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Marinello A, Tagliamento M, Pagliaro A, Conci N, Cella E, Vasseur D, Remon J, Levy A, Dall'Olio FG, Besse B. Circulating tumor DNA to guide diagnosis and treatment of localized and locally advanced non-small cell lung cancer. Cancer Treat Rev 2024; 129:102791. [PMID: 38963991 DOI: 10.1016/j.ctrv.2024.102791] [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: 04/23/2024] [Revised: 06/15/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
Liquid biopsy is a minimally invasive method for biomarkers detection in body fluids, particularly in blood, which offers an elevated and growing number of clinical applications in oncology. As a result of the improvement in the techniques for DNA analysis, above all next-generation sequencing (NGS) assays, circulating tumor DNA (ctDNA) has become the most informing tumor-derived material for most types of cancer, including non-small cell lung cancer (NSCLC). Although ctDNA concentration is higher in patients with advanced tumors, it can be detected even in patients with early-stage disease. Therefore, numerous clinical applications of ctDNA in the management of early-stage lung cancer are emerging, such as lung cancer screening, the identification of minimal residual disease (MRD), and the prediction of relapse before radiologic progression. Moreover, a high number of clinical trials are ongoing to better define the impact of ctDNA evaluation in this setting. Aim of this review is to offer a comprehensive overview of the most relevant implementations in using ctDNA for the management of early-stage lung cancer, addressing available data, technical aspects, limitations, and future perspectives.
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Affiliation(s)
- Arianna Marinello
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; INSERM Unit 1030 - Molecular Radiotherapy and Therapeutic Innovation, Gustave Roussy, Villejuif, France
| | - Marco Tagliamento
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy.
| | - Arianna Pagliaro
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Medical Oncology, IRCCS Istituto Clinico Humanitas, Rozzano, Italy
| | - Nicole Conci
- Department of Medical Oncology, IRCCS Sant'Orsola-Malpighi, Bologna, Italy
| | - Eugenia Cella
- Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy
| | - Damien Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Jordi Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Antonin Levy
- Department of Radiotherapy, Gustave Roussy, Villejuif, France
| | | | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
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2
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Thao DT, Thanh NP, Quyen DV, Khai LT, Song LH, Trung NT. Identification of breast cancer-associated PIK3CA H1047R mutation in blood circulation using an asymmetric PCR assay. PLoS One 2024; 19:e0309209. [PMID: 39197004 PMCID: PMC11356436 DOI: 10.1371/journal.pone.0309209] [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: 01/26/2024] [Accepted: 08/08/2024] [Indexed: 08/30/2024] Open
Abstract
PURPOSE To establish a highly sensitive and specific approach for the detection of circulating PIK3CA H1047R mutation in breast cancer (BC) patients and to investigate the association between the prevalence of PIK3CA H1047R mutation and clinical presentations. METHODS A proper blocker was designed in an allele-specific manner and optimized for PCR-based identification of the PIK3CA H1047R mutation. The established technique was validated in cell-free DNA samples from 196 recruited BC patients. RESULTS The allele-specific PCR assay with a properly designed blocker was able to detect the H1047R mutant variant with 0.01%. By applying the newly established assay, 62 cases (31.6% of the total recruited cases) were found to carry a blood-circulating H1047R mutant. Wherein, the detected mutant rates increased with disease stages from 2/18 (11.1%) of stage I to 17/71 (23.9%) of stage II, 20/53 (37.7%) of stage III, and 23/31 (42.6%) of stage IV (p = 0.025), respectively. Higher frequencies of H1047R mutation were associated with late-stage (p = 0.033) or recurrence (p = 0.045) or metastatic patients (p = 0.049) as well as radiation-treated human epidermal growth factor receptor 2 (HER2) positive BC (p = 0.004). PIK3CA mutant carriers were frequently observed in patients under the age of 50 who had liver-metastasized or brain metastases or lymph node-invaded (p < 0.05). CONCLUSION A novel allele-specific PCR assay with high sensitivity was established successfully for the detection of the PIK3CA H1047R mutation in clinical practice.
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Affiliation(s)
- Dinh Thi Thao
- Center for Genetic Consultation and Cancer Screening, 108 Military Center Hospital, Hai Ba Trung, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Cau Giay, Hanoi, Vietnam
| | - Nguyen Phu Thanh
- Center for Genetic Consultation and Cancer Screening, 108 Military Center Hospital, Hai Ba Trung, Hanoi, Vietnam
| | - Dong Van Quyen
- University of Science and Technology of Hanoi, Cau Giay, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Ly Tuan Khai
- Department of Hematology, Laboratory Center, 108 Military Center Hospital, Hai Ba Trung, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, 108 Military Center Hospital, Hai Ba Trung Hanoi, Vietnam
| | - Ngo Tat Trung
- Center for Genetic Consultation and Cancer Screening, 108 Military Center Hospital, Hai Ba Trung, Hanoi, Vietnam
- Vietnamese-German Center for Medical Research, 108 Military Center Hospital, Hai Ba Trung Hanoi, Vietnam
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3
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Wehrle CJ, Tocci NX, Sun K, Jiao C, Hong H, Gross A, Allkushi E, Uysal M, Linganna MW, Stackhouse K, Hashimoto K, Schlegel A, Walsh RM, Miller C, Kwon DCH, Aucejo F. Utility of circulating tumor DNA in secondary liver malignancies: What we know and what is to come. J Surg Oncol 2024. [PMID: 39155652 DOI: 10.1002/jso.27838] [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: 04/20/2024] [Accepted: 07/27/2024] [Indexed: 08/20/2024]
Abstract
Secondary liver malignancies are a serious and challenging global health concern. Secondary metastasis to the liver is most commonly from colorectal cancer that has metastatically spread through splanchnic circulation. Metastatic diseases can portend poor prognosis due to the progressive nature typically found on detection. Improvements in detection of disease, monitoring therapy response, and monitoring for recurrence are crucial to the improvement in the management of secondary liver malignancies. Assessment of ctDNA in these patient populations poses an opportunity to impact the management of secondary liver malignancies. In this review, we aim to discuss ctDNA, the current literature, and future directions of this technology within secondary liver malignancies.
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Affiliation(s)
- Chase J Wehrle
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Noah X Tocci
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Keyue Sun
- Cleveland Clinic Foundation, Lerner Research Institute, Inflammation & Immunity, Cleveland, Ohio, USA
| | - Chunbao Jiao
- Cleveland Clinic Foundation, Lerner Research Institute, Inflammation & Immunity, Cleveland, Ohio, USA
| | - Hanna Hong
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Abby Gross
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Erlind Allkushi
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Melis Uysal
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Maureen Whitsett Linganna
- Department of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Katheryn Stackhouse
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Koji Hashimoto
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Andrea Schlegel
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
- Cleveland Clinic Foundation, Lerner Research Institute, Inflammation & Immunity, Cleveland, Ohio, USA
| | - R Matthew Walsh
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Charles Miller
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - David C H Kwon
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
| | - Federico Aucejo
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Cleveland Clinic Foundation, Digestive Diseases and Surgery Institute, Cleveland, Ohio, USA
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Tocci NX, Wehrle CJ, Sun K, Jiao C, Hong H, Gross A, Allkushi E, Uysal M, Linganna MW, Stackhouse K, Hashimoto K, Schlegel A, Walsh RM, Miller C, Kwon DCH, Aucejo F. Circulating tumor DNA in management of primary liver malignancy: A review of the literature and future directions. J Surg Oncol 2024. [PMID: 39155663 DOI: 10.1002/jso.27825] [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: 04/22/2024] [Accepted: 06/14/2024] [Indexed: 08/20/2024]
Abstract
Primary liver malignancies are a serious and challenging global health concern. The most common primary tumors are hepatocellular carcinoma and cholangiocarcinoma. These diseases portend poor prognosis when presenting with progressive, extensive disease. There is a critical need for improved diagnosis, therapeutic intervention, and monitoring surveillance in liver-related malignancies. Liquid biopsy using ctDNA provides an opportunity for growth within these domains for liver-related malignancy. However, ctDNA is relatively understudied in this field compared with other solid tumor types, possibly due to the complex nature of the pathology. In this review, we aim to discuss ctDNA, the current literature, and future directions of this technology within primary liver malignancies.
