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Alsaab HO, Alzahrani MS, Bahauddin AA, Almutairy B. Circulating tumor DNA (ctDNA) application in investigation of cancer: Bench to bedside. Arch Biochem Biophys 2024; 758:110066. [PMID: 38906310 DOI: 10.1016/j.abb.2024.110066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Now, genomics forms the core of the precision medicine concept. Comprehensive investigations of tumor genomes have made it possible to characterize tumors at the molecular level and, specifically, to identify the fundamental processes that cause condition. A variety of kinds of tumors have seen better outcomes for patients as a result of the development of novel medicines to tackle these genetic-driving processes. Since therapy may exert selective pressure on cancers, non-invasive methods such as liquid biopsies can provide the opportunity for rich reservoirs of crucial and real-time genetic data. Liquid biopsies depend on the identification of circulating cells from tumors, circulating tumor DNA (ctDNA), RNA, proteins, lipids, and metabolites found in patient biofluids, as well as cell-free DNA (cfDNA), which exists in those with cancer. Although it is theoretically possible to examine biological fluids other than plasma, such as pleural fluid, urine, saliva, stool, cerebrospinal fluid, and ascites, we will limit our discussion to blood and solely cfDNA here for the sake of conciseness. Yet, the pace of wider clinical acceptance has been gradual, partly due to the increased difficulty of choosing the best analysis for the given clinical issue, interpreting the findings, and delaying proof of value from clinical trials. Our goal in this review is to discuss the current clinical value of ctDNA in cancers and how clinical oncology systems might incorporate procedures for ctDNA testing.
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Affiliation(s)
- Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, 21944, Saudi Arabia.
| | - Mohammad S Alzahrani
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.
| | - Ammar A Bahauddin
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Medina Al-Munawarah, Saudi Arabia.
| | - Bandar Almutairy
- Department of Pharmacology, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia.
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2
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Popescu I, Croitoru VM, Croitoru-Cazacu IM, Dudau AM, Herlea V, Dima SO, Croitoru AE. Dynamics of RAS Mutations in Liquid Biopsies in Metastatic Colorectal Cancer Patients-Case Series and Literature Review. J Pers Med 2024; 14:750. [PMID: 39064004 PMCID: PMC11278408 DOI: 10.3390/jpm14070750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/29/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Liquid biopsies can accurately identify molecular alterations in patients with colorectal cancer with high concordance with tissue analysis and shorter turnaround times. Circulating tumor (ct) DNA analysis can be used for diagnosing and monitoring tumor evolution in patients with metastatic colorectal cancer who are treated with EGFR inhibitors. In this article, we reported three clinical cases to illustrate the relevance of RAS mutations identified in ctDNA samples of patients with wild-type metastatic colorectal cancer who received an EGFR inhibitor plus chemotherapy as first-line treatment. The identification of RAS mutations in these patients is one of the most frequently identified mechanisms of acquired resistance. However, detecting a KRAS mutation via liquid biopsy can be caused by inter-tumor heterogeneity or it can be a false positive due to clonal hematopoiesis. More research is needed to determine whether ctDNA monitoring may help guide therapy options in metastatic colorectal cancer patients. We performed a literature review to assess the technologies that are used for analysis of RAS mutations on ctDNA, the degree of agreement between tissue and plasma and the importance of tissue/plasma discordant cases.
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Affiliation(s)
- Ionut Popescu
- Faculty of Medicine, Titu Maiorescu University, 031593 Bucharest, Romania; (I.P.); (V.M.C.)
| | - Vlad M. Croitoru
- Faculty of Medicine, Titu Maiorescu University, 031593 Bucharest, Romania; (I.P.); (V.M.C.)
- Department of Oncology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Irina M. Croitoru-Cazacu
- Department of Oncology, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania (S.O.D.)
| | - Ana-Maria Dudau
- Faculty of Medicine, Titu Maiorescu University, 031593 Bucharest, Romania; (I.P.); (V.M.C.)
- Department of Oncology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Vlad Herlea
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania (S.O.D.)
- Department of Pathology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Simona Olimpia Dima
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania (S.O.D.)
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
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Ronsley R, Karvonen KA, Cole B, Paulson V, Stevens J, Crotty EE, Hauptman J, Lee A, Stasi SM, Lockwood CM, Leary SES. Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors. J Neurooncol 2024; 168:215-224. [PMID: 38755519 DOI: 10.1007/s11060-024-04645-y] [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: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
PURPOSE Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. METHODS CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. RESULTS Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. CONCLUSIONS Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.
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Affiliation(s)
- Rebecca Ronsley
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US.
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US.
- Fred Hutchinson Cancer Research Center, Seattle, WA, US.
- Seattle Children's Hospital, Mail Stop MB.8.501, 4800 Sand Point Way NE, Seattle, WA, 98105, USA.
| | - Kristine A Karvonen
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Bonnie Cole
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
| | - Vera Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jeff Stevens
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
| | - Erin E Crotty
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Jason Hauptman
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Amy Lee
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Shannon M Stasi
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
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Stosic K, Senar OA, Tarfouss J, Bouchart C, Navez J, Van Laethem JL, Arsenijevic T. A Comprehensive Review of the Potential Role of Liquid Biopsy as a Diagnostic, Prognostic, and Predictive Biomarker in Pancreatic Ductal Adenocarcinoma. Cells 2023; 13:3. [PMID: 38201207 PMCID: PMC10778087 DOI: 10.3390/cells13010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most lethal malignant diseases, with a mortality rate being close to incidence. Due to its heterogeneity and plasticity, as well as the lack of distinct symptoms in the early phases, it is very often diagnosed at an advanced stage, resulting in poor prognosis. Traditional tissue biopsies remain the gold standard for making a diagnosis, but have an obvious disadvantage in their inapplicability for frequent sampling. Blood-based biopsies represent a non-invasive method which potentially offers easy and repeated sampling, leading to the early detection and real-time monitoring of the disease and hopefully an accurate prognosis. Given the urgent need for a reliable biomarker that can estimate a patient's condition and response to an assigned treatment, blood-based biopsies are emerging as a potential new tool for improving patients' survival and surveillance. In this article, we discuss the current advances and challenges in using liquid biopsies for pancreatic cancer, focusing on circulating tumour DNA (ctDNA), extracellular vesicles (EVs), and circulating tumour cells (CTCs), and compare the performance and reliability of different biomarkers and combinations of biomarkers.
