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Gromek P, Senkowska Z, Płuciennik E, Pasieka Z, Zhao LY, Gielecińska A, Kciuk M, Kłosiński K, Kałuzińska-Kołat Ż, Kołat D. Revisiting the standards of cancer detection and therapy alongside their comparison to modern methods. World J Methodol 2024; 14:92982. [DOI: 10.5662/wjm.v14.i2.92982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/15/2024] [Accepted: 04/28/2024] [Indexed: 06/13/2024] Open
Abstract
In accordance with the World Health Organization data, cancer remains at the forefront of fatal diseases. An upward trend in cancer incidence and mortality has been observed globally, emphasizing that efforts in developing detection and treatment methods should continue. The diagnostic path typically begins with learning the medical history of a patient; this is followed by basic blood tests and imaging tests to indicate where cancer may be located to schedule a needle biopsy. Prompt initiation of diagnosis is crucial since delayed cancer detection entails higher costs of treatment and hospitalization. Thus, there is a need for novel cancer detection methods such as liquid biopsy, elastography, synthetic biosensors, fluorescence imaging, and reflectance confocal microscopy. Conventional therapeutic methods, although still common in clinical practice, pose many limitations and are unsatisfactory. Nowadays, there is a dynamic advancement of clinical research and the development of more precise and effective methods such as oncolytic virotherapy, exosome-based therapy, nanotechnology, dendritic cells, chimeric antigen receptors, immune checkpoint inhibitors, natural product-based therapy, tumor-treating fields, and photodynamic therapy. The present paper compares available data on conventional and modern methods of cancer detection and therapy to facilitate an understanding of this rapidly advancing field and its future directions. As evidenced, modern methods are not without drawbacks; there is still a need to develop new detection strategies and therapeutic approaches to improve sensitivity, specificity, safety, and efficacy. Nevertheless, an appropriate route has been taken, as confirmed by the approval of some modern methods by the Food and Drug Administration.
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Affiliation(s)
- Piotr Gromek
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zuzanna Senkowska
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zbigniew Pasieka
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Lin-Yong Zhao
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Karol Kłosiński
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Żaneta Kałuzińska-Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
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Panet F, Papakonstantinou A, Borrell M, Vivancos J, Vivancos A, Oliveira M. Use of ctDNA in early breast cancer: analytical validity and clinical potential. NPJ Breast Cancer 2024; 10:50. [PMID: 38898045 PMCID: PMC11187121 DOI: 10.1038/s41523-024-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.
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Affiliation(s)
- François Panet
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcomas, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Borrell
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - Joan Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mafalda Oliveira
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain.
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Shi X, Guo S, Duan Q, Zhang W, Gao S, Jing W, Jiang G, Kong X, Li P, Li Y, Teng C, Xu X, Chen S, Nian B, Li Z, Zhong C, Yang X, Zhu G, Du Y, Zhang D, Jin G. Detection and characterization of pancreatic and biliary tract cancers using cell-free DNA fragmentomics. J Exp Clin Cancer Res 2024; 43:145. [PMID: 38750539 PMCID: PMC11094938 DOI: 10.1186/s13046-024-03067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Plasma cell-free DNA (cfDNA) fragmentomics has demonstrated significant differentiation power between cancer patients and healthy individuals, but little is known in pancreatic and biliary tract cancers. The aim of this study is to characterize the cfDNA fragmentomics in biliopancreatic cancers and develop an accurate method for cancer detection. METHODS One hundred forty-seven patients with biliopancreatic cancers and 71 non-cancer volunteers were enrolled, including 55 patients with cholangiocarcinoma, 30 with gallbladder cancer, and 62 with pancreatic cancer. Low-coverage whole-genome sequencing (median coverage: 2.9 ×) was performed on plasma cfDNA. Three cfDNA fragmentomic features, including fragment size, end motif and nucleosome footprint, were subjected to construct a stacked machine learning model for cancer detection. Integration of carbohydrate antigen 19-9 (CA19-9) was explored to improve model performance. RESULTS The stacked model presented robust performance for cancer detection (area under curve (AUC) of 0.978 in the training cohort, and AUC of 0.941 in the validation cohort), and remained consistent even when using extremely low-coverage sequencing depth of 0.5 × (AUC: 0.905). Besides, our method could also help differentiate biliopancreatic cancer subtypes. By integrating the stacked model and CA19-9 to generate the final detection model, a high accuracy in distinguishing biliopancreatic cancers from non-cancer samples with an AUC of 0.995 was achieved. CONCLUSIONS Our model demonstrated ultrasensitivity of plasma cfDNA fragementomics in detecting biliopancreatic cancers, fulfilling the unmet accuracy of widely-used serum biomarker CA19-9, and provided an affordable way for accurate noninvasive biliopancreatic cancer screening in clinical practice.
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Affiliation(s)
- Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Qiaonan Duan
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Wei Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Wei Jing
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Guojuan Jiang
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Xiangyu Kong
- Department of Gastroenterology, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Penghao Li
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Yikai Li
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Chuanqi Teng
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Xiaoya Xu
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Sheng Chen
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Baoning Nian
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Zhikuan Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China
| | - Chaoliang Zhong
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Xiaolu Yang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Guangyu Zhu
- Department of Interventional Radiology and Vascular Surgery, Zhongda Hospital, Southeast University, 87 Dingjiaqiao Road, Nanjing, Jiangsu Province, 210009, China.
| | - Yiqi Du
- Department of Gastroenterology, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China.
| | - Dadong Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc, 158 Xin Junhuan Road, Pujiang Hi-Tech Park, Shanghai, 201114, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University, 168 Changhai Road, Shanghai, 200433, China.
