1
|
Williams AL, Scorzo AV, Strawbridge RR, Davis SC, Niedre M. Two-color diffuse in vivo flow cytometer. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:065003. [PMID: 38818515 PMCID: PMC11138342 DOI: 10.1117/1.jbo.29.6.065003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Abstract
Significance Hematogenous metastasis is mediated by circulating tumor cells (CTCs) and CTC clusters (CTCCs). We recently developed "diffuse in vivo flow cytometry" (DiFC) to detect fluorescent protein (FP) expressing CTCs in small animals. Extending DiFC to allow detection of two FPs simultaneously would allow concurrent study of different CTC sub-populations or heterogeneous CTCCs in the same animal. Aim The goal of this work was to develop and validate a two-color DiFC system capable of non-invasively detecting circulating cells expressing two distinct FPs. Approach A DiFC instrument was designed and built to detect cells expressing either green FP (GFP) or tdTomato. We tested the instrument in tissue-mimicking flow phantoms in vitro and in multiple myeloma bearing mice in vivo. Results In phantoms, we could accurately differentiate GFP+ and tdTomato+ CTCs and CTCCs. In tumor-bearing mice, CTC numbers expressing both FPs increased during disease. Most CTCCs (86.5%) expressed single FPs with the remainder both FPs. These data were supported by whole-body hyperspectral fluorescence cryo-imaging of the mice. Conclusions We showed that two-color DiFC can detect two populations of CTCs and CTCCs concurrently. This instrument could allow study of tumor development and response to therapies for different sub-populations in the same animal.
Collapse
Affiliation(s)
- Amber L. Williams
- Northeastern University, Department of Bioengineering, Boston, Massachusetts, United States
| | - Augustino V. Scorzo
- Dartmouth College, Thayer School of Engineering, Hanover, New Hampshire, United States
| | | | - Scott C. Davis
- Dartmouth College, Thayer School of Engineering, Hanover, New Hampshire, United States
| | - Mark Niedre
- Northeastern University, Department of Bioengineering, Boston, Massachusetts, United States
| |
Collapse
|
2
|
Niu Y, Li Z, Chen Z, Huang W, Tan J, Tian F, Yang T, Fan Y, Wei J, Mu J. Efficient screening of pharmacological broad-spectrum anti-cancer peptides utilizing advanced bidirectional Encoder representation from Transformers strategy. Heliyon 2024; 10:e30373. [PMID: 38765108 PMCID: PMC11101728 DOI: 10.1016/j.heliyon.2024.e30373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024] Open
Abstract
In the vanguard of oncological advancement, this investigation delineates the integration of deep learning paradigms to refine the screening process for Anticancer Peptides (ACPs), epitomizing a new frontier in broad-spectrum oncolytic therapeutics renowned for their targeted antitumor efficacy and specificity. Conventional methodologies for ACP identification are marred by prohibitive time and financial exigencies, representing a formidable impediment to the evolution of precision oncology. In response, our research heralds the development of a groundbreaking screening apparatus that marries Natural Language Processing (NLP) with the Pseudo Amino Acid Composition (PseAAC) technique, thereby inaugurating a comprehensive ACP compendium for the extraction of quintessential primary and secondary structural attributes. This innovative methodological approach is augmented by an optimized BERT model, meticulously calibrated for ACP detection, which conspicuously surpasses existing BERT variants and traditional machine learning algorithms in both accuracy and selectivity. Subjected to rigorous validation via five-fold cross-validation and external assessment, our model exhibited exemplary performance, boasting an average Area Under the Curve (AUC) of 0.9726 and an F1 score of 0.9385, with external validation further affirming its prowess (AUC of 0.9848 and F1 of 0.9371). These findings vividly underscore the method's unparalleled efficacy and prospective utility in the precise identification and prognostication of ACPs, significantly ameliorating the financial and temporal burdens traditionally associated with ACP research and development. Ergo, this pioneering screening paradigm promises to catalyze the discovery and clinical application of ACPs, constituting a seminal stride towards the realization of more efficacious and economically viable precision oncology interventions.
