51
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Whitlock JH, Soelter TM, Williams AS, Hardigan AA, Lasseigne BN. Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics. Hum Cell 2022; 35:15-22. [PMID: 34694568 PMCID: PMC8732818 DOI: 10.1007/s13577-021-00624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/29/2021] [Indexed: 01/19/2023]
Abstract
Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.
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Affiliation(s)
- Jordan H Whitlock
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tabea M Soelter
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avery S Williams
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew A Hardigan
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Brittany N Lasseigne
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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52
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Panja S, Rahem S, Chu CJ, Mitrofanova A. Big Data to Knowledge: Application of Machine Learning to Predictive Modeling of Therapeutic Response in Cancer. Curr Genomics 2021; 22:244-266. [PMID: 35273457 PMCID: PMC8822229 DOI: 10.2174/1389202921999201224110101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/16/2020] [Accepted: 09/30/2020] [Indexed: 11/22/2022] Open
Abstract
Background In recent years, the availability of high throughput technologies, establishment of large molecular patient data repositories, and advancement in computing power and storage have allowed elucidation of complex mechanisms implicated in therapeutic response in cancer patients. The breadth and depth of such data, alongside experimental noise and missing values, requires a sophisticated human-machine interaction that would allow effective learning from complex data and accurate forecasting of future outcomes, ideally embedded in the core of machine learning design. Objective In this review, we will discuss machine learning techniques utilized for modeling of treatment response in cancer, including Random Forests, support vector machines, neural networks, and linear and logistic regression. We will overview their mathematical foundations and discuss their limitations and alternative approaches in light of their application to therapeutic response modeling in cancer. Conclusion We hypothesize that the increase in the number of patient profiles and potential temporal monitoring of patient data will define even more complex techniques, such as deep learning and causal analysis, as central players in therapeutic response modeling.
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Affiliation(s)
| | | | | | - Antonina Mitrofanova
- Address correspondence to this author at the Department of Health Informatics, Rutgers School of Health Professions, Rutgers Biomedical and Health Sciences, Newark, NJ 07107, USA; E-mail:
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53
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Mardis ER. The emergence of cancer genomics in diagnosis and precision medicine. NATURE CANCER 2021; 2:1263-1264. [PMID: 35121919 DOI: 10.1038/s43018-021-00305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Elaine R Mardis
- Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
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54
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Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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55
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Zhang Y, Wang Y, Su X, Wang P, Lin W. The Value of Circulating Circular RNA in Cancer Diagnosis, Monitoring, Prognosis, and Guiding Treatment. Front Oncol 2021; 11:736546. [PMID: 34722285 PMCID: PMC8551378 DOI: 10.3389/fonc.2021.736546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Liquid biopsy includes non-invasive analysis of circulating tumor-derived substances. It is a novel, innovative cancer screening tool that overcomes the limitations of current invasive tissue examinations in precision oncology. Circular RNA (circRNA) is a recent, novel, and attractive liquid biomarker showing stability, abundance, and high specificity in various diseases, especially in human cancers. This review focused on the emerging potential of human circRNA in body fluids as the liquid biopsy biomarkers for cancers and the methods used to detect the circRNA expression and summarized the construction of circRNA biomarkers in body fluids for treating human cancers and their limitations before they become part of routine clinical medicine. Furthermore, the future opportunities and challenges of translating circRNAs in liquid biopsy into clinical practices were explored.
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Affiliation(s)
- Yunjing Zhang
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
| | - Ying Wang
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
| | - Xinwan Su
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ping Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiqiang Lin
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
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56
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Aran V, Heringer M, da Mata PJ, Kasuki L, Miranda RL, Andreiuolo F, Chimelli L, Filho PN, Gadelha MR, Neto VM. Identification of mutant K-RAS in pituitary macroadenoma. Pituitary 2021; 24:746-753. [PMID: 33954928 DOI: 10.1007/s11102-021-01151-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE RAS genes are among the most frequently mutated genes in cancer, where their mutation frequency varies according to the distinct RAS isoforms and tumour types. Despite occurring more prevalent in malignant tumours, RAS mutations were also observed in few benign tumours. Pituitary adenomas are examples of benign tumours which vary in size and aggressiveness. The present study was performed to investigate, via liquid biopsy and tissue analysis, the presence of K-RAS mutations in a pituitary macroadenoma. METHODS Molecular analysis was performed to investigate K-RAS mutations using the droplet digital PCR (ddPCR) method by evaluating both plasma (liquid biopsy) and the solid tumour of a patient diagnosed with a giant clinically non-functioning pituitary tumour. RESULTS The patient underwent surgical resection due to visual loss, and the histopathological analysis showed a gonadotrophic pituitary macroadenoma. The molecular analysis revealed the presence of mutant K-RAS both in the plasma and in the tumour tissue which, to our knowledge, has not been previously reported in the literature. CONCLUSION Our findings highlight the exceptional capacity of the digital PCR in detecting low frequency mutations (below 1%), since we detected, for the first time, K-RAS mutations in pituitary macroadenoma. The potential impact of K-RAS mutations in these tumours should be further investigated.
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Affiliation(s)
- Veronica Aran
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil.
| | - Manoela Heringer
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil
| | - Paulo Jose da Mata
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Leandro Kasuki
- Neuroendocrine Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Endocrine Unit and Neuroendocrinology Research Center, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Felipe Andreiuolo
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Leila Chimelli
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Paulo Niemeyer Filho
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Monica Roberto Gadelha
- Neuroendocrine Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Endocrine Unit and Neuroendocrinology Research Center, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivaldo Moura Neto
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil
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57
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Wang Q, Liu J, Zeng J, Yang Z, Ran F, Wu L, Yang G, Mei Q, Wang X, Chen Q. Determination of miRNA derived from exosomes of prostate cancer via toehold-aided cyclic amplification combined with HRP enzyme catalysis and magnetic nanoparticles. Anal Biochem 2021; 630:114336. [PMID: 34400146 DOI: 10.1016/j.ab.2021.114336] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) play a significant role in tumorigenesis and tumor development. Exosomal microRNA-141 (miRNA-141, miR-141) has been reported to be overexpressed in prostate cancer (PCa) and has become a potential biomarker for the diagnosis of PCa. Herein, a novel fluorescent biosensor based on toehold-aided cyclic amplification combined with horseradish peroxidase (HRP) enzyme catalysis and magnetic nanoparticles (MNPs) was designed for determination of the exosomes-derived microRNA-141 (miRNA-141, miR-141). The synergy of HRP enzyme catalysis and toehold mediated strand display reaction (TSDR) increase the sensitivity of the method, and the good separation ability of MNPs ensures the specificity of the method. Therefore, under the optimized experimental conditions, the highly sensitive and specific detection of miRNA-141 can be realized, and the detection limit is as low as 10 fM. More importantly, the biosensor successfully determinates the exosomal miR-141 in the plasma of patients with PCa.
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Affiliation(s)
- Qinjun Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, China
| | - Jingjian Liu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Jiantao Zeng
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518101, China
| | - Zhiming Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Fengying Ran
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Lun Wu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Guangyi Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Quanxi Mei
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Xisheng Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, China.
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China.
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58
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Sun W, Wang Y, Zhu Z, Wang Y, Zhang M, Jiang L, Liu S, Yu J, Huang J. Accurate and Nonpurified Identification of Extracellular Vesicles Using Dual-Binding Recognition Mode. Anal Chem 2021; 93:12383-12390. [PMID: 34449197 DOI: 10.1021/acs.analchem.1c02259] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Circulating extracellular vesicles (EVs) are promising biomarkers for the early diagnosis and prognosis of cancer in a non-invasive manner. However, the rapid and accurate identification of EVs in complex biological samples is technically challenging, which is attributed to the requirement of extensive sample purification and unsatisfactory detection accuracy due to the disturbance of interfering proteins. Herein, a simultaneous binding of double-positive EV membrane protein-based recognition mode (DRM) is proposed. By the combination of DRM-mediated toehold activation and G-quadruplex DNAZyme-catalyzed etching of Au@Ag nanorods (Au@Ag NRs), we have developed an accurate, non-purified, low-cost, and visual strategy for EV identification. The synchronous binding of double-positive proteins on EV membranes is validated by confocal laser scanning microscopy analysis. This approach exhibits excellent specificity and sensitivity toward EVs ranging from 1.0 × 105 to 1.0 × 109 particles/mL with a detection limit of 6.31 × 104 particles/mL. Moreover, we have successfully realized non-purified EV quantification in complex biological media. In addition, target-initiated catalyzed hairpin assembly (CHA) is integrated with G-quadruplex DNAZyme-catalyzed color variation of Au@Ag NRs; thus, low-background EV detection can be achieved by the naked eye. Furthermore, our strategy is easy to adapt to high-throughput formats by using an automatic microplate reader, which could be expected to meet the requirements for high-throughput detection of clinical samples. With its capacities of rapidness, portability, affordability, high throughput, non-purification, and visual detection, this strategy could provide a practical tool for accurate identification of EVs and early diagnosis of cancer.