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Affiliation(s)
- Noah X Tocci
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Chase J Wehrle
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Keyue Sun
- Lerner Research Institute, Inflammation & Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Chunbao Jiao
- Lerner Research Institute, Inflammation & Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Hanna Hong
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Abby Gross
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Erlind Allkushi
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Melis Uysal
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Maureen Whitsett Linganna
- Department of Gastroenterology, Hepatology, and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Katheryn Stackhouse
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Koji Hashimoto
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Andrea Schlegel
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
- Lerner Research Institute, Inflammation & Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - R Matthew Walsh
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Charles Miller
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - David C H Kwon
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Federico Aucejo
- Department of Hepato-pancreato-biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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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; 42:2736-2740. [PMID: 38754043 DOI: 10.1200/jco.23.02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [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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6
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Seyhan AA. Circulating Liquid Biopsy Biomarkers in Glioblastoma: Advances and Challenges. Int J Mol Sci 2024; 25:7974. [PMID: 39063215 PMCID: PMC11277426 DOI: 10.3390/ijms25147974] [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: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Gliomas, particularly glioblastoma (GBM), represent the most prevalent and aggressive tumors of the central nervous system (CNS). Despite recent treatment advancements, patient survival rates remain low. The diagnosis of GBM traditionally relies on neuroimaging methods such as magnetic resonance imaging (MRI) or computed tomography (CT) scans and postoperative confirmation via histopathological and molecular analysis. Imaging techniques struggle to differentiate between tumor progression and treatment-related changes, leading to potential misinterpretation and treatment delays. Similarly, tissue biopsies, while informative, are invasive and not suitable for monitoring ongoing treatments. These challenges have led to the emergence of liquid biopsy, particularly through blood samples, as a promising alternative for GBM diagnosis and monitoring. Presently, blood and cerebrospinal fluid (CSF) sampling offers a minimally invasive means of obtaining tumor-related information to guide therapy. The idea that blood or any biofluid tests can be used to screen many cancer types has huge potential. Tumors release various components into the bloodstream or other biofluids, including cell-free nucleic acids such as microRNAs (miRNAs), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), proteins, extracellular vesicles (EVs) or exosomes, metabolites, and other factors. These factors have been shown to cross the blood-brain barrier (BBB), presenting an opportunity for the minimally invasive monitoring of GBM as well as for the real-time assessment of distinct genetic, epigenetic, transcriptomic, proteomic, and metabolomic changes associated with brain tumors. Despite their potential, the clinical utility of liquid biopsy-based circulating biomarkers is somewhat constrained by limitations such as the absence of standardized methodologies for blood or CSF collection, analyte extraction, analysis methods, and small cohort sizes. Additionally, tissue biopsies offer more precise insights into tumor morphology and the microenvironment. Therefore, the objective of a liquid biopsy should be to complement and enhance the diagnostic accuracy and monitoring of GBM patients by providing additional information alongside traditional tissue biopsies. Moreover, utilizing a combination of diverse biomarker types may enhance clinical effectiveness compared to solely relying on one biomarker category, potentially improving diagnostic sensitivity and specificity and addressing some of the existing limitations associated with liquid biomarkers for GBM. This review presents an overview of the latest research on circulating biomarkers found in GBM blood or CSF samples, discusses their potential as diagnostic, predictive, and prognostic indicators, and discusses associated challenges and future perspectives.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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7
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He D, Cui B, Lv H, Lu S, Zhu Y, Cheng Y, Dang L, Zhang H. Blood-Derived Extracellular Vesicles as a Promising Liquid Biopsy Diagnostic Tool for Early Cancer Detection. Biomolecules 2024; 14:847. [PMID: 39062561 PMCID: PMC11275243 DOI: 10.3390/biom14070847] [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: 04/14/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer poses a significant public health challenge worldwide, and timely screening has the potential to mitigate cancer progression and reduce mortality rates. Currently, early identification of most tumors relies on imaging techniques and tissue biopsies. However, the use of low-cost, highly sensitive, non-invasive detection methods for early cancer screening has become more attractive. Extracellular Vesicles (EVs) released by all living cells contain distinctive biological components, such as nucleic acids, proteins, and lipids. These vesicles play crucial roles in the tumor microenvironment and intercellular communication during tumor progression, rendering liquid biopsy a particularly suitable method for diagnosis. Nevertheless, challenges related to purification methods and validation of efficacy currently hinder its widespread clinical implementation. These limitations underscore the importance of refining isolation techniques and conducting comprehensive investigations on EVs. This study seeks to evaluate the potential of liquid biopsy utilizing blood-derived EVs as a practical, cost-effective, and secure approach for early cancer detection.
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Affiliation(s)
- Dan He
- Laboratory of Animal Center, Medical Experiment Center, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (D.H.); (S.L.); (Y.Z.)
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an 710038, China;
| | - Hongkai Lv
- Department of Clinical Medicine of Second Clinical Medical School, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (H.L.); (Y.C.)
| | - Shuxian Lu
- Laboratory of Animal Center, Medical Experiment Center, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (D.H.); (S.L.); (Y.Z.)
| | - Yuan Zhu
- Laboratory of Animal Center, Medical Experiment Center, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (D.H.); (S.L.); (Y.Z.)
| | - Yuqiang Cheng
- Department of Clinical Medicine of Second Clinical Medical School, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (H.L.); (Y.C.)
| | - Lin Dang
- Basic Medical Academy, Shaanxi University of Chinese Medicine, Xianyang 712046, China
| | - Hong Zhang
- Laboratory of Animal Center, Medical Experiment Center, Shaanxi University of Chinese Medicine, Xianyang 712046, China; (D.H.); (S.L.); (Y.Z.)
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8
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Turabi K, Klute K, Radhakrishnan P. Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies. Cancers (Basel) 2024; 16:2432. [PMID: 39001494 PMCID: PMC11240538 DOI: 10.3390/cancers16132432] [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: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.
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Affiliation(s)
- Khadija Turabi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey Klute
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Fu Y, Jiang J, Wu Y, Cao D, Jia Z, Zhang Y, Li D, Cui Y, Zhang Y, Cao X. Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer. Gastric Cancer 2024; 27:735-746. [PMID: 38584223 DOI: 10.1007/s10120-024-01493-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND 5-Hydroxymethylcytosine-enriched gene profiles and regions show tissue-specific and tumor specific. There is a potential value to explore cell-free DNA 5-hydroxymethylcytosine feature biomarkers for early gastric cancer detection. METHODS A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the different 5-hydroxymethylcytosine modification features of cell free DNA. Significantly differential 5-hydroxymethylcytosine modification genes were identified to construct a gastric cancer diagnostic model. Data set from GEO was used as an external testing set to test the robustness of the diagnostic model. RESULTS Accounting for more than 90% of 5-hydroxymethylcytosine peaks were distributed in the gene body in both the gastric cancer and control groups. The diagnostic model was developed based on five different 5-hydroxymethylcytosine modification genes, FBXL7, PDE3A, TPO, SNTG2 and STXBP5. The model could effectively distinguish gastric cancer patients from controls in the training (AUC = 0.95, sensitivity = 88.6%, specificity = 94.3%), validation (AUC = 0.87, sensitivity = 73.3%, specificity = 93.3%) and testing (AUC = 0.90, sensitivity = 81.9%, specificity = 90.2%) sets. The risk scores of the controls from the model were significantly lower than those of gastric cancer patients in both our own data (P < 0.001) and GEO external testing data (P < 0.001), and no significant difference between different TNM stage patients (P = 0.09 and 0.66). Furthermore, there was no significant difference between the healthy control and benign gastric disease patients in the testing set from GEO (P = 0.10). CONCLUSIONS The characteristics of 5-hydroxymethylcytosine in cell free DNA are specific to gastric cancer patients, and the diagnostic model constructed by five genes' 5-hydroxymethylcytosine features could effectively identify gastric cancer patients.
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Affiliation(s)
- Yingli Fu
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jing Jiang
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yanhua Wu
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Donghui Cao
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Zhifang Jia
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yangyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Dongming Li
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yingnan Cui
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yuzheng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China.
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Nam H, Lee E, Yang H, Lee K, Kwak T, Kim D, Kim H, Yang M, Yang Y, Son S, Nam YH, Minn I. PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. Biol Methods Protoc 2024; 9:bpae041. [PMID: 38938409 PMCID: PMC11208725 DOI: 10.1093/biomethods/bpae041] [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: 01/15/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
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Affiliation(s)
- Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Esder Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hichang Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Kyeyoon Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Taeho Kwak
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Dain Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hyemin Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Mihwa Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Younjoo Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Seungwan Son
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Young-Hyean Nam
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21287, United States
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11
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Hao MJ, Cheng ZY, Gao Y, Xin L, Yu CT, Wang TL, Li ZS, Wang LW. Liquid biopsy of oesophageal squamous cell carcinoma: implications in diagnosis, prognosis, and treatment monitoring. Scand J Gastroenterol 2024; 59:698-709. [PMID: 38466190 DOI: 10.1080/00365521.2024.2310167] [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: 10/20/2023] [Accepted: 01/20/2024] [Indexed: 03/12/2024]
Abstract
Oesophageal squamous cell carcinoma (ESCC) is a common malignant tumour of the gastrointestinal tract. Early detection and access to appropriate treatment are crucial for the long-term survival of patients. However, limited diagnostic and monitoring methods are available for identifying early stage ESCC. Endoscopic screening and surgical resection are commonly used to diagnose and treat early ESCC. However, these methods have disadvantages, such as high recurrence, lethality, and mortality rates. Therefore, methods to improve early diagnosis of ESCC and reduce its mortality rate are urgently required. In 1961, Gary et al. proposed a novel liquid biopsy approach for clinical diagnosis. This involved examining exosomes, circulating tumour cells, circulating free DNA, and circulating free RNA in body fluids. The ability of liquid biopsy to obtain samples repeatedly, wide detection range, and fast detection speed make it a feasible option for non-invasive tumour detection. In clinical practice, liquid biopsy technology has gained popularity for early screening, diagnosis, treatment efficacy monitoring, and prognosis assessment. Thus, this is a highly promising examination method. However, there have been no comprehensive reviews on the four factors of liquid biopsy in the context of ESCC. This review aimed to analyse the progress of liquid biopsy research for ESCC, including its classification, components, and potential future applications.
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Affiliation(s)
- Mei-Juan Hao
- University of Shanghai for Science and Technology, Shanghai, China
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Department of Anaesthesia and Surgery, Guiyang Fourth People's Hospital, Guiyang, China
| | - Zhi-Yuan Cheng
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Gao
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Lei Xin
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Chu-Ting Yu
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Ting-Lu Wang
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Zhao-Shen Li
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Luo-Wei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
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12
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Kudriavtsev A, Pastor B, Mirandola A, Pisareva E, Gricourt Y, Capdevila X, Thierry AR, Cuvillon P. Association of the immediate perioperative dynamics of circulating DNA levels and neutrophil extracellular traps formation in cancer patients. PRECISION CLINICAL MEDICINE 2024; 7:pbae008. [PMID: 38699382 PMCID: PMC11062027 DOI: 10.1093/pcmedi/pbae008] [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: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Objectives Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients. Methods We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI). Results The synergistic analytical information provided by these markers revealed that: (i) NETs formation contributes to post-surgery conditions; (ii) post-surgery cir-nDNA levels were highly associated with NE and MPO in colon cancer [r = 0.60 (P < 0.001) and r = 0.53 (P < 0.01), respectively], but not in prostate and breast cancer; (iii) each tumor type shows a specific pattern of cir-nDNA and NETs marker dynamics, but overall the pre- and post-surgery median values of cir-nDNA, NE, and MPO were significantly higher in cancer patients than in HI. Conclusion Taken as a whole, our work reveals the association of NETs formation with the elevated cir-nDNA release during a cancer patient's perioperative period, depending on surgical procedure or cancer type. By contrast, cir-mtDNA is poorly associated with NETs formation in the studied perioperative period, which would appear to indicate a different mechanism of release or suggest mitochondrial dysfunction.