Collapse
Affiliation(s)
- Yupeng Niu
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Zhenghao Li
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Ziao Chen
- College of Law, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Wenyuan Huang
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Jingxuan Tan
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Fa Tian
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
| | - Tao Yang
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Yamin Fan
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| | - Jiangshu Wei
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
| | - Jiong Mu
- College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China
- Artificial intelligence laboratory, Sichuan Agricultural University, Ya'an 625000, China
| |
Collapse
|
3
|
Scaini MC, Catoni C, Poggiana C, Pigozzo J, Piccin L, Leone K, Scarabello I, Facchinetti A, Menin C, Elefanti L, Pellegrini S, Aleotti V, Vidotto R, Schiavi F, Fabozzi A, Chiarion-Sileni V, Rosato A. A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance. NPJ Precis Oncol 2024; 8:78. [PMID: 38548846 PMCID: PMC10978909 DOI: 10.1038/s41698-024-00567-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Melanoma heterogeneity is a hurdle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcomes, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker for the real-time tracing of disease evolution. Thus, we aimed to correlate liquid biopsy dynamics with treatment response and progression by devising a multiplatform approach applied to longitudinal melanoma patient monitoring. We conceived an approach that exploits Next Generation Sequencing (NGS) and droplet digital PCR, as well as the FDA-cleared platform CellSearch, to analyze circulating tumor DNA (ctDNA) trend and circulating melanoma cell (CMC) count, together with their customized genetic and copy number variation analysis. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, followed for up to 28 months. BRAF mutations were detected in the plasma of 82% of patients. Single nucleotide variants known or suspected to confer resistance were identified in 70% of patients. Moreover, the amount of ctDNA, both at baseline and during response, correlated with the type and duration of the response itself, and the CMC count was confirmed to be a prognostic biomarker. This work provides proof of principle of the power of this approach and paves the way for a validation study aimed at evaluating early ctDNA-guided treatment decisions in stage IV melanoma. The NGS-based molecular profile complemented the analysis of ctDNA trend and, together with CMC analysis, revealed to be useful in capturing tumor evolution.
Collapse
Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Jacopo Pigozzo
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Luisa Piccin
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Kevin Leone
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Ilaria Scarabello
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Stefania Pellegrini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Riccardo Vidotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Francesca Schiavi
- Familial Cancer Clinic, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Oncology Unit 3, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | | | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| |
Collapse
|
4
|
Ayesa SL. Novel genetic assessments for cancer patients: where does medical imaging stand in the future of personalised medicine? J Med Radiat Sci 2024; 71:7-9. [PMID: 38356417 PMCID: PMC10920931 DOI: 10.1002/jmrs.762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
As our understanding of genetics in cancer care improves, the role of personalised medicine for patients continues to grow. With the increasing emergence of novel technologies for patient assessment, such as the evaluation of circulating tumour DNA, we must reflect on the potentially changing role that medical imaging will play in the future of optimal patient care.
Collapse
Affiliation(s)
- Sally L. Ayesa
- School of MedicineUniversity of SydneyCamperdownNew South WalesAustralia
- Department of Nuclear MedicineRoyal North Shore HospitalSt LeonardsNew South WalesAustralia
- Department of Medical Imaging & Nuclear MedicineGosford & Wyong HospitalsGosfordNew South WalesAustralia
| |
Collapse
|
5
|
Torresan S, de Scordilli M, Bortolot M, Di Nardo P, Foltran L, Fumagalli A, Guardascione M, Ongaro E, Puglisi F. Liquid biopsy in colorectal cancer: Onward and upward. Crit Rev Oncol Hematol 2024; 194:104242. [PMID: 38128627 DOI: 10.1016/j.critrevonc.2023.104242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide. In recent years, liquid biopsy has emerged as one of the most interesting areas of research in oncology, leading to innovative trials and practical changes in all aspects of CRC management. RNAs and cell free DNA (cfDNA) methylation are emerging as promising biomarkers for early diagnosis. Post-surgical circulating tumour DNA (ctDNA) can aid in evaluating minimal residual disease and personalising adjuvant treatment. In rectal cancer, ctDNA could improve response assessment to neoadjuvant therapy and risk stratification, especially in the era of organ-preservation trials. In the advanced setting, ctDNA analysis offers the opportunity to monitor treatment response and identify driver and resistance mutations more comprehensively than traditional tissue analysis, providing prognostic and predictive information. The aim of this review is to provide a detailed overview of the clinical applications and future perspectives of liquid biopsy in CRC.
