent molecular analyses and should meet certain standards to be applied in diagnostic work flows. Analytical considerations, such as analytical input and choice of assay, might vary based on the clinical application (i.e., screening, primary diagnosis, minimal residual disease [MRD], response monitoring, and resistance identification). In addition to practical procedures, variant interpretation and reporting ctDNA results should be harmonized. Collaborative efforts in (inter)national consortia and societies are essential for the establishment of standard operating procedures (SOPs) in attempts to standardize the plasma-based ctDNA analysis work flow. SUMMARY Development of universally applicable guidelines regarding the critical factors in liquid biopsy testing are necessary to pave the way to clinical implementation for routine diagnostics.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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10
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Geiger K, Joerger M, Roessler M, Hettwer K, Ritter C, Simon K, Uhlig S, Holdenrieder S. Relevance of tumor markers for prognosis and predicting therapy response in non-small cell lung cancer patients: A CEPAC-TDM biomarker substudy. Tumour Biol 2024; 46:S191-S206. [PMID: 38363625 DOI: 10.3233/tub-230014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Protein tumor markers are released in high amounts into the blood in advanced non-small cell lung cancer (NSCLC). OBJECTIVE To investigate the relevance of serum tumor markers (STM) for prognosis, prediction and monitoring of therapy response in NSCLC patients receiving chemotherapy. METHODS In a biomarker substudy of a prospective, multicentric clinical trial (CEPAC-TDM) on 261 advanced NSCLC patients, CYFRA 21-1, CEA, SCC, NSE, ProGRP, CA125, CA15-3 and HE4 were assessed in serial serum samples and correlated with radiological response after two cycles of chemotherapy and overall (OS) and progression-free survival (PFS). RESULTS While pretherapeutic STM levels at staging did not discriminate between progressive and non-progressive patients, CYFRA 21-1, CA125, NSE and SCC at time of staging did, and yielded AUCs of 0.75, 0.70, 0.69 and 0.67 in ROC curves, respectively. High pretherapeutic CA15-3 and CA125 as well as high CYFRA 21-1, SCC, CA125 and CA15-3 levels at staging were prognostic for shorter PFS and OS -also when clinical variables were added to the models. CONCLUSIONS STM at the time of first radiological staging and pretherapeutic CA15-3, CA125 are predictive for first-line treatment response and highly prognostic in patients with advanced NSCLC.
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Affiliation(s)
- Kimberly Geiger
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Centre, Technical University of Munich, Munich, Germany
| | - Markus Joerger
- Department of Oncology and Hematology, Cantonal Hospital St. Gallen, Switzerland
| | - Max Roessler
- Central European Society for Anticancer Drug Research (CESAR), Vienna, Austria
| | | | - Christoph Ritter
- Institute of Pharmacy, Clinical Pharmacy, University of Greifswald, Germany
| | - Kirsten Simon
- QuoData GmbH-Quality & Statistics, Dresden, Germany
- CEBIO GmbH - Center for Evaluation of Biomarkers, Munich, Germany
| | - Steffen Uhlig
- QuoData GmbH-Quality & Statistics, Dresden, Germany
- CEBIO GmbH - Center for Evaluation of Biomarkers, Munich, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Centre, Technical University of Munich, Munich, Germany
- CEBIO GmbH - Center for Evaluation of Biomarkers, Munich, Germany
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11
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Duffy MJ. Circulating tumor DNA (ctDNA) as a biomarker for lung cancer: Early detection, monitoring and therapy prediction. Tumour Biol 2024; 46:S283-S295. [PMID: 37270828 DOI: 10.3233/tub-220044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Circulating tumor DNA (ctDNA), i.e., DNA shed from tumor cells into the bloodstream, is emerging as one of the most useful plasma biomarkers in patients with multiple types of cancer, including patients with non-small cell lung cancer (NSCLC). Indeed, NSCLC was the first malignancy in which measurement of ctDNA was approved for clinical use, i.e., mutational testing of EGFR for predicting response to EGFR tyrosine kinase inhibitors in patients with advanced disease. Although historically the gold standard method for EGFR mutational analysis required tumor tissue, the use of ctDNA is more convenient and safer for patients, results in a faster turn-around-time for return of results, provides a more complete representation of genetic alteration in heterogeneous tumors and is less costly to perform. Emerging uses of ctDNA in patients with lung or suspected lung cancer include screening for early disease, surveillance following initial treatment and monitoring response to therapy in metastatic disease. For evaluating therapy response, ctDNA appears to be especially useful in patients receiving targeted therapies against driver oncogenes or immunotherapy. Further work should not only validate these emerging findings but also aim to optimize and standardize ctDNA assays.
