1
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [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: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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2
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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3
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Tong S, Ye L, Xu Y, Sun Q, Gao L, Cai J, Ye Z, Tian D, Chen Q. IRF2-ferroptosis related gene is associated with prognosis and EMT in gliomas. Transl Oncol 2022; 26:101544. [PMID: 36156371 PMCID: PMC9508157 DOI: 10.1016/j.tranon.2022.101544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/20/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022] Open
Abstract
Ferroptosis is a new type of programmed cell death that has excellent anti-tumor potential in different tumors. However, the research on ferroptosis in glioma is still incomplete. In this study, we aimed to revealed the relationship between ferroptosis-related genes (FRGs) and glioma. We collected gene expression profiles of glioma patients from the TCGA and CGGA databases. All glioma samples were classified into five subtypes using the R software ConsensusClusterPlus. Subsequently, we performed single sample gene set enrichment analysis (ssGSEA) to explore the correlation between different subtypes and immune status and ferroptosis. Then co-expression modules were constructed via weighted gene co-expression network analysis (WGCNA). A Gene Ontology (GO) analysis was conducted to analyze the potential biological functions of the genes in the modules. Finally, we identified 10 hub genes using the PPI network. The in vitro experiments were used to validate our predictions. We found that the expression level of IRF2 is positively correlated with the grade of glioma. The overexpression of IRF2 could protect glioma cells from ferroptosis and enhance the invasive and migratory abilities. Silence of IRF2 had the opposite effect. In conclusion, we demonstrated a novel ferroptosis-related signature for predicting prognosis, and IRF2 could be a potential biomarker for diagnosis and treatment in glioma.
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Affiliation(s)
- Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liguo Ye
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qian Sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jiayang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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5
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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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Frederico SC, Darling C, Zhang X, Huq S, Agnihotri S, Gardner PA, Snyderman CH, Wang EW, Zenonos GA. Circulating tumor DNA – A potential aid in the management of chordomas. Front Oncol 2022; 12:1016385. [PMID: 36338734 PMCID: PMC9632974 DOI: 10.3389/fonc.2022.1016385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Chordomas are a locally invasive, low-grade, CNS malignancy that are primarily found in the skull base, spine, and sacrum. They are thought to be derived from notochordal remnants and remain a significant clinical challenge due to their local invasiveness, resistance to chemoradiation, and difficulty in achieving a complete resection. Adjuvant therapy such as proton beam therapy is critical in preventing recurrence in patients who are at high risk, however this treatment is associated with increased risk of complication. Currently, intraoperative observation and imaging findings are used to determine recurrence and success of gross total resection. These methods can be unreliable due to limited operative view, bony and soft tissue involvement, and complex post-operative changes on MRI. Earlier detection of incomplete resection or recurrence will allow for earlier ability to intervene and potentially improve patient outcomes. Circulating-tumor DNA (ctDNA) is cell-free DNA that is released by tumor cells as they undergo cellular turn-over. Monitoring ctDNA has been shown to be more sensitive at predicting residual tumor than imaging in numerous solid malignancies. Furthermore, ctDNA could be detected earlier in peripheral blood as opposed to imaging changes, allowing for earlier intervention. In this review, we intend to give a brief overview of the current state of molecular diagnosis for skull base chordomas. We will then discuss current advances in the utilization of ctDNA for the management of CNS pathologies such as glioblastoma (GBM) and brain metastases. We will also discuss the role ctDNA has in the management of non-CNS pathologies such as osteosarcoma and Ewing sarcoma (EWS). Finally, we will discuss potential implications of ctDNA monitoring for chordoma management.
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Affiliation(s)
- Stephen C. Frederico
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Corbin Darling
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xiaoran Zhang
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sakibul Huq
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Paul A. Gardner
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carl H. Snyderman
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eric W. Wang
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Georgios A. Zenonos
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Georgios A. Zenonos,
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MGMT and Whole-Genome DNA Methylation Impacts on Diagnosis, Prognosis and Therapy of Glioblastoma Multiforme. Int J Mol Sci 2022; 23:ijms23137148. [PMID: 35806153 PMCID: PMC9266959 DOI: 10.3390/ijms23137148] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic changes in DNA methylation contribute to the development of many diseases, including cancer. In glioblastoma multiforme, the most prevalent primary brain cancer and an incurable tumor with a median survival time of 15 months, a single epigenetic modification, the methylation of the O6-Methylguanine-DNA Methyltransferase (MGMT) gene, is a valid biomarker for predicting response to therapy with alkylating agents and also, independently, prognosis. More recently, the progress from single gene to whole-genome analysis of DNA methylation has allowed a better subclassification of glioblastomas. Here, we review the clinically relevant information that can be obtained by studying MGMT gene and whole-genome DNA methylation changes in glioblastomas, also highlighting benefits, including those of liquid biopsy, and pitfalls of the different detection methods. Finally, we discuss how changes in DNA methylation, especially in glioblastomas bearing mutations in the Isocitrate Dehydrogenase (IDH) 1 and 2 genes, can be exploited as targets for tailoring therapy.