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Affiliation(s)
- Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China
| | - Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China
| | - Zhixue Zhu
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China
| | - Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P.R. China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P.R. China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P.R. China
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.,Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
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59
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Bortolini Silveira A, Bidard FC, Tanguy ML, Girard E, Trédan O, Dubot C, Jacot W, Goncalves A, Debled M, Levy C, Ferrero JM, Jouannaud C, Rios M, Mouret-Reynier MA, Dalenc F, Hego C, Rampanou A, Albaud B, Baulande S, Berger F, Lemonnier J, Renault S, Desmoulins I, Proudhon C, Pierga JY. Multimodal liquid biopsy for early monitoring and outcome prediction of chemotherapy in metastatic breast cancer. NPJ Breast Cancer 2021; 7:115. [PMID: 34504096 PMCID: PMC8429692 DOI: 10.1038/s41523-021-00319-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are two cancer-derived blood biomarkers that inform on patient prognosis and treatment efficacy in breast cancer. We prospectively evaluated the clinical validity of quantifying both CTCs (CellSearch) and ctDNA (targeted next-generation sequencing). Their combined value as prognostic and early monitoring markers was assessed in 198 HER2-negative metastatic breast cancer patients. All patients were included in the prospective multicenter UCBG study COMET (NCT01745757) and treated by first-line chemotherapy with weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline and before the second cycle of chemotherapy. At baseline, CTCs and ctDNA were respectively detected in 72 and 74% of patients and were moderately correlated (Kendall’s τ = 0.3). Only 26 (13%) patients had neither detectable ctDNA nor CTCs. Variants were most frequently observed in TP53 and PIK3CA genes. KMT2C/MLL3 variants detected in ctDNA were significantly associated with a lower CTC count, while the opposite trend was seen with GATA3 alterations. Both CTC and ctDNA levels at baseline and after four weeks of treatment were correlated with survival. For progression-free and overall survival, the best multivariate prognostic model included tumor subtype (triple negative vs other), grade (grade 3 vs other), ctDNA variant allele frequency (VAF) at baseline (per 10% increase), and CTC count at four weeks (≥5CTC/7.5 mL). Overall, this study demonstrates that CTCs and ctDNA have nonoverlapping detection profiles and complementary prognostic values in metastatic breast cancer patients. A comprehensive liquid-biopsy approach may involve simultaneous detection of ctDNA and CTCs.
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Affiliation(s)
| | - François-Clément Bidard
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France.,UVSQ, Université Paris-Saclay, Paris, France
| | | | - Elodie Girard
- INSERM U900, Institut Curie, Mines ParisTech, PSL Research University, Paris, France
| | - Olivier Trédan
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Coraline Dubot
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France
| | - William Jacot
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier University, IRCM INSERM, Montpellier, France
| | - Anthony Goncalves
- Department of Medical Oncology, Aix-Marseille Univ, INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Marc Debled
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - Christelle Levy
- Department of Medical Oncology, Centre François Baclesse, Caen, France
| | - Jean-Marc Ferrero
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | | | - Maria Rios
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | | | - Florence Dalenc
- Department of Medical Oncology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Caroline Hego
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Benoit Albaud
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | | | | | - Shufang Renault
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Isabelle Desmoulins
- Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,INSERM U934 CNRS UMR3215, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France. .,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France. .,Université de Paris, Paris, France.
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60
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Cortés-Hernández LE, Eslami-S Z, Costa-Silva B, Alix-Panabières C. Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles. Cells 2021; 10:2221. [PMID: 34571870 PMCID: PMC8465935 DOI: 10.3390/cells10092221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
In cancer, many analytes can be investigated through liquid biopsy. They play fundamental roles in the biological mechanisms underpinning the metastatic cascade and provide clinical information that can be monitored in real time during the natural course of cancer. Some of these analytes (circulating tumor cells and extracellular vesicles) share a key feature: the presence of a phospholipid membrane that includes proteins, lipids and possibly nucleic acids. Most cell-to-cell and cell-to-matrix interactions are modulated by the cell membrane composition. To understand cancer progression, it is essential to describe how proteins, lipids and nucleic acids in the membrane influence these interactions in cancer cells. Therefore, assessing such interactions and the phospholipid membrane composition in different liquid biopsy analytes might be important for future diagnostic and therapeutic strategies. In this review, we briefly describe some of the most important surface components of circulating tumor cells and extracellular vesicles as well as their interactions, putting an emphasis on how they are involved in the different steps of the metastatic cascade and how they can be exploited by the different liquid biopsy technologies.
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Affiliation(s)
- Luis Enrique Cortés-Hernández
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Zahra Eslami-S
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Bruno Costa-Silva
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal;
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
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61
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Andrieux G, Chakraborty S. Editorial: Integration of Multi-Omics Techniques in Cancer. Front Genet 2021; 12:733965. [PMID: 34434225 PMCID: PMC8380985 DOI: 10.3389/fgene.2021.733965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
- Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Freiburg, Germany
| | - Sajib Chakraborty
- Molecular Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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62
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Combes GF, Vučković AM, Perić Bakulić M, Antoine R, Bonačić-Koutecky V, Trajković K. Nanotechnology in Tumor Biomarker Detection: The Potential of Liganded Nanoclusters as Nonlinear Optical Contrast Agents for Molecular Diagnostics of Cancer. Cancers (Basel) 2021; 13:4206. [PMID: 34439360 PMCID: PMC8393257 DOI: 10.3390/cancers13164206] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the leading causes of premature death, and, as such, it can be prevented by developing strategies for early and accurate diagnosis. Cancer diagnostics has evolved from the macroscopic detection of malignant tissues to the fine analysis of tumor biomarkers using personalized medicine approaches. Recently, various nanomaterials have been introduced into the molecular diagnostics of cancer. This has resulted in a number of tumor biomarkers that have been detected in vitro and in vivo using nanodevices and corresponding imaging techniques. Atomically precise ligand-protected noble metal quantum nanoclusters represent an interesting class of nanomaterials with a great potential for the detection of tumor biomarkers. They are characterized by high biocompatibility, low toxicity, and suitability for controlled functionalization with moieties specifically recognizing tumor biomarkers. Their non-linear optical properties are of particular importance as they enable the visualization of nanocluster-labeled tumor biomarkers using non-linear optical techniques such as two-photon-excited fluorescence and second harmonic generation. This article reviews liganded nanoclusters among the different nanomaterials used for molecular cancer diagnosis and the relevance of this new class of nanomaterials as non-linear optical probe and contrast agents.
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Affiliation(s)
- Guillaume F. Combes
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, 21000 Split, Croatia; (G.F.C.); (A.-M.V.); (M.P.B.); (V.B.-K.)
- Mediterranean Institute for Life Sciences (MedILS), 21000 Split, Croatia
| | - Ana-Marija Vučković
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, 21000 Split, Croatia; (G.F.C.); (A.-M.V.); (M.P.B.); (V.B.-K.)
- Mediterranean Institute for Life Sciences (MedILS), 21000 Split, Croatia
| | - Martina Perić Bakulić
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, 21000 Split, Croatia; (G.F.C.); (A.-M.V.); (M.P.B.); (V.B.-K.)
| | - Rodolphe Antoine
- UMR 5306, Centre National de la Recherche Scientifique (CNRS), Institute Lumière Matière, Claude Bernard University Lyon 1, F-69622 Villeurbanne, France;
| | - Vlasta Bonačić-Koutecky
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, 21000 Split, Croatia; (G.F.C.); (A.-M.V.); (M.P.B.); (V.B.-K.)
- Interdisciplinary Center for Advanced Science and Technology (ICAST), University of Split, 21000 Split, Croatia
- Chemistry Department, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Katarina Trajković
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, 21000 Split, Croatia; (G.F.C.); (A.-M.V.); (M.P.B.); (V.B.-K.)
- Mediterranean Institute for Life Sciences (MedILS), 21000 Split, Croatia
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63
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Novel Prostate Cancer Biomarkers: Aetiology, Clinical Performance and Sensing Applications. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9080205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The review initially provides a short introduction to prostate cancer (PCa) incidence, mortality, and diagnostics. Next, the need for novel biomarkers for PCa diagnostics is briefly discussed. The core of the review provides details about PCa aetiology, alternative biomarkers available for PCa diagnostics besides prostate specific antigen and their biosensing. In particular, low molecular mass biomolecules (ions and metabolites) and high molecular mass biomolecules (proteins, RNA, DNA, glycoproteins, enzymes) are discussed, along with clinical performance parameters.
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Theakstone AG, Brennan PM, Jenkinson MD, Mills SJ, Syed K, Rinaldi C, Xu Y, Goodacre R, Butler HJ, Palmer DS, Smith BR, Baker MJ. Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours. Cancers (Basel) 2021; 13:cancers13153851. [PMID: 34359751 PMCID: PMC8345395 DOI: 10.3390/cancers13153851] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.