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Affiliation(s)
- Andrei Kudriavtsev
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Brice Pastor
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Alexia Mirandola
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Ekaterina Pisareva
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Yann Gricourt
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
| | - Xavier Capdevila
- Division of Anaesthesia Intensive Care, Pain and Emergency Medicine, Montpellier University Hospital, Montpellier 34090, France
- Montpellier NeuroSciences Institute, INSERM U1298, University of Montpellier, Montpellier 34295, France
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Philippe Cuvillon
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
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13
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Ding L, Cao S, Qu C, Wu Y, Yu S. Ratiometric CRISPR/Cas12a-Triggered CHA System Coupling with the MSRE to Detect Site-Specific DNA Methylation. ACS Sens 2024; 9:1877-1885. [PMID: 38573977 DOI: 10.1021/acssensors.3c02571] [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: 04/06/2024]
Abstract
The precise determination of DNA methylation at specific sites is critical for the timely detection of cancer, as DNA methylation is closely associated with the initiation and progression of cancer. Herein, a novel ratiometric fluorescence method based on the methylation-sensitive restriction enzyme (MSRE), CRISPR/Cas12a, and catalytic hairpin assembly (CHA) amplification were developed to detect site-specific methylation with high sensitivity and specificity. In detail, AciI, one of the commonly used MSREs, was employed to distinguish the methylated target from nonmethylated targets. The CRISPR/Cas12a system was utilized to recognize the site-specific target. In this process, the protospacer adjacent motif and crRNA-dependent identification, the single-base resolution of Cas12a, can effectively ensure detection specificity. The trans-cleavage ability of Cas12a can convert one target into abundant activators and can then trigger the CHA reaction, leading to the accomplishment of cascaded signal amplification. Moreover, with the structural change of the hairpin probe during CHA, two labeled dyes can be spatially separated, generating a change of the Förster resonance energy transfer signal. In general, the proposed strategy of tandem CHA after the CRISPR/Cas12a reaction not only avoids the generation of false-positive signals caused by the target-similar nucleic acid but can also improve the sensitivity. The use of ratiometric fluorescence can eradicate environmental effects by self-calibration. Consequently, the proposed approach had a detection limit of 2.02 fM. This approach could distinguish between colorectal cancer and precancerous tissue, as well as between colorectal patients and healthy people. Therefore, the developed method can serve as an excellent site-specific methylation detection tool, which is promising for biological and disease studies.
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Affiliation(s)
- Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shengnan Cao
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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14
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Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [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: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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15
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Kim YJ, Min J. Hydrogel-based technologies in liquid biopsy for the detection of circulating clinical markers: challenges and prospects. Anal Bioanal Chem 2024; 416:2065-2078. [PMID: 37963993 DOI: 10.1007/s00216-023-05025-7] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
Liquid biopsy, which promises noninvasive detection of tumor-derived material, has recently been highlighted because of its potential to lead us to an era of precision medicine. However, its development has encountered challenges owing to the extremely low frequency and low purity of circulating tumor markers, such as circulating tumor cells (CTCs), circulating exosomes, and circulating tumor nucleic acids (ctNAs). Much effort has been made to overcome this limitation over the last decade, and an increasing number of studies have shown interest in the special characteristics of hydrogels. This hydrophilic and biocompatible polymeric network, which absorbs a large amount of water, can aid in the isolation, protection, and analysis of these low-abundance and short-lived circulating biomarkers. The role of hydrogels in liquid biopsy is extensive and ranges from enrichment to encapsulation. This review provides an overview of hydrogel-based technologies to pave the way in liquid biopsy.
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Affiliation(s)
- Young Jun Kim
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea.
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16
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Lippert J, Smith G, Appenzeller S, Landwehr LS, Prete A, Steinhauer S, Asia M, Urlaub H, Elhassan YS, Kircher S, Arlt W, Fassnacht M, Altieri B, Ronchi CL. Circulating cell-free DNA-based biomarkers for prognostication and disease monitoring in adrenocortical carcinoma. Eur J Endocrinol 2024; 190:234-247. [PMID: 38451242 DOI: 10.1093/ejendo/lvae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/11/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024]
Abstract
OBJECTIVE Adrenocortical carcinoma (ACC) is a rare aggressive cancer with heterogeneous behaviour. Disease surveillance relies on frequent imaging, which comes with significant radiation exposure. The aim of the study was to investigate the role of circulating cell-free DNA (ccfDNA)-related biomarkers (BMs) for prognostication and monitoring of ACC. DESIGN AND METHODS We investigated 34 patients with ACC and 23 healthy subjects (HSs) as controls. Circulating cell-free DNA was extracted by commercial kits and ccfDNA concentrations were quantified by fluorimeter (BM1). Targeted sequencing was performed using a customized panel of 27 ACC-specific genes. Leucocyte DNA was used to discriminate somatic variants (BM2), while tumour DNA was sequenced in 22/34 cases for comparison. Serial ccfDNA samples were collected during follow-up in 19 ACC patients (median period 9 months) and analysed in relationship with standard radiological imaging. RESULTS Circulating cell-free DNA concentrations were higher in ACC than HS (mean ± SD, 1.15 ± 1.56 vs 0.05 ± 0.05 ng/µL, P < .0001), 96% of them being above the cut-off of 0.146 ng/µL (mean HS + 2 SD, positive BM1). At ccfDNA sequencing, 47% of ACC showed at least 1 somatic mutation (positive BM2). A combined ccfDNA-BM score was strongly associated with both progression-free and overall survival (hazard ratio [HR] = 2.63; 95% CI, 1.13-6.13; P = .010, and HR = 5.98; 95% CI, 2.29-15.6; P = .0001, respectively). During disease monitoring, positive BM2 showed the best specificity (100%) and sensitivity (67%) to detect ACC recurrence or progress compared with BM1. CONCLUSION ccfDNA-related BMs are frequently detected in ACC patients and represent a promising, minimally invasive tool to predict clinical outcome and complement surveillance imaging. Our findings will be validated in a larger cohort of ACCs with long-term follow-up.
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Affiliation(s)
- Juliane Lippert
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
- Institute of Human Genetics, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Gabrielle Smith
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
| | - Silke Appenzeller
- Core Unit Bioinformatics, Comprehensive Cancer Center Mainfranken, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Laura-Sophie Landwehr
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Alessandro Prete
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, B152TT Birmingham, United Kingdom
- NIHR Birmingham Biomedical Research Centre, University of Birmingham, University Hospitals Birmingham NHS Foundation Trust, B152GW Birmingham, United Kingdom
| | - Sonja Steinhauer
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Miriam Asia
- Endocrine Department, Queen Elizabeth Hospital Birmingham NHS Trust, B152GW Birmingham, United Kingdom
| | - Hanna Urlaub
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Yasir S Elhassan
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Endocrine Department, Queen Elizabeth Hospital Birmingham NHS Trust, B152GW Birmingham, United Kingdom
| | - Stefan Kircher
- Department of Pathology, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Wiebke Arlt
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- MRC Laboratory of Medical Sciences, W120TN London, United Kingdom
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, B152TT Birmingham, United Kingdom
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17
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Wang H, Yang S, Chen L, Li Y, He P, Wang G, Dong H, Ma P, Ding G. Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer. Bioact Mater 2024; 33:174-222. [PMID: 38034499 PMCID: PMC10684566 DOI: 10.1016/j.bioactmat.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.
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Affiliation(s)
- Hang Wang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Siwei Yang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Liangfeng Chen
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Yongqiang Li
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peng He
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Gang Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, PR China
| | - Hui Dong
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, PR China
| | - Guqiao Ding
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
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18
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Liu D, Yehia L, Dhawan A, Ni Y, Eng C. Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome. Cell Rep Med 2024; 5:101384. [PMID: 38242121 PMCID: PMC10897513 DOI: 10.1016/j.xcrm.2023.101384] [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: 06/09/2023] [Revised: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Individuals with PTEN hamartoma tumor syndrome (PHTS) harbor pathogenic germline PTEN variants that confer a significantly increased lifetime risk of various organ-specific cancers including second primary malignant neoplasms (SMNs). Currently, there are no reliable biomarkers that can predict individual-level cancer risk. Despite the highly promising value of cell-free DNA (cfDNA) as a biomarker for underlying sporadic cancers, the utility of cfDNA in individuals with known cancer-associated germline variants and subclinical cancers remains poorly understood. We perform ultra-low-pass whole-genome sequencing (ULP-WGS) of cfDNA from plasma samples from patients with PHTS and cancer as well as those without cancer. Analysis of cfDNA reveals that patients with PHTS and SMNs have distinct cfDNA size distribution, aberrant genome-wide fragmentation, and differential fragment end motif frequencies. Our work provides evidence that cfDNA profiles may be used as a marker for SMN risk in patients with PHTS.