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8
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Mukherkjee D, Saha P, Kaplun D, Sinitca A, Sarkar R. Brain tumor image generation using an aggregation of GAN models with style transfer. Sci Rep 2022; 12:9141. [PMID: 35650252 PMCID: PMC9160042 DOI: 10.1038/s41598-022-12646-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 05/11/2022] [Indexed: 12/21/2022] Open
Abstract
In the recent past, deep learning-based models have achieved tremendous success in computer vision-related tasks with the help of large-scale annotated datasets. An interesting application of deep learning is synthetic data generation, especially in the domain of medical image analysis. The need for such a task arises due to the scarcity of original data. Class imbalance is another reason for applying data augmentation techniques. Generative Adversarial Networks (GANs) are beneficial for synthetic image generation in various fields. However, stand-alone GANs may only fetch the localized features in the latent representation of an image, whereas combining different GANs might understand the distributed features. To this end, we have proposed AGGrGAN, an aggregation of three base GAN models-two variants of Deep Convolutional Generative Adversarial Network (DCGAN) and a Wasserstein GAN (WGAN) to generate synthetic MRI scans of brain tumors. Further, we have applied the style transfer technique to enhance the image resemblance. Our proposed model efficiently overcomes the limitation of data unavailability and can understand the information variance in multiple representations of the raw images. We have conducted all the experiments on the two publicly available datasets - the brain tumor dataset and the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset. Results show that the proposed model can generate fine-quality images with maximum Structural Similarity Index Measure (SSIM) scores of 0.57 and 0.83 on the said two datasets.
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Affiliation(s)
- Debadyuti Mukherkjee
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
| | - Pritam Saha
- Department of Electrical Engineering, Jadavpur University, Kolkata, 700032, India
| | - Dmitry Kaplun
- Department of Automation and Control Processes, Saint Petersburg Electrotechnical University "LETI", Saint Petersburg, 197022, Russian Federation.
| | - Aleksandr Sinitca
- Department of Automation and Control Processes, Saint Petersburg Electrotechnical University "LETI", Saint Petersburg, 197022, Russian Federation
| | - Ram Sarkar
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
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9
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McMahon JT, Studer M, Ulrich B, Revuelta Barbero JM, Pradilla I, Palacios-Ariza MA, Pradilla G. Circulating Tumor DNA in Adults With Glioma: A Systematic Review and Meta-Analysis of Biomarker Performance. Neurosurgery 2022; 91:231-238. [PMID: 35535984 DOI: 10.1227/neu.0000000000001982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/05/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a promising noninvasive biomarker to capture tumor genetics in patients with brain tumors. Research into its clinical utility, however, has not been standardized because the sensitivity and specificity of ctDNA remain undefined. OBJECTIVE To (1) review the primary literature about ctDNA in adults with glioma to compare the sensitivity and specificity of ctDNA in the cerebrospinal fluid vs the plasma and (2) to evaluate the effect of tumor grade on detection of ctDNA. METHODS PRISMA-guided systematic review and meta-analysis was performed using published studies that assessed ctDNA in either plasma or cerebrospinal fluid among adult patients with confirmed glioma. Summary receiver operating characteristic curves were generated using the Rücker-Schumacher method, and area under the curve (AUC) was calculated. RESULTS Meta-analysis revealed improved biomarker performance for CSF (AUC = 0.947) vs plasma (AUC = 0.741) ctDNA, although this did not reach statistical significance (P = .141). Qualitative analysis revealed greater sensitivities among single-allele PCR and small, targeted next-generation sequencing panels compared with broader panels. It additionally demonstrated higher sensitivity of ctDNA detection in high-grade vs low-grade gliomas, although these analyses were limited by a lack of specificity reporting in many studies. CONCLUSION ctDNA seems to be a highly sensitive and specific noninvasive biomarker among adults with gliomas. To maximize its performance, CSF should be studied with targeted genetic analysis platforms, particularly in high-grade gliomas. Further studies on ctDNA are needed to define its clinical utility in diagnosis, prognostication, glioblastoma pseudoprogression, and other scenarios wherein neoadjuvant therapies may be considered.
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Affiliation(s)
| | - Matthew Studer
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bryan Ulrich
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Ivan Pradilla
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Gustavo Pradilla
- Department of Neurosurgery, Emory University, Atlanta, Georgia, USA
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10
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Bonosi L, Ferini G, Giammalva GR, Benigno UE, Porzio M, Giovannini EA, Musso S, Gerardi RM, Brunasso L, Costanzo R, Paolini F, Graziano F, Scalia G, Umana GE, Di Bonaventura R, Sturiale CL, Iacopino DG, Maugeri R. Liquid Biopsy in Diagnosis and Prognosis of High-Grade Gliomas; State-of-the-Art and Literature Review. Life (Basel) 2022; 12:life12030407. [PMID: 35330158 PMCID: PMC8950809 DOI: 10.3390/life12030407] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022] Open
Abstract
Gliomas, particularly high-grade gliomas, represent the most common and aggressive tumors of the CNS and are still burdened by high mortality and a very poor prognosis, regardless of the type of therapy. Their diagnosis and monitoring rely on imaging techniques and direct biopsy of the pathological tissue; however, both procedures have inherent limitations. To address these limitations, liquid biopsies have been proposed in this field. They could represent an innovative tool that could help clinicians in the early diagnosis, monitoring, and prognosis of these tumors. Furthermore, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost, with improved accuracy, providing a molecular profile of cancer and leading to better survival results and less disease burden. This paper focuses on the current clinical application of liquid biopsy in the early diagnosis and prognosis of cancer, introduces NGS-related methods, reviews recent progress, and summarizes challenges and future perspectives.