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Affiliation(s)
- Ashton G. Theakstone
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK;
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
- Department of Pharmacology & Therapeutics, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha J. Mills
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Holly J. Butler
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - David S. Palmer
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK
| | - Benjamin R. Smith
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - Matthew J. Baker
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [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: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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66
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Alcoceba M, García-Álvarez M, Chillón MC, Jiménez C, Medina A, Antón A, Blanco O, Díaz LG, Tamayo P, González-Calle V, Vidal MJ, Cuello R, Díaz Gálvez FJ, Queizán JA, Martín A, González M, García-Sanz R, Sarasquete ME. Liquid biopsy: a non-invasive approach for Hodgkin lymphoma genotyping. Br J Haematol 2021; 195:542-551. [PMID: 34312841 DOI: 10.1111/bjh.17719] [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: 04/28/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022]
Abstract
The Hodgkin lymphoma (HL) genomic landscape is hardly known due to the scarcity of tumour cells in the tissue. Liquid biopsy employing circulating tumour DNA (ctDNA) can emerge as an alternative tool for non-invasive genotyping. By using a custom next generation sequencing (NGS) panel in combination with unique molecule identifiers, we aimed to identify somatic variants in the ctDNA of 60 HL at diagnosis. A total of 277 variants were detected in 36 of the 49 samples (73·5%) with a good quality ctDNA sample. The median number of variants detected per patient was five (range 1-23) with a median variant allele frequency of 4·2% (0·84-28%). Genotyping revealed somatic variants in the following genes: SOCS1 (28%), IGLL5 (26%), TNFAIP3 (23%), GNA13 (23%), STAT6 (21%) and B2M (19%). Moreover, several poor prognosis features (high LDH, low serum albumin, B-symptoms, IPI ≥ 3 or at an advanced stage) were related to significantly higher amounts of ctDNA. Variant detection in ctDNA by NGS is a feasible approach to depict the genetic features of HL patients at diagnosis. Our data favour the implementation of liquid biopsy genotyping for the routine evaluation of HL patients.
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Affiliation(s)
- Miguel Alcoceba
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - María García-Álvarez
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - M Carmen Chillón
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Cristina Jiménez
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Alejandro Medina
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Alicia Antón
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Oscar Blanco
- Department of Pathology, University Hospital of Salamanca (HUS/IBSAL), Spain
| | - Luis G Díaz
- Department of Nuclear Medicine, University Hospital of Salamanca (HUS/IBSAL),, Salamanca, Spain
| | - Pilar Tamayo
- Department of Nuclear Medicine, University Hospital of Salamanca (HUS/IBSAL),, Salamanca, Spain
| | - Verónica González-Calle
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | | | - Rebeca Cuello
- Department of Hematology, University Hospital of Valladolid,, Valladolid, Spain
| | | | | | - Alejandro Martín
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Marcos González
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Ramón García-Sanz
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - M Eugenia Sarasquete
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
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Xiao X, Wu K, Yan A, Wang JG, Zhang Z, Li D. Intelligent Probabilistic System for Digital Tracing Cellular Origin of Individual Clinical Extracellular Vesicles. Anal Chem 2021; 93:10343-10350. [PMID: 34264625 DOI: 10.1021/acs.analchem.1c01971] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are small vesicles secreted by various cell types to mediate cell-to-cell communication through the transfer of macromolecules. EVs carry multiple cargo molecules that reflect the origins of their donor cells; thus, they can be considered reliable biomarkers for early cancer diagnosis. However, the diverse cellular origin of EV masks the detection signals generated by both tumor- and nontumor-derived cells. Thereby, the capability to recognize the cellular origin of EVs is the prerequisite for their diagnostic applications. In the present study, we develop an intelligent probabilistic system for tracing the cellular origin of individual EVs using single-molecule multicolor imaging. Through the analysis of the expression profile of two typical membrane protein markers, CD9 and CD63, on single EVs, accurate and rapid probabilistic recognition of EVs derived from individual tumor and nontumor cells in clinical samples is achieved. The correlation between cellular origin and surface protein phenotyping on single EVs is also exemplified. The proposed system holds great potential for advancing EVs as reliable clinical indicators and exploring their biological functions.
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Affiliation(s)
- Xia Xiao
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Kun Wu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - An Yan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Jun-Gang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Zhanxia Zhang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.,Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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Mebendazole disrupts stromal desmoplasia and tumorigenesis in two models of pancreatic cancer. Oncotarget 2021; 12:1326-1338. [PMID: 34262644 PMCID: PMC8274724 DOI: 10.18632/oncotarget.28014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
The five-year survival rate for metastatic pancreatic cancer is currently only 3%, which increases to 13% with local invasion only and to 39% with localized disease at diagnosis. Here we evaluated repurposed mebendazole, an approved anthelminthic drug, to determine how mebendazole might work at the different stages of pancreatic cancer formation and progression. We asked if mebendazole could prevent initiation of pancreatic intraepithelial neoplasia precursor lesions, interfere with stromal desmoplasia, or suppress tumor growth and liver metastasis. In both the Kras LSL.G12D/+; Pdx1-Cre (KC) mouse model of caerulein-induced inflammatory pancreatitis and the Kras LSL.G12D/+; Tp53 R172H/+; Pdx1-Cre (KPC) mouse model of advanced pancreatic cancer, mebendazole significantly reduced pancreas weight, dysplasia and intraepithelial neoplasia formation, compared to controls. Mebendazole significantly reduced trichrome-positive fibrotic connective tissue and α-SMA-positive activated pancreatic stellate cells that heralds fibrogenesis. In the aggressive KPC model, mebendazole significantly suppressed pancreatic tumor growth, both as an early and late intervention. Mebendazole reduced the overall incidence of pancreatic cancer and severity of liver metastasis in KPC mice. Using early models of pancreatic cancer, treatment with mebendazole resulted in less inflammation, decreased dysplasia, with the later stage model additionally showing a decreased tumor burden, less advanced tumors, and a reduction of metastasis. We conclude that mebendazole should be investigated further as a component of adjuvant therapy to slow progression and prevent metastasis, and well as for primary prevention in the highest risk patients.
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69
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Kabzinski J, Maczynska M, Majsterek I. MicroRNA as a Novel Biomarker in the Diagnosis of Head and Neck Cancer. Biomolecules 2021; 11:844. [PMID: 34198889 PMCID: PMC8228566 DOI: 10.3390/biom11060844] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Head and neck squamous cell carcinoma is the sixth most common cancer worldwide, with 890,000 new cases and 450,000 deaths in 2018, and although the survival statistics for some patient groups are improving, there is still an urgent need to find a fast and reliable biomarker that allows early diagnosis. This niche can be filled by microRNA, small single-stranded non-coding RNA molecules, which are expressed in response to specific events in the body. This article presents the potential use of microRNAs in the diagnosis of HNSCC, compares the advances in this field to other diseases, especially other cancers, and discusses the detailed use of miRNA as a biomarker in profiling and predicting the treatment outcome with radiotherapy and immunotherapy. Potential problems and difficulties related to the development of this promising technology, and areas on which future research should be focused in order to overcome these difficulties, were also indicated.
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Affiliation(s)
| | | | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, al. Kościuszki 4, 90-419 Łódź, Poland; (J.K.); (M.M.)
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70
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Bertokova A, Bertok T, Jane E, Hires M, Ďubjaková P, Novotná O, Belan V, Fillo J, Tkac J. Detection of N,N-diacetyllactosamine (LacdiNAc) containing free prostate-specific antigen for early stage prostate cancer diagnostics and for identification of castration-resistant prostate cancer patients. Bioorg Med Chem 2021; 39:116156. [PMID: 33894508 DOI: 10.1016/j.bmc.2021.116156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is one of the most common cancer types among men and also acommon cause of death globally. With an increasing incidence, there is aneed for low-cost, reliable biomarkers present in samples, which could be provided non-invasively (without a need to perform prostate biopsy). Glycosylation changes of free-PSA (fPSA) are considered cancer-specific, while the level of different PSA forms can increase under other than cancerous conditions. In the present study, we investigated the role ofN,N-diacetyllactosamine (LacdiNAc) epitope of fPSA (i.e. glycoprofile of fPSA or gPSA) in combination with total-PSA (tPSA), prostate volume, and tPSA density (tPSA level divided by prostate volume i.e. PSAd) as biomarkers for monitoring of PCa development and progression in 105 men. Furthermore, we applied an genetic (evolutionary) algorithm to identify any suspicious individuals in abenign cohort having benign prostatic hyperplasia (BPH). We identified 3 suspicious men originally diagnosed with BPH using gPSA analysis. In thefollow-up we found out that two men should not be considered as BPH patients since multiparametric magnetic resonance imaging (mpMRI) identified one man with clinically significant PCa via Prostate Imaging - Reporting and Data System (PI RADS v2 = 4) and the second man was with High-gradeprostatic intraepithelial neoplasia (HG PIN), commonly described as apre-cancerous stage. Moreover, in the study we described for the first time that changed LacdiNAc on PSA can be applied to identify prostatitis patients and most importantly this is the first study suggesting that changed glycosylation on PSA can be applied to identify castration-resistant prostate cancer (CRPCa) patients.
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Affiliation(s)
- Aniko Bertokova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Eduard Jane
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Michal Hires
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia
| | - Petra Ďubjaková
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | - Oľga Novotná
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | | | - Juraj Fillo
- University Hospital Bratislava, Mickiewiczova 13, 811 07 Bratislava, Slovakia
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovakia; Glycanostics, Ltd., Dubravska cesta 9, Bratislava 845 38, Slovakia.
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71
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Peneder P, Stütz AM, Surdez D, Krumbholz M, Semper S, Chicard M, Sheffield NC, Pierron G, Lapouble E, Tötzl M, Ergüner B, Barreca D, Rendeiro AF, Agaimy A, Boztug H, Engstler G, Dworzak M, Bernkopf M, Taschner-Mandl S, Ambros IM, Myklebost O, Marec-Bérard P, Burchill SA, Brennan B, Strauss SJ, Whelan J, Schleiermacher G, Schaefer C, Dirksen U, Hutter C, Boye K, Ambros PF, Delattre O, Metzler M, Bock C, Tomazou EM. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat Commun 2021; 12:3230. [PMID: 34050156 PMCID: PMC8163828 DOI: 10.1038/s41467-021-23445-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.