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Affiliation(s)
- Kosta Stosic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Oier Azurmendi Senar
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Jawad Tarfouss
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Christelle Bouchart
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Radiation Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Julie Navez
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Hepato-Biliary-Pancreatic Surgery, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Tatjana Arsenijevic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Xing S, Zhu Y, You Y, Wang S, Wang H, Ning M, Jin H, Liu Z, Zhang X, Yu C, Lu ZJ. Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1791. [PMID: 37086051 DOI: 10.1002/wrna.1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Gastrointestinal (GI) cancer includes many cancer types, such as esophageal, liver, gastric, pancreatic, and colorectal cancer. As the cornerstone of personalized medicine for GI cancer, liquid biopsy based on noninvasive biomarkers provides promising opportunities for early diagnosis and dynamic treatment management. Recently, a growing number of studies have demonstrated the potential of cell-free RNA (cfRNA) as a new type of noninvasive biomarker in body fluids, such as blood, saliva, and urine. Meanwhile, transcriptomes based on high-throughput RNA detection technologies keep discovering new cfRNA biomarkers. In this review, we introduce the origins and applications of cfRNA, describe its detection and qualification methods in liquid biopsy, and summarize a comprehensive list of cfRNA biomarkers in different GI cancer types. Moreover, we also discuss perspective studies of cfRNA to overcome its current limitations in clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
| | - Yumin Zhu
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Yaxian You
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng Ning
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Heyue Jin
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Zhengxia Liu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinhua Zhang
- Department of Health Care, Jiangsu Women and Children Health Hospital, the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, Jiangsu, China
| | - Chunzhao Yu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
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Mangum R, Reuther J, Baksi KS, Gandhi I, Zabriskie RC, Recinos A, Raesz-Martinez R, Lin FY, Potter SL, Sher AC, Kralik SF, Mohila CA, Chintagumpala MM, Muzny D, Hu J, Gibbs RA, Fisher KE, Bernini JC, Gill J, Griffin TC, Tomlinson GE, Vallance KL, Plon SE, Roy A, Parsons DW. Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. Pediatr Hematol Oncol 2023; 40:719-738. [PMID: 37366551 PMCID: PMC10592361 DOI: 10.1080/08880018.2023.2228837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Jacquelyn Reuther
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Koel Sen Baksi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ilavarasi Gandhi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Ryan C. Zabriskie
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alva Recinos
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Robin Raesz-Martinez
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Frank Y. Lin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Samara L. Potter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Andrew C. Sher
- Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | | | - Carrie A. Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Murali M. Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Fisher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Juan Carlos Bernini
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy C. Griffin
- Department of Hematology Oncology, The Children’s Hospital of San Antonio, Baylor College of Medicine, San Antonio, Texas
| | - Gail E Tomlinson
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Kelly L. Vallance
- Hematology and Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Sharon E. Plon
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - D. Williams Parsons
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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8
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Bou Zerdan M, Kassab J, Saba L, Haroun E, Bou Zerdan M, Allam S, Nasr L, Macaron W, Mammadli M, Abou Moussa S, Chaulagain CP. Liquid biopsies and minimal residual disease in lymphoid malignancies. Front Oncol 2023; 13:1173701. [PMID: 37228488 PMCID: PMC10203459 DOI: 10.3389/fonc.2023.1173701] [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: 02/25/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Minimal residual disease (MRD) assessment using peripheral blood instead of bone marrow aspirate/biopsy specimen or the biopsy of the cancerous infiltrated by lymphoid malignancies is an emerging technique with enormous interest of research and technological innovation at the current time. In some lymphoid malignancies (particularly ALL), Studies have shown that MRD monitoring of the peripheral blood may be an adequate alternative to frequent BM aspirations. However, additional studies investigating the biology of liquid biopsies in ALL and its potential as an MRD marker in larger patient cohorts in treatment protocols are warranted. Despite the promising data, there are still limitations in liquid biopsies in lymphoid malignancies, such as standardization of the sample collection and processing, determination of timing and duration for liquid biopsy analysis, and definition of the biological characteristics and specificity of the techniques evaluated such as flow cytometry, molecular techniques, and next generation sequencies. The use of liquid biopsy for detection of minimal residual disease in T-cell lymphoma is still experimental but it has made significant progress in multiple myeloma for example. Recent attempt to use artificial intelligence may help simplify the algorithm for testing and may help avoid inter-observer variation and operator dependency in these highly technically demanding testing process.
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Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Joseph Kassab
- Cleveland Clinic, Research Institute, Cleveland, OH, United States
| | - Ludovic Saba
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
| | - Elio Haroun
- Department of Medicine, State University of New York (SUNY) Upstate Medical University, New York, NY, United States
| | | | - Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Balamand, Lebanon
| | - Lewis Nasr
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Walid Macaron
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Mahinbanu Mammadli
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | | | - Chakra P. Chaulagain
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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10
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Soscia R, Della Starza I, De Novi LA, Ilari C, Ansuinelli M, Cavalli M, Bellomarino V, Cafforio L, Di Trani M, Cazzaniga G, Fazio G, Santoro A, Salemi D, Spinelli O, Tosi M, Terragna C, Robustelli V, Bellissimo T, Colafigli G, Breccia M, Chiaretti S, Di Rocco A, Martelli M, Guarini A, Del Giudice I, Foà R. Circulating cell-free DNA for target quantification in hematologic malignancies: Validation of a protocol to overcome pre-analytical biases. Hematol Oncol 2023; 41:50-60. [PMID: 36251440 DOI: 10.1002/hon.3087] [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: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 02/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has become the most investigated analyte in blood. It is shed from the tumor into the circulation and represents a subset of the total cell-free DNA (cfDNA) pool released into the peripheral blood. In order to define if ctDNA could represent a useful tool to monitor hematologic malignancies, we analyzed 81 plasma samples from patients affected by different diseases. The results showed that: (i) the comparison between two different extraction methods Qiagen (Hilden, Germany) and Promega (Madison, WI) showed no significant differences in cfDNA yield, though the first recovered higher amounts of larger DNA fragments; (ii) cfDNA concentrations showed a notable inter-patient variability and differed among diseases: acute lymphoblastic leukemia and chronic myeloid leukemia released higher amounts of cfDNA than chronic lymphocytic leukemia, and diffuse large B-cell lymphoma released higher cfDNA quantities than localized and advanced follicular lymphoma; (iii) focusing on the tumor fraction of cfDNA, the quantity of ctDNA released was insufficient for an adequate target quantification for minimal residual disease monitoring; (iv) an amplification system proved to be free of analytical biases and efficient in increasing ctDNA amounts at diagnosis and in follow-up samples as shown by droplet digital PCR target quantification. The protocol has been validated by quality control rounds involving external laboratories. To conclusively document the feasibility of a ctDNA-based monitoring of patients with hematologic malignancies, more post-treatment samples need to be evaluated. This will open new possibilities for ctDNA use in the clinical practice.
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Affiliation(s)
- Roberta Soscia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,GIMEMA Foundation, Rome, Italy
| | - Lucia Anna De Novi
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Caterina Ilari
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Michela Ansuinelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Marzia Cavalli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Vittorio Bellomarino
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Luciana Cafforio
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Mariangela Di Trani
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Grazia Fazio
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Alessandra Santoro
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Domenico Salemi
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Carolina Terragna
- Seràgnoli Institute of Hematology, Azienda Ospedaliero-Universitaria Sant'Orsola-Malpighi, Bologna, Italy
| | - Valentina Robustelli
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Teresa Bellissimo
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Gioia Colafigli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Massimo Breccia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Alice Di Rocco
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Maurizio Martelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Anna Guarini
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
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11
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El Hejjioui B, Bouguenouch L, Melhouf MA, El Mouhi H, Bennis S. Clinical Evidence of Circulating Tumor DNA Application in Aggressive Breast Cancer. Diagnostics (Basel) 2023; 13:470. [PMID: 36766575 PMCID: PMC9914403 DOI: 10.3390/diagnostics13030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is clinically and biologically heterogeneous and is classified into different subtypes according to the molecular landscape of the tumor. Triple-negative breast cancer is a subtype associated with higher tumor aggressiveness, poor prognosis, and poor response to treatment. In metastatic breast cancer, approximately 6% to 10% of new breast cancer cases are initially staged IV (de novo metastatic disease). The number of metastatic recurrences is estimated to be 20-30% of all existing breast tumor cases, whereby the need to develop specific genetic markers to improve the prognosis of patients suffering from these deadly forms of breast cancer. As an alternative, liquid biopsy methods can minutely identify the molecular architecture of breast cancer, including aggressive forms, which provides new perspectives for more precise diagnosis and more effective therapeutics. This review aimed to summarize the current clinical evidence for the application of circulating tumor DNA in managing breast cancer by detailing the increased usefulness of this biomarker as a diagnostic, prognostic, monitoring, and surveillance marker for breast cancer.
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Affiliation(s)
- Brahim El Hejjioui
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Laila Bouguenouch
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | | | - Hind El Mouhi
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Sanae Bennis
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
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12
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Cao XS, Zheng WQ, Hu ZD. Diagnostic value of soluble biomarkers for parapneumonic pleural effusion. Crit Rev Clin Lab Sci 2023; 60:233-247. [PMID: 36593742 DOI: 10.1080/10408363.2022.2158779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Parapneumonic pleural effusion (PPE) is a common complication in patients with pneumonia. Timely and accurate diagnosis of PPE is of great value for its management. Measurement of biomarkers in circulating and pleural fluid have the advantages of easy accessibility, short turn-around time, objectiveness and low cost and thus have utility for PPE diagnosis and stratification. To date, many biomarkers have been reported to be of value for the management of PPE. Here, we review the values of pleural fluid and circulating biomarkers for the diagnosis and stratification PPE. The biomarkers discussed are C-reactive protein, procalcitonin, presepsin, soluble triggering receptor expressed on myeloid cells 1, lipopolysaccharide-binding protein, inflammatory markers, serum amyloid A, soluble urokinase plasminogen activator receptor, matrix metalloproteinases, pentraxin-3 and cell-free DNA. We found that none of the available biomarkers has adequate performance for diagnosing and stratifying PPE. Therefore, further work is needed to identify and validate novel biomarkers, and their combinations, for the management of PPE.