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Affiliation(s)
- Lapo Bonosi
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
- Correspondence: ; Tel.: +39-0916554656
| | - Gianluca Ferini
- Department of Radiation Oncology, REM Radioterapia srl, 95125 Catania, Italy;
| | - Giuseppe Roberto Giammalva
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Umberto Emanuele Benigno
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Massimiliano Porzio
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Evier Andrea Giovannini
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Sofia Musso
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Rosa Maria Gerardi
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Lara Brunasso
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Roberta Costanzo
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Federica Paolini
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Francesca Graziano
- Unit of Neurosurgery, Garibaldi Hospital, 95124 Catania, Italy; (F.G.); (G.S.)
| | - Gianluca Scalia
- Unit of Neurosurgery, Garibaldi Hospital, 95124 Catania, Italy; (F.G.); (G.S.)
| | - Giuseppe Emmanuele Umana
- Trauma Center, Gamma Knife Center, Department of Neurosurgery, Cannizzaro Hospital, 95125 Catania, Italy;
| | - Rina Di Bonaventura
- Department of Neurosurgery, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (R.D.B.); (C.L.S.)
| | - Carmelo Lucio Sturiale
- Department of Neurosurgery, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (R.D.B.); (C.L.S.)
| | - Domenico Gerardo Iacopino
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Rosario Maugeri
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
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Mettler E, Fottner C, Bakhshandeh N, Trenkler A, Kuchen R, Weber MM. Quantitative Analysis of Plasma Cell-Free DNA and Its DNA Integrity and Hypomethylation Status as Biomarkers for Tumor Burden and Disease Progression in Patients with Metastatic Neuroendocrine Neoplasias. Cancers (Basel) 2022; 14:cancers14041025. [PMID: 35205773 PMCID: PMC8870292 DOI: 10.3390/cancers14041025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Neuroendocrine neoplasias (NEN) are a heterogeneous group of frequent slow-progressing malignant tumors for which a reliable marker for tumor relapse and progression is still lacking. Previously, circulating cell-free DNA and its global methylation status and fragmentation rate have been proposed to be valuable prognostic tumor markers in a variety of malignancies. In the current study, we compared plasma cell-free DNA (cfDNA) properties of NEN patients with a healthy control group and a group of surgically cured patients. Our results revealed significantly higher plasma cfDNA concentrations with increased fragmentation and hypomethylation in patients with advanced metastatic NEN, which was strongly associated with tumor load and could help to differentiate between metastasized disease and presumably cured patients. This suggests that the combined analysis of plasma cfDNA characteristics is a potent and sensitive prognostic and therapeutic biomarker for tumor burden and disease progression in patients with neuroendocrine neoplasias. Abstract Background: Neuroendocrine neoplasia (NEN) encompasses a diverse group of malignancies marked by histological heterogeneity and highly variable clinical outcomes. Apart from Chromogranin A, specific biomarkers predicting residual tumor disease, tumor burden, and disease progression in NEN are scant. Thus, there is a strong clinical need for new and minimally invasive biomarkers that allow for an evaluation of the prognosis, clinical course, and response to treatment of NEN patients, thereby helping implement individualized treatment decisions in this heterogeneous group of patients. In the current prospective study, we evaluated the role of plasma cell-free DNA concentration and its global hypomethylation and fragmentation as possible diagnostic and prognostic biomarkers in patients with neuroendocrine neoplasias. Methods: The plasma cfDNA concentration, cfDNA Alu hypomethylation, and LINE-1 cfDNA integrity were evaluated prospectively in 63 NEN patients with presumably cured or advanced metastatic disease. The cfDNA characteristics in NEN patients were compared to the results of a group of 29 healthy controls and correlated with clinical and histopathological data of the patients. Results: Patients with advanced NEN showed a significantly higher cfDNA concentration and percentage of Alu hypomethylation and a reduced LINE-1 cfDNA integrity as compared to the surgically cured NET patients and the healthy control group. The increased hypomethylation and concentration of cfDNA and the reduced cfDNA integrity in NEN patients were strongly associated with tumor burden and poor prognosis, while no correlation with tumor grading, differentiation, localization, or hormonal activity could be found. Multiparametric ROC analysis of plasma cfDNA characteristics was able to distinguish NEN patients with metastatic disease from the control group and the cured NEN patients with AUC values of 0.694 and 0.908, respectively. This was significant even for the group with only a low tumor burden. Conclusions: The present study, for the first time, demonstrates that the combination of plasma cfDNA concentration, global hypomethylation, and fragment length pattern has the potential to serve as a potent and sensitive prognostic and therapeutic “liquid biopsy” biomarker for tumor burden and disease progression in patients with neuroendocrine neoplasias.
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Affiliation(s)
- Esther Mettler
- Department of Endocrinology and Metabolism, I Medical Clinic, University Hospital, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany; (C.F.); (N.B.); (A.T.); (M.M.W.)