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Affiliation(s)
- Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Sabine Semper
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Mathieu Chicard
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Heidrun Boztug
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Gernot Engstler
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Michael Dworzak
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Inge M Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Perrine Marec-Bérard
- Pediatric Department, Hematology and Oncology Pediatric Institute, Centre Léon Bérard, Lyon, France
| | - Susan Ann Burchill
- Children's Cancer Research Group, Leeds Institute of Medical Research, St. James's University Hospital, Leeds, UK
| | - Bernadette Brennan
- Department of Pediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK
| | - Sandra J Strauss
- Department of Oncology, UCL Cancer Institute, London, UK
- Department of Oncology, University College London Hospital, London, UK
| | - Jeremy Whelan
- Department of Oncology, University College London Hospital, London, UK
| | - Gudrun Schleiermacher
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Christiane Schaefer
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Uta Dirksen
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Caroline Hutter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Peter F Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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72
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Pereira B, Chen CT, Goyal L, Walmsley C, Pinto CJ, Baiev I, Allen R, Henderson L, Saha S, Reyes S, Taylor MS, Fitzgerald DM, Broudo MW, Sahu A, Gao X, Winckler W, Brannon AR, Engelman JA, Leary R, Stone JR, Campbell CD, Juric D. Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer. Nat Commun 2021; 12:3199. [PMID: 34045463 PMCID: PMC8160338 DOI: 10.1038/s41467-021-23394-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
In patients with metastatic cancer, spatial heterogeneity of somatic alterations may lead to incomplete assessment of a cancer's mutational profile when analyzing a single tumor biopsy. In this study, we perform sequencing of cell-free DNA (cfDNA) and distinct metastatic tissue samples from ten rapid autopsy cases with pre-treated metastatic cancer. We show that levels of heterogeneity in genetic biomarkers vary between patients but that gene expression signatures representative of the tumor microenvironment are more consistent. Across nine patients with plasma samples available, we are able to detect 62/62 truncal and 47/121 non-truncal point mutations in cfDNA. We observe that mutation clonality in cfDNA is correlated with the number of metastatic lesions in which the mutation is detected and use this result to derive a clonality threshold to classify truncal and non-truncal driver alterations with reasonable specificity. In contrast, mutation truncality is more often incorrectly assigned when studying single tissue samples. Our results demonstrate the utility of a single cfDNA sample relative to that of single tissue samples when treating patients with metastatic cancer.
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Affiliation(s)
- Bernard Pereira
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Christopher T Chen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Charlotte Walmsley
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Christopher J Pinto
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Islam Baiev
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Read Allen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Laura Henderson
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Supriya Saha
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephanie Reyes
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Donna M Fitzgerald
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Maida Williams Broudo
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Avinash Sahu
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xin Gao
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wendy Winckler
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - A Rose Brannon
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Rebecca Leary
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA.
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73
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Shanmugam A, Hariharan AK, Hasina R, Nair JR, Katragadda S, Irusappan S, Ravichandran A, Veeramachaneni V, Bettadapura R, Bhati M, Ramaswamy V, Rao VUS, Bagadia RK, Manjunath A, NML M, Solomon MC, Maji S, Bahadur U, Bettegowda C, Papadopoulos N, Lingen MW, Hariharan R, Gupta V, Agrawal N, Izumchenko E. Ultrasensitive detection of tumor-specific mutations in saliva of patients with oral cavity squamous cell carcinoma. Cancer 2021; 127:1576-1589. [PMID: 33405231 PMCID: PMC8084899 DOI: 10.1002/cncr.33393] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Oral cavity squamous cell carcinoma (OCSCC) is the most common head and neck malignancy. Although the survival rate of patients with advanced-stage disease remains approximately 20% to 60%, when detected at an early stage, the survival rate approaches 80%, posing a pressing need for a well validated profiling method to assess patients who have a high risk of developing OCSCC. Tumor DNA detection in saliva may provide a robust biomarker platform that overcomes the limitations of current diagnostic tests. However, there is no routine saliva-based screening method for patients with OCSCC. METHODS The authors designed a custom next-generation sequencing panel with unique molecular identifiers that covers coding regions of 7 frequently mutated genes in OCSCC and applied it on DNA extracted from 121 treatment-naive OCSCC tumors and matched preoperative saliva specimens. RESULTS By using stringent variant-calling criteria, mutations were detected in 106 tumors, consistent with a predicted detection rate ≥88%. Moreover, mutations identified in primary malignancies were also detected in 93% of saliva samples. To ensure that variants are not errors resulting in false-positive calls, a multistep analytical validation of this approach was performed: 1) re-sequencing of 46 saliva samples confirmed 88% of somatic variants; 2) no functionally relevant mutations were detected in saliva samples from 11 healthy individuals without a history of tobacco or alcohol; and 3) using a panel of 7 synthetic loci across 8 sequencing runs, it was confirmed that the platform developed is reproducible and provides sensitivity on par with droplet digital polymerase chain reaction. CONCLUSIONS The current data highlight the feasibility of somatic mutation identification in driver genes in saliva collected at the time of OCSCC diagnosis.
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Affiliation(s)
| | | | - Rifat Hasina
- University of Chicago, Section of Otolaryngology-Head and Neck Surgery, Chicago, USA
| | | | | | | | | | | | | | | | | | - Vishal US Rao
- HealthCare Global (HCG) Cancer Centre, Bangalore, India
| | | | | | - Manjunath NML
- HealthCare Global (HCG) Cancer Centre, Bangalore, India
| | | | | | | | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mark W. Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | | | | | - Nishant Agrawal
- University of Chicago, Section of Otolaryngology-Head and Neck Surgery, Chicago, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
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74
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Chua IS, Gaziel-Yablowitz M, Korach ZT, Kehl KL, Levitan NA, Arriaga YE, Jackson GP, Bates DW, Hassett M. Artificial intelligence in oncology: Path to implementation. Cancer Med 2021; 10:4138-4149. [PMID: 33960708 PMCID: PMC8209596 DOI: 10.1002/cam4.3935] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, the field of artificial intelligence (AI) in oncology has grown exponentially. AI solutions have been developed to tackle a variety of cancer‐related challenges. Medical institutions, hospital systems, and technology companies are developing AI tools aimed at supporting clinical decision making, increasing access to cancer care, and improving clinical efficiency while delivering safe, high‐value oncology care. AI in oncology has demonstrated accurate technical performance in image analysis, predictive analytics, and precision oncology delivery. Yet, adoption of AI tools is not widespread, and the impact of AI on patient outcomes remains uncertain. Major barriers for AI implementation in oncology include biased and heterogeneous data, data management and collection burdens, a lack of standardized research reporting, insufficient clinical validation, workflow and user‐design challenges, outdated regulatory and legal frameworks, and dynamic knowledge and data. Concrete actions that major stakeholders can take to overcome barriers to AI implementation in oncology include training and educating the oncology workforce in AI; standardizing data, model validation methods, and legal and safety regulations; funding and conducting future research; and developing, studying, and deploying AI tools through multidisciplinary collaboration.
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Affiliation(s)
- Isaac S Chua
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Michal Gaziel-Yablowitz
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Zfania T Korach
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Kenneth L Kehl
- Harvard Medical School, Boston, MA, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gretchen P Jackson
- IBM Watson Health, Cambridge, MA, USA.,Department of Pediatric Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David W Bates
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Michael Hassett
- Harvard Medical School, Boston, MA, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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75
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Tao R, Cao W, Zhu F, Nie J, Wang H, Wang L, Liu P, Chen H, Hong B, Zhao D. Liquid biopsies to distinguish malignant from benign pulmonary nodules. Thorac Cancer 2021; 12:1647-1655. [PMID: 33960710 PMCID: PMC8169297 DOI: 10.1111/1759-7714.13982] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022] Open
Abstract
Over the past decades, low-dose computed tomography (LD-CT) screening has been widely used for the early detection of lung cancer. Increasing numbers of indeterminate pulmonary nodules are now being discovered. However, it remains challenging to distinguish malignant from benign pulmonary nodules, especially those considered to be small or ground-glass (GGN) nodules. Liquid biopsies have been successfully applied in the diagnosis of advanced lung cancer, and the potential value for early detection of lung cancer has made great progress. Recent studies have demonstrated the value of various blood-based tumor biomarkers in determining the nature of pulmonary nodules, including cell-free DNA (cfDNA), microRNAs (miRNAs), circulating tumor cells (CTCs) and tumor-associated autoantibodies (AAbs). In this review, we summarize the latest progress of liquid biopsies, and their potential applications and challenges in the diagnosis of malignant pulmonary nodules.