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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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de Queiroz LF, Silva MSDME, de Souza HSP, Rosas SLB, Carvalho MDGDC. hTERT gene methylation in circulating DNA, tumor, and surrounding tissue in breast cancer: a prospective study. SAO PAULO MED J 2024; 142:e2023140. [PMID: 38747873 PMCID: PMC11087006 DOI: 10.1590/1516-3180.2023.0140.r1.04032024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/08/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND The human telomerase reverse transcriptase (hTERT) enzyme, encoded by the hTERT gene, synthesizes protective telomeric sequences on chromosomes and plays a fundamental role in cancer formation. Methylation of the hTERT gene has an upregulatory effect, increasing hTERT enzyme synthesis and allowing continuous tumor cell division. OBJECTIVE In a group of patients with breast cancer, we aimed to analyze the methylation status of hTERT in the tumor, surrounding tissue, and circulating free deoxyribonucleic acid (cfDNA) of blood collected on the day of mastectomy and then approximately one year later. DESIGN AND SETTING A prospective study was conducted at a university hospital in Rio de Janeiro, Brazil. METHODS Samples were collected from 15 women with breast cancer on the day of mastectomy and approximately one year postoperatively. cfDNA was analyzed by sodium bisulfite conversion, followed by polymerase chain reaction, electrophoresis, and silver nitrate staining. RESULTS Methylation of hTERT was detected in the tumors and surrounding tissues of all 15 patients. Five patients displayed hTERT methylation in the cfDNA from the blood of the first collection. Of the ten patients who returned for the second collection, three showed methylation. Two patients with methylation in the first collection did not display methylation in the second collection. One patient with no methylation in the first collection displayed methylation in the second collection, and one patient had a diminished level of methylation in the second collection. CONCLUSION Only one-third of patients displayed methylation in their cfDNA, which may be related to the success of chemotherapy.
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Affiliation(s)
- Luiz Fernando de Queiroz
- MD, PhD. Molecular Biologist, Department of Pathology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Marcelo Soares da Mota e Silva
- MD, PhD. Molecular Biologist, Department of Pathology, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Heitor Siffert Pereira de Souza
- MD, PhD. Physician and Full Professor, Department of Internal Medicine, School of Medicine, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Siane Lopes Bittencourt Rosas
- MD, PhD. Molecular Biologist, Department of Internal Medicine, School of Medicine, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
| | - Maria da Glória da Costa Carvalho
- MD, PhD. Physician and Associate Professor, Department of Pathology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro (RJ), Brazil
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Bang G, Park M, Seon JY, Park SY. Comparative analysis of genetic testing utilization rates among people with and without disabilities in South Korea from 2016 to 2019, focusing on malignant neoplasms: A national population-based study. Cancer Med 2024; 13:e7102. [PMID: 38711356 DOI: 10.1002/cam4.7102] [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: 07/26/2023] [Revised: 02/13/2024] [Accepted: 03/02/2024] [Indexed: 05/08/2024] Open
Abstract
INTRODUCTION Oncogene testing is widely used to detect or direct cancer treatments. Compared to people without disabilities, people with disabilities in Korea have a lower cancer incidence rate but a fivefold higher cancer mortality rate, implying delayed detection. METHODS We used an administrative database combining disability status and care utilization to analyze every case of cancer-related genetic testing paid for by the National Health Insurance Services of Korea between 2016 and 2019. We first compared percentages of individuals who had taken a registered genetic test by their disability statuses. We then compared the most frequently utilized tests between individuals with and without disabilities. RESULTS Korean citizens, 175,000 in total, underwent at least one of the 192 registered cancer-related genetic tests between 2016 and 2019. People with disabilities utilized these genetic tests at higher rates than those without disabilities, regardless of sex or age. Among people aged ≥40 years, lung and colorectal cancer-related tests were most frequently utilized, regardless of disability status. CONCLUSION Although the cancer-related genetic test uptake rate is higher among people with disabilities than among those without disabilities, it is still possible that information on these tests is not as readily available to people with disabilities. Therefore, it is imperative for the government to actively devise strategies to enhance national cancer screening rates among people with disabilities.
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Affiliation(s)
- Gwanwook Bang
- Department of Medical Education and Humanities, College of Medicine, Kyunghee University, Seoul, South Korea
- Disability Health Research Center of Kyunghee University, Seoul, South Korea
| | - Minji Park
- Kyunghee University Hospital at Gangdong, Seoul, South Korea
| | - Jeong-Yeon Seon
- Health Insurance Research Institute, National Health Insurance Service, Wonju, South Korea
| | - So-Youn Park
- Department of Medical Education and Humanities, College of Medicine, Kyunghee University, Seoul, South Korea
- Disability Health Research Center of Kyunghee University, Seoul, South Korea
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Bao Y, Zhang D, Guo H, Ma W. Beyond blood: Advancing the frontiers of liquid biopsy in oncology and personalized medicine. Cancer Sci 2024; 115:1060-1072. [PMID: 38308498 PMCID: PMC11007055 DOI: 10.1111/cas.16097] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Liquid biopsy is emerging as a pivotal tool in precision oncology, offering a noninvasive and comprehensive approach to cancer diagnostics and management. By harnessing biofluids such as blood, urine, saliva, cerebrospinal fluid, and pleural effusions, this technique profiles key biomarkers including circulating tumor DNA, circulating tumor cells, microRNAs, and extracellular vesicles. This review discusses the extended scope of liquid biopsy, highlighting its indispensable role in enhancing patient outcomes through early detection, continuous monitoring, and tailored therapy. While the advantages are notable, we also address the challenges, emphasizing the necessity for precision, cost-effectiveness, and standardized methodologies in its broader application. The future trajectory of liquid biopsy is set to expand its reach in personalized medicine, fueled by technological advancements and collaborative research.
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Affiliation(s)
- Ying Bao
- Key Laboratory for Translational MedicineThe First Hospital Affiliated with Huzhou UniversityHuzhouChina
| | - Dejing Zhang
- Department of General SurgeryPuyang Oilfield General HospitalPuyangChina
| | - Huihui Guo
- Key Laboratory for Translational MedicineThe First Hospital Affiliated with Huzhou UniversityHuzhouChina
| | - Wenxue Ma
- Department of Medicine, Moores Cancer Center, and Sanford Stem Cell InstituteUniversity of California San DiegoLa JollaCaliforniaUSA
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8
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Malakar S, Gontor EN, Dugbaye MY, Shah K, Sinha S, Sutaoney P, Chauhan NS. Cancer treatment with biosimilar drugs: A review. CANCER INNOVATION 2024; 3:e115. [PMID: 38946928 PMCID: PMC11212292 DOI: 10.1002/cai2.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 07/02/2024]
Abstract
Biosimilars are biological drugs created from living organisms or that contain living components. They share an identical amino-acid sequence and immunogenicity. These drugs are considered to be cost-effective and are utilized in the treatment of cancer and other endocrine disorders. The primary aim of biosimilars is to predict biosimilarity, efficacy, and treatment costs; they are approved by the Food and Drug Administration (FDA) and have no clinical implications. They involve analytical studies to understand the similarities and dissimilarities. A biosimilar manufacturer sets up FDA-approved reference products to evaluate biosimilarity. The contribution of next-generation sequencing is evolving to study the organ tumor and its progression with its impactful therapeutic approach on cancer patients to showcase and target rare mutations. The study shall help to understand the future perspectives of biosimilars for use in gastro-entero-logic diseases, colorectal cancer, and thyroid cancer. They also help target specific organs with essential mutational categories and drug prototypes in clinical practices with blood and liquid biopsy, cell treatment, gene therapy, recombinant therapeutic proteins, and personalized medications. Biosimilar derivatives such as monoclonal antibodies like trastuzumab and rituximab are common drugs used in cancer therapy. Escherichia coli produces more than six antibodies or antibody-derived proteins to treat cancer such as filgrastim, epoetin alfa, and so on.