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Affiliation(s)
- Xi-Shan Cao
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Wen-Qi Zheng
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhi-De Hu
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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13
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Zhong L, Yin R, Song L. Resistance to PARP Inhibitors After First-Line Platinum-Based Chemotherapy in a Patient with Advanced Ovarian Cancer with a Pathogenic Somatic BRCA1 Mutation. Pharmgenomics Pers Med 2023; 16:195-200. [PMID: 36942084 PMCID: PMC10024533 DOI: 10.2147/pgpm.s397827] [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: 11/16/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
PARP inhibitors (PARPi) are the maintenance therapy after first line platinum-based chemotherapy for patients with advanced epithelial ovarian cancer (EOC) with germline and pathogenic somatic BRCA1/2 mutations. However, as with chemotherapy, patients can develop resistance to PARPi. The selective pressure generated by heterogeneous somatic BRCA mutations may give rise to chemotherapy or PARPi resistant tumors. Here, we present the case of a patient harboring a pathogenic p.Glu143* (c.427G>T) somatic BRCA1 mutation conferring resistance to olaparib following cytoreductive surgery and platinum-based chemotherapy. We ordered a plasma ctDNA analysis (tissue biopsy of recurrent lesions was contraindicated due to their anatomical location) to figure out the possible resistance mechanism. Analysis of ctDNA did not detect the pathogenic somatic BRCA1 p.Glu143* (c.427G>T) mutation seen before. The tumor cells harboring the pathogenic BRCA1 mutation were probably eliminated by the platinum-based chemotherapy, leaving only those without BRCA mutations to proliferate.
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Affiliation(s)
- Lan Zhong
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Rutie Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Liang Song
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, 610041, People’s Republic of China
- Correspondence: Liang Song, Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, No. 20 The Third Section of South Renmin Road, Chengdu, Sichuan, 610041, People’s Republic of China, Tel +86-19828966121, Email
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14
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A narrative review of cancer molecular diagnostics: past, present, and future. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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15
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Wardana T, Chasanah SN, Oktriani R, Herawati C, Anwar SL, Astuti I, Mubarika Haryana S. Circulation microRNA expression profiles in patients with complete responses to chemoradiotherapy in nasopharyngeal carcinoma. Noncoding RNA Res 2022; 7:233-241. [PMID: 36203524 PMCID: PMC9519485 DOI: 10.1016/j.ncrna.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background Aims Methods Results Conclusion
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Affiliation(s)
- Tirta Wardana
- Department of Biomedicine, Faculty of Medicine, Jenderal Soedirman University, Purwokerto, Central Java, Indonesia
- Corresponding author.
| | - Siti Nur Chasanah
- Graduate Student, Biomedical Science, Faculty of Medicine, Nursing, and Public Health, Gadjah Mada University, Yogyakarta, Indonesia
| | - Risky Oktriani
- Department of Biochemistry, Faculty of Medicine, Nursing, and Public Health, Gadjah Mada University, Yogyakarta, Indonesia
| | - Cita Herawati
- Department of THT, Dharmais Hospital National Cancer Center, West Jakarta, Indonesia
| | - Sumadi Lukman Anwar
- Department of Surgery, Faculty of Medicine, Nursing, and Public Health, Gadjah Mada University, Yogyakarta, Indonesia
| | - Indwiani Astuti
- Department of Pharmacology and Therapy, Faculty of Medicine, Nursing, and Public Health, Gadjah Mada University, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine, Nursing, and Public Health, Gadjah Mada University, Yogyakarta, Indonesia
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16
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Abstract
Over the last decade, molecular markers have become an integral part in the management of Central Nervous System (CNS) tumors. Somatic mutations that identify and prognosticate tumors are also detected in the bio-fluids especially the serum and CSF; the sampling of which is known as liquid biopsy (LB). These tumor-derived biomarkers include plasma circulating tumor cells (CTCs), cell-free DNA (cf/ctDNAs), circulating cell-free microRNAs (cfmiRNAs), circulating extracellular vesicles, or exosomes (EVs), proteins, and tumor educated platelets. Established in the management of other malignancies, liquid biopsy is becoming an important tool in the management of CNS tumors as well. This review presents a snapshot of the current state of LB research its potential and the possible pitfalls.
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Affiliation(s)
- Amitava Ray
- Senior Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City and Apollo Secunderabad, Hyderabad 500089, Telangana, India
| | - Tarang K Vohra
- Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City, Hyderabad 500089, Telangana, India
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17
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Global Trends in Research on Cell-Free Nucleic Acids in Obstetrics and Gynecology during 2017–2021. J Clin Med 2022; 11:jcm11195545. [PMID: 36233412 PMCID: PMC9572904 DOI: 10.3390/jcm11195545] [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: 07/12/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Objectives. The objectives of this study were to identify global trends in research on cell-free deoxyribonucleic acid (cfDNA) from a bibliometric perspective and provide researchers with new research hotspots. Methods. In all, we extracted 5038 pieces of literature from PubMed and 527 articles from the Web of Science Core Collection (WoSCC) database related to cfDNA published from 1 January 2017 to 31 December 2021. For PubMed literature, we employed co-word, biclustering, and strategic diagram analysis to describe the trends in research on cfDNA in the said five years. Then, we used VOSviewer analysis for the WoSCC database to display the trends in research on cfDNA in obstetrics and gynecology during 2017–2021. Results. Strategy diagram analysis of 95 major Medical Subject Headings terms extracted from 5038 pieces of literature indicated that cfDNA sequence analysis for non-invasive prenatal and genetic testing and its application in the fields of neoplasm genetics and diagnosis is a newly emerging immature theme of cfDNA. VOSviewer analysis of 527 articles showed the global trends in research on cfDNA in obstetrics and gynecology, for example, in terms of most influential authors, institutions, countries, journals, and five research hotspots: (1) cfDNA application in prenatal screening and prenatal diagnosis, (2) cfDNA application in assisted reproductive technology, (3) cfDNA application in pre-eclampsia, DNA methylation, etc., (4) cfDNA application in placental dysfunction and fetal growth restriction, and (5) cfDNA application in fetal chromosomal abnormalities (fetal aneuploidy). Conclusions. Comprehensive visual analysis provides information regarding authors, organizations, countries/regions, journals, research hotspots, and emerging topics in the field of cfDNA for obstetrics and gynecology research. This comprehensive study could make it easier to find a partner for project development and build a network of knowledge on this emerging topic.
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18
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Werner TV, Kock S, Weber I, Kayser G, Werner M, Lassmann S. Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples. J Mol Diagn 2022; 24:784-802. [PMID: 35787794 DOI: 10.1016/j.jmoldx.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/26/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.