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Affiliation(s)
- Darren Liu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Andrew Dhawan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ying Ni
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA; Center for Immunotherapy and Precision Immuno-oncology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA; Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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Bixby B, Vrba L, Lenka J, Oshiro MM, Watts GS, Hughes T, Erickson H, Chopra M, Knepler JL, Knox KS, Jarnagin L, Alalawi R, Kala M, Bernert R, Routh J, Roe DJ, Garland LL, Futscher BW, Nelson MA. Cell-free DNA methylation analysis as a marker of malignancy in pleural fluid. Sci Rep 2024; 14:2939. [PMID: 38316884 PMCID: PMC10844328 DOI: 10.1038/s41598-024-53132-x] [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: 10/23/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024] Open
Abstract
Diagnosis of malignant pleural effusion (MPE) is made by cytological examination of pleural fluid or histological examination of pleural tissue from biopsy. Unfortunately, detection of malignancy using cytology has an overall sensitivity of 50%, and is dependent upon tumor load, volume of fluid assessed, and cytopathologist experience. The diagnostic yield of pleural fluid cytology is also compromised by low abundance of tumor cells or when morphology is obscured by inflammation or reactive mesothelial cells. A reliable molecular marker that may complement fluid cytology for the diagnosis of malignant pleural effusion is needed. The purpose of this study was to establish a molecular diagnostic approach based on pleural effusion cell-free DNA methylation analysis for the differential diagnosis of malignant pleural effusion and benign pleural effusion. This was a blind, prospective case-control biomarker study. We recruited 104 patients with pleural effusion for the study. We collected pleural fluid from patients with: MPE (n = 48), indeterminate pleural effusion in subjects with known malignancy or IPE (n = 28), and benign PE (n = 28), and performed the Sentinel-MPE liquid biopsy assay. The methylation level of Sentinel-MPE was markedly higher in the MPE samples compared to BPE control samples (p < 0.0001) and the same tendency was observed relative to IPE (p = 0.004). We also noted that the methylation signal was significantly higher in IPE relative to BPE (p < 0.001). We also assessed the diagnostic efficiency of the Sentinel-MPE test by performing receiver operating characteristic analysis (ROC). For the ROC analysis we combined the malignant and indeterminate pleural effusion groups (n = 76) and compared against the benign group (n = 28). The detection sensitivity and specificity of the Sentinel-MPE test was high (AUC = 0.912). The Sentinel-MPE appears to have better performance characteristics than cytology analysis. However, combining Sentinel-MPE with cytology analysis could be an even more effective approach for the diagnosis of MPE. The Sentinel-MPE test can discriminate between BPE and MPE. The Sentinel-MPE liquid biopsy test can detect aberrant DNA in several different tumor types. The Sentinel-MPE test can be a complementary tool to cytology in the diagnosis of MPE.
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Affiliation(s)
- Billie Bixby
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | | | - Jyoti Lenka
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Marc M Oshiro
- Boyer Liver Institute, Department of Medicine, University of Arizona, Tucson, USA
| | - George S Watts
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, USA
| | - Trina Hughes
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Heidi Erickson
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Madhav Chopra
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - James L Knepler
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Kenneth S Knox
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Lisa Jarnagin
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Raed Alalawi
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Mrinalini Kala
- Department of Internal Medicine, University of Arizona, Phoenix, USA
| | | | | | - Denise J Roe
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | - Linda L Garland
- Hematology Oncology, Department of Medicine, University of Arizona, Tucson, USA
| | - Bernard W Futscher
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, USA
| | - Mark A Nelson
- Department of Pathology, University of Arizona, Tucson, AZ, 85724, USA.
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21
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Deal BR, Ma R, Narum S, Ogasawara H, Duan Y, Kindt JT, Salaita K. Heteromultivalency enables enhanced detection of nucleic acid mutations. Nat Chem 2024; 16:229-238. [PMID: 37884668 DOI: 10.1038/s41557-023-01345-4] [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: 04/29/2022] [Accepted: 09/15/2023] [Indexed: 10/28/2023]
Abstract
Detecting genetic mutations such as single nucleotide polymorphisms (SNPs) is necessary to prescribe effective cancer therapies, perform genetic analyses and distinguish similar viral strains. Traditionally, SNP sensing uses short oligonucleotide probes that differentially bind the SNP and wild-type targets. However, DNA hybridization-based techniques require precise tuning of the probe's binding affinity to manage the inherent trade-off between specificity and sensitivity. As conventional hybridization offers limited control over binding affinity, here we generate heteromultivalent DNA-functionalized particles and demonstrate optimized hybridization specificity for targets containing one or two mutations. By investigating the role of oligo lengths, spacer lengths and binding orientation, we reveal that heteromultivalent hybridization enables fine-tuned specificity for a single SNP and dramatic enhancements in specificity for two non-proximal SNPs empowered by highly cooperative binding. Capitalizing on these abilities, we demonstrate straightforward discrimination between heterozygous cis and trans mutations and between different strains of the SARS-CoV-2 virus. Our findings indicate that heteromultivalent hybridization offers substantial improvements over conventional monovalent hybridization-based methods.
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Affiliation(s)
- Brendan R Deal
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Steven Narum
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - James T Kindt
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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22
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Du S, Cao K, Yan Y, Wang Y, Wang Z, Lin D. Developments and current status of cell-free DNA in the early detection and management of hepatocellular carcinoma. J Gastroenterol Hepatol 2024; 39:231-244. [PMID: 37990622 DOI: 10.1111/jgh.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
Nowadays, hepatocellular carcinoma (HCC) is still a major threat to human health globally, with a disappointing prognosis. Regular monitoring of patients at high risk, utilizing abdominal ultrasonography combined with alpha-fetoprotein (AFP) serum analysis, enables the early detection of potentially treatable tumors. However, the approach has limitations due to its lack of sensitivity. Meanwhile, the current standard procedure for obtaining a tumor biopsy in cases of HCC is invasive and lacks the ability to assess the dynamic progression of cancer or account for tumor heterogeneity. Hence, there is a pressing need to develop non-invasive, highly sensitive biomarkers for HCC which can improve the accuracy of early diagnosis, assess treatment response and accurately predict the prognosis. In contrast to the conventional method of tissue biopsy, liquid biopsy offers a non-invasive approach that can be readily repeated. As a liquid biopsy approach, the analysis of cell-free DNA (cfDNA) offers real-time insights that can accurately portray the tumor burden and provide a comprehensive depiction of the genetic profile associated with HCC. In this review, we present a comprehensive summary of the recent research findings pertaining to the significance and potential practicality of cfDNA analysis in the early detection and effective management of HCC.
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Affiliation(s)
- Sihao Du
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ke Cao
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yadong Yan
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yupeng Wang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhenshun Wang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Dongdong Lin
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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Cui JZ, Chew ZH, Lim LHK. New insights into nucleic acid sensor AIM2: The potential benefit in targeted therapy for cancer. Pharmacol Res 2024; 200:107079. [PMID: 38272334 DOI: 10.1016/j.phrs.2024.107079] [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: 11/06/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The AIM2 inflammasome represents a multifaceted oligomeric protein complex within the innate immune system, with the capacity to perceive double-stranded DNA (dsDNA) and engage in diverse physiological reactions and disease contexts, including cancer. While originally conceived as a discerning DNA sensor, AIM2 has demonstrated its capability to discern various nucleic acid variations, encompassing RNA and DNA-RNA hybrids. Through its interaction with nucleic acids, AIM2 orchestrates the assembly of a complex involving multiple proteins, aptly named the AIM2 inflammasome, which facilitates the enzymatic cleavage of proinflammatory cytokines, namely pro-IL-1β and pro-IL-18. This process, in turn, underpins its pivotal biological role. In this review, we provide a systematic summary and discussion of the latest advancements in AIM2 sensing various types of nucleic acids. Additionally, we discuss the modulation of AIM2 activation, which can cause cell death, including pyroptosis, apoptosis, and autophagic cell death. Finally, we fully illustrate the evidence for the dual role of AIM2 in different cancer types, including both anti-tumorigenic and pro-tumorigenic functions. Considering the above information, we uncover the therapeutic promise of modulating the AIM2 inflammasome in cancer treatment.
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Affiliation(s)
- Jian-Zhou Cui
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS-Cambridge Immunophenotyping Centre, Life Science Institute, National University of Singapore, Singapore.
| | - Zhi Huan Chew
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lina H K Lim
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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24
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Soliman N, Saharia A, Abdelrahim M, Connor AA. Molecular profiling in the management of hepatocellular carcinoma. Curr Opin Organ Transplant 2024; 29:10-22. [PMID: 38038621 DOI: 10.1097/mot.0000000000001124] [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: 12/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to both summarize the current knowledge of hepatocellular carcinoma molecular biology and to suggest a framework in which to prospectively translate this knowledge into patient care. This is timely as recent guidelines recommend increased use of these technologies to advance personalized liver cancer care. RECENT FINDINGS The main themes covered here address germline and somatic genetic alterations recently discovered in hepatocellular carcinoma, largely owing to next generation sequencing technologies, and nascent efforts to translate these into contemporary practice. SUMMARY Early efforts of translating molecular profiling to hepatocellular carcinoma care demonstrate a growing number of potentially actionable alterations. Still lacking are a consensus on what biomarkers and technologies to adopt, at what scale and cost, and how to integrate them most effectively into care.
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Lu J, Feng Y, Guo K, Sun L, Ruan S, Zhang K. Prognostic value of preoperative circulating tumor DNA in non-small cell lung cancer: a systematic review and meta-analysis. J Cancer Res Clin Oncol 2024; 150:25. [PMID: 38252173 PMCID: PMC10803397 DOI: 10.1007/s00432-023-05550-z] [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: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Several recent studies have reported the increasing application of preoperative circulating tumor DNA (ctDNA) as a biomarker of tumor burden for guiding potential postoperative treatment strategies. METHODS A meta-analysis of prospective/retrospective cohort studies was conducted to compare the prognosis of preoperatively genetically positive and genetically negative NSCLC patients. The endpoints used in the included studies were overall survival (OS) and recurrence-free survival (RFS). The objective of the meta-analysis was to comprehensively explore the prognostic value of preoperative ctDNA for patients with non-small-cell lung cancer (NSCLC) and its significance in guiding postoperative adjuvant therapy (AT) in patients with NSCLC. RESULTS The preliminary analysis identified 1565 studies, among which only 11 studies fulfilled the eligibility criteria and were finally included in the present systematic review and meta-analysis. The statistical results revealed that the expression of preoperative ctDNA was associated with worse RFS (HR = 3.00; 95% CI 2.26-3.98; I2 = 0%) and OS (HR = 2.77; 95% CI 1.67-4.58; I2 = 0%), particularly in lung adenocarcinoma (LUAD) patients (RFS: HR = 3.46; 95% CI 2.37-5.05; I2 = 0%; OS: HR = 3.52; 95% CI 1.91-6.49; I2 = 0%) and patients with I-II stage of NSCLC (RFS: HR = 2.84; 95% CI 1.88-4.29; I2 = 0%; OS: HR = 2.60; 95% CI 1.43-4.74; I2 = 0%). Moreover, compared to patients with negative preoperative ctDNA, patients with positive preoperative ctDNA presented greater survival benefits (HR = 0.39; 95% CI 0.22-0.67; I2 = 2%) from postoperative AT. CONCLUSION The evaluation of the prognostic value of preoperative ctDNA revealed that preoperative ctDNA might be used as a prognostic biomarker for patients with LUAD or those with stage I-II NSCLC. In addition, postoperative AT is recommended for NSCLC patients with positive preoperative ctDNA, regardless of the disease stage and subtype.