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Affiliation(s)
- Michael J Duffy
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin and UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Qian X, Meng QH. Circulating lung cancer biomarkers: From translational research to clinical practice. Tumour Biol 2024; 46:S27-S33. [PMID: 37927289 DOI: 10.3233/tub-230012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Fundamental studies on biomarkers as well as developed assays for their detection can provide valuable information facilitating clinical decisions. For patients with lung cancer, there are established circulating biomarkers such as serum progastrin-releasing peptide (ProGRP), neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCC-Ag), carcinoembryonic antigen (CEA), and cytokeratin-19 fragment (CYFRA21-1). There are also molecular biomarkers for targeted therapy such as epidermal growth factor receptor (EGFR) gene, anaplastic lymphoma kinase (ALK) gene, KRAS gene, and BRAF gene. However, there is still an unmet need for biomarkers that can be used for early detection and predict treatment response and survival. In this review, we describe the lung cancer biomarkers that are currently being used in clinical practice. We also discuss emerging preclinical and clinical studies on new biomarkers such as omics-based biomarkers for their potential clinical use to detect, predict, or monitor subtypes of lung cancer. Additionally, between-method differences in tumor markers warrant further development and improvement of the standardization and harmonization for each assay.
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Affiliation(s)
- Xu Qian
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Qing-He Meng
- Department of Laboratory Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Merath K, Tiwari A, Parikh AA, Pawlik TM. Molecular targeted and systemic therapy for intrahepatic cholangiocarcinoma: a multi-disciplinary approach. Future Oncol 2023; 19:2607-2621. [PMID: 38108100 DOI: 10.2217/fon-2023-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Most patients with intrahepatic cholangiocarcinoma (ICC) are diagnosed with advanced disease. For individuals with resectable tumors, R0 resection with lymphadenectomy is the best potentially curative-intent treatment. After resection, adjuvant therapy with capecitabine is the current standard of care. For patients with unresectable or distant metastatic disease, doublet chemotherapy with gemcitabine and cisplatin is the most utilized first-line regimen, but recent studies using triplet regimens and even the addition of immunotherapy have begun to shift the paradigm of systemic therapy. Molecular therapies have recently received US FDA approval for second-line treatment for patients harboring actionable genomic alterations. This review focuses on the multidisciplinary approach to the treatment of ICC with an emphasis on molecular targeted and systemic therapy.