- Correspondence:
| | - Christian Fottner
- Department of Endocrinology and Metabolism, I Medical Clinic, University Hospital, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany; (C.F.); (N.B.); (A.T.); (M.M.W.)
| | - Neda Bakhshandeh
- Department of Endocrinology and Metabolism, I Medical Clinic, University Hospital, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany; (C.F.); (N.B.); (A.T.); (M.M.W.)
| | - Anja Trenkler
- Department of Endocrinology and Metabolism, I Medical Clinic, University Hospital, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany; (C.F.); (N.B.); (A.T.); (M.M.W.)
| | - Robert Kuchen
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany;
| | - Matthias M. Weber
- Department of Endocrinology and Metabolism, I Medical Clinic, University Hospital, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany; (C.F.); (N.B.); (A.T.); (M.M.W.)
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12
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Di Santo R, Quagliarini E, Digiacomo L, Pozzi D, Di Carlo A, Caputo D, Cerrato A, Montone CM, Mahmoudi M, Caracciolo G. Protein corona profile of graphene oxide allows detection of glioblastoma multiforme using a simple one-dimensional gel electrophoresis technique: a proof-of-concept study. Biomater Sci 2021; 9:4671-4678. [PMID: 34018505 DOI: 10.1039/d1bm00488c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glioblastoma multiforme (GBM) is the most aggressive form of gliomas. The development of supplementary approaches for glioblastoma diagnosis, limited to imaging techniques and tissue biopsies so far, is a necessity of clinical relevance. In this context, nanotechnology might afford tools to enable early diagnosis. Upon exposure to biological media, nanoparticles are coated with a layer of proteins, the protein corona (PC), whose composition is individual and personalized. Here we show that the PC of graphene oxide nanosheets has a capacity to detect GBM using a simple one-dimensional gel electrophoresis technique. In a range of molecular weights between 100 and 120 kDa, the personalized PC from GBM patients is completely discernible from that of healthy donors and that of cancer patients affected by pancreatic adenocarcinoma and colorectal cancer. Using tandem mass spectrometry, we found that inter-alpha-trypsin inhibitor (ITI) heavy chain H4 is enriched in the PC of all tested individuals but not in the GBM patients. Overall, if confirmed on a larger cohort series, this approach could be advantageous at the first level of investigation to decide whether to carry out more invasive analyses and/or to follow up patients after surgery and/or pharmacological treatment.
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Affiliation(s)
- Riccardo Di Santo
- Nanodelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
| | | | - Luca Digiacomo
- Nanodelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniela Pozzi
- Nanodelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
| | - Angelina Di Carlo
- Department of Medico-Surgical Sciences and Biotechnologies, "Sapienza" University of Rome, Viale del Policlinico 155, 00161 Latina, Italy
| | - Damiano Caputo
- University Campus Bio-Medico di Roma, General Surgery, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Morteza Mahmoudi
- Precision Health Program, Michigan State University, East Lansing, MI, USA.
| | - Giulio Caracciolo
- Nanodelivery Lab, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
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Ali H, Harting R, de Vries R, Ali M, Wurdinger T, Best MG. Blood-Based Biomarkers for Glioma in the Context of Gliomagenesis: A Systematic Review. Front Oncol 2021; 11:665235. [PMID: 34150629 PMCID: PMC8211985 DOI: 10.3389/fonc.2021.665235] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Gliomas are the most common and aggressive tumors of the central nervous system. A robust and widely used blood-based biomarker for glioma has not yet been identified. In recent years, a plethora of new research on blood-based biomarkers for glial tumors has been published. In this review, we question which molecules, including proteins, nucleic acids, circulating cells, and metabolomics, are most promising blood-based biomarkers for glioma diagnosis, prognosis, monitoring and other purposes, and align them to the seminal processes of cancer. METHODS The Pubmed and Embase databases were systematically searched. Biomarkers were categorized in the identified biomolecules and biosources. Biomarker characteristics were assessed using the area under the curve (AUC), accuracy, sensitivity and/or specificity values and the degree of statistical significance among the assessed clinical groups was reported. RESULTS 7,919 references were identified: 3,596 in PubMed and 4,323 in Embase. Following screening of titles, abstracts and availability of full-text, 262 articles were included in the final systematic review. Panels of multiple biomarkers together consistently reached AUCs >0.8 and accuracies >80% for various purposes but especially for diagnostics. The accuracy of single biomarkers, consisting of only one measurement, was far more variable, but single microRNAs and proteins are generally more promising as compared to other biomarker types. CONCLUSION Panels of microRNAs and proteins are most promising biomarkers, while single biomarkers such as GFAP, IL-10 and individual miRNAs also hold promise. It is possible that panels are more accurate once these are involved in different, complementary cancer-related molecular pathways, because not all pathways may be dysregulated in cancer patients. As biomarkers seem to be increasingly dysregulated in patients with short survival, higher tumor grades and more pathological tumor types, it can be hypothesized that more pathways are dysregulated as the degree of malignancy of the glial tumor increases. Despite, none of the biomarkers found in the literature search seem to be currently ready for clinical implementation, and most of the studies report only preliminary application of the identified biomarkers. Hence, large-scale validation of currently identified and potential novel biomarkers to show clinical utility is warranted.