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Affiliation(s)
- Jiamin Lu
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Yuqian Feng
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kaibo Guo
- Department of Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Leitao Sun
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Shanming Ruan
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Kai Zhang
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
- Anji Traditional Chinese Medical Hospital, Huzhou, Zhejiang, China.
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26
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Diez-Feijóo R, Andrade-Campos M, Gibert J, Sánchez-González B, Fernández-Ibarrondo L, Fernández-Rodríguez C, Garcia-Gisbert N, Camacho L, Lafuente M, Vázquez I, Colomo L, Salar A, Bellosillo B. Cell-Free DNA as a Biomarker at Diagnosis and Follow-Up in 256 B and T-Cell Lymphomas. Cancers (Basel) 2024; 16:321. [PMID: 38254810 PMCID: PMC10813584 DOI: 10.3390/cancers16020321] [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: 12/09/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis has become a promising tool for the diagnosis, prognosis, and monitoring of lymphoma cases. Until now, research in this area has mainly focused on aggressive lymphomas, with scanty information from other lymphoma subtypes. METHODS We selected 256 patients diagnosed with lymphomas, including a large variety of B-cell and T-cell non-Hodgkin and Hodgkin lymphomas, and quantified cfDNA from plasma at the time of diagnosis. We further selected 49 large B-cell lymphomas (LBCL) and analyzed cfDNA levels at diagnosis (pre-therapy) and after therapy. In addition, we performed NGS on cfDNA and tissue in this cohort of LBCL. RESULTS Lymphoma patients showed a statistically significant higher cfDNA concentration than healthy controls (mean 53.0 ng/mL vs. 5.6 ng/mL, p < 0.001). The cfDNA concentration was correlated with lymphoma subtype, lactate dehydrogenase, the International Prognostic Index (IPI) score, Ann Arbor (AA), and B-symptoms. In 49 LBCL cases, the cfDNA concentration decreased after therapy in cases who achieved complete response (CR) and increased in non-responders. The median cfDNA at diagnosis of patients who achieved CR and later relapsed was higher (81.5 ng/mL) compared with levels of those who did not (38.6 ng/mL). A concordance of 84% was observed between NGS results in tumor and cfDNA samples. Higher VAF in cfDNA is correlated with advanced stage and bulky disease. CONCLUSIONS cfDNA analysis can be easily performed in almost all lymphoma cases. The cfDNA concentration correlated with the characteristics of the aggressiveness of the lymphomas and, in LBCL, with the response achieved after therapy. These results support the utility of cfDNA analysis as a complementary tool in the management of lymphoma patients.
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Affiliation(s)
- Ramón Diez-Feijóo
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Marcio Andrade-Campos
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Joan Gibert
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Blanca Sánchez-González
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Lierni Fernández-Ibarrondo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Concepción Fernández-Rodríguez
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Nieves Garcia-Gisbert
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Laura Camacho
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Marta Lafuente
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Ivonne Vázquez
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Luis Colomo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Antonio Salar
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Beatriz Bellosillo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
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Li JH, Zhang DY, Zhu JM, Dong L. Clinical applications and perspectives of circulating tumor DNA in gastric cancer. Cancer Cell Int 2024; 24:13. [PMID: 38184573 PMCID: PMC10770949 DOI: 10.1186/s12935-024-03209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024] Open
Abstract
Gastric cancer remains a leading cause of cancer-related death worldwide, largely due to inadequate screening methods, late diagnosis, and limited treatment options. Liquid biopsy has emerged as a promising non-invasive approach for cancer screening and prognosis by detecting circulating tumor components like circulating tumor DNA (ctDNA) in the blood. Numerous gastric cancer-specific ctDNA biomarkers have now been identified. CtDNA analysis provides insight into genetic and epigenetic alterations in tumors, holding promise for predicting treatment response and prognosis in gastric cancer patients. This review summarizes current research on ctDNA biology and detection technologies, while highlighting clinical applications of ctDNA for gastric cancer diagnosis, prognosis, and guiding treatment decisions. Current challenges and future perspectives for ctDNA analysis are also discussed.
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Affiliation(s)
- Jing-Han Li
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dan-Ying Zhang
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ji-Min Zhu
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Ling Dong
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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28
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Lygre KB, Forthun RB, Høysæter T, Hjelle SM, Eide GE, Gjertsen BT, Pfeffer F, Hovland R. Assessment of postoperative circulating tumour DNA to predict early recurrence in patients with stage I-III right-sided colon cancer: prospective observational study. BJS Open 2024; 8:zrad146. [PMID: 38242575 PMCID: PMC10799327 DOI: 10.1093/bjsopen/zrad146] [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: 08/28/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Right-sided colon cancer (RCC) differs in mutation profile and risk of recurrence compared to distal colon cancer. Circulating tumour DNA (ctDNA) present after surgery can identify patients with residual disease after curative surgery and predict risk of early recurrence. METHODS This is a prospective observational biomarker trial with exploration of ctDNA in 50 non-metastatic RCC patients for which oncological right-sided colectomy was performed. Blood samples were collected preoperatively, within 1 month post surgery, 3 months (not mandatory), 6 months and every 6 months thereafter. Plasma cell free DNA and/or tumour was investigated for cancer-related mutations by the next-generation sequencing (NGS) panel AVENIO surveillance specifically designed for ctDNA analysis. Detected mutations were quantified using digital droplet PCR (ddPCR) for follow-up. Recurrence-free survival was explored. RESULTS 50 patients were recruited. Somatic cancer-related mutations were detected in 47/50 patients. ddPCR validated results from NGS for 27/34 (plasma) and 72/72 samples (tumour). Preoperative ctDNA was detected in 31/47 of the stage I/III patients and the majority of ctDNA positive patients showed reduction of ctDNA after surgery (27/31). ctDNA-positive patients at first postoperative sample had high recurrence risk compared to patients without measurable ctDNA (adjusted hazard ratio: 172.91; 95% c.i.: 8.70 to 3437.24; P: 0.001). CONCLUSION ctDNA was detectable in most patients with non-metastatic RCC before surgery. Positive postoperative ctDNA was strongly associated with early recurrence. Detectable postoperative ctDNA is a prognostic factor with high (100%) positive predictive value for recurrence in this cohort of non-metastatic RCC. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov ID: NCT03776591.
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Affiliation(s)
- Kristin B Lygre
- Department of Gastrointestinal Surgery, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Gastrointestinal Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Rakel B Forthun
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
| | - Trude Høysæter
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sigrun M Hjelle
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Geir E Eide
- Centre for Clinical Research, Haukeland University Hospital, Bergen, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Bjørn T Gjertsen
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frank Pfeffer
- Department of Gastrointestinal Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Randi Hovland
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Biosciences, University of Bergen, Bergen, Norway
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29
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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Stosic K, Senar OA, Tarfouss J, Bouchart C, Navez J, Van Laethem JL, Arsenijevic T. A Comprehensive Review of the Potential Role of Liquid Biopsy as a Diagnostic, Prognostic, and Predictive Biomarker in Pancreatic Ductal Adenocarcinoma. Cells 2023; 13:3. [PMID: 38201207 PMCID: PMC10778087 DOI: 10.3390/cells13010003] [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: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most lethal malignant diseases, with a mortality rate being close to incidence. Due to its heterogeneity and plasticity, as well as the lack of distinct symptoms in the early phases, it is very often diagnosed at an advanced stage, resulting in poor prognosis. Traditional tissue biopsies remain the gold standard for making a diagnosis, but have an obvious disadvantage in their inapplicability for frequent sampling. Blood-based biopsies represent a non-invasive method which potentially offers easy and repeated sampling, leading to the early detection and real-time monitoring of the disease and hopefully an accurate prognosis. Given the urgent need for a reliable biomarker that can estimate a patient's condition and response to an assigned treatment, blood-based biopsies are emerging as a potential new tool for improving patients' survival and surveillance. In this article, we discuss the current advances and challenges in using liquid biopsies for pancreatic cancer, focusing on circulating tumour DNA (ctDNA), extracellular vesicles (EVs), and circulating tumour cells (CTCs), and compare the performance and reliability of different biomarkers and combinations of biomarkers.