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Affiliation(s)
- Katiuscha Merath
- Division of Surgical Oncology, University of Texas Health Science Center San Antonio MD Anderson Cancer Center, San Antonio, TX, USA
| | - Ankur Tiwari
- Division of Surgical Oncology, University of Texas Health Science Center San Antonio MD Anderson Cancer Center, San Antonio, TX, USA
| | - Alexander A Parikh
- Division of Surgical Oncology, University of Texas Health Science Center San Antonio MD Anderson Cancer Center, San Antonio, TX, USA
| | - Timothy M Pawlik
- Division of Surgical Oncology, The Ohio State University Wexner Medical Center & James Comprehensive Cancer Center, Columbus, OH 43210, USA
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Bi Y, Xia C, Zhang X, Liu H. Targeted treatments after chemoradiotherapy failure in a patient with relapsed, advanced non‑small cell lung cancer with on‑therapy circulating tumor biomarker monitoring: A case report. Oncol Lett 2023; 26:407. [PMID: 37600327 PMCID: PMC10436159 DOI: 10.3892/ol.2023.13993] [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: 02/10/2023] [Accepted: 06/30/2023] [Indexed: 08/22/2023] Open
Abstract
Ongoing investigations of targeted therapeutic agents and their increased clinical applications, together with research in genomics and proteomics, have explored a variety of novel approaches for treatment of lung cancer, and 'molecular subtypes' have been defined based on specific actionable genetic aberrations. Liquid biopsies, including circulating tumor DNA (ctDNA) testing, are of value for cancer diagnosis and comprehensive genomic profiling, such as the identification of cancer subtypes and major genetic alterations in cancer cells. The case of a 66-year-old male patient with newly-diagnosed driver mutation-negative advanced non-small cell lung cancer (NSCLC) who underwent conventional therapy is described in the present report. The patient underwent regular monitoring, including continuous ctDNA analysis, imaging and assessment of tumor marker levels such as carcinoembryonic antigen (CEA). The patient initially presented with deep vein thrombosis which affected both lower extremities and without any symptoms in the lung, with a positron emission tomography scan identifying irregular pulmonary nodules in the right lower lobe and enlarged right supraclavicular lymph nodes. Subsequent ultrasound-guided fine-needle aspiration with nodule biopsy indicated advanced unresectable disease at stage IIIB based on the Tumor-Node-Metastasis staging system by the American Joint Committee on Cancer. Next-generation sequencing of tumor tissue and peripheral blood confirmed driver mutation-negative genes, including epidermal growth factor receptor, rat sarcoma, ALK receptor tyrosine kinase, ROS1 proto-oncogene receptor tyrosine kinase and rearrangement during transfection (RET). After 5 years of chemoradiotherapy and surveillance of ctDNA and CEA levels, detectable kinesin family member 5B (KIF5B)-RET fusion in ctDNA and rising CEA levels prompted early scans, which identified disease progression. The patient subsequently received the oral RET inhibitor pralsetinib, with treatment being currently ongoing for ≥17 months without detectable KIF5B-RET ctDNA or elevated CEA levels, with an ongoing minor response and stable disease based on Response Evaluation Criteria in Solid Tumors v1.1 on imaging. The present case illustrates the potential role of on-therapy circulating tumor biomarker monitoring as a non-traumatic method to evaluate therapy response and detect early disease progression in patients with advanced NSCLC. Integration of circulating tumor biomarker testing into the management of patients with advanced NSCLC requires additional prospective studies to actively assess and elucidate optimal treatment strategies.
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Affiliation(s)
- Yinghui Bi
- Department of Oncology, Qingdao Municipal Hospital, Qingdao, Shandong 266012, P.R. China
| | - Chaoran Xia
- Zhejiang Shaoxing Topgen Biomedical Technology Co. Ltd., Shanghai 200120, P.R. China
| | - Xinglin Zhang
- Department of Oncology, Qingdao Municipal Hospital, Qingdao, Shandong 266012, P.R. China
| | - Haixin Liu
- Department of Oncology, Qingdao Municipal Hospital, Qingdao, Shandong 266012, P.R. China
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Matou-Nasri S, Aldawood M, Alanazi F, Khan AL. Updates on Triple-Negative Breast Cancer in Type 2 Diabetes Mellitus Patients: From Risk Factors to Diagnosis, Biomarkers and Therapy. Diagnostics (Basel) 2023; 13:2390. [PMID: 37510134 PMCID: PMC10378597 DOI: 10.3390/diagnostics13142390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is usually the most malignant and aggressive mammary epithelial tumor characterized by the lack of expression for estrogen receptors and progesterone receptors, and the absence of epidermal growth factor receptor (HER)2 amplification. Corresponding to 15-20% of all breast cancers and well-known by its poor clinical outcome, this negative receptor expression deprives TNBC from targeted therapy and makes its management therapeutically challenging. Type 2 diabetes mellitus (T2DM) is the most common ageing metabolic disorder due to insulin deficiency or resistance resulting in hyperglycemia, hyperinsulinemia, and hyperlipidemia. Due to metabolic and hormonal imbalances, there are many interplays between both chronic disorders leading to increased risk of breast cancer, especially TNBC, diagnosed in T2DM patients. The purpose of this review is to provide up-to-date information related to epidemiology and clinicopathological features, risk factors, diagnosis, biomarkers, and current therapy/clinical trials for TNBC patients with T2DM compared to non-diabetic counterparts. Thus, in-depth investigation of the diabetic complications on TNBC onset, development, and progression and the discovery of biomarkers would improve TNBC management through early diagnosis, tailoring therapy for a better outcome of T2DM patients diagnosed with TNBC.