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Affiliation(s)
- Hamza Ali
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Romée Harting
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Ralph de Vries
- Medical Library, Vrije Universiteit, Amsterdam, Netherlands
| | - Meedie Ali
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Myron G. Best
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
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14
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Díaz Méndez AB, Tremante E, Regazzo G, Brandner S, Rizzo MG. Time to focus on circulating nucleic acids for diagnosis and monitoring of gliomas: A systematic review of their role as biomarkers. Neuropathol Appl Neurobiol 2021; 47:471-487. [PMID: 33403678 DOI: 10.1111/nan.12691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022]
Abstract
Gliomas are diffusely growing tumours arising from progenitors within the central nervous system. They encompass a range of different molecular types and subtypes, many of which have a well-defined profile of driver mutations, copy number changes and DNA methylation patterns. A majority of gliomas will require surgical intervention to relieve raised intracranial pressure and reduce tumour burden. A proportion of tumours, however, are located in neurologically sensitive areas and a biopsy poses a significant risk of a deficit. A majority of gliomas recur after surgery, and monitoring tumour burden of the recurrence is currently achieved by imaging. However, most imaging modalities have limitations in assessing tumour burden and infiltration into adjacent brain, and sometimes imaging is unable to discriminate between tumour recurrence and pseudo-progression. Liquid biopsies, obtained from body fluids such as cerebrospinal fluid or blood, contain circulating nucleic acids or extracellular vesicles containing tumour-derived components. The studies for this systematic review were selected according to PRISMA criteria, and suggest that the detection of circulating tumour-derived nucleic acids holds great promises as biomarker to aid diagnosis and prognostication by monitoring tumour progression, and thus can be considered a pathway towards personalized medicine.
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Affiliation(s)
- Ana Belén Díaz Méndez
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Elisa Tremante
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Regazzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.,Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Maria G Rizzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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15
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Birkó Z, Nagy B, Klekner Á, Virga J. Novel Molecular Markers in Glioblastoma-Benefits of Liquid Biopsy. Int J Mol Sci 2020; 21:ijms21207522. [PMID: 33053907 PMCID: PMC7589793 DOI: 10.3390/ijms21207522] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma is a primary Central Nervous System (CNS) malignancy with poor survival. Treatment options are scarce and despite the extremely heterogeneous nature of the disease, clinicians lack prognostic and predictive markers to characterize patients with different outcomes. Certain immunohistochemistry, FISH, or PCR-based molecular markers, including isocitrate dehydrogenase1/2 (IDH1/2) mutations, epidermal growth factor receptor variant III (EGFRvIII) mutation, vascular endothelial growth factor overexpression (VEGF) overexpression, or (O6-Methylguanine-DNA methyltransferase promoter) MGMT promoter methylation status, are well-described; however, their clinical usefulness and accuracy is limited, and tumor tissue samples are always necessary. Liquid biopsy is a developing field of diagnostics and patient follow up in multiple types of cancer. Fragments of circulating nucleic acids are collected in various forms from different bodily fluids, including serum, urine, or cerebrospinal fluid in order to measure the quality and quantity of these markers. Multiple types of nucleic acids can be analyzed using liquid biopsy. Circulating cell-free DNA, mitochondrial DNA, or the more stable long and small non-coding RNAs, circular RNAs, or microRNAs can be identified and measured by novel PCR and next-generation sequencing-based methods. These markers can be used to detect the previously described alterations in a minimally invasive method. These markers can be used to differentiate patients with poor or better prognosis, or to identify patients who do not respond to therapy. Liquid biopsy can be used to detect recurrent disease, often earlier than using imaging modalities. Liquid biopsy is a rapidly developing field, and similarly to other types of cancer, measuring circulating tumor-derived nucleic acids from biological fluid samples could be the future of differential diagnostics, patient stratification, and follow up in the future in glioblastoma as well.
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Affiliation(s)
- Zsuzsanna Birkó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Correspondence:
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Álmos Klekner
- Department of Neurosurgery, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - József Virga
- Department of Oncology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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Zeggar HR, How-Kit A, Daunay A, Bettaieb I, Sahbatou M, Rahal K, Adouni O, Gammoudi A, Douik H, Deleuze JF, Kharrat M. Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. Oncol Lett 2020; 20:1999-2006. [PMID: 32724446 PMCID: PMC7377197 DOI: 10.3892/ol.2020.11745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P<0.03). DNA hypomethylation of LINE-1 was also indicated to be associated with low grade (P=0.023). To the best of our knowledge, the current study is the first study regarding DNA methylation of LINE-1 and Alu repeats element in breast cancer of the Tunisian population. The results of the current study suggest that, since hypomethylation of LINE-1 is associated with low grade, it could be used as a biomarker for prognosis for patients with breast cancer.