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Affiliation(s)
- Shilpa Malakar
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | | | - Moses Y. Dugbaye
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | - Kamal Shah
- Institute of Pharmaceutical ResearchGLA UniversityMathuraUttar PradeshIndia
| | - Sakshi Sinha
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | - Priya Sutaoney
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
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Stanley KE, Jatsenko T, Tuveri S, Sudhakaran D, Lannoo L, Van Calsteren K, de Borre M, Van Parijs I, Van Coillie L, Van Den Bogaert K, De Almeida Toledo R, Lenaerts L, Tejpar S, Punie K, Rengifo LY, Vandenberghe P, Thienpont B, Vermeesch JR. Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology. Nat Commun 2024; 15:2220. [PMID: 38472221 PMCID: PMC10933257 DOI: 10.1038/s41467-024-46435-0] [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: 08/10/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
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Affiliation(s)
- Kate E Stanley
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Stefania Tuveri
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Dhanya Sudhakaran
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Marie de Borre
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Ilse Van Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Van Coillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Liesbeth Lenaerts
- Department of Oncology, Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura Y Rengifo
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [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: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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11
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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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12
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Çalışkan M, Tazaki K. AI/ML advances in non-small cell lung cancer biomarker discovery. Front Oncol 2023; 13:1260374. [PMID: 38148837 PMCID: PMC10750392 DOI: 10.3389/fonc.2023.1260374] [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: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths among both men and women, representing approximately 25% of cancer fatalities each year. The treatment landscape for non-small cell lung cancer (NSCLC) is rapidly evolving due to the progress made in biomarker-driven targeted therapies. While advancements in targeted treatments have improved survival rates for NSCLC patients with actionable biomarkers, long-term survival remains low, with an overall 5-year relative survival rate below 20%. Artificial intelligence/machine learning (AI/ML) algorithms have shown promise in biomarker discovery, yet NSCLC-specific studies capturing the clinical challenges targeted and emerging patterns identified using AI/ML approaches are lacking. Here, we employed a text-mining approach and identified 215 studies that reported potential biomarkers of NSCLC using AI/ML algorithms. We catalogued these studies with respect to BEST (Biomarkers, EndpointS, and other Tools) biomarker sub-types and summarized emerging patterns and trends in AI/ML-driven NSCLC biomarker discovery. We anticipate that our comprehensive review will contribute to the current understanding of AI/ML advances in NSCLC biomarker research and provide an important catalogue that may facilitate clinical adoption of AI/ML-derived biomarkers.
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Affiliation(s)
- Minal Çalışkan
- Translational Science Department, Precision Medicine Function, Daiichi Sankyo, Inc., Basking Ridge, NJ, United States
| | - Koichi Tazaki
- Translational Science Department I, Precision Medicine Function, Daiichi Sankyo, Tokyo, Japan
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13
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Zhang F, Zhang X, Zhang H, Lin D, Fan H, Guo S, An F, Zhao Y, Li J, Schrodi SJ, Zhang D. Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis. Epigenetics 2023; 18:2231222. [PMID: 37393582 DOI: 10.1080/15592294.2023.2231222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K-Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.
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Affiliation(s)
- Feifan Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Xin Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Haikun Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Dongdong Lin
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Fang An
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
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14
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Huang Q, Mitsiades I, Dowst H, Zarrin-Khameh N, Noor AB, Castro P, Scheurer ME, Godoy G, Mims MP, Mitsiades N. Incidental detection of FGFR3 fusion via liquid biopsy leading to earlier diagnosis of urothelial carcinoma. NPJ Precis Oncol 2023; 7:123. [PMID: 37980380 PMCID: PMC10657397 DOI: 10.1038/s41698-023-00467-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/13/2023] [Indexed: 11/20/2023] Open
Abstract
The rising utilization of circulating tumor DNA (ctDNA) assays in Precision Oncology may incidentally detect genetic material from secondary sources. It is important that such findings are recognized and properly leveraged for both diagnosis and monitoring of response to treatment. Here, we report a patient in whom serial cell-free DNA (cfDNA) monitoring for his known prostate adenocarcinoma uncovered the emergence of an unexpected FGFR3-TACC3 gene fusion, a BRCA1 frameshift mutation, and other molecular abnormalities. Due to the rarity of FGFR3 fusions in prostate cancer, a workup for a second primary cancer was performed, leading to the diagnosis of an otherwise-asymptomatic urothelial carcinoma (UC). Once UC-directed treatment was initiated, the presence of these genetic abnormalities in cfDNA allowed for disease monitoring and early detection of resistance, well before radiographic progression. These findings also uncovered opportunities for targeted therapies against FGFR and BRCA1. Overall, this report highlights the multifaceted utility of longitudinal ctDNA monitoring in early cancer diagnosis, disease prognostication, therapeutic target identification, monitoring of treatment response, and early detection of emergence of resistance.
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Affiliation(s)
- Quillan Huang
- Dept. of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Ben Taub General Hospital, Harris Health System, Houston, TX, 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
| | - Irene Mitsiades
- Harvard Medical School, Boston, MA, 02115, USA
- Boston University School of Arts and Sciences, Boston, MA, 02215, USA
| | - Heidi Dowst
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
| | - Neda Zarrin-Khameh
- Ben Taub General Hospital, Harris Health System, Houston, TX, 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
- Dept. of Pathology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Attiya Batool Noor
- Ben Taub General Hospital, Harris Health System, Houston, TX, 77030, USA
| | - Patricia Castro
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
- Dept. of Pathology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael E Scheurer
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
- Dept. of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Guilherme Godoy
- Ben Taub General Hospital, Harris Health System, Houston, TX, 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
- Dept. of Urology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martha P Mims
- Dept. of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Ben Taub General Hospital, Harris Health System, Houston, TX, 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Houston, TX, 77030, USA
| | - Nicholas Mitsiades
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, 95817, USA.