Collapse
Affiliation(s)
- Sara Torresan
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Marco de Scordilli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy.
| | - Martina Bortolot
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Paola Di Nardo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Luisa Foltran
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Arianna Fumagalli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Michela Guardascione
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Elena Ongaro
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Fabio Puglisi
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| |
Collapse
|
6
|
Huang L, Xu Y, Wang N, Yi K, Xi X, Si H, Zhang Q, Xiang M, Rong Y, Yuan Y, Wang F. Next-Generation Preclinical Functional Testing Models in Cancer Precision Medicine: CTC-Derived Organoids. SMALL METHODS 2024; 8:e2301009. [PMID: 37882328 DOI: 10.1002/smtd.202301009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/10/2023] [Indexed: 10/27/2023]
Abstract
Basic and clinical cancer research requires tumor models that consistently recapitulate the characteristics of prima tumors. As ex vivo 3D cultures of patient tumor cells, patient-derived tumor organoids possess the biological properties of primary tumors and are therefore excellent preclinical models for cancer research. Patient-derived organoids can be established using primary tumor tissues, peripheral blood, pleural fluid, ascites, and other samples containing tumor cells. Circulating tumor cells acquired by non-invasive sampling feature dynamic circulation and high heterogeneity. Circulating tumor cell-derived organoids are prospective tools for the dynamic monitoring of tumor mutation evolution profiles because they reflect the heterogeneity of the original tumors to a certain extent. This review discusses the advantages and applications of patient-derived organoids. Meanwhile, this work highlights the biological functions of circulating tumor cells, the latest advancement in research of circulating tumor cell-derived organoids, and potential application and challenges of this technology.
Collapse
Affiliation(s)
- Lanxiang Huang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yaqi Xu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Na Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Kezhen Yi
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaodan Xi
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Huaqi Si
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qian Zhang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ming Xiang
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuan Rong
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, 430071, China
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| |
Collapse
|
7
|
Ngo HKC, Le H, Surh YJ. Nrf2, A Target for Precision Oncology in Cancer Prognosis and Treatment. J Cancer Prev 2023; 28:131-142. [PMID: 38205365 PMCID: PMC10774478 DOI: 10.15430/jcp.2023.28.4.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Activating nuclear factor-erythroid 2-related factor (Nrf2), a master regulator of redox homeostasis, has been shown to suppress initiation of carcinogenesis in normal cells. However, this transcription factor has recently been reported to promote proliferation of some transformed or cancerous cells. In tumor cells, Nrf2 is prone to mutations that result in stabilization and concurrent accumulation of its protein product. A hyperactivated mutant form of Nrf2 could support the cancer cells for enhanced proliferation, invasiveness, and resistance to chemotherapeutic agents and radiotherapy, which are associated with a poor clinical outcome. Hence understanding mutations in Nrf2 would have a significant impact on the prognosis and treatment of cancer in the era of precision medicine. This perspective would provide an insight into the genetic alterations in Nrf2 and suggest the application of small molecules, RNAi, and genome editing technologies, particularly CRISR-Cas9, in therapeutic intervention of cancer in the context of the involvement of Nrf2 mutations.
Collapse
Affiliation(s)
- Hoang Kieu Chi Ngo
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hoang Le
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Young-Joon Surh
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| |
Collapse
|
8
|
Wang D, Rausch C, Buerger SA, Tschuri S, Rothenberg-Thurley M, Schulz M, Hasenauer J, Ziemann F, Metzeler KH, Marr C. Modeling early treatment response in AML from cell-free tumor DNA. iScience 2023; 26:108271. [PMID: 38047080 PMCID: PMC10690559 DOI: 10.1016/j.isci.2023.108271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.