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Affiliation(s)
- Hayet Radia Zeggar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Ilhem Bettaieb
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Khaled Rahal
- Service de Chirurgie Carcinologique, Institut Salah Azaiz de Tunis, 1006 Tunis, Tunisia
| | - Olfa Adouni
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Amor Gammoudi
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Hayet Douik
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Le Commissariat à l'énergie atomique et aux énergies alternatives-Institut François Jacob, 92265 Evry, France
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
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Ghodsi M, Shahmohammadi M, Modarressi MH, Karami F. Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients. Exp Brain Res 2020; 238:1903-1909. [PMID: 32556427 DOI: 10.1007/s00221-020-05848-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/08/2020] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Despite advanced diagnostic and therapeutic techniques, many brain tumors are still diagnosed at high grades and, therefore finding novel molecular markers may assist in early detection and reducing brain tumors-related mortality rate. Owing to the previous reports on the importance of MCPH1 gene in tumorigenesis, the present study was aimed to study the promoter methylation of MCPH1 gene in paired circulating cell-free DNA (cfDNA) and tumor tissues of brain tumor patients. MATERIALS AND METHODS Fourteen fresh paired serum and tumor tissue samples in addition to 18 isolated serum samples were collected from patients affected by different grades of brain tumor. Genomic DNA and cfDNA was isolated from tissue and serum samples using QIAamp DNA Mini Kit Norgen Bioteck Kit, respectively. Methylation DNA immunoprecipitation Real-time polymerization chain reaction (MeDIP-Real-time PCR) was performed on isolated DNA samples using EpiQuik MeDIP Ultra Kit and specific primer pairs. cfDNA quantity was determined through Real-time PCR analysis using specific primer pairs designed for GAPDH gene. RESULTS MCPH1 was methylated in 54% of cfDNA samples which was significantly associated with tumor grade, as well (P-value = 0.02). The methylation rate of MCPH1 was found as 78% in the tissue samples which was meaningfully associated with tumor grade (P-value = 0.03). Moreover, methylation of the MCPH1 gene was consistent in 57% of the same cfDNA and tissue samples. Methylation of MCPH1 gene in neither tumor tissues nor cfDNA was not correlated with age and sex of the patients. DISCUSSION AND CONCLUSION Due to the conformity of methylation of MCPH1 gene in cfDNA and tissue samples in more than half of the enrolled patients, especially in higher grades of tumors, it seems that MCPH1 promoter methylation could be a potential epimarker in not only detection of brain tumors but also in response to chemo- and radiotherapy which warranted further assessment.
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Affiliation(s)
- Marjan Ghodsi
- Department of Biology, School of Basic Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammadreza Shahmohammadi
- Functional Neurosurgery Research Center, Shohada Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Karami
- Department of Medical Genetics, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran.
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Liu J, Liu H, Tang Z, Gui W, Ma T, Gong S, Gao Q, Xie Y, Niyoyita JP. IOUC-3DSFCNN: Segmentation of Brain Tumors via IOU Constraint 3D Symmetric Full Convolution Network with Multimodal Auto-context. Sci Rep 2020; 10:6256. [PMID: 32277141 PMCID: PMC7148375 DOI: 10.1038/s41598-020-63242-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/27/2020] [Indexed: 11/26/2022] Open
Abstract
Accurate segmentation of brain tumors from magnetic resonance (MR) images play a pivot role in assisting diagnoses, treatments and postoperative evaluations. However, due to its structural complexities, e.g., fuzzy tumor boundaries with irregular shapes, accurate 3D brain tumor delineation is challenging. In this paper, an intersection over union (IOU) constraint 3D symmetric full convolutional neural network (IOUC-3DSFCNN) model fused with multimodal auto-context is proposed for the 3D brain tumor segmentation. IOUC-3DSFCNN incorporates 3D residual groups into the classic 3DU-Net to further deepen the network structure to obtain more abstract voxel features under a five-layer cohesion architecture to ensure the model stability. The IOU constraint is used to address the issue of extremely unbalanced tumor foreground and background regions in MR images. In addition, to obtain more comprehensive and stable 3D brain tumor profiles, the multimodal auto-context information is fused into the IOUC-3DSFCNN model to achieve end-to-end 3D brain tumor profiles. Extensive confirmatory and comparative experiments conducted on the benchmark BRATS 2017 dataset demonstrate that the proposed segmentation model is superior to classic 3DU-Net-relevant and other state-of-the-art segmentation models, which can achieve accurate 3D tumor profiles on multimodal MRI volumes even with blurred tumor boundaries and big noise.
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Affiliation(s)
- Jinping Liu
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, Hunan, 410081, China.
| | - Hui Liu
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Zhaohui Tang
- School of Automation, Central South University, Changsha, Hunan, 410083, China
| | - Weihua Gui
- School of Automation, Central South University, Changsha, Hunan, 410083, China
| | - Tianyu Ma
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Subo Gong
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
| | - Quanquan Gao
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Yongfang Xie
- School of Automation, Central South University, Changsha, Hunan, 410083, China
| | - Jean Paul Niyoyita
- College of Science and Technology, University of Rwanda, Kigali, 3286, Rwanda
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Ye D, Jiang D, Zhang X, Mao Y. Alu Methylation and Risk of Cancer: A Meta-analysis. Am J Med Sci 2020; 359:271-280. [PMID: 32268941 DOI: 10.1016/j.amjms.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The association between Alu methylation and risk of cancer remains uncertain. This meta-analysis was conducted to elucidate this issue. MATERIALS AND METHODS PubMed and Web of Science up to December 31, 2018, and the reference lists of studies, as well as those presented in relevant meta-analyses and reviews were systematically searched. Standardized mean difference (SMD) in Alu methylation level between cases and controls were pooled using random effects model and assessed heterogeneity between strata by stratified factors using meta-regression model. Sensitivity analysis and publication bias test were also conducted. RESULTS Twenty-five articles, including 2719 cases and 3018 controls were included in the meta-analysis. The significant difference in Alu methylation level between cancer cases and controls was greater in tissue (SMD = -1.89, 95% CI: -2.72, -1.05) than blood (SMD = -0.46, 95% CI: -0.82, -0.09), and heterogeneity was found in materials (P = 0.038). In tissue samples, Alu hypomethylation was found in carcinoma (SMD = -2.50, 95% CI: -3.51, -1.48), while not in non-carcinoma. The inverse associations were consistently found in subgroups stratified by data sources and quality score in tissue samples, and publication year was considered to be the potential source of between-study heterogeneity. Moreover, reduced Alu methylation level was found in the European subgroup, detection method of SIRPH and COBRA, and original data source in blood samples. CONCLUSIONS Alu hypomethylation was associated with increased risk of cancer, which could be a potential biomarker for cancer.