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Affiliation(s)
- Rui Tao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Wei Cao
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Feng Zhu
- Department of Thoracic Surgery, Anhui Chest Hospital, Thoracic Clinical College of Anhui Medical University, Hefei, China
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Heath & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Hefei Cancer Hospital, Chinese Academy of Science, Hefei, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Heath & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Hefei Cancer Hospital, Chinese Academy of Science, Hefei, China
| | - Lixiang Wang
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Pengcheng Liu
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Hailong Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Bo Hong
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Heath & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Hefei Cancer Hospital, Chinese Academy of Science, Hefei, China
| | - Dahai Zhao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
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76
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Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands. Nat Biotechnol 2021; 39:1220-1227. [PMID: 33941929 DOI: 10.1038/s41587-021-00900-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Identification and quantification of low-frequency mutations remain challenging despite improvements in the baseline error rate of next-generation sequencing technologies. Here, we describe a method, termed SaferSeqS, that addresses these challenges by (1) efficiently introducing identical molecular barcodes in the Watson and Crick strands of template molecules and (2) enriching target sequences with strand-specific PCR. The method achieves high sensitivity and specificity and detects variants at frequencies below 1 in 100,000 DNA template molecules with a background mutation rate of <5 × 10-7 mutants per base pair (bp). We demonstrate that it can evaluate mutations in a single amplicon or simultaneously in multiple amplicons, assess limited quantities of cell-free DNA with high recovery of both strands and reduce the error rate of existing PCR-based molecular barcoding approaches by >100-fold.
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77
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Hajian R, DeCastro J, Parkinson J, Kane A, Camelo AFR, Chou PP, Yang J, Wong N, Hernandez EDO, Goldsmith B, Conboy I, Aran K. Rapid and Electronic Identification and Quantification of Age-Specific Circulating Exosomes via Biologically Activated Graphene Transistors. Adv Biol (Weinh) 2021; 5:e2000594. [PMID: 33929095 DOI: 10.1002/adbi.202000594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/23/2021] [Indexed: 12/12/2022]
Abstract
Increasing access to modern clinical practices concomitantly extends lifespan, ironically revealing new classes of degenerative and inflammatory diseases of later years. Here, an electronic graphene field-effect transistor (gFET) is reported, termed EV-chip, for label-free, rapid identification and quantification of exosomes (EV) associated with aging through specific surface markers, CD63 and CD151. Studies suggest that blood-derived exosomes carry specific biomolecules that can be used toward diagnostic applications of age and health. However, to observe improvements in patient outcomes, earlier detection at the point-of-care (POC) is required. Unfortunately, conventional techniques and other electronic-based platforms for exosome sensing are burdensome and inept for the POC distinction of aged blood factors. It is shown that EV-chip can quantitatively detect purified exosomes from plasma, with a limit of detection (LOD) of 2 × 104 particles mL-1 and a limit of quantification (LOQ) of 6 × 104 particles mL-1 . The sensitivity and compact electronics of the EV-chip improves upon previously published electronic biosensors, making it ideal for a physician's office or a simple biological laboratory. The sensitivity, selectivity, and portability of the EV-chip demonstrate the potential of the biosensor as a powerful point-of-care diagnostic and prognostic tool for age-related diseases.
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Affiliation(s)
- Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA.,Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | - Jonalyn DeCastro
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA
| | | | - Alex Kane
- Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | | | - Peichi Peggy Chou
- Keck Science Department, Pitzer College, The Claremont Colleges, Claremont, CA, 91711, USA
| | - Jielin Yang
- Keck Science Department, Claremont McKenna College, The Claremont Colleges, Claremont, CA, 91711, USA
| | - Nathan Wong
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Brett Goldsmith
- Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | - Irina Conboy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA.,Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
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78
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Chen Z, Zhao G, Wang K, Wang X, Ma Y, Xiong S, Zheng M, Fei S. Blood leukocytes methylation levels analysis indicate methylated plasma test is a promising tool for colorectal cancer early detection. J Cancer 2021; 12:3678-3685. [PMID: 33995643 PMCID: PMC8120172 DOI: 10.7150/jca.57114] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/22/2021] [Indexed: 12/19/2022] Open
Abstract
Background: A number of plasma methylated DNA biomarkers related to colorectal cancer (CRC) have been identified. However, the effect of methylation level in leukocytes on plasma-based methylation test was rarely reported. Methods: Blood samples from 213 individuals including 91 CRC patients were collected and separated into 3.5 mL of plasma and paired leukocyte fractions. DNA were extracted from plasma and leukocytes and bisulfite converted, followed by ColoDefense test that detects methylated SEPT9 (mSEPT9) and methylated SDC2 (mSDC2) simultaneously in a single qPCR reaction. Results: Both mSEPT9 and mSDC2 levels in leukocytes exhibited no significant difference among CRC, benign tumors and healthy controls. However, mSEPT9 and mSDC2 levels in plasma were significantly higher in CRC group than those in other groups. The sensitivities of mSEPT9 and mSDC2 alone for detecting CRC with plasma samples were 75.8% and 60.4% with specificities of 94.7% and 86.8%, respectively. These two markers in combination exhibited an improved sensitivity of 85.7% for CRC detection with a specificity of 86.8%, mostly attributable to increased sensitivity of 81.8% for detecting stage 0-II CRC. AUC values for mSEPT9 and mSDC2 alone were 0.864 (95% CI: 0.798 - 0.929) and 0.796 (95% CI: 0.719 - 0.874), respectively, but improved to 0.972 (95% CI: 0.949 - 0.996) when combined for ColoDefense test. Conclusions: The leukocytes gDNA will not affect the performance of plasma ColoDefense test, and plasma ColoDefense test exhibited high sensitivity and specificity in a validation set, demonstrating its potential as a non-invasive and cost-effective method for CRC early detection.
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Affiliation(s)
- Zhiliang Chen
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Jiangsu 221002, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou Jiangsu 221002, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210009, China.,Suzhou VersaBio Technologies Co. Ltd., Kunshan Jiangsu 215300, China
| | - Kai Wang
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China
| | - Xiaomei Wang
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China
| | - Yong Ma
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou Jiangsu 215163, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China.,Suzhou VersaBio Technologies Co. Ltd., Kunshan Jiangsu 215300, China
| | - Minxue Zheng
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan Jiangsu 215300, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou Jiangsu 215163, China
| | - Sujuan Fei
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Jiangsu 221002, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou Jiangsu 221002, China
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79
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Henriksen SD, Thorlacius-Ussing O. Cell-Free DNA Methylation as Blood-Based Biomarkers for Pancreatic Adenocarcinoma—A Literature Update. EPIGENOMES 2021; 5:epigenomes5020008. [PMID: 34968295 PMCID: PMC8594668 DOI: 10.3390/epigenomes5020008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic adenocarcinoma has a horrible prognosis, which is partly due to difficulties in diagnosing the disease in an early stage. Additional blood-born biomarkers for pancreatic adenocarcinoma are needed. Epigenetic modifications, as changes in DNA methylation, is a fundamental part of carcinogenesis. The aim of this paper is to do an update on cell-free DNA methylation as blood-based biomarkers for pancreatic adenocarcinoma. The current literature including our studies clearly indicates that cell-free DNA methylation has the potential as blood-based diagnostic and prognostic biomarkers for pancreatic adenocarcinoma. However, still no clinical applicable biomarker for pancreatic adenocarcinoma based on DNA methylation do exist. Further well-designed validation studies are needed.
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Affiliation(s)
- Stine Dam Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark
- Correspondence:
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark
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80
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Ferreira D, Miranda J, Martins-Lopes P, Adega F, Chaves R. Future Perspectives in Detecting EGFR and ALK Gene Alterations in Liquid Biopsies of Patients with NSCLC. Int J Mol Sci 2021; 22:ijms22083815. [PMID: 33916986 PMCID: PMC8067613 DOI: 10.3390/ijms22083815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a major cause of death worldwide. Alterations in such genes as EGFR and ALK are considered important biomarkers in NSCLC due to the existence of targeted therapies with specific tyrosine kinase inhibitors (TKIs). However, specific resistance-related mutations can occur during TKI treatment, which often result in therapy inefficacy. Liquid biopsies arise as a reliable tool for the early detection of these types of alterations, allowing a non-invasive follow-up of the patients. Furthermore, they can be essential for cancer screening, initial diagnosis and to check surgery success. Despite the great advantages of liquid biopsies in NSCLC and the high input that next-generation sequencing (NGS) approaches can provide in this field, its use in oncology is still limited. With improvement of assay sensitivity and the establishment of clinical guidelines for liquid biopsy analysis, it is expected that they will be used in routine procedures. This review focuses on the usefulness of liquid biopsies of NSCLC patients as a means to detect alterations in EGFR and ALK genes and in disease management, highlighting the impact of NGS methods.
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Affiliation(s)
- Daniela Ferreira
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Juliana Miranda
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Paula Martins-Lopes
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filomena Adega
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Raquel Chaves
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Correspondence: ; Tel.: +351-259-350936
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81
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Fishbein L, Del Rivero J, Else T, Howe JR, Asa SL, Cohen DL, Dahia PLM, Fraker DL, Goodman KA, Hope TA, Kunz PL, Perez K, Perrier ND, Pryma DA, Ryder M, Sasson AR, Soulen MC, Jimenez C. The North American Neuroendocrine Tumor Society Consensus Guidelines for Surveillance and Management of Metastatic and/or Unresectable Pheochromocytoma and Paraganglioma. Pancreas 2021; 50:469-493. [PMID: 33939658 DOI: 10.1097/mpa.0000000000001792] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ABSTRACT This manuscript is the result of the North American Neuroendocrine Tumor Society consensus conference on the medical management and surveillance of metastatic and unresectable pheochromocytoma and paraganglioma held on October 2 and 3, 2019. The panelists consisted of endocrinologists, medical oncologists, surgeons, radiologists/nuclear medicine physicians, nephrologists, pathologists, and radiation oncologists. The panelists performed a literature review on a series of questions regarding the medical management of metastatic and unresectable pheochromocytoma and paraganglioma as well as questions regarding surveillance after resection. The panelists voted on controversial topics, and final recommendations were sent to all panel members for final approval.