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Affiliation(s)
- Tamara V Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Isabel Weber
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gian Kayser
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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19
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Hu D, Guo E, Yang B, Qin X, Fu Y, Fan J, Zhuang X, Yao Q, Lu F, Li W, Xiao R, Wu X, Yang X, Wang Z, Liu C, You L, Zang R, Zhou Q, Zhao W, Chen G, Sun C. Mutation profiles in circulating cell‐free
DNA
predict acquired resistance to Olaparib in high‐grade serous ovarian carcinoma. Cancer Sci 2022; 113:2849-2861. [PMID: 35661486 PMCID: PMC9357630 DOI: 10.1111/cas.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xu Qin
- Department of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xucui Zhuang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qianqian Yao
- Department of Medical Science Shanghai AccuraGen Biotechnology Co., Ltd Shanghai China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xue Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Lixin You
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rongyu Zang
- Department of Gynecologic Oncology, Zhongshan Hospital Fudan University Shanghai China
| | - Qi Zhou
- Department of Gynecology Oncology Chongqing University Cancer Hospital Chongqing China
| | - Weidong Zhao
- Department of Gynecologic Oncology Anhui Provincial Cancer Hospital Hefei China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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20
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Liu MC, MacKay M, Kase M, Piwowarczyk A, Lo C, Schaeffer J, Finkle JD, Mason CE, Beaubier N, Blackwell KL, Park BH. Longitudinal Shifts of Solid Tumor and Liquid Biopsy Sequencing Concordance in Metastatic Breast Cancer. JCO Precis Oncol 2022; 6:e2100321. [PMID: 35721584 PMCID: PMC9200387 DOI: 10.1200/po.21.00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/17/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue-based next-generation sequencing (NGS) in metastatic breast cancer (mBC) is limited by the inability to noninvasively track tumor evolution. Cell-free DNA (cfDNA) NGS has made sequential testing feasible; however, the relationship between cfDNA and tissue-based testing in mBC is not well understood. Here, we evaluate concordance between tissue and cfDNA NGS relative to cfDNA sampling frequency in a large, clinically annotated mBC data set. METHODS Tempus LENS was used to analyze deidentified records of mBC cases with Tempus xT (tissue) and xF (cfDNA) sequencing results. Then, various metrics of concordance were assessed within overlapping probe regions of the tissue and cfDNA assays (104 genes), focusing on pathogenic variants. Variant allele frequencies of discordant and concordant pathogenic variants were also compared. Analyses were stratified by mBC subtype and time between tests. RESULTS Records from 300 paired tissue and liquid biopsies were analyzed. Median time between tissue and blood collection was 78.5 days (standard deviation = 642.99). The median number of pathogenic variants/patient was one for cfDNA and two for tissue. Across the cohort, 77.8% of pathogenic tissue variants were found in cfDNA and 75.7% of pathogenic cfDNA variants were found in tissue when tests were ≤ 7 days apart, which decreased to 50.3% and 51.8%, respectively, for > 365 days. Furthermore, the median patient-level variant concordance was 67% when tests were ≤7 days apart and 30%-37% when > 30 days. The median variant allele frequencies of discordant variants were generally lower than those of concordant variants within the same time frame. CONCLUSION We observed high concordances between tissue and cfDNA results that generally decreased with longer durations between tests. Thus, cfDNA NGS reliably measures tissue genomics and is likely beneficial for longitudinal monitoring of molecular changes in mBC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, TN
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21
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Evaluation of cfDNA as an early detection assay for dense tissue breast cancer. Sci Rep 2022; 12:8458. [PMID: 35589867 PMCID: PMC9120463 DOI: 10.1038/s41598-022-12457-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
A cell-free DNA (cfDNA) assay would be a promising approach to early cancer diagnosis, especially for patients with dense tissues. Consistent cfDNA signatures have been observed for many carcinogens. Recently, investigations of cfDNA as a reliable early detection bioassay have presented a powerful opportunity for detecting dense tissue screening complications early. We performed a prospective study to evaluate the potential of characterizing cfDNA as a central element in the early detection of dense tissue breast cancer (BC). Plasma samples were collected from 32 consenting subjects with dense tissue and positive mammograms, 20 with positive biopsies and 12 with negative biopsies. After screening and before biopsy, cfDNA was extracted, and whole-genome next-generation sequencing (NGS) was performed on all samples. Copy number alteration (CNA) and single nucleotide polymorphism (SNP)/insertion/deletion (Indel) analyses were performed to characterize cfDNA. In the positive-positive subjects (cases), a total of 5 CNAs overlapped with 5 previously
reported BC-related oncogenes (KSR2, MAP2K4, MSI2, CANT1 and MSI2). In addition, 1 SNP was detected in KMT2C, a BC oncogene, and 9 others were detected in or near 10 genes (SERAC1, DAGLB, MACF1, NVL, FBXW4, FANK1, KCTD4, CAVIN1; ATP6V0A1 and ZBTB20-AS1) previously associated with non-BC cancers. For the positive–negative subjects (screening), 3 CNAs were detected in BC genes (ACVR2A, CUL3 and PIK3R1), and 5 SNPs were identified in 6 non-BC cancer genes (SNIP1, TBC1D10B, PANK1, PRKCA and RUNX2; SUPT3H). This study presents evidence of the potential of using cfDNA somatic variants as dense tissue BC biomarkers from a noninvasive liquid bioassay for early cancer detection.
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22
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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23
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Deverka PA, Douglas MP, Phillips KA. Multicancer Screening Tests: Anticipating And Addressing Considerations For Payer Coverage And Patient Access. Health Aff (Millwood) 2022; 41:383-389. [PMID: 35254936 DOI: 10.1377/hlthaff.2021.01316] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There is a tremendous public health need to identify potentially lethal cancers at earlier stages, when there is a greater chance for improved survival. Although in the US there are currently screening recommendations for only five cancers (breast, colorectal, cervical, lung, and prostate), new tests can screen for up to fifty cancers simultaneously based on a simple blood draw. However, these multicancer screening tests (also called "liquid biopsy" tests) will also present challenges to payers because of intrinsic features of the tests and the complexity of payer coverage assessments for screening tests. We describe these considerations while also offering potential solutions that can inform payers' decision making if these tests prove to be beneficial.
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Affiliation(s)
- Patricia A Deverka
- Patricia A. Deverka , University of California San Francisco, San Francisco, California
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24
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Edwards RL, Menteer J, Lestz RM, Baxter-Lowe LA. Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches. Biomark Med 2022; 16:401-415. [PMID: 35195028 DOI: 10.2217/bmm-2021-0968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-quality biomarkers that detect emergent graft damage and/or rejection after solid-organ transplantation offer new opportunities to improve post-transplant monitoring, allow early therapeutic intervention and facilitate personalized patient management. Donor-derived cell-free DNA (DD-cfDNA) is a particularly exciting minimally invasive biomarker because it has the potential to be quantitative, time-sensitive and cost-effective. Increased DD-cfDNA has been associated with graft damage and rejection episodes. Efforts are underway to further improve sensitivity and specificity. This review summarizes the procedures used to process and detect DD-cfDNA, measurement of DD-cfDNA in clinical transplantation, approaches for improving sensitivity and specificity and long-term prospects as a transplant biomarker to supplement traditional organ monitoring and invasive biopsies.
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Affiliation(s)
- Rebecca L Edwards
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Cardiology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Rachel M Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Nephrology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Lee Ann Baxter-Lowe
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
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25
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Karabacak NM, Zheng Y, Dubash TD, Burr R, Micalizzi DS, Wittner BS, Lin M, Wiley DF, Comaills V, Emmons E, Niederhoffer KL, Ho U, Ukleja J, Che D, Stowe H, Nieman LT, Haas W, Stott SL, Lawrence MS, Ting DT, Miyamoto DT, Haber DA, Toner M, Maheswaran S. Differential kinase activity across prostate tumor compartments defines sensitivity to target inhibition. Cancer Res 2022; 82:1084-1097. [DOI: 10.1158/0008-5472.can-21-2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/03/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022]
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26
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Rykov SV, Filippova EA, Loginov VI, Braga EA. Gene Methylation in Circulating Cell-Free DNA from the Blood Plasma as Prognostic and Predictive Factor in Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Tieng FYF, Abu N, Nasir SN, Lee LH, Ab Mutalib NS. Liquid Biopsy-Based Colorectal Cancer Screening via Surface Markers of Circulating Tumor Cells. Diagnostics (Basel) 2021; 11:2136. [PMID: 34829483 PMCID: PMC8618170 DOI: 10.3390/diagnostics11112136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is ranked second for cancer-related deaths worldwide with approximately half of the patients being diagnosed at the late stages. The untimely detection of CRC results in advancement to the metastatic stage and nearly 90% of cancer-related deaths. The early detection of CRC is crucial to decrease its overall incidence and mortality rates. The recent introduction of circulating tumor cells (CTCs) has enabled a less invasive sampling method from liquid biopsies, besides revealing key information toward CRC metastasis. The current gold standard for CTC identification is the CellSearch® system (Veridex). This first-generation instrumentation relies on a single cell surface marker (CSM) to capture and count CTCs. Detection of CTCs allows the identification of patients at risk for metastasis, whereas CTC enumeration could improve risk assessment, monitoring of systemic therapy, and detection of therapy resistance in advanced metastatic CRC. In this review, we compared the pros and cons between single CSM-based CTC enrichment techniques and multi-marker-based systems. We also highlighted the challenges faced in the routine implementation of CSM-dependent CTC detection methods in CRC screening, prediction, prognosis, disease monitoring, and therapy selection toward precision medicine, as well as the dwelling on post-CTC analysis and characterization methods.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.); (S.N.N.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.); (S.N.N.)
| | - Siti Nurmi Nasir
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.); (S.N.N.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.); (S.N.N.)