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Affiliation(s)
- Kosta Stosic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Oier Azurmendi Senar
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Jawad Tarfouss
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Christelle Bouchart
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Radiation Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Julie Navez
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Hepato-Biliary-Pancreatic Surgery, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Tatjana Arsenijevic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
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Foster JB, Koptyra MP, Bagley SJ. Recent Developments in Blood Biomarkers in Neuro-oncology. Curr Neurol Neurosci Rep 2023; 23:857-867. [PMID: 37943477 DOI: 10.1007/s11910-023-01321-y] [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] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE OF REVIEW Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system (CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors. RECENT FINDINGS We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier. Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz P Koptyra
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, 10th Floor Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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Bu Q, Luo X, He L, Ma J, He S, Lei W, Zhou W, Deng H, Lin Y, Zhang L, Hong X. Septin9 DNA methylation as a promising biomarker for cervical cancer. J OBSTET GYNAECOL 2023; 43:2151356. [PMID: 36476308 DOI: 10.1080/01443615.2022.2151356] [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: 12/13/2022]
Abstract
Aberrant Septin9 methylation in cervical cancer has been rarely studied. We aimed to identify its diagnostic value in cervical cancer using cervical scrapings, and its predictive potential in plasma for pelvic nodal metastasis of cervical cancer. The statuses of methylated Septin9 in fresh cervical lesions and cervical scrapings were first evaluated by using quantitative methylation-specific PCR. Subsequently, the relationship between Septin9 methylation in 113 plasma samples and pelvic nodal metastasis of cervical cancer was evaluated. Methylated Septin9 was detected in all cancerous tissues, but not in cervicitis. The degrees of Septin9 methylation increased with growing severity of cervical lesions in cervical scrapings. The sensitivity of methylated Septin9 was lower than that of cytology, while it yielded a high specificity and area under the curve in detecting high-grade squamous intraepithelial lesion or cervical cancer; and when Septin9 methylation combined with HPV16/18 genotyping, the sensitivity would increase from 70.42% to 82.39%. Plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%. In conclusion, we demonstrated methylated Septin9 to be an innovative diagnostic biomarker for cervical cancer and its non-invasive predictive potential in plasma for pelvic nodal metastasis of cervical cancer.Impact statementWhat is already known on this subject? The occurrence of cervical cancer is related to Septin9 methylation. In fresh specimens and cervical scrapings, we found the degrees of methylated Septin9 increased with growing severity of cervical lesions. Compared with HPV16/18 genotyping and cytological detection, Septin9 methylation had a better specificity and AUC in detecting ≥ HSIL. Furthermore, plasma-based Septin9 methylation also had a high specificity for pelvic lymphatic metastasis prediction.What the results of this study add? Methylation analysis of Septin9 indicated a similar sensitivity, specificity and AUC in detecting ≥ HSIL, relative to HPV16/18 genotyping. Compared with cytological method, Septin9 methylation also yielded a higher specificity and AUC in detecting ≥ HSIL. And we also found plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%; additionally an increasing sensitivity from 50% to nearly 80% was found when combined with SCCAg.What the implications are of these findings for clinical practice and/or further research? This study aimed to evaluate the relationship between Septin9 methylation and cervical cancer, and to explore the value of methylated Septin9 in the detection of cervical (pre)cancerous lesions. Moreover, we would explore plasma-based ctDNA biomarkers for pelvic lymphatic metastasis prediction of cervical cancer, to improve non-invasive predictive accuracy of pelvic nodal metastasis and reduce the complications caused by pelvic lymphadenectomy.
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Affiliation(s)
- Qiaowen Bu
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiping Luo
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lulu He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jian Ma
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shaoyi He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Weiping Zhou
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yu Lin
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaoshan Hong
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
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Chauhan US, Kohale MG, Jaiswal N, Wankhade R. Emerging Applications of Liquid Biopsies in Ovarian Cancer. Cureus 2023; 15:e49880. [PMID: 38174205 PMCID: PMC10762500 DOI: 10.7759/cureus.49880] [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: 10/06/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Liquid biopsy is a new diagnostic tool in precision oncology that can be used as a complementary or alternative method to surgical biopsies. It is a cutting-edge sampling technique that examines distinct cancer components, such as exosomes and circulating tumor cells discharged into the peripheral circulation, to identify tumor biomarkers through various methods, including polymerase chain reaction (PCR). Liquid biopsy has several benefits, including its non-invasiveness and practicality, which permit serial sampling and long-term monitoring of dynamic tumor changes. Ovarian cancer (OC), the most lethal gynecologic malignancy in the world, is typically diagnosed at stages II and III, which makes recovery and treatment extremely difficult. Relapsed OC and chemotherapy resistance of ovarian tumor cells are other clinical challenges. Although liquid biopsy is not a routinely used diagnostic test, it should be utilized in the diagnosis and prognosis of OC for early detection and treatment. It is less intrusive than conventional tissue biopsies, allowing for the continuous collection of serial blood samples to track cancer development in real time. Before therapeutic application, more investigation is required to pinpoint the particular release processes, the source tissue, and the biological significance of the bulk of liquid biopsy contents.
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Affiliation(s)
- Urvi S Chauhan
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Mangesh G Kohale
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Neha Jaiswal
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Rashmi Wankhade
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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Pu W, Wang F, Li K, Xing C, Zhuang Z, Wang H, Bian H, Zhang R, Xiao L. Novel Method for Detection of PIK3CA Mutations in Circulating Tumor DNA of Patients with Colorectal Cancer. Appl Biochem Biotechnol 2023; 195:7821-7831. [PMID: 37093531 DOI: 10.1007/s12010-023-04488-9] [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] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
The PIK3CA mutation is considered a potential target for treatment of colorectal cancer. We evaluated a PIK3CA mutation assay on plasma cell-free DNA (cfDNA) using a newly developed PCR with restriction digestion integrated and followed by Sanger's sequencing. We analyzed PIK3CA mutation in plasma with our newly developed assays and in matching tumor tissues by routine methods. We detected the PIK3CA gene mutation status by both methods in samples from 40 colorectal cancer patients. Three H1047R mutations of PIK3CA gene were detected in the cfDNA of the 40 patients by restriction digestion PCR. Neither E545K nor H1047R mutations were detected in the cfDNA by routine PCR/sequencing. The PIK3CA H1047R and E545K mutations in cfDNA can be sensitively detected with our newly developed assays. The colorectal cancer has been used as a clinical example in testing our new assays, which indicates that the new assays may have wider applications in detecting mutations in precision oncology. Trial registration: Current Controlled Trials ChiCTR-DDT-12002848, 8 October 2012.
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Affiliation(s)
- Wangyang Pu
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Fengjiao Wang
- Department of Pharmacy, The Affiliated Children's Hospital of Soochow University, Suzhou, 215004, China
| | - Kai Li
- Molecular Medicine Center, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhixiang Zhuang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Hui Wang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Huahui Bian
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Li Xiao
- Molecular Medicine Center, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
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Adams AM, Vreeland TJ, Newhook TE. Circulating Tumor DNA: Towards More Individualized Treatment for Patients with Resectable Colorectal Cancer. J Gastrointest Cancer 2023; 54:1071-1081. [PMID: 36562938 DOI: 10.1007/s12029-022-00888-y] [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] [Accepted: 11/13/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Despite curative-intent treatment, recurrence is common for patients with colorectal cancer (CRC). Currently, prediction of disease recurrence and prognostication following surgery is based upon vague clinical factors and more precise and dynamic biomarkers for risk stratification and treatment decisions are urgently needed. Circulating tumor DNA (ctDNA) is a promising biomarker for patients undergoing treatment for resectable CRC. METHODS In this review, we provide an overview of the data supporting current uses of ctDNA for CRC, including localized CRC and resectable colorectal liver metastases (CLM), as well as descriptions of important ongoing clinical trials using ctDNA in the care of patients with CRC. RESULTS The detection of ctDNA following curative-intent therapy is associated with disease recurrence, and multiple trials are investigating its role in determining need and duration for adjuvant therapy for localized CRC. In addition, ctDNA reliably predicts prognosis for patients with CLM, with trials underway studying ctDNA-guided treatment sequencing and intensity. CONCLUSION The detection of ctDNA is a sensitive and dynamic biomarker for disease recurrence in CRC. Many investigations are underway into ctDNA's potential role in surveillance and treatment algorithms, and it has the potential to become a critical biomarker to determine individualized strategies for treatment sequencing, choice, and duration of therapies.
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Affiliation(s)
- Alexandra M Adams
- Department of Surgery, Brooke Army Medical Center, San Antonio, TX, USA
| | - Timothy J Vreeland
- Department of Surgery, Uniformed Services University of Health Sciences, Bethesda, MD, USA
- Department of Surgical Oncology, Brooke Army Medical Center, San Antonio, TX, USA
| | - Timothy E Newhook
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Temilola DO, Adeola HA, Grobbelaar J, Chetty M. Liquid Biopsy in Head and Neck Cancer: Its Present State and Future Role in Africa. Cells 2023; 12:2663. [PMID: 37998398 PMCID: PMC10670726 DOI: 10.3390/cells12222663] [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: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The rising mortality and morbidity rate of head and neck cancer (HNC) in Africa has been attributed to factors such as the poor state of health infrastructures, genetics, and late presentation resulting in the delayed diagnosis of these tumors. If well harnessed, emerging molecular and omics diagnostic technologies such as liquid biopsy can potentially play a major role in optimizing the management of HNC in Africa. However, to successfully apply liquid biopsy technology in the management of HNC in Africa, factors such as genetic, socioeconomic, environmental, and cultural acceptability of the technology must be given due consideration. This review outlines the role of circulating molecules such as tumor cells, tumor DNA, tumor RNA, proteins, and exosomes, in liquid biopsy technology for the management of HNC with a focus on studies conducted in Africa. The present state and the potential opportunities for the future use of liquid biopsy technology in the effective management of HNC in resource-limited settings such as Africa is further discussed.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Henry Ademola Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Johan Grobbelaar
- Division of Otorhinolaryngology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Manogari Chetty
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
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Shuai Y, Ma Z, Ju J, Wei T, Gao S, Kang Y, Yang Z, Wang X, Yue J, Yuan P. Liquid-based biomarkers in breast cancer: looking beyond the blood. J Transl Med 2023; 21:809. [PMID: 37957623 PMCID: PMC10644618 DOI: 10.1186/s12967-023-04660-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, including breast cancer (BC). To date, efforts in the area of liquid biopsy predominantly focus on the analysis of blood-based markers. It is worth noting that the identifications of markers from non-blood sources provide unique advantages beyond the blood and these alternative sources may be of great significance in offering supplementary information in certain settings. Here, we outline the latest advances in the analysis of non-blood biomarkers, predominantly including urine, saliva, cerebrospinal fluid, pleural fluid, stool and etc. The unique advantages of such testings, their current limitations and the appropriate use of non-blood assays and blood assays in different settings are further discussed. Finally, we propose to highlight the challenges of these alternative assays from basic to clinical implementation and explore the areas where more investigations are warranted to elucidate its potential utility.