Collapse
Affiliation(s)
- Dantong Wang
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Simon A. Buerger
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Melanie Schulz
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Jan Hasenauer
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
- Computational Health Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Faculty of Mathematics and Natural Sciences, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Klaus H. Metzeler
- Department of Hematology and Cell Therapy, University Hospital Leipzig (UHL) 04103, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| |
Collapse
|
9
|
Lee S, Verkhoturov DS, Eller MJ, Verkhoturov SV, Shaw MA, Gwon K, Kim Y, Lucien F, Malhi H, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry Enables Multiplexed Analysis of Individual Hepatic Extracellular Vesicles. ACS NANO 2023; 17:23584-23594. [PMID: 38033295 PMCID: PMC10985841 DOI: 10.1021/acsnano.3c06604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state, which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for statistical analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate and then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags colocalized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nanoenvironment where targeted moieties colocalized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
Collapse
Affiliation(s)
- Seonhwa Lee
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Michael J. Eller
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | | | - Michael A. Shaw
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | - Kihak Gwon
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yohan Kim
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fabrice Lucien
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| |
Collapse
|
10
|
Di Cosimo S, De Marco C, Silvestri M, Busico A, Vingiani A, Pruneri G, Cappelletti V. Can we define breast cancer HER2 status by liquid biopsy? INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 381:23-56. [PMID: 37739483 DOI: 10.1016/bs.ircmb.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Human Epidermal growth factor Receptor 2 (HER2) assessment is crucial for breast cancer treatment. Therapeutic decisions for recurrent cases often rely on primary tumor status. However, mounting evidence suggests that tumors show dynamic changes and up to 10% of breast cancer modify their initial status during progression. It is still debated whether these changes reflect a biological evolution of the disease or are secondary to primary tumor heterogeneity. Certainly, repeating HER2 assessment during breast cancer trajectory is important for the increasing availability of effective anti-HER2 drugs. In response to this need, circulating biomarkers such as circulating tumor cells (CTCs) and cell-free circulating tumor DNA (ctDNA) offer the potential to safely and repeatedly assess HER2 status over time. This chapter outlines current methods for testing HER2 in CTCs and ctDNA, and reviews clinical trials evaluating its prognostic and predictive value in patients with breast cancer, as well as recent advances in the field.
Collapse
Affiliation(s)
- Serena Di Cosimo
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Cinzia De Marco
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Marco Silvestri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Adele Busico
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Andrea Vingiani
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Giancarlo Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Vera Cappelletti
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
| |
Collapse
|
11
|
Lee S, Verkhoturov DS, Eller MJ, Verkhoturov SV, Shaw MA, Gwon K, Kim Y, Lucien F, Malhi H, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry Enables Multiplexed Analysis of Individual Hepatic Extracellular Vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554053. [PMID: 37662200 PMCID: PMC10473594 DOI: 10.1101/2023.08.21.554053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags co-localized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nano-environment where targeted moieties co-localized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
Collapse
|
12
|
Mut M, Adiguzel Z, Cakir-Aktas C, Hanalioğlu Ş, Gungor-Topcu G, Kiyga E, Isikay I, Sarac A, Soylemezoglu F, Strobel T, Ampudia-Mesias E, Cameron C, Aslan T, Tekirdas E, Hayran M, Oguz KK, Henzler C, Saydam N, Saydam O. Extracellular-Vesicle-Based Cancer Panels Diagnose Glioblastomas with High Sensitivity and Specificity. Cancers (Basel) 2023; 15:3782. [PMID: 37568598 PMCID: PMC10417317 DOI: 10.3390/cancers15153782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Glioblastoma is one of the most devastating neoplasms of the central nervous system. This study focused on the development of serum extracellular vesicle (EV)-based glioblastoma tumor marker panels that can be used in a clinic to diagnose glioblastomas and to monitor tumor burden, progression, and regression in response to treatment. RNA sequencing studies were performed using RNA isolated from serum EVs from both patients (n = 85) and control donors (n = 31). RNA sequencing results for preoperative glioblastoma EVs compared to control EVs revealed 569 differentially expressed genes (DEGs, 2XFC, FDR < 0.05). By using these DEGs, we developed serum-EV-based biomarker panels for the following glioblastomas: wild-type IDH1 (96% sensitivity/80% specificity), MGMT promoter methylation (91% sensitivity/73% specificity), p53 gene mutation (100% sensitivity/89% specificity), and TERT promoter mutation (89% sensitivity/100% specificity). This is the first study showing that serum-EV-based biomarker panels can be used to diagnose glioblastomas with a high sensitivity and specificity.