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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28
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Hackshaw A, Cohen SS, Reichert H, Kansal AR, Chung KC, Ofman JJ. Estimating the population health impact of a multi-cancer early detection genomic blood test to complement existing screening in the US and UK. Br J Cancer 2021; 125:1432-1442. [PMID: 34426664 PMCID: PMC8575970 DOI: 10.1038/s41416-021-01498-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multi-cancer early detection (MCED) next-generation-sequencing blood tests represent a potential paradigm shift in screening. METHODS We estimated the impact of screening in the US and UK. We used country-specific parameters for uptake, and test-specific sensitivity and false-positive rates for current screening: breast, colorectal, cervical and lung (US only) cancers. For the MCED test, we used cancer-specific sensitivities by stage. Outcomes included the true-positive:false-positive (TP:FP) ratio; and the cost of diagnostic investigations among screen positives, per cancer detected (Diagcost). Outcomes were estimated for recommended screening only, and then when giving the MCED test to anyone without cancer detected by current screening plus similarly aged adults ineligible for recommended screening. RESULTS In the US, current screening detects an estimated 189,498 breast, cervical, colorectal and lung cancers. An MCED test with 25-100% uptake detects an additional 105,526-422,105 cancers (multiple types). The estimated TP:FP (Diagcost) was 1.43 ($89,042) with current screening but only 1:1.8 ($7060) using an MCED test. For the UK the corresponding estimates were 1:18 (£10,452) for current screening, and 1:1.6 (£2175) using an MCED test. CONCLUSIONS Adding an MCED blood test to recommended screening can potentially be an efficient strategy. Ongoing randomised studies are required for full efficacy and cost-effectiveness evaluations.
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Affiliation(s)
- Allan Hackshaw
- Cancer Research UK & University College London Cancer Trials Centre, London, UK.
| | - Sarah S Cohen
- EpidStrategies, A Division of ToxStrategies, Inc, Cary, NC, USA
| | - Heidi Reichert
- EpidStrategies, A Division of ToxStrategies, Inc, Ann Arbor, MI, USA
| | | | - Karen C Chung
- GRAIL, Inc., 1525 O'Brien Drive, Menlo Park, CA, USA
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29
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Honoré N, Galot R, van Marcke C, Limaye N, Machiels JP. Liquid Biopsy to Detect Minimal Residual Disease: Methodology and Impact. Cancers (Basel) 2021; 13:5364. [PMID: 34771526 PMCID: PMC8582541 DOI: 10.3390/cancers13215364] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
One reason why some patients experience recurrent disease after a curative-intent treatment might be the persistence of residual tumor cells, called minimal residual disease (MRD). MRD cannot be identified by standard radiological exams or clinical evaluation. Tumor-specific alterations found in the blood indirectly diagnose the presence of MRD. Liquid biopsies thus have the potential to detect MRD, allowing, among other things, the detection of circulating tumor DNA (ctDNA), circulating tumor cells (CTC), or tumor-specific microRNA. Although liquid biopsy is increasingly studied, several technical issues still limit its clinical applicability: low sensitivity, poor standardization or reproducibility, and lack of randomized trials demonstrating its clinical benefit. Being able to detect MRD could give clinicians a more comprehensive view of the risk of relapse of their patients and could select patients requiring treatment escalation with the goal of improving cancer survival. In this review, we are discussing the different methodologies used and investigated to detect MRD in solid cancers, their respective potentials and issues, and the clinical impacts that MRD detection will have on the management of cancer patients.
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Affiliation(s)
- Natasha Honoré
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
| | - Rachel Galot
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Cédric van Marcke
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | - Jean-Pascal Machiels
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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30
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Zhang S, Zhang T, Liu H, Zhao J, Zhou H, Su X, Liu X, Li L, Qiu L, Qian Z, Zhou S, Gong W, Meng B, Ren X, He J, Wang X, Zhang H. Tracking the evolution of untreated high-intermediate/high-risk diffuse large B-cell lymphoma by circulating tumour DNA. Br J Haematol 2021; 196:617-628. [PMID: 34664256 DOI: 10.1111/bjh.17894] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/25/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a highly heterogenous malignancy, early identification of patients for relapse remains challenging. The potential to non-invasively monitor tumour evolutionary dynamics of DLBCL needs to be further established. In the present study, 17 tumour biopsy and 38 plasma samples from 38 patients with high-intermediate/high-risk DLBCL were evaluated at baseline. Longitudinal blood samples were also collected during therapy. Circulating tumour DNA (ctDNA) was analysed using targeted sequencing based on a gene panel via a recently developed methodology, circulating single-molecule amplification and re-sequencing technology (cSMART). We found that the most frequently mutated genes were tumour protein p53 (TP53; 42·1%), histone-lysine N-methyltransferase 2D (KMT2D; 28·9%), caspase recruitment domain family member 11 (CARD11; 21·1%), cAMP response element-binding protein binding protein (CREBBP; 15·8%), β2 -microglobulin (B2M; 15·8%), and tumour necrosis factor alpha-induced protein 3 (TNFAIP3; 15·8%). The mutation profiles between ctDNA and matched tumour tissue showed good concordance; however, more mutation sites were detected in ctDNA samples. Either TP53 or B2M mutations before treatment predicted poor prognosis. Analysis of dynamic blood samples confirmed the utility of ctDNA for the real-time assessment of treatment response and revealed that the increases in ctDNA levels and changes in KMT2D mutation status could be useful predictors of disease progression. Our present results suggest that ctDNA is a promising method for the detection of mutation spectrum and serves as a biomarker for disease monitoring and predicting clinical recurrence.
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Affiliation(s)
- Sicong Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Tingting Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Hengqi Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jing Zhao
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | | | | | - Xianming Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lanfang Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lihua Qiu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Zhengzi Qian
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Shiyong Zhou
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Wenchen Gong
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bin Meng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiubao Ren
- Department of Immunology/Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jin He
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
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31
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Malapelle U, Pisapia P, Addeo A, Arrieta O, Bellosillo B, Cardona AF, Cristofanilli M, De Miguel-Perez D, Denninghoff V, Durán I, Jantus-Lewintre E, Nuzzo PV, O'Byrne K, Pauwels P, Pickering EM, Raez LE, Russo A, Serrano MJ, Gandara DR, Troncone G, Rolfo C. Liquid biopsy from research to clinical practice: focus on non-small cell lung cancer. Expert Rev Mol Diagn 2021; 21:1165-1178. [PMID: 34570988 DOI: 10.1080/14737159.2021.1985468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the current era of personalized medicine, liquid biopsy has acquired a relevant importance in patient management of advanced stage non-small cell lung cancer (NSCLC). As a matter of fact, liquid biopsy may supplant the problem of inadequate tissue for molecular testing. The term 'liquid biopsy' refers to a number of different biological fluids, but is most clearly associated with plasma-related platforms. It must be taken into account that pre-analytical processing and the selection of the appropriate technology according to the clinical context may condition the results obtained. In addition, novel clinical applications beyond the evaluation of the molecular status of predictive biomarkers are currently under investigation. AREAS COVERED This review summarizes the available evidence on pre-analytical issues and different clinical applications of liquid biopsies in NSCLC patients. EXPERT OPINION Liquid biopsy should be considered not only as a valid alternative but as complementary to tissue-based molecular approaches. Careful attention should be paid to the optimization and standardization of all phases of liquid biopsy samples management in order to determine a significant improvement in either sensitivity or specificity, while significant reducing the number of 'false negative' or 'false positive' molecular results.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), México City, México
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar, Barcelona, Spain.,Department of Pathology, Ciberonc, Madrid, Spain
| | - Andres F Cardona
- Department of Oncology, Clinical and Translational Oncology Group, Clínica Del Country, Bogotá, Colombia.,Department of Oncology, Foundation for Clinical and Applied Cancer Research (Ficmac), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-g/oncolgroup), Universidad el Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diego De Miguel-Perez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria Denninghoff
- Department of Pathology, University of Buenos Aires - National Council for Scientific and Technical Research (Conicet), Buenos Aires, Argentina
| | - Ignacio Durán
- Department of Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Eloísa Jantus-Lewintre
- Department of Pathology, Ciberonc, Madrid, Spain.,Molecular Oncology Laboratory, Fundación Para La Investigación Del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ken O'Byrne
- Medical Oncology, Princess Alexandra Hospital, Queensland University of Technology, Brisbane City, Australia
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (Core), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (Uantwerp), Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Edward M Pickering
- Divison of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, FL, USA
| | - Alessandro Russo
- Department of Oncology, Medical Oncology Unit, A.O. Papardo, Messina, Italy
| | - Maria José Serrano
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain
| | - David R Gandara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
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Guo Y, Wu D, Zhang X, Zhang K, Luo Y. Biomolecules in cell-derived extracellular vesicle chariots as warriors to repair damaged tissues. NANOSCALE 2021; 13:16017-16033. [PMID: 34570853 DOI: 10.1039/d1nr04999b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this review, we highlight the innovative applications of biomolecules from parent cell-derived extracellular vesicles (EVs) for tissue repair that have been developed in recent years. We evaluate the underlying mechanisms and therapeutic efficacy of each therapy. In previous literature reviews, it was most common to classify the use of EVs in tissue repair by disease type. This article reviews the role of three biomolecules in EVs in tissue repair. This review first summarizes the definitions and classifications of EVs. Then, the importance and significance of treating tissue damage with EVs are discussed. In particular, EV contents for tissue repair are three main types of biomolecules: proteins, RNAs and cell growth factors. The therapeutic and repair mechanisms of the biomolecules are discussed respectively. Finally, the development prospect and potential challenges of EV contents from highly differentiated cells as specific agents for tissue repair are summarized. When EVs are used to treat diseases such as tissue or organ damage, EVs play a role in delivery, and the real repair effect is effected by the various biomolecules carried by EVs. We believe that EV biomolecules have unparalleled advantages and clinical transformation potential for tissue repair and expect this review to inspire more intensive research work in this field.