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Affiliation(s)
- Lauren Fishbein
- From the Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jaydira Del Rivero
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Tobias Else
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - James R Howe
- Division of Surgical Oncology and Endocrine Surgery, Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Sylvia L Asa
- Department of Pathology, University Hospitals Cleveland Medical Center and University Health Network, Toronto, Case Western Reserve University, Cleveland, OH
| | - Debbie L Cohen
- Renal Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Patricia L M Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX
| | - Douglas L Fraker
- Division of Endocrine and Oncologic Surgery, Department of Surgery, University of Pennsylvania and Abramson Cancer Center, Philadelphia, PA
| | - Karyn A Goodman
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Thomas A Hope
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA
| | - Pamela L Kunz
- Division of Oncology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Kimberly Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Nancy D Perrier
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel A Pryma
- Department of Radiology and Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Mabel Ryder
- Endocrine Oncology Tumor Group, Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - Aaron R Sasson
- Division of Surgical Oncology, Department of Surgery, Stony Brook University Medical Center, Stony Brook, NY
| | - Michael C Soulen
- Department of Radiology, University of Pennsylvania, Philadelphia, PA
| | - Camilo Jimenez
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX
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82
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Beltraminelli T, Perez CR, De Palma M. Disentangling the complexity of tumor-derived extracellular vesicles. Cell Rep 2021; 35:108960. [PMID: 33826890 DOI: 10.1016/j.celrep.2021.108960] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/21/2021] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
The tumor microenvironment encompasses an intertwined ensemble of both transformed cancer cells and non-transformed host cells, which together establish a signaling network that regulates tumor progression. By conveying both homo- and heterotypic cell-to-cell communication cues, tumor-derived extracellular vesicles (tEVs) modulate several cancer-associated processes, such as immunosuppression, angiogenesis, invasion, and metastasis. Herein we discuss how recent methodological advances in the isolation and characterization of tEVs may help to broaden our understanding of their functions in tumor biology and, potentially, establish their utility as cancer biomarkers.
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Affiliation(s)
- Tim Beltraminelli
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland; Swiss Cancer Center Léman (SCCL), Lausanne, Switzerland
| | - Caleb R Perez
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland; Swiss Cancer Center Léman (SCCL), Lausanne, Switzerland; Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michele De Palma
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland; Swiss Cancer Center Léman (SCCL), Lausanne, Switzerland.
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83
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Human Plasma Extracellular Vesicle Isolation and Proteomic Characterization for the Optimization of Liquid Biopsy in Multiple Myeloma. Methods Mol Biol 2021; 2261:151-191. [PMID: 33420989 DOI: 10.1007/978-1-0716-1186-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer cells secrete membranous extracellular vesicles (EVs) which contain specific oncogenic molecular cargo (including oncoproteins, oncopeptides, and RNA) into their microenvironment and the circulation. As such, EVs including exosomes (small EVs) and microvesicles (large EVs) represent important circulating biomarkers for various diseases, including cancer and its progression. These circulating biomarkers offer a potentially minimally invasive and repeatable targets for analysis (liquid biopsy) that could aid in the diagnosis, risk stratification, and monitoring of cancer. Although their potential as cancer biomarkers has been promising, the identification and quantification of EVs in clinical samples remain challenging. Like EVs, other types of circulating biomarkers (including cell-free nucleic acids, cf-NAs; or circulating tumor cells, CTCs) may represent a complementary or alternative approach to cancer diagnosis. In the context of multiple myeloma (MM), a systemic cancer type that causes cancer cells to accumulate in the bone marrow, the specific role for EVs as biomarkers for diagnosis and monitoring remains undefined. Tumor heterogeneity along with the various subtypes of MM (such as non-secretory MM) that cannot be monitored using conventional testing (e.g. sequential serological testing and bone marrow biopsies) render liquid biopsy and circulating tumor-derived EVs a promising approach. In this protocol, we describe the isolation and purification of EVs from peripheral blood plasma (PBPL) collected from healthy donors and patients with MM for a biomarker discovery strategy. Our results demonstrate detection of circulating EVs from as little as 1 mL of MM patients' PBPL. High-resolution mass spectrometry (MS)-based proteomics promises to provide new avenues in identifying novel markers for detection, monitoring, and therapeutic intervention of disease. We describe biophysical characterization and quantitative proteomic profiling of disease-specific circulating EVs which may provide important implications for the development of cancer diagnostics in MM.
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84
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Al-Shaheri FN, Alhamdani MSS, Bauer AS, Giese N, Büchler MW, Hackert T, Hoheisel JD. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer. Cancer Treat Rev 2021; 96:102193. [PMID: 33865174 DOI: 10.1016/j.ctrv.2021.102193] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany.
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Markus W Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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85
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Arechederra M, Recalde M, Gárate-Rascón M, Fernández-Barrena MG, Ávila MA, Berasain C. Epigenetic Biomarkers for the Diagnosis and Treatment of Liver Disease. Cancers (Basel) 2021; 13:1265. [PMID: 33809263 PMCID: PMC7998165 DOI: 10.3390/cancers13061265] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Research in the last decades has demonstrated the relevance of epigenetics in controlling gene expression to maintain cell homeostasis, and the important role played by epigenome alterations in disease development. Moreover, the reversibility of epigenetic marks can be harnessed as a therapeutic strategy, and epigenetic marks can be used as diagnosis biomarkers. Epigenetic alterations in DNA methylation, histone post-translational modifications (PTMs), and non-coding RNA (ncRNA) expression have been associated with the process of hepatocarcinogenesis. Here, we summarize epigenetic alterations involved in the pathogenesis of chronic liver disease (CLD), particularly focusing on DNA methylation. We also discuss their utility as epigenetic biomarkers in liquid biopsy for the diagnosis and prognosis of hepatocellular carcinoma (HCC). Finally, we discuss the potential of epigenetic therapeutic strategies for HCC treatment.
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Affiliation(s)
- María Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Miriam Recalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
| | - María Gárate-Rascón
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Matías A. Ávila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.A.); (M.R.); (M.G.-R.); (M.G.F.-B.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
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86
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Chen D, Wu Y, Hoque S, Tilley RD, Gooding JJ. Rapid and ultrasensitive electrochemical detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles. Chem Sci 2021; 12:5196-5201. [PMID: 34163756 PMCID: PMC8179593 DOI: 10.1039/d1sc01044a] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
An accurate and robust method for quantifying the levels of circulating tumor DNA (ctDNA) is vital if this potential biomarker is to be used for the early diagnosis of cancer. The analysis of ctDNA presents unique challenges because of its short half-life and ultralow abundance in early stage cancers. Here we develop an ultrasensitive electrochemical biosensor for rapid detection of ctDNA in whole blood. The sensing of ctDNA is based on hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles (DNA-Au@MNPs). This DNA-Au@MNPs biosensor can selectively detect short- and long-strand DNA targets. It has a broad dynamic range (2 aM to 20 nM) for 22 nucleotide DNA target with an ultralow detection limit of 3.3 aM. For 101 nucleotide ctDNA target, a dynamic range from 200 aM to 20 nM was achieved with a detection limit of 5 fM. This DNA-Au@MNPs based sensor provides a promising method to achieve 20 min response time and minimally invasive cancer early diagnosis.
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Affiliation(s)
- Dongfei Chen
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Yanfang Wu
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Sharmin Hoque
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Richard D Tilley
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales Sydney NSW 2052 Australia
| | - J Justin Gooding
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
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87
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Kenner B, Chari ST, Kelsen D, Klimstra DS, Pandol SJ, Rosenthal M, Rustgi AK, Taylor JA, Yala A, Abul-Husn N, Andersen DK, Bernstein D, Brunak S, Canto MI, Eldar YC, Fishman EK, Fleshman J, Go VLW, Holt JM, Field B, Goldberg A, Hoos W, Iacobuzio-Donahue C, Li D, Lidgard G, Maitra A, Matrisian LM, Poblete S, Rothschild L, Sander C, Schwartz LH, Shalit U, Srivastava S, Wolpin B. Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. Pancreas 2021; 50:251-279. [PMID: 33835956 PMCID: PMC8041569 DOI: 10.1097/mpa.0000000000001762] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ABSTRACT Despite considerable research efforts, pancreatic cancer is associated with a dire prognosis and a 5-year survival rate of only 10%. Early symptoms of the disease are mostly nonspecific. The premise of improved survival through early detection is that more individuals will benefit from potentially curative treatment. Artificial intelligence (AI) methodology has emerged as a successful tool for risk stratification and identification in general health care. In response to the maturity of AI, Kenner Family Research Fund conducted the 2020 AI and Early Detection of Pancreatic Cancer Virtual Summit (www.pdac-virtualsummit.org) in conjunction with the American Pancreatic Association, with a focus on the potential of AI to advance early detection efforts in this disease. This comprehensive presummit article was prepared based on information provided by each of the interdisciplinary participants on one of the 5 following topics: Progress, Problems, and Prospects for Early Detection; AI and Machine Learning; AI and Pancreatic Cancer-Current Efforts; Collaborative Opportunities; and Moving Forward-Reflections from Government, Industry, and Advocacy. The outcome from the robust Summit conversations, to be presented in a future white paper, indicate that significant progress must be the result of strategic collaboration among investigators and institutions from multidisciplinary backgrounds, supported by committed funders.