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Affiliation(s)
- Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Danjie Jiang
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xinhan Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Yingying Mao
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China.
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McEwen AE, Leary SES, Lockwood CM. Beyond the Blood: CSF-Derived cfDNA for Diagnosis and Characterization of CNS Tumors. Front Cell Dev Biol 2020; 8:45. [PMID: 32133357 PMCID: PMC7039816 DOI: 10.3389/fcell.2020.00045] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic data are rapidly becoming part of tumor classification and are integral to prognosis and predicting response to therapy. Current molecular tumor profiling relies heavily on tissue resection or biopsy. Tissue profiling has several disadvantages in tumors of the central nervous system, including the challenge associated with invasive biopsy, the heterogeneous nature of many malignancies where a small biopsy can underrepresent the mutational profile, and the frequent lack of obtaining a repeat biopsy, which limits routine monitoring to assess therapy response and/or tumor evolution. Circulating tumor, cell-free DNA (cfDNA), has been proposed as a liquid biopsy to address some limitations of tissue-based genetics. In cancer patients, a portion of cfDNA is tumor-derived and may contain somatic genetic alterations. In central nervous system (CNS) neoplasia, plasma tumor-derived cfDNA is very low or absent, likely due to the blood brain barrier. Interrogating cfDNA in cerebrospinal fluid (CSF) has several advantages. Compared to blood, CSF is paucicellular and therefore predominantly lacks non-tumor cfDNA; however, patients with CNS-limited tumors have significantly enriched tumor-derived cfDNA in CSF. In patients with metastatic CNS disease, mutations in CSF cfDNA are most concordant with the intracranial process. CSF cfDNA can also occasionally uncover additional genetic alterations absent in concurrent biopsy specimens, reflecting tumor heterogeneity. Although CSF is enriched for tumor-derived cfDNA, absolute quantities are low. Highly sensitive, targeted methods including next-generation sequencing and digital PCR are required to detect mutations in CSF cfDNA. Additional technical and bioinformatic approaches also facilitate enhanced ability to detect tumor mutations in CSF cfDNA.
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Affiliation(s)
- Abbye E McEwen
- Department of Pathology, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Sarah E S Leary
- Brotman Baty Institute for Precision Medicine, Seattle, WA, United States.,Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
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21
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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22
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Liquid Biopsy in Glioblastoma: Opportunities, Applications and Challenges. Cancers (Basel) 2019; 11:cancers11070950. [PMID: 31284524 PMCID: PMC6679205 DOI: 10.3390/cancers11070950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy represents a minimally invasive procedure that can provide similar information from body fluids to what is usually obtained from a tissue biopsy sample. Its implementation in the clinical setting might significantly renew the field of medical oncology, facilitating the introduction of the concepts of precision medicine and patient-tailored therapies. These advances may be useful in the diagnosis of brain tumors that currently require surgery for tissue collection, or to perform genetic tumor profiling for disease classification and guidance of therapy. In this review, we will summarize the most recent advances and putative applications of liquid biopsy in glioblastoma, the most common and malignant adult brain tumor. Moreover, we will discuss the remaining challenges and hurdles in terms of technology and biology for its clinical application.