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Affiliation(s)
- Yingshu Guo
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Di Wu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
| | - Xu Zhang
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China.
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Kothari P, Sauerhaft T, Bouvier N, Rodriguez-Sanchez MI, Shia J, Price A, Morjaria S, Gerstle JT, Shukla NN, Ortiz MV. Identification of a TP53 Deletion in an Undifferentiated Embryonal Sarcoma of the Liver Provides Clinically Relevant Longitudinal Detection of Circulating Tumor DNA. JCO Precis Oncol 2021; 5:PO.21.00102. [PMID: 34527851 PMCID: PMC8437221 DOI: 10.1200/po.21.00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 07/30/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Talia Sauerhaft
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita Price
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sejal Morjaria
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J Theodore Gerstle
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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Krasic J, Abramovic I, Vrtaric A, Nikolac Gabaj N, Kralik-Oguic S, Katusic Bojanac A, Jezek D, Sincic N. Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics. Front Cell Dev Biol 2021; 9:686149. [PMID: 34552921 PMCID: PMC8451956 DOI: 10.3389/fcell.2021.686149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/13/2021] [Indexed: 01/18/2023] Open
Abstract
While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Sasa Kralik-Oguic
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Clinical Institute of Laboratory Diagnostics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
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Xu Y, Jiang Y, Yu M, Lou J, Song M, Xu H, Cui Y, Zeng X, Wang Q, Ma H, Wang Z, Zhu S, Li G, Zhao A. Meta-Analysis of the Diagnostic Value of Cell-free DNA for Renal Cancer. Front Mol Biosci 2021; 8:683844. [PMID: 34458320 PMCID: PMC8385273 DOI: 10.3389/fmolb.2021.683844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Cell-free DNA (cf-DNA) has been reported to represent a suitable material for liquid biopsy in the diagnosis and prognosis of various cancers. We performed a meta-analysis of published data to investigate the diagnostic value of cf-DNA for renal cancer (RCa). Systematic searches were conducted using Pubmed, Embase databases, Web of Science, Medline and Cochrane Library to identify relevant publications until the 31st March 2021. For all patients, we evaluated the true diagnostic value of cf-DNA by calculating the number of true positive, false positive, true negative, and false negative, diagnoses by extracting specificity and sensitivity data from the selected literature. In total, 8 studies, featuring 754 RCa patients, and 355 healthy controls, met our inclusion criteria. The overall diagnostic sensitivity and specificity for cf-DNA was 0.71 (95% confidence interval (CI), 0.55–0.83) and 0.79 (95% CI, 0.66–0.88), respectively. The pooled positive likelihood ratio and pooled negative likelihood ratio were 3.42 (95% CI, 2.04–5.72) and 0.36 (95% CI, 0.23–0.58), respectively. The area under the summary receiver operating characteristic curve was 0.82 (95% CI, 0.79–0.85), and the diagnostic odds ratio was 7.80 (95% CI, 4.40–13.85). Collectively, our data demonstrate that cf-DNA has high specificity and sensitivity for diagnosing RCa. Therefore, cf-DNA is a useful biomarker for the diagnosis of RCa.
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Affiliation(s)
- Yipeng Xu
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzho, China
| | - Yingjun Jiang
- Hangzhou Traditional Chinese Medicine Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Mingke Yu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianmin Lou
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Mei Song
- Department of Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China
| | - Han Xu
- Central Research Laboratory, Children's Hospital of Nanchang University, Hangzhou, China
| | - Yingying Cui
- Translational Radiation Oncology Research Laboratory, Department of Radiooncology and Radiotherapy, Charite University Hospital, Berlin, Germany
| | - Xiaowei Zeng
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzho, China.,Hangzhou Traditional Chinese Medicine Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qibo Wang
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzho, China
| | - Hanyun Ma
- Comprehensive Cancer Center, Charité Universitätsmedizin, Berlin, Germany
| | - Zongping Wang
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzho, China
| | - Shaoxing Zhu
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzho, China
| | - Guorong Li
- Department of Urology, North Hospital, University of Jean-Monnet, Saint-Etienne, France
| | - An Zhao
- Experimental Research Center, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China
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Lin C, Liu X, Zheng B, Ke R, Tzeng CM. Liquid Biopsy, ctDNA Diagnosis through NGS. Life (Basel) 2021; 11:life11090890. [PMID: 34575039 PMCID: PMC8468354 DOI: 10.3390/life11090890] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsy with circulating tumor DNA (ctDNA) profiling by next-generation sequencing holds great promise to revolutionize clinical oncology. It relies on the basis that ctDNA represents the real-time status of the tumor genome which contains information of genetic alterations. Compared to tissue biopsy, liquid biopsy possesses great advantages such as a less demanding procedure, minimal invasion, ease of frequent sampling, and less sampling bias. Next-generation sequencing (NGS) methods have come to a point that both the cost and performance are suitable for clinical diagnosis. Thus, profiling ctDNA by NGS technologies is becoming more and more popular since it can be applied in the whole process of cancer diagnosis and management. Further developments of liquid biopsy ctDNA testing will be beneficial for cancer patients, paving the way for precision medicine. In conclusion, profiling ctDNA with NGS for cancer diagnosis is both biologically sound and technically convenient.
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Affiliation(s)
- Chen Lin
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Xuzhu Liu
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Bingyi Zheng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
- Correspondence: (R.K.); (C.-M.T.)
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
- Correspondence: (R.K.); (C.-M.T.)
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Kojadinovic A, Laderian B, Mundi PS. Targeting TRK: A fast-tracked application of precision oncology and future directions. Crit Rev Oncol Hematol 2021; 165:103451. [PMID: 34389458 DOI: 10.1016/j.critrevonc.2021.103451] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/14/2022] Open
Abstract
The NTRK genes encode the tropomyosin-related receptor tyrosine kinases TrkA, TrkB and TrkC. TRK receptors regulate the proliferation, differentiation, and survival of many neuronal and non-neuronal glial cells during embryogenesis, thus playing a critical role in synaptic plasticity and the development of nociceptive pathways. Recurrent genomic alterations in NTRK genes, typically fusions involving the 3' region encoding the kinase domain juxtaposed to 5' sequences from numerous partner genes, occur at a low frequency in a wide diversity of adult and pediatric cancers. The contributions of the resulting constitutively activated kinase to oncogenesis and cancer progression are being elucidated. Larotrectinib and entrectinib are potent first-generation TRK inhibitors with IC50 values in the nanomolar range across cancer cell lines harboring NTRK fusions. Larotrectinib is highly selective for TRK receptors, whereas entrectinib also potently inhibits ROS1 and ALK. Clinical trials of both drugs demonstrated significant and durable responses in patients with tumors harboring NTRK alterations, leading to first of its kind cancer agnostic FDA approvals in the United States for drugs targeting a genomic alteration. Unfortunately, acquired resistance inevitably develops. The second-generation TRK inhibitors selitrectinib and repotrectinib are designed to overcome known mechanisms of resistance.
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Affiliation(s)
- Arsenije Kojadinovic
- Icahn School of Medicine at Mount Sinai, United States; James J. Peters VA Medical Center, United States
| | | | - Prabhjot S Mundi
- James J. Peters VA Medical Center, United States; Columbia University Irving Medical Center, United States.
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38
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Voss T, Ullius A, Schönborn M, Oelmüller U. Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal. PLoS One 2021; 16:e0253401. [PMID: 34228726 PMCID: PMC8260181 DOI: 10.1371/journal.pone.0253401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.