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15
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van den Ende T, van der Pol Y, Creemers A, Moldovan N, Boers D, van Berge Henegouwen MI, Hulshof MC, Cillessen SA, van Grieken NC, Pegtel DM, Derks S, Bijlsma MF, Mouliere F, van Laarhoven HW. Genome-wide and panel-based cell-free DNA characterization of patients with resectable esophageal adenocarcinoma. J Pathol 2023; 261:286-297. [PMID: 37615198 DOI: 10.1002/path.6175] [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: 03/13/2023] [Revised: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 08/25/2023]
Abstract
Circulating tumor DNA (ctDNA) holds promise in resectable esophageal adenocarcinoma (EAC) to predict patient outcome but is not yet sensitive enough to be clinically applicable. Our aim was to combine ctDNA mutation data with shallow whole-genome sequencing (sWGS)-derived copy number tumor fraction estimates (ichorCNA) to improve pathological response and survival prediction in EAC. In total, 111 stage II/III EAC patients with baseline (n = 111), post-neoadjuvant chemoradiotherapy (nCRT) (n = 68), and pre-surgery (n = 92) plasma samples were used for ctDNA characterization. sWGS (<5× coverage) was performed on all time-point samples, and copy number aberrations were estimated using ichorCNA. Baseline and pre-surgery samples were sequenced using a custom amplicon panel for mutation detection. Detection of baseline ctDNA was successful in 44.3% of patients by amplicon sequencing and 10.5% by ichorCNA. Combining both, ctDNA could be detected in 50.5% of patients. Baseline ctDNA positivity was related to higher T stage (cT3, 4) (p = 0.017). There was no relationship between pathological response and baseline ctDNA positivity. However, baseline ctDNA metrics (variant allele frequency > 1% or ichorCNA > 3%) were associated with a high risk of disease progression [HR = 2.23 (95% CI 1.22-4.07), p = 0.007]. The non-clearance of a baseline variant or ichorCNA > 3% in pre-surgery samples was related to early progression [HR = 4.58 (95% CI 2.22-9.46), p < 0.001]. Multi-signal analysis improves detection of ctDNA and can be used for prognostication of resectable EAC patients. Future studies should explore the potential of multi-modality sequencing for risk stratification and treatment adaptation based on ctDNA results. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tom van den Ende
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Ymke van der Pol
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Aafke Creemers
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Norbert Moldovan
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Dries Boers
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Mark I van Berge Henegouwen
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Maarten Ccm Hulshof
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Radiotherapy, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Saskia Agm Cillessen
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Nicole Ct van Grieken
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Sarah Derks
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Department of Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Florent Mouliere
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Hanneke Wm van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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16
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Kim SY, Jeong S, Lee W, Jeon Y, Kim YJ, Park S, Lee D, Go D, Song SH, Lee S, Woo HG, Yoon JK, Park YS, Kim YT, Lee SH, Kim KH, Lim Y, Kim JS, Kim HP, Bang D, Kim TY. Cancer signature ensemble integrating cfDNA methylation, copy number, and fragmentation facilitates multi-cancer early detection. Exp Mol Med 2023; 55:2445-2460. [PMID: 37907748 PMCID: PMC10689759 DOI: 10.1038/s12276-023-01119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 11/02/2023] Open
Abstract
Cell-free DNA (cfDNA) sequencing has demonstrated great potential for early cancer detection. However, most large-scale studies have focused only on either targeted methylation sites or whole-genome sequencing, limiting comprehensive analysis that integrates both epigenetic and genetic signatures. In this study, we present a platform that enables simultaneous analysis of whole-genome methylation, copy number, and fragmentomic patterns of cfDNA in a single assay. Using a total of 950 plasma (361 healthy and 589 cancer) and 240 tissue samples, we demonstrate that a multifeature cancer signature ensemble (CSE) classifier integrating all features outperforms single-feature classifiers. At 95.2% specificity, the cancer detection sensitivity with methylation, copy number, and fragmentomic models was 77.2%, 61.4%, and 60.5%, respectively, but sensitivity was significantly increased to 88.9% with the CSE classifier (p value < 0.0001). For tissue of origin, the CSE classifier enhanced the accuracy beyond the methylation classifier, from 74.3% to 76.4%. Overall, this work proves the utility of a signature ensemble integrating epigenetic and genetic information for accurate cancer detection.
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Affiliation(s)
| | | | | | - Yujin Jeon
- IMBdx Inc., Seoul, 08506, Republic of Korea
| | | | | | - Dongin Lee
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Dayoung Go
- IMBdx Inc., Seoul, 08506, Republic of Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
| | - Sanghoo Lee
- Seoul Clinical Laboratories Healthcare Inc., Yongin-si, Gyenggi-do, 16954, Republic of Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Jung-Ki Yoon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Young Sik Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Young Tae Kim
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, 03063, Republic of Korea
| | - Kwang Hyun Kim
- Department of Urology, Ewha Womans University Seoul Hospital, Seoul, 07804, Republic of Korea
| | - Yoojoo Lim
- IMBdx Inc., Seoul, 08506, Republic of Korea
| | - Jin-Soo Kim
- IMBdx Inc., Seoul, 08506, Republic of Korea
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, 07061, Republic of Korea
| | | | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Tae-You Kim
- IMBdx Inc., Seoul, 08506, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea.