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Affiliation(s)
| | - Suresh T. Chari
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephen J. Pandol
- Basic and Translational Pancreas Research Program, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Anil K. Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, NewYork-Presbyterian/Columbia University Irving Medical Center, New York, NY
| | | | - Adam Yala
- Department of Electrical Engineering and Computer Science
- Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA
| | - Noura Abul-Husn
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Dana K. Andersen
- Division of Digestive Diseases and Nutrition, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | | | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marcia Irene Canto
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Yonina C. Eldar
- Department of Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Elliot K. Fishman
- Department of Radiology and Radiological Science, Johns Hopkins Medicine, Baltimore, MD
| | | | - Vay Liang W. Go
- UCLA Center for Excellence in Pancreatic Diseases, University of California, Los Angeles, Los Angeles, CA
| | | | - Bruce Field
- From the Kenner Family Research Fund, New York, NY
| | - Ann Goldberg
- From the Kenner Family Research Fund, New York, NY
| | | | - Christine Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Debiao Li
- Biomedical Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Lawrence H. Schwartz
- Department of Radiology, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - Uri Shalit
- Faculty of Industrial Engineering and Management, Technion—Israel Institute of Technology, Haifa, Israel
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Brian Wolpin
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA
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88
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Martins I, Ribeiro IP, Jorge J, Gonçalves AC, Sarmento-Ribeiro AB, Melo JB, Carreira IM. Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring. Genes (Basel) 2021; 12:349. [PMID: 33673461 PMCID: PMC7997281 DOI: 10.3390/genes12030349] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The minimally-or non-invasive detection of circulating tumor-derived components in biofluids, such as blood, liquid biopsy is a revolutionary approach with significant potential for the management of cancer. Genomic and transcriptomic alterations can be accurately detected through liquid biopsies, which provide a more comprehensive characterization of the heterogeneous tumor profile than tissue biopsies alone. Liquid biopsies could assist diagnosis, prognosis, and treatment selection, and hold great potential to complement current surveilling strategies to monitor disease evolution and treatment response in real-time. In particular, these are able to detect minimal residual disease, to predict progression, and to identify mechanisms of resistance, allowing to re-orient treatment strategies in a timelier manner. In this review we gathered current knowledge regarding the role and potential of liquid biopsies for the diagnosis and follow-up of cancer patients. The presented findings emphasize the strengths of liquid biopsies, revealing their chance of improving the diagnosis and monitoring of several tumor types in the near future. However, despite growing evidence supporting their value as a management tool in oncology, some limitations still need to be overcome for their implementation in the routine clinical setting.
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Affiliation(s)
- Ivana Martins
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Joana Jorge
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Haematology Department, Coimbra University Hospital Centre (CHUC), 3004-531 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
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89
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Damascelli B, Tichà V, Repetti E, Dorji T. Beyond Standard Practice in Liquid Biopsy: Selective Venous Sampling. J Vasc Interv Radiol 2021; 32:668-671. [PMID: 33621662 DOI: 10.1016/j.jvir.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/01/2021] [Accepted: 02/13/2021] [Indexed: 10/22/2022] Open
Abstract
Liquid biopsy is a molecular diagnostic procedure that aims to provide readily accessible genetic profiling of tumors for primary diagnosis, detection of minimal residual or metastatic disease, and therapeutic decision-making, especially for molecularly targeted treatments. Cancers release various biological markers into the circulation, although the most widely used are cell-free tumor DNA and circulating tumor cells. The paucity of biological material means that laboratory methods mainly based on genetic sequencing expose this innovative diagnostic method to a considerable incidence of false negatives. The 3 cases presented here show how the sensitivity and specificity of liquid biopsy may be improved through selective venous sampling.
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Affiliation(s)
- Bruno Damascelli
- Department of Interventional Oncology EMO GVM Centrocuore Columbus, Milano, Italy.
| | - Vladimira Tichà
- Department of Interventional Oncology EMO GVM Centrocuore Columbus, Milano, Italy
| | - Elena Repetti
- Chief Geneticist, TOMA Advanced Biomedical Assays S.p.A., Busto Arsizio (VA), Italy
| | - Tshering Dorji
- Chief Pathologist, TOMA Advanced Biomedical Assays S.p.A., Busto Arsizio (VA), Italy
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90
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Prognostic Significance of Gene Expression and DNA Methylation Markers in Circulating Tumor Cells and Paired Plasma Derived Exosomes in Metastatic Castration Resistant Prostate Cancer. Cancers (Basel) 2021; 13:cancers13040780. [PMID: 33668490 PMCID: PMC7918693 DOI: 10.3390/cancers13040780] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary “Liquid biopsy”, based on the analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), provides non-invasive real-time monitoring of tumor evolution and therapeutic efficacy. We performed for the first time a direct comparison study on gene expression and DNA methylation markers in CTCs and paired plasma-derived exosomes and evaluated their prognostic significance in metastatic castration resistant prostate cancer. Our results revealed for the first time a significantly higher positivity of all markers in EpCAM-positive CTCs compared to plasma-derived exosomes. We report that in EpCAM-positive CTCs, CK-19, PSMA, TWIST1 expression and GSTP1 methylation are significantly correlated with worse overall survival (OS), while in exosomes, CK-8 expression and GSTP1 and RASSF1A methylation status were significantly correlated with a lower OS. We also enumerated CTC and tumor-derived extracellular vesicles (tdEVs) using CellSearch (CS) and found a correlation between the CTC and tumor-derived extracellular vesicles (tdEVs) enumeration values. Abstract Liquid biopsy, based on the analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), provides non-invasive real-time monitoring of tumor evolution and therapeutic efficacy. We performed for the first time a direct comparison study on gene expression and DNA methylation markers in CTCs and paired plasma-derived exosomes and evaluated their prognostic significance in metastatic castration resistant prostate cancer. This prospective liquid biopsy (LB) study was based on a group of 62 metastatic castration resistant prostate cancer (mCRPC) patients and 10 healthy donors (HD) as controls. Identical blood draws were used to: (a) enumerate CTC and tumor-derived extracellular vesicles (tdEVs) using CellSearch (CS) and (b) analyze CTCs and paired plasma-derived exosomes at the gene expression and DNA methylation level. CTCs were enumerated using CellSearch in 57/62 patients, with values ranging from 5 to 854 cells/7.5 mL PB. Our results revealed for the first time a significantly higher positivity of gene expression markers (CK-8, CK-18, TWIST1, PSMA, AR-FL, AR-V7, AR-567 and PD-L1 mRNA) in EpCAM-positive CTCs compared to plasma-derived exosomes. GSTP1, RASSF1A and SCHLAFEN were methylated both in CTC and exosomes. In CTCs, Kaplan–Meier analysis revealed that CK-19 (p = 0.009), PSMA (p = 0.001), TWIST1 (p = 0.001) expression and GSTP1 (p = 0.001) methylation were correlated with OS, while in exosomes GSTP1 (p = 0.007) and RASSF1A (p = 0.001) methylation was correlated with OS. Our direct comparison study of CTCs and exosomes at gene expression and DNA methylation level, revealed for the first time a significantly higher positivity in EpCAM-positive CTCs compared to plasma-derived exosomes. Future perspective of this study should be the evaluation of clinical utility of molecular biomarkers in CTCs and exosomes on independent multicentric cohorts with mCRPC patients.
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91
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Menyhárt O, Győrffy B. Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis. Comput Struct Biotechnol J 2021; 19:949-960. [PMID: 33613862 PMCID: PMC7868685 DOI: 10.1016/j.csbj.2021.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
While cost-effective high-throughput technologies provide an increasing amount of data, the analyses of single layers of data seldom provide causal relations. Multi-omics data integration strategies across different cellular function levels, including genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes offer unparalleled opportunities to understand the underlying biology of complex diseases, such as cancer. We review some of the most frequently used data integration methods and outline research areas where multi-omics significantly benefit our understanding of the process and outcome of the malignant transformation. We discuss algorithmic frameworks developed to reveal cancer subtypes, disease mechanisms, and methods for identifying driver genomic alterations and consider the significance of multi-omics in tumor classifications, diagnostics, and prognostications. We provide a comprehensive summary of each omics strategy's most recent advances within the clinical context and discuss the main challenges facing their clinical implementations. Despite its unparalleled advantages, multi-omics data integration is slow to enter everyday clinics. One major obstacle is the uneven maturity of different omics approaches and the growing gap between generating large volumes of data compared to data processing capacity. Progressive initiatives to enforce the standardization of sample processing and analytical pipelines, multidisciplinary training of experts for data analysis and interpretation are vital to facilitate the translatability of theoretical findings.