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Affiliation(s)
- Thorsten Voss
- R&D Department, QIAGEN GmbH, Hilden, Germany
- * E-mail:
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39
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Gonzalez D, Mateo J, Stenzinger A, Rojo F, Shiller M, Wyatt AW, Penault‐Llorca F, Gomella LG, Eeles R, Bjartell A. Practical considerations for optimising homologous recombination repair mutation testing in patients with metastatic prostate cancer. J Pathol Clin Res 2021; 7:311-325. [PMID: 33630412 PMCID: PMC8185363 DOI: 10.1002/cjp2.203] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 01/07/2023]
Abstract
Analysis of the genomic landscape of prostate cancer has identified different molecular subgroups with relevance for novel or existing targeted therapies. The recent approvals of the poly(ADP-ribose) polymerase (PARP) inhibitors olaparib and rucaparib in the metastatic castration-resistant prostate cancer (mCRPC) setting signal the need to embed molecular diagnostics in the clinical pathway of patients with mCRPC to identify those who can benefit from targeted therapies. Best practice guidelines in overall biospecimen collection and processing for molecular analysis are widely available for several tumour types. However, there is no standard protocol for molecular diagnostic testing in prostate cancer. Here, we provide a series of recommendations on specimen handling, sample pre-analytics, laboratory workflow, and testing pathways to maximise the success rates for clinical genomic analysis in prostate cancer. Early involvement of a multidisciplinary team of pathologists, urologists, oncologists, radiologists, nurses, molecular scientists, and laboratory staff is key to enable optimal workflow for specimen selection and preservation at the time of diagnosis so that samples are available for molecular analysis when required. Given the improved outcome of patients with mCRPC and homologous recombination repair gene alterations who have been treated with PARP inhibitors, there is an urgent need to incorporate high-quality genomic testing in the routine clinical pathway of these patients.
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Affiliation(s)
- David Gonzalez
- Patrick G Johnston Centre for Cancer ResearchQueen's UniversityBelfastUK
| | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology (VHIO)Vall d'Hebron University HospitalBarcelonaSpain
| | | | - Federico Rojo
- Department of PathologyIIS‐Hospital Universitario Fundación Jiménez Díaz‐CIBERONCMadridSpain
| | - Michelle Shiller
- Department of PathologyBaylor University Medical CenterDallasTXUSA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Frédérique Penault‐Llorca
- Centre Jean PerrinUniversité Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies ThéranostiquesClermont FerrandFrance
| | - Leonard G Gomella
- Department of Urology, Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Ros Eeles
- Division of Genetics and EpidemiologyThe Institute of Cancer Research and The Royal Marsden NHS Foundation TrustLondonUK
| | - Anders Bjartell
- Division of Urological Cancers, Department of Translational MedicineLund UniversityLundSweden
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40
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Deepak Singh D, Han I, Choi EH, Yadav DK. CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer. Comput Struct Biotechnol J 2021; 19:2384-2397. [PMID: 34025931 PMCID: PMC8120801 DOI: 10.1016/j.csbj.2021.04.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women at the global level and the highest mortality rate has been observed with triple-negative breast cancer (TNBC). Accumulation of genetic lesions an aberrant gene expression and protein degradation are considered to underlie the onset of tumorigenesis and metastasis. Therefore, the challenge to identify the genes and molecules that could be potentially used as potent biomarkers for personalized medicine against TNBC with minimal or no associated side effects. Discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) arrangement and an increasing repertoire of its new variants has provided a much-needed fillip towards editing TNBC genomes. In this review, we discuss the CRISPR/Cas9 genome editing, CRISPR Technology for diagnosis of (Triple-negative breast cancer) TNBC, Drug Resistance, and potential applications of CRISPR/Cas9 and its variants in deciphering or engineering intricate molecular and epigenetic mechanisms associated with TNBC. Furthermore, we have also explored the TNBC and CRISPR/Cas9 genome editing potential for repairing, genetic modifications in TNBC.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon City, Republic of Korea
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41
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Omics in Seminal Plasma: An Effective Strategy for Predicting Sperm Retrieval Outcome in Non-obstructive Azoospermia. Mol Diagn Ther 2021; 25:315-325. [PMID: 33860468 DOI: 10.1007/s40291-021-00524-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
Non-obstructive azoospermia (NOA) is a severe form of male factor infertility resulting from the impairment of sperm production. Surgical sperm retrieval followed by intracytoplasmic sperm injection (ICSI) is the only alternative for NOA patients to have their own genetic children. Nevertheless, due to an approximately 50% chance of success, harvesting sperm from these patients remains challenging. Thus, discovering noninvasive biomarkers, which are able to reliably predict the probability of sperm acquisition, not only can eliminate the risk of surgery but also can lower the costs of NOA diagnosis and treatment. Seminal plasma is the non-cellular and liquid portion of the ejaculate that consists of the secretions originating from testes and male accessory glands. In past years, a wide range of biomolecules including DNAs, RNAs, proteins, and metabolic intermediates have been identified by omics techniques in human seminal plasma. The current review aimed to briefly describe genomic, transcriptomic, proteomic, and metabolomic profiles of human seminal plasma in an attempt to introduce potential candidate noninvasive biomarkers for sperm-retrieval success in men with NOA.
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42
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Liu L, Chen X, Wong KC. Early Cancer Detection from Genome-wide Cell-free DNA Fragmentation via Shuffled Frog Leaping Algorithm and Support Vector Machine. Bioinformatics 2021; 37:3099-3105. [PMID: 33837381 DOI: 10.1093/bioinformatics/btab236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/19/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Early cancer detection is significant for the patient mortality rate reduction. Although machine learning has been widely employed in that context, there are still deficiencies. In this work, we studied different machine learning algorithms for early cancer detection and proposed an Adaptive Support Vector Machine (ASVM) method by synergizing Shuffled Frog Leaping Algorithm (SFLA) and Support Vector Machine (SVM) in this paper. RESULTS As ASVM regulates SVM for parameter adaption based on data characteristics, the experimental results demonstrated the robust generalization capability of ASVM on different datasets under different settings; for instance, ASVM can enhance the sensitivity by over 10% for early cancer detection compared with SVM. Besides, our proposed ASVM outperformed Grid Search + SVM and Random Search + SVM by significant margins in terms of the area under the ROC curve (AUC) (0.938 vs. 0.922 vs. 0.921). AVAILABILITY The proposed algorithm and dataset are available at https://github.com/ElaineLIU-920/ASVM-for-Early-Cancer-Detection. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Linjing Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
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43
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Tieng FYF, Abu N, Lee LH, Ab Mutalib NS. Microsatellite Instability in Colorectal Cancer Liquid Biopsy-Current Updates on Its Potential in Non-Invasive Detection, Prognosis and as a Predictive Marker. Diagnostics (Basel) 2021; 11:544. [PMID: 33803882 PMCID: PMC8003257 DOI: 10.3390/diagnostics11030544] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly-diagnosed cancer in the world and ranked second for cancer-related mortality in humans. Microsatellite instability (MSI) is an indicator for Lynch syndrome (LS), an inherited cancer predisposition, and a prognostic marker which predicts the response to immunotherapy. A recent trend in immunotherapy has transformed cancer treatment to provide medical alternatives that have not existed before. It is believed that MSI-high (MSI-H) CRC patients would benefit from immunotherapy due to their increased immune infiltration and higher neo-antigenic loads. MSI testing such as immunohistochemistry (IHC) and PCR MSI assay has historically been a tissue-based procedure that involves the testing of adequate tissue with a high concentration of cancer cells, in addition to the requirement for paired normal tissues. The invasive nature and specific prerequisite of such tests might hinder its application when surgery is not an option or when the tissues are insufficient. The application of next-generation sequencing, which is highly sensitive, in combination with liquid biopsy, therefore, presents an interesting possibility worth exploring. This review aimed to discuss the current body of evidence supporting the potential of liquid biopsy as a tool for MSI testing in CRC.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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44
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Asrat T, Cho W, Liu FA, Shapiro SM, Bracht JR, Zestos AG. Direct Detection of DNA and RNA on Carbon Fiber Microelectrodes Using Fast-Scan Cyclic Voltammetry. ACS OMEGA 2021; 6:6571-6581. [PMID: 33748569 PMCID: PMC7970473 DOI: 10.1021/acsomega.0c04845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 02/18/2021] [Indexed: 05/04/2023]
Abstract
DNA and RNA have been measured with many techniques but often with relatively long analysis times. In this study, we utilize fast-scan cyclic voltammetry (FSCV) for the subsecond codetection of adenine, guanine, and cytosine, first as free nucleosides, and then within custom synthesized oligos, plasmid DNA, and RNA from the nematode Caenorhabditis elegans. Previous studies have shown the detection of adenosine and guanosine with FSCV with high spatiotemporal resolution, while we have extended the assay to include cytidine and adenine, guanine, and cytosine in RNA and single- and double-stranded DNA (ssDNA and dSDNA). We find that FSCV testing has a higher sensitivity and yields higher peak oxidative currents when detecting shorter oligonucleotides and ssDNA samples at equivalent nucleobase concentrations. This is consistent with an electrostatic repulsion from negatively charged oxide groups on the surface of the carbon fiber microelectrode (CFME), the negative holding potential, and the negatively charged phosphate backbone. Moreover, as opposed to dsDNA, ssDNA nucleobases are not hydrogen-bonded to one another and thus are free to adsorb onto the surface of the carbon electrode. We also demonstrate that the simultaneous determination of nucleobases is not masked even in biologically complex serum samples. This is the first report demonstrating that FSCV, when used with CFMEs, is able to codetect nucleobases when polymerized into DNA or RNA and could potentially pave the way for future uses in clinical, diagnostic, or research applications.