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Affiliation(s)
- You Shuai
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tong Wei
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yikun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zixuan Yang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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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: 7] [Impact Index Per Article: 7.0] [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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Hallermayr A, Keßler T, Fujera M, Liesfeld B, Bernstein S, von Ameln S, Schanze D, Steinke-Lange V, Pickl JMA, Neuhann TM, Holinski-Feder E. Impact of cfDNA Reference Materials on Clinical Performance of Liquid Biopsy NGS Assays. Cancers (Basel) 2023; 15:5024. [PMID: 37894392 PMCID: PMC10605119 DOI: 10.3390/cancers15205024] [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: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Liquid biopsy enables the non-invasive analysis of genetic tumor variants in circulating free DNA (cfDNA) in plasma. Accurate analytical validation of liquid biopsy NGS assays is required to detect variants with low variant allele frequencies (VAFs). METHODS Six types of commercial cfDNA reference materials and 42 patient samples were analyzed using a duplex-sequencing-based liquid biopsy NGS assay. RESULTS We comprehensively evaluated the similarity of commercial cfDNA reference materials to native cfDNA. We observed significant differences between the reference materials in terms of wet-lab and sequencing quality as well as background noise. No reference material resembled native cfDNA in all performance metrics investigated. Based on our results, we established guidelines for the selection of appropriate reference materials for the different steps in performance evaluation. The use of inappropriate materials and cutoffs could eventually lead to a lower sensitivity for variant detection. CONCLUSION Careful consideration of commercial reference materials is required for performance evaluation of liquid biopsy NGS assays. While the similarity to native cfDNA aids in the development of experimental protocols, reference materials with well-defined variants are preferable for determining sensitivity and precision, which are essential for accurate clinical interpretation.
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Affiliation(s)
- Ariane Hallermayr
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Thomas Keßler
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Moritz Fujera
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Ben Liesfeld
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Samuel Bernstein
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Simon von Ameln
- Immune-Oncological Centre Cologne (IOZK), 50674 Cologne, Germany;
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Verena Steinke-Lange
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Julia M. A. Pickl
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
| | - Teresa M. Neuhann
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Elke Holinski-Feder
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
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Bixby B, Vrba L, Lenka J, Oshiro M, Watts GS, Hughes T, Erickson H, Chopra M, Knepler JL, Knox KS, Jarnagin L, Alalawi R, Kala M, Bernert R, Routh J, Roe DJ, Garland LL, Futscher BW, Nelson MA. Cell-Free DNA Methylation Analysis as a Marker of Malignancy in Pleural Fluid. RESEARCH SQUARE 2023:rs.3.rs-3390107. [PMID: 37886511 PMCID: PMC10602127 DOI: 10.21203/rs.3.rs-3390107/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Diagnosis of malignant pleural effusion (MPE) is made by cytological examination of pleural fluid or histological examination of pleural tissue from biopsy. Unfortunately, detection of malignancy using cytology has an overall sensitivity of 50%, and is dependent upon tumor load, volume of fluid assessed, and cytopathologist experience. The diagnostic yield of pleural fluid cytology is also compromised by low abundance of tumor cells or when morphology is obscured by inflammation or reactive mesothelial cells. A reliable molecular marker that may complement fluid cytology malignant pleural effusion diagnosis is needed. The purpose of this study was to establish a molecular diagnostic approach based on pleural effusion cell-free DNA methylation analysis for the differential diagnosis of malignant pleural effusion and benign pleural effusion. Results This was a blind, prospective case-control biomarker study. We recruited 104 patients with pleural effusion for the study. We collected pleural fluid from patients with: MPE (n = 48), PPE (n = 28), and benign PE (n = 28), and performed the Sentinel-MPE liquid biopsy assay. The methylation level of Sentinel-MPE was markedly higher in the MPE samples compared to BPE control samples (p < 0.0001) and the same tendency was observed relative to PPE (p = 0.004). We also noted that the methylation signal was significantly higher in PPE relative to BPE (p < 0.001). We also assessed the diagnostic efficiency of the Sentinel-MPE test by performing receiver operating characteristic analysis (ROC). For the ROC analysis we combined the malignant and paramalignant groups (n = 76) and compared against the benign group (n = 28). The detection sensitivity and specificity of the Sentinel-MPE test was high (AUC = 0.912). The Sentinel-MPE appears to have better performance characteristics than cytology analysis. However, combining Sentinel-MPE with cytology analysis could be an even more effective approach for the diagnosis of MPE. Conclusions The Sentinel-MPE test can discriminate between BPE and MPE. The Sentinel-MPE liquid biopsy test can detect aberrant DNA in several different tumor types. The Sentinel-MPE test can be a complementary tool to cytology in the diagnosis of MPE.
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42
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Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023; 13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Cell-free DNA (cfDNA) concentrations from patients with cancer are often elevated compared with those of healthy controls, but the sources of this extra cfDNA have never been determined. To address this issue, we assessed cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary and 64 patients without cancer. Eighty-three of these individuals had cfDNA concentrations much greater than those generally observed in healthy subjects. The major contributor of cfDNA in all samples was leukocytes, accounting for ∼76% of cfDNA, with neutrophils predominating. This was true regardless of whether the samples were derived from patients with cancer or the total plasma cfDNA concentration. High levels of cfDNA observed in patients with cancer did not come from either neoplastic cells or surrounding normal epithelial cells from the tumor's tissue of origin. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. SIGNIFICANCE The origin of excess cfDNA in patients with cancer is unknown. Using cfDNA methylation patterns, we determined that neither the tumor nor the surrounding normal tissue contributes this excess cfDNA-rather it comes from leukocytes. This finding suggests that cancers have a systemic impact on cell turnover or DNA clearance. See related commentary by Thierry and Pisareva, p. 2122. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Austin K. Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Steve Lu
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H. Pearlman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kamel Lahouel
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Cristian Tomasetti
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Peiyong Jiang
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K.C. Allen Chan
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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43
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Thierry AR, Pisareva E. A New Paradigm of the Origins of Circulating DNA in Patients with Cancer. Cancer Discov 2023; 13:2122-2124. [PMID: 37794839 DOI: 10.1158/2159-8290.cd-23-0824] [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: 10/06/2023]
Abstract
SUMMARY By shedding light on the cellular origins of circulating DNA (cirDNA), this research provides important insights into the mechanisms of cirDNA production in cancer. Contrary to expectations, the increased cirDNA in patients with cancer was not derived predominantly from neoplastic cells or surrounding nonneoplastic epithelial cells; rather, the excess cirDNA originated primarily from leukocytes, implying a systemic impact of cancer on cell turnover or DNA clearance. See related article by Mattox et al., p. 2166 (1).
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Affiliation(s)
- Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, France
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44
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Funderburk K, Bang-Christensen SR, Miller BF, Tan H, Margolin G, Petrykowska HM, Baugher C, Farney SK, Grimm SA, Jameel N, Holland DO, Altman NS, Elnitski L. Evaluating Stacked Methylation Markers for Blood-Based Multicancer Detection. Cancers (Basel) 2023; 15:4826. [PMID: 37835520 PMCID: PMC10571530 DOI: 10.3390/cancers15194826] [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: 08/02/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The ability to detect several types of cancer using a non-invasive, blood-based test holds the potential to revolutionize oncology screening. We mined tumor methylation array data from the Cancer Genome Atlas (TCGA) covering 14 cancer types and identified two novel, broadly-occurring methylation markers at TLX1 and GALR1. To evaluate their performance as a generalized blood-based screening approach, along with our previously reported methylation biomarker, ZNF154, we rigorously assessed each marker individually or combined. Utilizing TCGA methylation data and applying logistic regression models within each individual cancer type, we found that the three-marker combination significantly increased the average area under the ROC curve (AUC) across the 14 tumor types compared to single markers (p = 1.158 × 10-10; Friedman test). Furthermore, we simulated dilutions of tumor DNA into healthy blood cell DNA and demonstrated increased AUC of combined markers across all dilution levels. Finally, we evaluated assay performance in bisulfite sequenced DNA from patient tumors and plasma, including early-stage samples. When combining all three markers, the assay correctly identified nine out of nine lung cancer plasma samples. In patient plasma from hepatocellular carcinoma, ZNF154 alone yielded the highest combined sensitivity and specificity values averaging 68% and 72%, whereas multiple markers could achieve higher sensitivity or specificity, but not both. Altogether, this study presents a comprehensive pipeline for the identification, testing, and validation of multi-cancer methylation biomarkers with a considerable potential for detecting a broad range of cancer types in patient blood samples.
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Affiliation(s)
- Karen Funderburk
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara R. Bang-Christensen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brendan F. Miller
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gennady Margolin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanna M. Petrykowska
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine Baugher
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - S. Katie Farney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA
| | - Nader Jameel
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David O. Holland
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomi S. Altman
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Wu G, Song M, Wang K, Cui T, Jiao Z, Ji L, Gao X, Wang J, Liu T, Xia X, Fang H, Guan Y, Yi X. DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations. Brief Bioinform 2023; 24:bbad277. [PMID: 37539831 DOI: 10.1093/bib/bbad277] [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: 03/12/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Duplex sequencing technology has been widely used in the detection of low-frequency mutations in circulating tumor deoxyribonucleic acid (DNA), but how to determine the sequencing depth and other experimental parameters to ensure the stable detection of low-frequency mutations is still an urgent problem to be solved. The mutation detection rules of duplex sequencing constrain not only the number of mutated templates but also the number of mutation-supportive reads corresponding to each forward and reverse strand of the mutated templates. To tackle this problem, we proposed a Depth Estimation model for stable detection of Low-Frequency MUTations in duplex sequencing (DELFMUT), which models the identity correspondence and quantitative relationships between templates and reads using the zero-truncated negative binomial distribution without considering the sequences composed of bases. The results of DELFMUT were verified by real duplex sequencing data. In the case of known mutation frequency and mutation detection rule, DELFMUT can recommend the combinations of DNA input and sequencing depth to guarantee the stable detection of mutations, and it has a great application value in guiding the experimental parameter setting of duplex sequencing technology.