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Affiliation(s)
- Otília Menyhárt
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, H-1094 Budapest, Hungary
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, H-1094 Budapest, Hungary
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
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92
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Kraaijpoel N, Mulder FI, Carrier M, van Lieshout A, Würdinger T, Best MG, van Vlijmen BJ, Mohammed Y, Jara-Palomares L, Kamphuisen PW, Di Nisio M, Ageno W, Beyer-Westendorf J, Vanassche T, Klokm FA, Otten HM, Peters MJ, Cosmi B, Wolde MT, Bossuyt PM, Büller HR, van Es N. Novel biomarkers to detect occult cancer in patients with unprovoked venous thromboembolism: Rationale and design of the PLATO-VTE study. THROMBOSIS UPDATE 2021. [DOI: 10.1016/j.tru.2020.100030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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93
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Piña-Sánchez P, Chávez-González A, Ruiz-Tachiquín M, Vadillo E, Monroy-García A, Montesinos JJ, Grajales R, Gutiérrez de la Barrera M, Mayani H. Cancer Biology, Epidemiology, and Treatment in the 21st Century: Current Status and Future Challenges From a Biomedical Perspective. Cancer Control 2021; 28:10732748211038735. [PMID: 34565215 PMCID: PMC8481752 DOI: 10.1177/10732748211038735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Since the second half of the 20th century, our knowledge about the biology of cancer has made extraordinary progress. Today, we understand cancer at the genomic and epigenomic levels, and we have identified the cell that starts neoplastic transformation and characterized the mechanisms for the invasion of other tissues. This knowledge has allowed novel drugs to be designed that act on specific molecular targets, the immune system to be trained and manipulated to increase its efficiency, and ever more effective therapeutic strategies to be developed. Nevertheless, we are still far from winning the war against cancer, and thus biomedical research in oncology must continue to be a global priority. Likewise, there is a need to reduce unequal access to medical services and improve prevention programs, especially in countries with a low human development index.
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Affiliation(s)
- Patricia Piña-Sánchez
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | | | - Martha Ruiz-Tachiquín
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Eduardo Vadillo
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Alberto Monroy-García
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Juan José Montesinos
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Rocío Grajales
- Department of Medical Oncology, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Marcos Gutiérrez de la Barrera
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
- Clinical Research Division, Oncology Hospital, Mexican Institute of Social Security, Mexico
| | - Hector Mayani
- Oncology Research Unit, Oncology Hospital, Mexican Institute of Social Security, Mexico
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94
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Monosomy 3 Influences Epithelial-Mesenchymal Transition Gene Expression in Uveal Melanoma Patients; Consequences for Liquid Biopsy. Int J Mol Sci 2020; 21:ijms21249651. [PMID: 33348918 PMCID: PMC7767066 DOI: 10.3390/ijms21249651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Despite outstanding advances in diagnosis and the treatment of primary uveal melanoma (UM), nearly 50% of UM patients develop metastases via hematogenous dissemination, driven by the epithelial-mesenchymal transition (EMT). Despite the failure in UM to date, a liquid biopsy may offer a feasible non-invasive approach for monitoring metastatic disease progression and addressing protracted dormancy. To detect circulating tumor cells (CTCs) in UM patients, we evaluated the mRNA expression of EMT-associated transcription factors in CD45-depleted blood fraction, using qRT-PCR. ddPCR was employed to assess UM-specific GNA11, GNAQ, PLCβ4, and CYSLTR2 mutations in plasma DNA. Moreover, microarray analysis was performed on total RNA isolated from tumor tissues to estimate the prognostic value of EMT-associated gene expression. In total, 42 primary UM and 11 metastatic patients were enrolled. All CD45-depleted samples were negative for CTC when compared to the peripheral blood fraction of 60 healthy controls. Tumor-specific mutations were detected in the plasma of 21.4% patients, merely, in 9.4% of primary UM, while 54.5% in metastatic patients. Unsupervised hierarchical clustering of differentially expressed EMT genes showed significant differences between monosomy 3 and disomy 3 tumors. Newly identified genes can serve as non-invasive prognostic biomarkers that can support therapeutic decisions.
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95
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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96
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Adeoye J, Wan CCJ, Thomson P. An appraisal of pivotal evaluation designs in validating noninvasive biomarkers for head and neck cancer detection. Acta Oncol 2020; 59:1500-1502. [PMID: 32924723 DOI: 10.1080/0284186x.2020.1820077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- John Adeoye
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
- Oral Cancer Research Group, The University of Hong Kong, Hong Kong SAR, China
| | - Chi Ching Joan Wan
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Peter Thomson
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
- Oral Cancer Research Group, The University of Hong Kong, Hong Kong SAR, China
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97
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Bresalier RS, Grady WM, Markowitz SD, Nielsen HJ, Batra SK, Lampe PD. Biomarkers for Early Detection of Colorectal Cancer: The Early Detection Research Network, a Framework for Clinical Translation. Cancer Epidemiol Biomarkers Prev 2020; 29:2431-2440. [PMID: 32299850 PMCID: PMC7572434 DOI: 10.1158/1055-9965.epi-20-0234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/26/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022] Open
Abstract
Early detection by screening significantly reduces mortality from colorectal cancer, but 40% of guideline-eligible patients are not screened as recommended in the United States. Novel strategies to improve screening uptake overall and efforts to deploy best practices to underserved populations are a high priority for health care. This review focuses on existing biomarkers in practice and those in development with clinical relevance to early detection of colorectal neoplasia, with an emphasis on those developed by investigators of the NCI's Early Detection Research Network. Aberrantly methylated DNA markers (blood and stool), stool-based markers (including fecal immunochemical test-DNA), and a variety of blood-based marker assays in development (protein markers, glycoproteins including mucins, and cell-free DNA tests) are reviewed. Individual markers and biomarker panels, sample resources, and barriers to translating biomarkers to clinical practice are discussed.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center and the Department of Medicine, Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington
| | - Sanford D Markowitz
- Case Comprehensive Cancer Center and the Division of Hematology-Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
- The Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, Omaha, Nebraska
| | - Paul D Lampe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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98
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Cohen JD, Diergaarde B, Papadopoulos N, Kinzler KW, Schoen RE. Tumor DNA as a Cancer Biomarker through the Lens of Colorectal Neoplasia. Cancer Epidemiol Biomarkers Prev 2020; 29:2441-2453. [PMID: 33033144 PMCID: PMC7710619 DOI: 10.1158/1055-9965.epi-20-0549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/06/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022] Open
Abstract
Biomarkers have a wide range of applications in the clinical management of cancer, including screening and therapeutic management. Tumor DNA released from neoplastic cells has become a particularly active area of cancer biomarker development due to the critical role somatic alterations play in the pathophysiology of cancer and the ability to assess released tumor DNA in accessible clinical samples, in particular blood (i.e., liquid biopsy). Many of the early applications of tumor DNA as a biomarker were pioneered in colorectal cancer due to its well-defined genetics and common occurrence, the effectiveness of early detection, and the availability of effective therapeutic options. Herein, in the context of colorectal cancer, we describe how the intended clinical application dictates desired biomarker test performance, how features of tumor DNA provide unique challenges and opportunities for biomarker development, and conclude with specific examples of clinical application of tumor DNA as a biomarker with particular emphasis on early detection.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Joshua D Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kenneth W Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert E Schoen
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
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99
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Avanzini S, Kurtz DM, Chabon JJ, Moding EJ, Hori SS, Gambhir SS, Alizadeh AA, Diehn M, Reiter JG. A mathematical model of ctDNA shedding predicts tumor detection size. SCIENCE ADVANCES 2020; 6:eabc4308. [PMID: 33310847 PMCID: PMC7732186 DOI: 10.1126/sciadv.abc4308] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/29/2020] [Indexed: 05/12/2023]
Abstract
Early cancer detection aims to find tumors before they progress to an incurable stage. To determine the potential of circulating tumor DNA (ctDNA) for cancer detection, we developed a mathematical model of tumor evolution and ctDNA shedding to predict the size at which tumors become detectable. From 176 patients with stage I to III lung cancer, we inferred that, on average, 0.014% of a tumor cell's DNA is shed into the bloodstream per cell death. For annual screening, the model predicts median detection sizes of 2.0 to 2.3 cm representing a ~40% decrease from the current median detection size of 3.5 cm. For informed monthly cancer relapse testing, the model predicts a median detection size of 0.83 cm and suggests that treatment failure can be detected 140 days earlier than with imaging-based approaches. This mechanistic framework can help accelerate clinical trials by precomputing the most promising cancer early detection strategies.
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Affiliation(s)
- Stefano Avanzini
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - David M Kurtz
- Division of Oncology, Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob J Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Everett J Moding
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon Seiko Hori
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanjiv Sam Gambhir
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Bio-X Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering and Department of Materials Science and Engineering, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Bio-X Program, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Biophysics Program, Stanford University, Stanford, CA 94305, USA
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100
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Dudley JC, Diehn M. Detection and Diagnostic Utilization of Cellular and Cell-Free Tumor DNA. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 16:199-222. [PMID: 33228464 DOI: 10.1146/annurev-pathmechdis-012419-032604] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Because cancer is caused by an accumulation of genetic mutations, mutant DNA released by tumors can be used as a highly specific biomarker for cancer. Although this principle was described decades ago, the advent and falling costs of next-generation sequencing have made the use of tumor DNA as a biomarker increasingly practical. This review surveys the use of cellular and cell-free DNA for the detection of cancer, with a focus on recent technological developments and applications to solid tumors. It covers (a) key principles and technology enabling the highly sensitive detection of tumor DNA; (b) assessment of tumor DNA in plasma, including for genotyping, minimal residual disease detection, and early detection of localized cancer; (c) detection of tumor DNA in body cavity fluids, such as urine or cerebrospinal fluid; and (d) challenges posed to the use of tumor DNA as a biomarker by the phenomenon of benign clonal expansions.
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Affiliation(s)
- Jonathan C Dudley
- Ludwig Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA;
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