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17
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [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: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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Nguyen VTC, Nguyen TH, Doan NNT, Pham TMQ, Nguyen GTH, Nguyen TD, Tran TTT, Vo DL, Phan TH, Jasmine TX, Nguyen VC, Nguyen HT, Nguyen TV, Nguyen THH, Huynh LAK, Tran TH, Dang QT, Doan TN, Tran AM, Nguyen VH, Nguyen VTA, Ho LMQ, Tran QD, Pham TTT, Ho TD, Nguyen BT, Nguyen TNV, Nguyen TD, Phu DTB, Phan BHH, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Le TK, Tran THT, Duong ML, Bach HPT, Kim VV, Pham TA, Tran DH, Le TNA, Pham TVN, Le MT, Vo DH, Tran TMT, Nguyen MN, Van TTV, Nguyen AN, Tran TT, Tran VU, Le MP, Do TT, Phan TV, Nguyen HDL, Nguyen DS, Cao VT, Do TTT, Truong DK, Tang HS, Giang H, Nguyen HN, Phan MD, Tran LS. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife 2023; 12:RP89083. [PMID: 37819044 PMCID: PMC10567114 DOI: 10.7554/elife.89083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Aziz M, Arora A, Li F, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DTW. Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection. Biomark Res 2023; 11:90. [PMID: 37817261 PMCID: PMC10566128 DOI: 10.1186/s40364-023-00524-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. METHODS In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. RESULTS Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). CONCLUSION These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Akanksha Arora
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Sung Kim
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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Citarella A, Besharat ZM, Trocchianesi S, Autilio TM, Verrienti A, Catanzaro G, Splendiani E, Spinello Z, Cantara S, Zavattari P, Loi E, Romei C, Ciampi R, Pezzullo L, Castagna MG, Angeloni A, Elisei R, Durante C, Po A, Ferretti E. Circulating cell-free DNA (cfDNA) in patients with medullary thyroid carcinoma is characterized by specific fragmentation and methylation changes with diagnostic value. Biomark Res 2023; 11:82. [PMID: 37726827 PMCID: PMC10510276 DOI: 10.1186/s40364-023-00522-4] [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: 06/02/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
Medullary Thyroid Carcinoma (MTC) is a rare neuroendocrine tumour whose diagnosis includes evaluating calcitonin serum levels, which can present fluctuations unrelated to MTC. Here, we investigated circulating DNA fragmentation and methylation changes as potential biomarkers using ddPCR on cell-free DNA (cfDNA) isolated from the plasma of MTC patients. For cfDNA fragmentation analysis, we investigated the fragment size distribution of a gene family and calculated short fragment fraction (SFF). Methylation analyses evaluated the methylation levels of CG_16698623, a CG dinucleotide in the MGMT gene that we found hypermethylated in MTC tissues by analyzing public databases. The SFF ratio and methylation of CG_16698623 were significantly increased in plasma from MTC patients at diagnosis, and patients with clinical remission or stable disease at follow-up showed no significant SFF difference compared with healthy subjects. Our data support the diagnostic value of cfDNA traits that could enable better management of MTC patients.
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Affiliation(s)
- Anna Citarella
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Sofia Trocchianesi
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Tanja Milena Autilio
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Elena Splendiani
- Department of Movement, Human and Health Sciences, University of Foro Italico, 00135, Rome, Italy
| | - Zaira Spinello
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, 53100, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, 09042, Italy
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, 09042, Italy
| | - Cristina Romei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, 56126, Italy
| | - Raffaele Ciampi
- Endocrine Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, 56126, Italy
| | - Luciano Pezzullo
- Thyroid Surgical Unit, IRCCS Fondazione G.Pascale, Naples, 80131, Italy
| | - Maria Grazia Castagna
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, 53100, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Rosella Elisei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, 56126, Italy
| | - Cosimo Durante
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, 00161, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University of Rome, Rome, 00161, Italy.
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, 00161, Italy
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Biglari N, Soltani-Zangbar MS, Mohammadian J, Mehdizadeh A, Abbasi K. ctDNA as a novel and promising approach for cancer diagnosis: a focus on hepatocellular carcinoma. EXCLI JOURNAL 2023; 22:752-780. [PMID: 37720239 PMCID: PMC10502204 DOI: 10.17179/excli2023-6277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 09/19/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent forms of cancer worldwide. Therefore, it is essential to diagnose and treat HCC patients promptly. As a novel discovery, circulating tumor DNA (ctDNA) can be used to analyze the tumor type and the cancer location. Additionally, ctDNA assists the cancer stage determination, which enables medical professionals to provide patients with the most appropriate treatment. This review will discuss the HCC-related mutated genes diagnosed by ctDNA. In addition, we will introduce the different and the most appropriate ctDNA diagnosis approaches based on the facilities.
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Affiliation(s)
- Negin Biglari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Sadegh Soltani-Zangbar
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamal Mohammadian
- School of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khadijeh Abbasi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Ma Y, Gan J, Bai Y, Cao D, Jiao Y. Minimal residual disease in solid tumors: an overview. Front Med 2023; 17:649-674. [PMID: 37707677 DOI: 10.1007/s11684-023-1018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/24/2023] [Indexed: 09/15/2023]
Abstract
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Affiliation(s)
- Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jingbo Gan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yinlei Bai
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, 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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23
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Xia T, Fang C, Chen Y. Advances in application of circulating tumor DNA in ovarian cancer. Funct Integr Genomics 2023; 23:250. [PMID: 37479960 DOI: 10.1007/s10142-023-01181-2] [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: 03/15/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Ovarian cancer is the third most common gynecologic cancer worldwide and has the highest mortality rate among gynecologic cancers. Identifying timely and effective biomarkers at different stages of the disease is the key to improve the prognosis of ovarian cancer patients. Circulating tumor DNA (ctDNA) is a fragment of free DNA produced by tumor cells in the blood. Current techniques for detecting ctDNA mainly include quantitative polymerase chain reaction (PCR), targeted next-generation sequencing (NGS), and non-targeted NGS (such as whole exon or whole genome sequencing). As a non-invasive liquid biopsy technique, ctDNA has a good application prospect in the ovarian cancer diagnosis, monitoring of treatment response and efficacy evaluation, detection of reverse mutation and related medication guidance, and prognosis evaluation. This article reviews the advances in application of ctDNA in ovarian cancer.
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Affiliation(s)
- Ting Xia
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Chenyan Fang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Yaqing Chen
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
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24
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Li F, Aziz M, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DT. Multi-Faceted Attributes of Salivary Cell-free DNA as Liquid Biopsy Biomarkers for Gastric Cancer Detection. RESEARCH SQUARE 2023:rs.3.rs-3154388. [PMID: 37503289 PMCID: PMC10371094 DOI: 10.21203/rs.3.rs-3154388/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. Methods In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. Results Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). Conclusion These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David T.W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Cohen SA, Liu MC, Aleshin A. Practical recommendations for using ctDNA in clinical decision making. Nature 2023; 619:259-268. [PMID: 37438589 DOI: 10.1038/s41586-023-06225-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/16/2023] [Indexed: 07/14/2023]
Abstract
The continuous improvement in cancer care over the past decade has led to a gradual decrease in cancer-related deaths. This is largely attributed to improved treatment and disease management strategies. Early detection of recurrence using blood-based biomarkers such as circulating tumour DNA (ctDNA) is being increasingly used in clinical practice. Emerging real-world data shows the utility of ctDNA in detecting molecular residual disease and in treatment-response monitoring, helping clinicians to optimize treatment and surveillance strategies. Many studies have indicated ctDNA to be a sensitive and specific biomarker for recurrence. However, most of these studies are largely observational or anecdotal in nature, and peer-reviewed data regarding the use of ctDNA are mainly indication-specific. Here we provide general recommendations on the clinical utility of ctDNA and how to interpret ctDNA analysis in different treatment settings, especially in patients with solid tumours. Specifically, we provide an understanding around the implications, strengths and limitations of this novel biomarker and how to best apply the results in clinical practice.