Collapse
Affiliation(s)
- Melike Mut
- Department of Neurosurgery, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; (Ş.H.); (I.I.); (T.A.); (E.T.)
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara 06230, Turkey;
| | - Zelal Adiguzel
- TUBİTAK, GEBI, Gebze, Kocaeli 41470, Turkey; (Z.A.); (G.G.-T.); (E.K.); (A.S.)
- Faculty of Medicine KUTTAM, Koç University, Davutpaşa Street No. 4 Topkapi, Istanbul 34010, Turkey
| | - Canan Cakir-Aktas
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara 06230, Turkey;
| | - Şahin Hanalioğlu
- Department of Neurosurgery, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; (Ş.H.); (I.I.); (T.A.); (E.T.)
| | - Gamze Gungor-Topcu
- TUBİTAK, GEBI, Gebze, Kocaeli 41470, Turkey; (Z.A.); (G.G.-T.); (E.K.); (A.S.)
| | - Ezgi Kiyga
- TUBİTAK, GEBI, Gebze, Kocaeli 41470, Turkey; (Z.A.); (G.G.-T.); (E.K.); (A.S.)
| | - Ilkay Isikay
- Department of Neurosurgery, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; (Ş.H.); (I.I.); (T.A.); (E.T.)
| | - Aydan Sarac
- TUBİTAK, GEBI, Gebze, Kocaeli 41470, Turkey; (Z.A.); (G.G.-T.); (E.K.); (A.S.)
| | - Figen Soylemezoglu
- Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey;
| | - Thomas Strobel
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Elisabet Ampudia-Mesias
- Division of Hematology and Oncology, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55455, USA; (E.A.-M.); (C.C.)
| | - Charles Cameron
- Division of Hematology and Oncology, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55455, USA; (E.A.-M.); (C.C.)
| | - Tulay Aslan
- Department of Neurosurgery, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; (Ş.H.); (I.I.); (T.A.); (E.T.)
| | - Eray Tekirdas
- Department of Neurosurgery, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; (Ş.H.); (I.I.); (T.A.); (E.T.)
| | - Mutlu Hayran
- Department of Preventive Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey;
| | - Kader Karli Oguz
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey;
| | - Christine Henzler
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | | | - Okay Saydam
- Division of Hematology and Oncology, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55455, USA; (E.A.-M.); (C.C.)
| |
Collapse
|
13
|
Condoluci A, Rossi D. Special issue on circulating tumor DNA: Introductory editorial. Semin Hematol 2023; 60:125-131. [PMID: 37620237 DOI: 10.1053/j.seminhematol.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Adalgisa Condoluci
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland; Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland; Università della Svizzera Italiana, Lugano, Switzerland
| | - Davide Rossi
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland; Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland; Università della Svizzera Italiana, Lugano, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
| |
Collapse
|
14
|
Anzinger I, Nagel D, De Toni EN, Ofner A, Philipp AB, Holdt LM, Teupser D, Kolligs FT, Herbst A. Cell-free circulating ALU repeats in serum have a prognostic value for colorectal cancer patients. Cancer Biomark 2023:CBM210536. [PMID: 37302022 DOI: 10.3233/cbm-210536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Carcinoembryonic antigen (CEA) is the only established serum biomarker for colorectal cancer (CRC). To facilitate therapy decisions and improve the overall survival of CRC patients, prognostic biomarkers are required. OBJECTIVE We studied the prognostic value of five different cell free circulating DNA (fcDNA) fragments. The potential markers were ALU115, ALU247, LINE1-79, LINE1-300 and ND1-mt. METHODS The copy numbers of the DNA fragments were measured in the peripheral blood serum of 268 CRC patients using qPCR, the results were compared to common and previously described markers. RESULTS We found that ALU115 and ALU247 fcDNA levels correlate significantly with several clinicopathological parameters. An increased amount of ALU115 and ALU247 fcDNA fragments coincides with methylation of HPP1 (P< 0.001; P< 0.01), which proved to be a prognostic marker itself in former studies and also with increased CEA level (P< 0.001). ALU115 and ALU247 can define patients with poor survival in UICC stage IV (Alu115: HR = 2.9; 95% Cl 1.8-4.8, P< 0.001; Alu247: HR = 2.2; 95% Cl 1.3-3.6; P= 0.001). Combining ALU115 and HPP1, the prognostic value in UICC stage IV is highly significant (P< 0.001). CONCLUSIONS This study shows that an increased level of ALU fcDNA is an independent prognostic biomarker for advanced colorectal cancer disease.