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Affiliation(s)
- Sabine Matou-Nasri
- Blood and Cancer Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
- Biosciences Department, Faculty of the School for Systems Biology, George Mason University, Manassas, VA 22030, USA
| | - Maram Aldawood
- Blood and Cancer Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
- Post Graduate and Zoology Department, King Saud University, Riyadh 12372, Saudi Arabia
| | - Fatimah Alanazi
- Blood and Cancer Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
- Biosciences Department, Faculty of the School for Systems Biology, George Mason University, Manassas, VA 22030, USA
| | - Abdul Latif Khan
- Tissue Biobank, KAIMRC, MNG-HA, Riyadh 11481, Saudi Arabia
- Pathology and Clinical Laboratory Medicine, King Abdulaziz Medical City (KAMC), Riyadh 11564, Saudi Arabia
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Trinidad EM, Juan-Ribelles A, Pisano G, Castel V, Cañete A, Gut M, Heath S, Font de Mora J. Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas. Front Oncol 2023; 13:1037342. [PMID: 37251933 PMCID: PMC10213460 DOI: 10.3389/fonc.2023.1037342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, and response to treatment. DNA methylation profiling is also a potential solution for sensitive and specific detection of many cancers. The combination of both approaches, DNA methylation analysis from ctDNA, provides an extremely useful and minimally invasive tool with high relevance in patients with childhood cancer. Neuroblastoma is an extracranial solid tumor most common in children and responsible for up to 15% of cancer-related deaths. This high death rate has prompted the scientific community to search for new therapeutic targets. DNA methylation also offers a new source for identifying these molecules. However, the limited blood sample size which can be obtained from children with cancer and the fact that ctDNA content may occasionally be diluted by non-tumor cell-free DNA (cfDNA) complicate optimal quantities of material for high-throughput sequencing studies. Methods In this article, we present an improved method for ctDNA methylome studies of blood-derived plasma from high-risk neuroblastoma patients. We assessed the electropherogram profiles of ctDNA-containing samples suitable for methylome studies, using 10 ng of plasma-derived ctDNA from 126 samples of 86 high-risk neuroblastoma patients, and evaluated several bioinformatic approaches to analyze DNA methylation sequencing data. Results We demonstrated that enzymatic methyl-sequencing (EM-seq) outperformed bisulfite conversion-based method, based on the lower proportion of PCR duplicates and the higher percentage of unique mapping reads, mean coverage, and genome coverage. The analysis of the electropherogram profiles revealed the presence of nucleosomal multimers, and occasionally high molecular weight DNA. We established that 10% content of the mono-nucleosomal peak is sufficient ctDNA for successful detection of copy number variations and methylation profiles. Quantification of mono-nucleosomal peak also showed that samples at diagnosis contained a higher amount of ctDNA than relapse samples. Conclusions Our results refine the use of electropherogram profiles to optimize sample selection for subsequent high-throughput analysis and support the use of liquid biopsy followed by enzymatic conversion of unmethylated cysteines to assess the methylomes of neuroblastoma patients.