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Affiliation(s)
- Stacey A Cohen
- Fred Hutchinson Cancer Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
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26
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Xue R, Yang L, Yang M, Xue F, Li L, Liu M, Ren Y, Qi Y, Zhao J. Circulating cell-free DNA sequencing for early detection of lung cancer. Expert Rev Mol Diagn 2023; 23:589-606. [PMID: 37318381 DOI: 10.1080/14737159.2023.2224504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Lung cancer is a leading cause of death in patients with cancer. Early diagnosis is crucial to improve the prognosis of patients with lung cancer. Plasma circulating cell-free DNA (cfDNA) contains comprehensive genetic and epigenetic information from tissues throughout the body, suggesting that early detection of lung cancer can be done non-invasively, conveniently, and cost-effectively using high-sensitivity techniques such as sequencing. AREAS COVERED In this review, we summarize the latest technological innovations, coupled with next-generation sequencing (NGS), regarding genomic alterations, methylation, and fragmentomic features of cfDNA for the early detection of lung cancer, as well as their clinical advances. Additionally, we discuss the suitability of study designs for diagnostic accuracy evaluation for different target populations and clinical questions. EXPERT OPINION Currently, cfDNA-based early screening and diagnosis of lung cancer faces many challenges, such as unsatisfactory performance, lack of quality control standards, and poor repeatability. However, the progress of several large prospective studies employing epigenetic features has shown promising predictive performance, which has inspired cfDNA sequencing for future clinical applications. Furthermore, the development of multi-omics markers for lung cancer, including genome-wide methylation and fragmentomics, is expected to play an increasingly important role in the future.
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Affiliation(s)
- Ruyue Xue
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lu Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Meijia Yang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Xue
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yong Ren
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhao
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Zhang H, Dong P, Fan H, Liang H, Zhang K, Zhao Y, Guo S, Schrodi SJ, Fan Y, Zhang D. Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma. Funct Integr Genomics 2023; 23:198. [PMID: 37273114 DOI: 10.1007/s10142-023-01114-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023]
Abstract
Programmed cell death (PCD) resistance is a key driver of cancer occurrence and development. The prognostic relevance of PCD-related genes in hepatocellular carcinoma (HCC) has attracted considerable attention in recent years. However, there is still a lack of efforts to compare the methylation status of different types of PCD genes in HCC and their roles in its surveillance. The methylation status of genes related to pyroptosis, apoptosis, autophagy, necroptosis, ferroptosis, and cuproptosis was analyzed in tumor and non-tumor tissues from TCGA. Whole-genome bisulfite sequencing (WGBS) data of paired tumor tissue and buffy coat samples were used to filter the potential interference of blood leukocytes in cell-free DNA (cfDNA). The WGBS data of healthy individuals' and early-stage HCC patients' cfDNA were analyzed to evaluate the distinguishing ability. The average gene body methylation (gbDNAme) of pyroptosis-related genes (PRGs) was significantly altered in HCC tissues relative to normal tissues, and their distinguishing ability was higher compared to the other types of PCD-related genes. The gbDNAme of NLRP7, NLRP2, and NLRP3 was reflective of the hypomethylation in HCC tissues, and methylation levels of NLRP3 correlated positively with its expression level (r=0.51). The candidate hypomethylated PRGs could discriminate between early HCC patients and healthy controls in cfDNA analysis with high accuracy (area under the receiver operation curve, AUC=0.94). Furthermore, the hypomethylation of PRGs was associated with poor prognosis of HCC. Gene body hypomethylation of PRGs is a promising biomarker for early HCC detection, monitoring of tumor recurrence, and prognosis prediction.
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Affiliation(s)
- Haikun Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Peiling Dong
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Hao Liang
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Ke Zhang
- SCG Cell Therapy Pte. Ltd, Singapore, Singapore
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100191, China.
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Fairley JA, Badrick T, Denis MG, Dimitrova L, Goodall R, Maas J, Normanno N, Patton SJ, Rouleau E, Russo A, Stockley TL, Deans ZC. Implementation of circulating tumour DNA multi-target mutation testing in plasma: a perspective from an external quality assessment providers' survey. Virchows Arch 2023:10.1007/s00428-023-03558-x. [PMID: 37202567 DOI: 10.1007/s00428-023-03558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/02/2023] [Accepted: 05/06/2023] [Indexed: 05/20/2023]
Abstract
Demand for large-scale tumour profiling across cancer types has increased in recent years, driven by the emergence of targeted drug therapies. Analysing alternations in plasma circulating tumour DNA (ctDNA) for cancer detection can improve survival; ctDNA testing is recommended when tumour tissue is unavailable. An online survey of molecular pathology testing was circulated by six external quality assessment members of IQN Path to registered laboratories and all IQN Path collaborative corporate members. Data from 275 laboratories across 45 countries were collected; 245 (89%) perform molecular pathology testing, including 177 (64%) which perform plasma ctDNA diagnostic service testing. The most common tests were next-generation sequencing-based (n = 113). Genes with known stratified treatment options, including KRAS (n = 97), NRAS (n = 84), and EGFR (n = 130), were common targets. The uptake of ctDNA plasma testing and plans to implement further testing demonstrates the importance of support from a well-designed EQA scheme.