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Digital PCR in Myeloid Malignancies: Ready to Replace Quantitative PCR? Int J Mol Sci 2019; 20:ijms20092249. [PMID: 31067725 PMCID: PMC6540058 DOI: 10.3390/ijms20092249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
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25
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Orsini P, Impera L, Parciante E, Cumbo C, Minervini CF, Minervini A, Zagaria A, Anelli L, Coccaro N, Casieri P, Tota G, Brunetti C, Ricco A, Carluccio P, Specchia G, Albano F. Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies. Diagn Pathol 2018; 13:98. [PMID: 30579366 PMCID: PMC6303857 DOI: 10.1186/s13000-018-0777-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
Background Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) class, contain about 25% of CpG sites in the human genome. Alu sequences lie in gene-rich regions, so their methylation is an important transcriptional regulation mechanism. Aberrant Alu methylation has been associated with tumor aggressiveness, and also previously discussed in hematological malignancies, by applying different approaches. Moreover, today different techniques designed to measure global DNA methylation are focused on the methylation level of specific repeat elements. In this work we propose a new method of investigating Alu differential methylation, based on droplet digital PCR (ddPCR) technology. Methods Forty-six patients with hematological neoplasms were included in the study: 30 patients affected by chronic lymphocytic leukemia, 7 patients with myelodysplastic syndromes at intermediate/high risk, according with the International Prognostic Scoring System, and 9 patients with myelomonocytic leukemia. Ten healthy donors were included as controls. Acute promyelocytic leukemia-derived NB4 cell line, either untreated or treated with decitabine (DEC) hypomethylating agent, was also analyzed. DNA samples were investigated for Alu methylation level by digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation, followed by ddPCR. Results Using ddPCR, a significant decrease of the global Alu methylation level in DNA extracted from NB4 cells treated with DEC, as compared to untreated cells, was observed. Moreover, comparing the global Alu methylation levels at diagnosis and after azacytidine (AZA) treatment in MDS patients, a statistically significant decrease of Alu sequences methylation after therapy as compared to diagnosis was evident. We also observed a significant decrease of the Alu methylation level in CLL patients compared to HD, and, finally, for CMML patients, a decrease of Alu sequences methylation was observed in patients harboring the SRSF2 hotspot gene mutation c.284C>D. Conclusions In our work, we propose a method to investigate Alu differential methylation based on ddPCR technology. This assay introduces ddPCR as a more sensitive and immediate technique for Alu methylation analysis. To date, this is the first application of ddPCR to study DNA repetitive elements. This approach may be useful to profile patients affected by hematologic malignancies for diagnostic/prognostic purpose. Electronic supplementary material The online version of this article (10.1186/s13000-018-0777-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paola Orsini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Crescenzio F Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Alessandra Ricco
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Paola Carluccio
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy.
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Bonner ER, Bornhorst M, Packer RJ, Nazarian J. Liquid biopsy for pediatric central nervous system tumors. NPJ Precis Oncol 2018; 2:29. [PMID: 30588509 PMCID: PMC6297139 DOI: 10.1038/s41698-018-0072-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Central nervous system (CNS) tumors are the most common solid tumors in children, and the leading cause of cancer-related death. Over the past decade, molecular profiling has been incorporated into treatment for pediatric CNS tumors, allowing for a more personalized approach to therapy. Through the identification of tumor-specific changes, it is now possible to diagnose, assign a prognostic subgroup, and develop targeted chemotherapeutic treatment plans for many cancer types. The successful incorporation of informative liquid biopsies, where the liquid biome is interrogated for tumor-associated molecular clues, has the potential to greatly complement the precision-based approach to treatment, and ultimately, to improve clinical outcomes for children with CNS tumors. In this article, the current application of liquid biopsy in cancer therapy will be reviewed, as will its potential for the diagnosis and therapeutic monitoring of pediatric CNS tumors.
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Affiliation(s)
- Erin R Bonner
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,2Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
| | - Miriam Bornhorst
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Roger J Packer
- 3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Javad Nazarian
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA.,4Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
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ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease. Int J Mol Sci 2018; 19:ijms19061734. [PMID: 29895733 PMCID: PMC6032270 DOI: 10.3390/ijms19061734] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/04/2018] [Accepted: 06/09/2018] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis (ATH) and coronary artery disease (CAD) are chronic inflammatory diseases with an important genetic background; they derive from the cumulative effect of multiple common risk alleles, most of which are located in genomic noncoding regions. These complex diseases behave as nonlinear dynamical systems that show a high dependence on their initial conditions; thus, long-term predictions of disease progression are unreliable. One likely possibility is that the nonlinear nature of ATH could be dependent on nonlinear correlations in the structure of the human genome. In this review, we show how chaos theory analysis has highlighted genomic regions that have shared specific structural constraints, which could have a role in ATH progression. These regions were shown to be enriched with repetitive sequences of the Alu family, genomic parasites that have colonized the human genome, which show a particular secondary structure and are involved in the regulation of gene expression. Here, we show the impact of Alu elements on the mechanisms that regulate gene expression, especially highlighting the molecular mechanisms via which the Alu elements alter the inflammatory response. We devote special attention to their relationship with the long noncoding RNA (lncRNA); antisense noncoding RNA in the INK4 locus (ANRIL), a risk factor for ATH; their role as microRNA (miRNA) sponges; and their ability to interfere with the regulatory circuitry of the (nuclear factor kappa B) NF-κB response. We aim to characterize ATH as a nonlinear dynamic system, in which small initial alterations in the expression of a number of repetitive elements are somehow amplified to reach phenotypic significance.
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Abstract
INTRODUCTION Minimally invasive methods will augment the clinical approach for establishing the diagnosis or monitoring treatment response of central nervous system tumors. Liquid biopsy by blood or cerebrospinal fluid sampling holds promise in this regard. Areas covered: In this literature review, the authors highlight recent studies describing the analysis of circulating tumor cells, cell free nucleic acids, and extracellular vesicles as strategies to accomplish liquid biopsy in glioblastoma and metastatic tumors. The authors then discuss the continued efforts to improve signal detection, standardize the liquid biopsy handling and preparation, develop platforms for clinical application, and establish a role for liquid biopsies in personalized medicine. Expert commentary: As the technologies used to analyze these biomarkers continue to evolve, we propose that there is a future potential to precisely diagnose and monitor treatment response with liquid biopsies.
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Affiliation(s)
- Ganesh M. Shankar
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Shannon L. Stott
- Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brian Nahed
- Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Bob S. Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
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