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Affiliation(s)
- Guiying Wu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Mengmeng Song
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Ke Wang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tianyu Cui
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Zicong Jiao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tao Liu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Huan Fang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
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46
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Kampel L, Feldstein S, Tsuriel S, Hannes V, Carmel Neiderman NN, Horowitz G, Warshavsky A, Leider-Trejo L, Hershkovitz D, Muhanna N. Mutated TP53 in Circulating Tumor DNA as a Risk Level Biomarker in Head and Neck Squamous Cell Carcinoma Patients. Biomolecules 2023; 13:1418. [PMID: 37759818 PMCID: PMC10527516 DOI: 10.3390/biom13091418] [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: 06/25/2023] [Revised: 08/28/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has been suggested as a surrogate biomarker for early detection of cancer recurrence. We aimed to explore the utility of ctDNA as a noninvasive prognostic biomarker in newly diagnosed head and neck squamous cell carcinoma (HNSCC) patients. Seventy HNSCC specimens were analysed for the detection of TP53 genetic alterations utilizing next-generation sequencing (NGS). TP53 mutations were revealed in 55 (79%). Upon detection of a significant TP53 mutation, circulating cell-free DNA was scrutinized for the presence of the tumor-specific mutation. ctDNA was identified at a minimal allele frequency of 0.08% in 21 out of 30 processed plasma samples. Detectable ctDNA correlated with regional spread (N stage ≥ 1, p = 0.011) and poorer 5-year progression-free survival (20%, 95% CI 10.9 to 28.9, p = 0.034). The high-risk worst pattern of invasion (WPOI grade 4-5) and deep invasion were frequently found in patients whose ctDNA was detected (p = 0.087 and p = 0.072, respectively). Detecting mutated TP53 ctDNA was associated with poor progression-free survival and regional metastases, indicating its potential role as a prognostic biomarker. However, ctDNA detectability in early-stage disease and the mechanisms modulating its release into the bloodstream must be further elucidated.
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Affiliation(s)
- Liyona Kampel
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
| | - Sara Feldstein
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Shlomo Tsuriel
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Victoria Hannes
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Narin N. Carmel Neiderman
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
| | - Gilad Horowitz
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Anton Warshavsky
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Leonor Leider-Trejo
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Dov Hershkovitz
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Nidal Muhanna
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
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Tan K, Chen L, Cao D, Xiao W, Lv Q, Zou L. A rapid and highly sensitive ctDNA detection platform based on locked nucleic acid-assisted catalytic hairpin assembly circuits. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4548-4554. [PMID: 37642516 DOI: 10.1039/d3ay01150j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
As a promising biomarker of liquid biopsy, circulating tumor DNA (ctDNA) plays a paramount role in the early diagnosis of noninvasive cancer. The isothermal catalytic hairpin assembly (CHA) strategy has great potential for in vitro detection of ctDNA in low abundance. However, a traditional CHA strategy for ctDNA detection at the earlier stages of cancer remains extremely challenging, as annoying signal leakage from the 'breathing' phenomenon and nuclease degradation occur. Herein, we report a locked nucleic acid (LNA)-incorporated CHA circuit for the rapid and sensitive detection of target ctDNA. The target ctDNA intelligently catalyzed LNA-modified hairpins H1 and H2via a range of toehold-mediated strand displacement processes, leading to the continuous generation of an H1-H2 hybrid for the amplified fluorescence signal. In comparison to conventional CHA circuits, the stronger binding affinity of LNA-DNA bases greatly inhibited the breathing effect, which endowed it with greater thermodynamic stability and resistance to nuclease degradation in the LNA-assisted CHA system, thus achieving a high signal gain. The developed CHA circuit demonstrated excellent performance during target ctDNA detection, with a linear range from 10 pM to 5 nM, and its target detection limit was reached at 3.3 pM. Moreover, this LNA-assisted CHA system was successfully applied to the analysis of target ctDNA in clinical serum samples of breast cancer patients. This updated CHA system provides a general and robust platform for the sensitive detection of biomarkers of interest, thus facilitating the accurate identification and diagnosis of cancers.
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Affiliation(s)
- Kaiyue Tan
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Longsheng Chen
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou 510500, China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou 510500, China
| | - Qian Lv
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Lili Zou
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
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Fan W, Ren W, Jia D, Shi J, Liu C. Digital-like Enzyme Inhibition Mechanism-Based Strategy for the Digital Sensing of Heparin-Specific Biomarkers. Anal Chem 2023; 95:13690-13697. [PMID: 37632468 DOI: 10.1021/acs.analchem.3c02983] [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: 08/28/2023]
Abstract
A new microbead (MB)-based digital flow cytometric sensing system is proposed for the sensitive detection of heparin-specific biomarkers, including heparin-binding protein (HBP) and heparinase. This strategy takes advantage of the inherent space-confined enzymatic behavior of T4 polynucleotide kinase phosphatase (T4 PNKP) around a single MB and the heparin's digital-like inhibitory effect on T4 PNKP. By integrating with an on-bead terminal deoxynucleotidyl transferase (TdT)-catalyzed fluorescence signal amplification technology, the concentration of HBP and heparinase can be digitally determined by the number of fluorescence-positive/-negative MBs which can be easily counted by flow cytometry. This is not only the first test to expand the application scenario of T4 PNKP to the digital detection of different biomarkers but also pioneers a new direction for fabricating digital biosensing platforms based on the enzyme inhibition mechanism.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Jingjing Shi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
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Bittla P, Kaur S, Sojitra V, Zahra A, Hutchinson J, Folawemi O, Khan S. Exploring Circulating Tumor DNA (CtDNA) and Its Role in Early Detection of Cancer: A Systematic Review. Cureus 2023; 15:e45784. [PMID: 37745752 PMCID: PMC10516512 DOI: 10.7759/cureus.45784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023] Open
Abstract
There is a significant increase in the need for an efficient screening method that might identify cancer at an early stage and could improve patients' long-term survival due to the continued rise in cancer incidence and associated mortality. One such effort involved using circulating tumor DNA (ctDNA) as a rescue agent for a non-invasive blood test that may identify many tumors. A tumor marker called ctDNA is created by cells with the same DNA alterations. Due to its shorter half-life, it may be useful for both early cancer detection and real-time monitoring of tumor development, therapeutic response, and tumor outcomes. We obtained 156 papers from PUBMED using the MeSH approach in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) criteria and ten articles from additional online resources. After removing articles with irrelevant titles and screening the abstract and full text of the articles that contained information unrelated to or not specific to the title query using inclusion and exclusion criteria, 18 out of 166 articles were chosen for the quality check. Fourteen medium to high-quality papers were chosen out of the 18 publications to be included in the study design. The reviewed literature showed no significant utility of ctDNA in detecting early-stage tumors of size less than 1 cm diameter. Still, the ideal screening test would require the assay to detect a size <5 mm tumor, which is nearly impossible with the current data. The sensitivity and specificity of the assay ranged from 69% to 98% and 99%, respectively. Furthermore, CancerSEEK achieves tumor origin localization in 83% of cases, while targeted error correction sequencing (TEC-Seq) assays demonstrate a cancer detection rate ranging from 59% to 71%, depending on the type of cancer. However, it could be of great value as a prognostic indicator, and the levels are associated with progression-free survival (PFS) and overall survival (OS) rates, wherein the positive detection of ctDNA is associated with worse OS compared to the tumors detected through standard procedures, with an odds ratio (OS) of 4.83. We conclude that ctDNA could be better applied in cancer patients for prognosis, disease progression monitoring, and treatment outcomes compared to its use in early cancer detection. Due to its specific feature of recognizing the tumor-related mutations, it could be implemented as a supplemental tool to assess the nature of the tumor, grade, and size of the tumor and for predicting the outcomes by pre-operative and post-operative evaluation of the tumor marker, ctDNA, and thereby estimating PFS and OS depending on the level of marker present. A vast amount of research is required in early detection to determine the sensitivity, specificity, false positive rates, and false negative rates in evaluating its true potential as a screening tool. Even if the test could detect the mutations, an extensive workup for the search of tumor is required as the assay could only detect but cannot localize the disease. Establishing the clinical validity and utility of ctDNA is imperative for its implementation in future clinical practice.
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Affiliation(s)
- Parikshit Bittla
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Simran Kaur
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Vani Sojitra
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Anam Zahra
- Surgery, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Jhenelle Hutchinson
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Oluwa Folawemi
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Safeera Khan
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
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Xu M, Shi T, Xu R, Chen G, He W. The potential role of minimal/molecular residual disease in colorectal cancer: curative surgery, radiotherapy and beyond. JOURNAL OF THE NATIONAL CANCER CENTER 2023; 3:203-210. [PMID: 39035199 PMCID: PMC11256684 DOI: 10.1016/j.jncc.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/23/2023] [Accepted: 05/18/2023] [Indexed: 07/23/2024] Open
Abstract
Detection of minimal/molecular residual disease (MRD) based on ctDNA assay develops from hematological malignancies to solid tumors. Generally, there are two mainstream assays in MRD testing technology: tumor-informed and tumor-agnostic. For colorectal cancer (CRC), MRD is used not only to monitor recurrence and predict prognosis, but also to help in clinical decision making and assessment of clinical efficacy in the settings of curative surgery, radiotherapy, chemotherapy and surveillance. Accumulated clinical trials are exploring roles of MRD in early or advanced stages of CRC. Here, we give an overview of how MRD is and will be used in CRC.
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Affiliation(s)
- Meiyi Xu
- Department of Oncology, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Tianhao Shi
- Department of Biology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Ruilian Xu
- Department of Oncology, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Gong Chen
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wan He
- Department of Oncology, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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