Collapse
Affiliation(s)
- Isabel Anzinger
- Department of Urology, St. Elisabeth Hospital, Straubing, Germany
| | - Dorothea Nagel
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Enrico N De Toni
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Andrea Ofner
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Alexander B Philipp
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | | | - Andreas Herbst
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| |
Collapse
|
15
|
Yu Y, Zhang Y, Chen Y, Wang X, Kang K, Zhu N, Wu Y, Yi Q. Floating Immunomagnetic Microspheres for Highly Efficient Circulating Tumor Cell Isolation under Facile Magnetic Manipulation. ACS Sens 2023; 8:1858-1866. [PMID: 37067910 DOI: 10.1021/acssensors.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Among circulating tumor cell enrichment strategies, immunomagnetic beads (IMBs) have received great attention due to their excellent performance. However, traditional strategies using IMBs normally require an additional mechanical stirring device to fully mix the IMBs and specimens, and this step may cause mechanical cellular damage. In this study, by changing the architecture and motion trajectory control strategy of the IMBs, floating immunomagnetic microspheres (FIMMs) and their matching rotary magnetic manipulation device were proposed to achieve highly efficient CTC capture under a cell-friendly condition. Generally, the FIMMs were prepared through layer-by-layer assembly of the individual functional components, and their stress state governed by either buoyancy or magnetic force was tuned by the rotary magnetic manipulation device. Consequently, recognition of FIMMs and target cells as well as CTC recovery can be simply realized through external magnetic manipulation. Accordingly, satisfactory enrichment efficiencies for CTCs with varied epithelial expression levels were obtained as 92.93 ± 3.23% for MCF-7, 79.93 ± 3.31% for A549, and 92.57 ± 5.22% for HepG2. Besides, an extremely low detection limitation of 5 cells mL-1 can be achieved from complex sample conditions, even the whole blood. In addition, FIMMs successfully enriched 23-56 CTCs from 1.5 mL of blood samples from cancer patients.
Collapse
Affiliation(s)
- Yue Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Yujia Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Yu Chen
- Department of Cardiology, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, P. R. China
| | - Xuekang Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Ke Kang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Nanhang Zhu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| | - Qiangying Yi
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China
| |
Collapse
|
16
|
Jin J, Shao Y, Zhang J, Cao J, Tao Z, Hu X. High-purity isolation platelets by gradient centrifugation plus filtration. Int J Lab Hematol 2023; 45:187-194. [PMID: 36470678 DOI: 10.1111/ijlh.13998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Platelets can be used as a liquid biopsy source to provide rapid, up-to-date, and relevant information on tumor pathology and treatment response. However, there is still a lack of high efficiency methods for platelet isolation with high purity. METHODS Three platelet isolation methods were evaluated by platelet recovery and purity. The platelet inhibition cocktail (PIC) was added into peripheral blood, or was not allowed to access the effect of the platelet activation. The CD61, CD45, and CD62P labelled platelets, leukocytes and activated platelets were detected by flow cytometry. Quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS) were employed to determine the gene expression levels. A time-dependent experiment combined with qPCR was used to determine the time limit for platelet isolation at room temperature. RESULTS Compared to the gradient centrifugation alone, and gradient centrifugation plus filtration and magnetic beads separation, gradient centrifugation plus filtration was the preferred method for more efficient and high-purity platelet isolation, with a recovery rate of 9.1% and a purity of 99.98%. Furthermore, there was no difference in platelet activation level, regardless of whether PIC was used. Moreover, the rate of platelet RNA degradation did not differ when platelets were isolated within 48 h of blood collection. CONCLUSION Gradient centrifugation plus filtration at room temperature within 48 h of blood collection, without PIC, is a novel protocol with high recovery and purity rate to isolate platelets.