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Affiliation(s)
- Eva María Trinidad
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Giulia Pisano
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
- School of Medicine, University of Valencia, Valencia, Spain
| | - Marta Gut
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
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Udagawa S, Ooki A, Shinozaki E, Fukuda K, Yamaguchi K, Osumi H. Circulating Tumor DNA: The Dawn of a New Era in the Optimization of Chemotherapeutic Strategies for Metastatic Colo-Rectal Cancer Focusing on RAS Mutation. Cancers (Basel) 2023; 15:1473. [PMID: 36900264 PMCID: PMC10001242 DOI: 10.3390/cancers15051473] [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: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Genotyping of tumor tissues to assess RAS and BRAF V600E mutations enables us to select optimal molecularly targeted therapies when considering treatment strategies for patients with metastatic colorectal cancer. Tissue-based genetic testing is limited by the difficulty of performing repeated tests, due to the invasive nature of tissue biopsy, and by tumor heterogeneity, which can limit the usefulness of the information it yields. Liquid biopsy, represented by circulating tumor DNA (ctDNA), has attracted attention as a novel method for detecting genetic alterations. Liquid biopsies are more convenient and much less invasive than tissue biopsies and are useful for obtaining comprehensive genomic information on primary and metastatic tumors. Assessing ctDNA can help track genomic evolution and the status of alterations in genes such as RAS, which are sometimes altered following chemotherapy. In this review, we discuss the potential clinical applications of ctDNA, summarize clinical trials focusing on RAS, and present the future prospects of ctDNA analysis that could change daily clinical practice.
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Affiliation(s)
| | | | | | | | | | - Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
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Urine Molecular Biomarkers for Detection and Follow-Up of Small Renal Masses. Int J Mol Sci 2022; 23:ijms232416110. [PMID: 36555747 PMCID: PMC9785854 DOI: 10.3390/ijms232416110] [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: 11/15/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Active surveillance (AS) is the best strategy for small renal masses (SRMs) management; however, reliable methods for early detection and disease aggressiveness prediction are urgently needed. The aim of the present study was to validate DNA methylation biomarkers for non-invasive SRM detection and prognosis. The levels of methylated genes TFAP2B, TAC1, PCDH8, ZNF677, FLRT2, and FBN2 were evaluated in 165 serial urine samples prospectively collected from 39 patients diagnosed with SRM, specifically renal cell carcinoma (RCC), before and during the AS via quantitative methylation-specific polymerase chain reaction. Voided urine samples from 92 asymptomatic volunteers were used as the control. Significantly higher methylated TFAP2B, TAC1, PCDH8, ZNF677, and FLRT2 levels and/or frequencies were detected in SRM patients' urine samples as compared to the control. The highest diagnostic power (AUC = 0.74) was observed for the four biomarkers panel with 92% sensitivity and 52% specificity. Methylated PCDH8 level positively correlated with SRM size at diagnosis, while TFAP2B had the opposite effect and was related to SRM progression. To sum up, SRMs contribute significantly to the amount of methylated DNA detectable in urine, which might be used for very early RCC detection. Moreover, PCDH8 and TFAP2B methylation have the potential to be prognostic biomarkers for SRMs.
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Patient Selection Approaches in FGFR Inhibitor Trials-Many Paths to the Same End? Cells 2022; 11:cells11193180. [PMID: 36231142 PMCID: PMC9563413 DOI: 10.3390/cells11193180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 12/16/2022] Open
Abstract
Inhibitors of fibroblast growth factor receptor (FGFR) signaling have been investigated in various human cancer diseases. Recently, the first compounds received FDA approval in biomarker-selected patient populations. Different approaches and technologies have been applied in clinical trials, ranging from protein (immunohistochemistry) to mRNA expression (e.g., RNA in situ hybridization) and to detection of various DNA alterations (e.g., copy number variations, mutations, gene fusions). We review, here, the advantages and limitations of the different technologies and discuss the importance of tissue and disease context in identifying the best predictive biomarker for FGFR targeting therapies.
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