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Affiliation(s)
- Jennifer A Fairley
- GenQA, Department of Laboratory Medicine, NHS Lothian, Nine Bioquarter, Little France Rd, Edinburgh, EH16 4UX, UK
| | - Tony Badrick
- The Royal College of Pathologists of Australasia, Quality Assurance Programs (RCPAQAP), St. Leonards, Australia
| | - Marc G Denis
- Nantes Université, CHU Nantes, Department of Biochemistry, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, Nantes, France
| | | | - Rebecca Goodall
- EMQN CIC, Unit 4, Enterprise House, Manchester Science Park, Pencroft Way, Manchester, M15 6SE, UK
| | - Joerg Maas
- Deutsche Gesellschaft für Pathologie E.V. (DGP), Berlin, Germany
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - "Fondazione G. Pascale", Via Mariano Semola, 80131, Napoli, Italy
| | - Simon J Patton
- EMQN CIC, Unit 4, Enterprise House, Manchester Science Park, Pencroft Way, Manchester, M15 6SE, UK
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Tracy L Stockley
- Laboratory Medicine Program, University Health Network; Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Zandra C Deans
- GenQA, Department of Laboratory Medicine, NHS Lothian, Nine Bioquarter, Little France Rd, Edinburgh, EH16 4UX, UK.
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Thompson JC, Vachani A. Could DNA Fragments Be the Key to Early Detection of Lung Cancer? Am J Respir Crit Care Med 2023; 207:1120-1122. [PMID: 36883946 PMCID: PMC10161741 DOI: 10.1164/rccm.202303-0387ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Affiliation(s)
- Jeffrey C Thompson
- Department of Medicine University of Pennsylvania Philadelphia, Pennsylvania and Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center Philadelphia, Pennsylvania
| | - Anil Vachani
- Department of Medicine University of Pennsylvania Philadelphia, Pennsylvania and Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center Philadelphia, Pennsylvania
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Talotta D, Almasri M, Cosentino C, Gaidano G, Moia R. Liquid biopsy in hematological malignancies: current and future applications. Front Oncol 2023; 13:1164517. [PMID: 37152045 PMCID: PMC10157039 DOI: 10.3389/fonc.2023.1164517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
The assessment of the cancer mutational profile is crucial for patient management, stratification, and therapeutic decisions. At present, in hematological malignancies with a solid mass, such as lymphomas, tumor genomic profiling is generally performed on the tissue biopsy, but the tumor may harbor genetic lesions that are unique to other anatomical compartments. The analysis of circulating tumor DNA (ctDNA) on the liquid biopsy is an emerging approach that allows genotyping and monitoring of the disease during therapy and follow-up. This review presents the different methods for ctDNA analysis and describes the application of liquid biopsy in different hematological malignancies. In diffuse large B-cell lymphoma (DLBCL) and Hodgkin lymphoma (HL), ctDNA analysis on the liquid biopsy recapitulates the mutational profile of the tissue biopsy and can identify mutations otherwise absent on the tissue biopsy. In addition, changes in the ctDNA amount after one or two courses of chemotherapy significantly predict patient outcomes. ctDNA analysis has also been tested in myeloid neoplasms with promising results. In addition to mutational analysis, liquid biopsy also carries potential future applications of ctDNA, including the analysis of ctDNA fragmentation and epigenetic patterns. On these grounds, several clinical trials aiming at incorporating ctDNA analysis for treatment tailoring are currently ongoing in hematological malignancies.
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Affiliation(s)
| | | | | | | | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
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Guil-Luna S, Sánchez-Céspedes R, Rivas Crespo A, Dolores Fernández M, Fernández Sarmiento JA, Rodríguez-Ariza A, Millán Y. Analysis of cell-free DNA concentration, fragmentation patterns and TP53 gene expression in mammary tumor-bearing dogs: A pilot study. Front Vet Sci 2023; 10:1157878. [PMID: 37065257 PMCID: PMC10090457 DOI: 10.3389/fvets.2023.1157878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
IntroductionLiquid biopsy based on the analysis of circulating cell-free DNA (cfDNA), as well as on detection of point mutations by digital droplet PCR (ddPCR), has revolutionized the research in oncology. In recent years, this technique has been pioneering in veterinary medicine since it is a minimally invasive approach with very promising results for characterization of tumors.MethodsThe aim of this study was, firstly, to analyze the concentration and the fragmentation pattern of cfDNA of dogs with mammary tumors (n = 36) and healthy dogs (n = 5) and its correlation with clinicopathological data. Secondly, analysis of TP53 gene expression and the point mutation in the codon 245 were performed in cfDNA and in tumor tissues to assess their potential as plasma biomarkers.Results and discussionOur results highlighted that those dogs with worse clinicopathological characteristics (simple or undifferentiated carcinomas, higher histological grade and presence of peritumoral inflammation) shown higher cfDNA concentration and higher concentrations of short-fragments (<190 bp) than healthy dogs. In addition, although no detection of the point mutation in codon 245 of TP53 gene could be detected neither in plasma nor tumor tissue, an increased TP53 expression was detected in animals with tumors bearing malignant characteristics. Finally, a high concordance with TP53 gene expression in plasma and tumor tissue and cfDNA concentration was also found. The results derived from this work confirm the valuable potential of cfDNA and its fragments, as well as the analysis of TP53 expression in plasma as useful liquid biomarkers for clinical application in veterinary oncology.
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Affiliation(s)
- Silvia Guil-Luna
- Grupo Nuevas Terapias en cáncer, Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria de Córdoba, Universidad de Córdoba, Córdoba, Spain
- *Correspondence: Silvia Guil-Luna
| | - Raquel Sánchez-Céspedes
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | - Aurora Rivas Crespo
- Grupo Nuevas Terapias en cáncer, Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
| | - María Dolores Fernández
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | | | - Antonio Rodríguez-Ariza
- Grupo Nuevas Terapias en cáncer, Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Yolanda Millán
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria de Córdoba, Universidad de Córdoba, Córdoba, Spain
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32
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Cao Z, An L, Han Y, Jiao S, Zhou Z. The Hippo signaling pathway in gastric cancer. Acta Biochim Biophys Sin (Shanghai) 2023. [PMID: 36924251 DOI: 10.3724/abbs.2023038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Gastric cancer (GC) is an aggressive malignant disease which still lacks effective early diagnosis markers and targeted therapies, representing the fourth-leading cause of cancer-associated death worldwide. The Hippo signaling pathway plays crucial roles in organ size control and tissue homeostasis under physiological conditions, yet its aberrations have been closely associated with several hallmarks of cancer. The last decade witnessed a burst of investigations dissecting how Hippo dysregulation contributes to tumorigenesis, highlighting the therapeutic potential of targeting this pathway for tumor intervention. In this review, we systemically document studies on the Hippo pathway in the contexts of gastric tumor initiation, progression, metastasis, acquired drug resistance, and the emerging development of Hippo-targeting strategies. By summarizing major open questions in this field, we aim to inspire further in-depth understanding of Hippo signaling in GC development, as well as the translational implications of targeting Hippo for GC treatment.