Collapse
Affiliation(s)
- Jia Jin
- Department of Lymphoma, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yilin Shao
- Department of Oncology, Shanghai Tenth People's Hospital, Shanghai, China
| | - Jian Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Phase I Clinical Trial Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Junning Cao
- Department of Lymphoma, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhonghua Tao
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast and Urological Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xichun Hu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast and Urological Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| |
Collapse
|
17
|
Roi A, Boia S, Rusu LC, Roi CI, Boia ER, Riviș M. Circulating miRNA as a Biomarker in Oral Cancer Liquid Biopsy. Biomedicines 2023; 11:biomedicines11030965. [PMID: 36979943 PMCID: PMC10046112 DOI: 10.3390/biomedicines11030965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/10/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Oral cancer is currently challenging the healthcare system, with a high incidence among the population and a poor survival rate. One of the main focuses related to this malignancy is the urge to implement a viable approach for improving its early diagnosis. By introducing the use of liquid biopsy and the identification of potential biomarkers, aiming for a noninvasive approach, new advancements offer promising perspectives in the diagnosis of oral cancer. The present review discusses the potential of circulating miRNAs as oral cancer biomarkers identified in body fluids such as serum, plasma, and saliva samples of oral cancer patients. Existing results reveal an important implication of different miRNA expressions involved in the initiation, development, progression, and metastasis rate of oral malignancy. Liquid biomarkers can play a crucial role in the development of the concept of personalized medicine, providing a wide range of clinical applications and future targeted therapies.
Collapse
Affiliation(s)
- Alexandra Roi
- Department of Oral Pathology, Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, "Victor Babes" University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania
| | - Simina Boia
- Department of Periodontology, "Victor Babes" University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania
| | - Laura-Cristina Rusu
- Department of Oral Pathology, Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, "Victor Babes" University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania
| | - Ciprian Ioan Roi
- Department of Anesthesiology and Oral Surgery, Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, "Victor Babes" University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 30041 Timisoara, Romania
| | - Eugen Radu Boia
- Department of Ear, Nose and Throat, "Victor Babes" University of Medicine and Pharmacy Timisoara, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania
| | - Mircea Riviș
- Department of Anesthesiology and Oral Surgery, Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, "Victor Babes" University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 30041 Timisoara, Romania
| |
Collapse
|
18
|
He S, Ding L, Yuan H, Zhao G, Yang X, Wu Y. A review of sensors for classification and subtype discrimination of cancer: Insights into circulating tumor cells and tumor-derived extracellular vesicles. Anal Chim Acta 2023; 1244:340703. [PMID: 36737145 DOI: 10.1016/j.aca.2022.340703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Liquid biopsy can reflect the state of tumors in vivo non-invasively, thus providing a strong basis for the early diagnosis, individualized treatment monitoring and prognosis of tumors. Circulating tumor cells (CTCs) and tumor-derived extracellular vesicles (tdEVs) contain information-rich components, such as nucleic acids and proteins, and they are essential markers for liquid biopsies. Their capture and analysis are of great importance for the study of disease occurrence and development and, consequently, have been the subject of many reviews. However, both CTCs and tdEVs carry the biological characteristics of their original tissue, and few reviews have focused on their function in the staging and classification of cancer. In this review, we focus on state-of-the-art sensors based on the simultaneous detection of multiple biomarkers within CTCs and tdEVs, with clinical applications centered on cancer classification and subtyping. We also provide a thorough discussion of the current challenges and prospects for novel sensors with the ultimate goal of cancer classification and staging. It is hoped that these most advanced technologies will bring new insights into the clinical practice of cancer screening and diagnosis.
Collapse
Affiliation(s)
- Sitian He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Huijie Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Gaofeng Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiaonan Yang
- School of Information Engineering, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
19
|
Hanna M, Dey N, Grady WM. Emerging Tests for Noninvasive Colorectal Cancer Screening. Clin Gastroenterol Hepatol 2023; 21:604-616. [PMID: 36539002 PMCID: PMC9974876 DOI: 10.1016/j.cgh.2022.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC) is among the most common cancers globally and a major cause of cancer-related deaths. The American Cancer Society estimates that CRC will kill 1 in 60 Americans, and CRC screening is recommended for all Americans ≥45 years of age. Current CRC screening methods are effective for preventing CRC and have been shown to reduce CRC-related mortality. However, none of the currently available tests is ideal, and many people are not compliant with screening recommendations. Novel screening tests based on advances in CRC molecular biology, genetics, and epigenetics, combined with developments in sequencing technologies and computational analytic methods, have been developed to address the shortcomings of current CRC screening tests. These emerging tests include blood-based assays that use plasma-derived circulating tumor DNA and serum proteins to detect early CRC and advanced adenomas, assays that use stool DNA or mRNA, and methods for profiling the gut microbiome. Here we review current screening modalities, and we discuss the principles behind the most promising emerging CRC screening tests and the data supporting their potential to be used in clinical practice.