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Affiliation(s)
- Thomas
M. Asrat
- Department
of Chemistry, American University, Washington, D.C. 20016, United States
| | - Whirang Cho
- Department
of Chemistry, American University, Washington, D.C. 20016, United States
| | - Favian A. Liu
- Department
of Chemistry, American University, Washington, D.C. 20016, United States
| | - Sarah M. Shapiro
- Department
of Biology, American University, Washington, D.C. 20016, United States
| | - John R. Bracht
- Department
of Biology, American University, Washington, D.C. 20016, United States
| | - Alexander G. Zestos
- Department
of Chemistry, American University, Washington, D.C. 20016, United States
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45
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Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
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Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
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46
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Keup C, Suryaprakash V, Storbeck M, Hoffmann O, Kimmig R, Kasimir-Bauer S. Longitudinal Multi-Parametric Liquid Biopsy Approach Identifies Unique Features of Circulating Tumor Cell, Extracellular Vesicle, and Cell-Free DNA Characterization for Disease Monitoring in Metastatic Breast Cancer Patients. Cells 2021; 10:212. [PMID: 33494385 PMCID: PMC7912374 DOI: 10.3390/cells10020212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Dynamics of mRNA from circulating tumor cells (CTCs), mRNA from extracellular vesicles (EVs), and cell-free DNA (cfDNA) were assessed to examine the relevance of a longitudinal multi-parametric liquid biopsy strategy. Eighteen milliliters of blood was drawn from 27 hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) patients at disease progression and at two subsequent radiologic staging time points. CTC mRNA and EV mRNA were analyzed using multi-marker qPCR, and cfDNA was analyzed using targeted next-generation sequencing (NGS). The presence of ERBB2 or ERBB3 overexpression signals in CTCs significantly correlated with disease progression (87% specificity, 36% sensitivity, p-value = 0.023), and the presence of either ERBB3 signals in CTCs or EVs or cfDNA variants in ERBB3 also showed a significant association with progressive MBC. Fluctuations during treatment were detected in the EV fraction with the appearance of hitherto undetected ERCC1 signals correlating with progressive disease (97% specificity, 18% sensitivity, p-value = 0.030). Allele frequency development of ESR1 and PIK3CA variants detected at subsequent staging time points could be used as a predictor for therapy success and, importantly, might help guide therapy decisions. The three analytes, each with their own unique features for disease monitoring, were shown to be complementary, underlining the usefulness of the longitudinal multi-parametric liquid biopsy approach.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | | | | | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
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47
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Hu Z, Chen H, Long Y, Li P, Gu Y. The main sources of circulating cell-free DNA: Apoptosis, necrosis and active secretion. Crit Rev Oncol Hematol 2021; 157:103166. [DOI: 10.1016/j.critrevonc.2020.103166] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/05/2023] Open
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48
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Wang Y, Wang Y, Guo C, Xie X, Liang S, Zhang R, Pang W, Huang L. Cancer genotypes prediction and associations analysis from imaging phenotypes: a survey on radiogenomics. Biomark Med 2020; 14:1151-1164. [PMID: 32969248 DOI: 10.2217/bmm-2020-0248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this paper, we present a survey on the progress of radiogenomics research, which predicts cancer genotypes from imaging phenotypes and investigates the associations between them. First, we present an overview of the popular technology modalities for obtaining diagnostic medical images. Second, we summarize recently used methodologies for radiogenomics analysis, including statistical analysis, radiomics and deep learning. And then, we give a survey on the recent research based on several types of cancers. Finally, we discuss these studies and propose possible future research directions. In conclusion, we have identified strong correlations between cancer genotypes and imaging phenotypes. In addition, with the rapid growth of medical data, deep learning models show great application potential for radiogenomics.
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Affiliation(s)
- Yao Wang
- Key Laboratory of Symbol Computation & Knowledge Engineering, Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, 130012, PR China
| | - Yan Wang
- Key Laboratory of Symbol Computation & Knowledge Engineering, Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, 130012, PR China.,School of Artificial Intelligence, Jilin University, Changchun 130012, PR China
| | - Chunjie Guo
- Department of Radiology, The First Hospital of Jilin University, Changchun 130012, PR China
| | - Xuping Xie
- Key Laboratory of Symbol Computation & Knowledge Engineering, Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, 130012, PR China
| | - Sen Liang
- State Key Lab of CAD & CG, Zhejiang University, Hangzhou 310058, PR China
| | - Ruochi Zhang
- School of Artificial Intelligence, Jilin University, Changchun 130012, PR China
| | - Wei Pang
- School of Mathematical & Computer Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Lan Huang
- Key Laboratory of Symbol Computation & Knowledge Engineering, Ministry of Education, College of Computer Science & Technology, Jilin University, Changchun, 130012, PR China.,Zhuhai Laboratory of Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Department of Computer Science & Technology, Zhuhai College of Jilin University, Zhuhai 519041, China
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49
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Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
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Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
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50
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Mentis AFA, Grivas PD, Dardiotis E, Romas NA, Papavassiliou AG. Circulating tumor cells as Trojan Horse for understanding, preventing, and treating cancer: a critical appraisal. Cell Mol Life Sci 2020; 77:3671-3690. [PMID: 32333084 PMCID: PMC11104835 DOI: 10.1007/s00018-020-03529-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/29/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Circulating tumor cells (CTCs) are regarded as harbingers of metastases. Their ability to predict response to therapy, relapse, and resistance to treatment has proposed their value as putative diagnostic and prognostic indicators. CTCs represent one of the zeniths of cancer evolution in terms of cell survival; however, the triggers of CTC generation, the identification of potentially metastatic CTCs, and the mechanisms contributing to their heterogeneity and aggressiveness represent issues not yet fully deciphered. Thus, prior to enabling liquid biopsy applications to reach clinical prime time, understanding how the above mechanistic information can be applied to improve treatment decisions is a key challenge. Here, we provide our perspective on how CTCs can provide mechanistic insights into tumor pathogenesis, as well as on CTC clinical value. In doing so, we aim to (a) describe how CTCs disseminate from the primary tumor, and their link to epithelial-mesenchymal transition (EMT); (b) trace the route of CTCs through the circulation, focusing on tumor self-seeding and the possibility of tertiary metastasis; (c) describe possible mechanisms underlying the enhanced metastatic potential of CTCs; (d) discuss how CTC could provide further information on the tissue of origin, especially in cancer of unknown primary origin. We also provide a comprehensive review of meta-analyses assessing the prognostic significance of CTCs, to highlight the emerging role of CTCs in clinical oncology. We also explore how cell-free circulating tumor DNA (ctDNA) analysis, using a combination of genomic and phylogenetic analysis, can offer insights into CTC biology, including our understanding of CTC heterogeneity and tumor evolution. Last, we discuss emerging technologies, such as high-throughput quantitative imaging, radiogenomics, machine learning approaches, and the emerging breath biopsy. These technologies could compliment CTC and ctDNA analyses, and they collectively represent major future steps in cancer detection, monitoring, and management.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
- Department of Microbiology, University Hospital of Thessaly, Larissa, Greece
| | - Petros D Grivas
- Division of Oncology, Department of Medicine, University of Washington School of Medicine, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Nicholas A Romas
- Department of Urology, Columbia University Medical Center, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street-Bldg. 16, 11527, Athens, Greece.
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