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Affiliation(s)
- Zhifa Cao
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China.,CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Liwei An
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China
| | - Yi Han
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China
| | - Shi Jiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China.,Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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33
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Cao M, Shi J, Xia C, Li H, Cai W, Qi X, Dai C, Chen W. Efficacy of ctDNA methylation combined with traditional detection modality to detect liver cancer among high-risk patients: A multicenter diagnostic trial. Chin J Cancer Res 2023; 35:58-65. [PMID: 36910858 PMCID: PMC9993000 DOI: 10.21147/j.issn.1000-9604.2023.01.06] [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: 10/25/2022] [Accepted: 01/05/2023] [Indexed: 03/10/2023] Open
Abstract
Objective Circulating tumor DNA (ctDNA) and alpha-fetoprotein (AFP) plus ultrasound (US) have been considered to have high diagnostic accuracy for cancer detection, however, the efficacy of ctDNA methylation combined with the traditional detection modality of liver cancer has not been tested in a Chinese independent cohort. Methods The high-risk individuals aged between 35 and 70 years who were diagnosed with liver cirrhosis or had moderate and severe fatty liver were eligible for inclusion. All participants were invited to receive a traditional examination [referring to AFP plus US], and ctDNA methylation, respectively. The sensitivity and specificity of different diagnostic tools were calculated. The logistic regression model was applied to estimate the area under the curve (AUC), which was further validated by 10-fold internal cross-validation. Results A total of 1,205 individuals were recruited in our study, and 39 participants were diagnosed with liver cancer. The sensitivity of AFP, US, US plus AFP, and the combination of US, AFP, and ctDNA methylation was 33.33%, 56.41%, 66.67%, and 87.18%, respectively. The corresponding specificity of AFP, US, US plus AFP, and the combination of all modalities was 98.20%, 99.31%, 97.68%, and 97.68%, respectively. The AUCs of AFP, US, US plus AFP, and the combination of AFP, US, and ctDNA methylation were 65.77%, 77.86%, 82.18%, and 92.43%, respectively. The internally validated AUCs of AFP, US, US plus AFP, and the combination of AFP, US, and ctDNA methylation were 67.57%, 83.26%, 86.54%, and 93.35%, respectively. Conclusions The ctDNA methylation is a good complementary to AFP and US for the detection of liver cancer.
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Affiliation(s)
- Maomao Cao
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jufang Shi
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Changfa Xia
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - He Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wei Cai
- Department of Prevention and Control of Chronic Noncommunicable Diseases, Binhai County Center for Disease Control and Prevention, Binhai 224521, China
| | - Xianyun Qi
- Chronic Noncommunicable Diseases Prevention and Treatment Department, Yingdong District Center for Disease Control and Prevention, Fuyang 236142, China
| | - Chunyun Dai
- Department for Chronic Non-communicable Diseases Control, Sheyang Center for Disease Control and Prevention, Sheyang 224300, China
| | - Wanqing Chen
- Office of Cancer Screening, 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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Grant BM, Pugh TJ, Oza AM. Molecular Monitoring in Endometrial Cancer-Ready for Prime Time? Clin Cancer Res 2023; 29:305-308. [PMID: 36354753 DOI: 10.1158/1078-0432.ccr-22-2781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022]
Abstract
SUMMARY Efforts are under way to define the role of minimally invasive strategies for molecular monitoring and risk stratification in endometrial cancer. A recent publication aims to define the association between circulating tumor DNA level and disease stage in patients with newly diagnosed endometrial cancer and determine whether sequencing of longitudinal cell-free DNA samples can be used for disease monitoring and detection of progression or recurrence. These results accelerate the current knowledge of molecular follow-up in endometrial cancer. See related article by Ashley et al., p. 410.
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Affiliation(s)
- Brooke M Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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35
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Pancreatic Cancer Cells Induce MicroRNA Deregulation in Platelets. Int J Mol Sci 2022; 23:ijms231911438. [PMID: 36232741 PMCID: PMC9569638 DOI: 10.3390/ijms231911438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer is a pathology with a high mortality rate since it is detected at advanced stages, so the search for early-stage diagnostic biomarkers is essential. Liquid biopsies are currently being explored for this purpose and educated platelets are a good candidate, since they are known to present a bidirectional interaction with tumor cells. In this work, we analyzed the effects of platelets on cancer cells’ viability, as determined by MTT, migration using transwell assays, clonogenicity in soft agar and stemness by dilution assays and stem markers’ expression. We found that the co-culture of platelets and pancreatic cancer cells increased the proliferation and migration capacity of BXCP3 cells, augmented clonogenicity and induced higher levels of Nanog, Sox2 and Oct4 expression. As platelets can provide horizontal transfer of microRNAs, we also determined the differential expression of miRNAs in platelets obtained from a small cohort of pancreatic cancer patients and healthy subjects. We found clear differences in the expression of several miRNAs between platelets of patients with cancer healthy subjects. Moreover, when we analyzed microRNAs from the platelets of the pancreatic juice and blood derived from each of the cancer patients, interestingly we find differences between the blood- and pancreatic juice-derived platelets suggesting the presence of different subpopulations of platelets in cancer patients, which warrant further analysis.
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36
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Choi EJ, Kim YJ. Liquid biopsy for early detection and therapeutic monitoring of hepatocellular carcinoma. JOURNAL OF LIVER CANCER 2022; 22:103-114. [PMID: 37383403 PMCID: PMC10035729 DOI: 10.17998/jlc.2022.09.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/30/2023]
Abstract
Advances in our knowledge of the molecular characteristics of hepatocellular carcinoma (HCC) have enabled significant progress in the detection and therapeutic prediction of HCC. As a non-invasive alternative to tissue biopsy, liquid biopsy examines circulating cellular components such as exosomes, nucleic acids, and cell-free DNA found in body fluids (e.g., urine, saliva, ascites, and pleural effusions) and provides information about tumor characteristics. Technical advances in liquid biopsy have led to the increasing adoption of diagnostic and monitoring applications for HCC. This review summarizes the various analytes, ongoing clinical trials, and case studies of United States Food and Drug Administrationapproved in vitro diagnostic applications for liquid biopsy, and provides insight into its implementation in managing HCC.
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Affiliation(s)
| | - Young-Joon Kim
- LepiDyne Co., Ltd., Seoul, Korea
- Department of Biochemistry, Yonsei University, Seoul, Korea
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