Collapse
Affiliation(s)
- Marina Hanna
- Department of Medicine, University of Washington, Seattle, Washington
| | - Neelendu Dey
- Department of Medicine, University of Washington, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington; Microbiome Research Initiative, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - William M Grady
- Department of Medicine, University of Washington, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington.
| |
Collapse
|
20
|
Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
Collapse
|
21
|
Westphal, M, Pantel K, Ricklefs FL, Maire C, Riethdorf S, Mohme M, Wikman H, Lamszus K. Circulating tumor cells and extracellular vesicles as liquid biopsy markers in neuro-oncology: prospects and limitations. Neurooncol Adv 2022; 4:ii45-ii52. [PMID: 36380859 PMCID: PMC9650476 DOI: 10.1093/noajnl/vdac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For many tumor entities, tumor biology and response to therapy are reflected by components that can be detected and captured in the blood stream. The so called “liquid biopsy” has been stratified over time into the analysis of circulating tumor cells (CTC), extracellular vesicles (EVs), and free circulating components such as cell-free nucleic acids or proteins. In neuro-oncology, two distinct areas need to be distinguished, intrinsic brain tumors and tumors metastatic to the brain. For intrinsic brain tumors, specifically glioblastoma, CTCs although present in low abundance, contain highly relevant, yet likely incomplete biological information for the whole tumor. For brain metastases, CTCs can have clinical relevance for patients especially with oligometastatic disease and brain metastasis in cancers like breast and lung cancer. EVs shed from the tumor cells and the tumor environment provide complementary information. Sensitive technologies have become available that are able to detect both, CTCs and EVs in the peripheral blood of patients with intrinsic and metastatic brain tumors despite the blood brain barrier. In reference to glioblastoma EVs, being shed by tumor cells and microenvironment and being more diffusible than CTCs may yield a more complete reflection of the whole tumor compared to low-abundance CTCs representing only a fraction of the multiclonal tumor heterogeneity. We here review the emerging aspects of CTCs and EVs as liquid biopsy biomarkers in neuro-oncology.
Collapse
Affiliation(s)
- Manfred Westphal,
- Department of Neurosurgery, Hans-Dietrich Herrmann Laboratory for Brain Tumor Research , Hamburg , Germany
| | - Klaus Pantel
- Institute for Tumor Biology, University of Hamburg Medical Center Eppendorf , Hamburg , Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, Hans-Dietrich Herrmann Laboratory for Brain Tumor Research , Hamburg , Germany
| | - Cecile Maire
- Department of Neurosurgery, Hans-Dietrich Herrmann Laboratory for Brain Tumor Research , Hamburg , Germany
| | - Sabine Riethdorf
- Institute for Tumor Biology, University of Hamburg Medical Center Eppendorf , Hamburg , Germany
| | - Malte Mohme
- Department of Neurosurgery, Hans-Dietrich Herrmann Laboratory for Brain Tumor Research , Hamburg , Germany
| | - Harriet Wikman
- Institute for Tumor Biology, University of Hamburg Medical Center Eppendorf , Hamburg , Germany
| | - Katrin Lamszus
- Department of Neurosurgery, Hans-Dietrich Herrmann Laboratory for Brain Tumor Research , Hamburg , Germany
| |
Collapse
|
22
|
Kobayashi S, Sugasaki A, Yamamoto Y, Shigenoi Y, Udaka A, Yamamoto A, Tanaka M. Enrichment of Cancer Cells Based on Antibody-Free Selective Cell Adhesion. ACS Biomater Sci Eng 2022; 8:4547-4556. [PMID: 36153975 DOI: 10.1021/acsbiomaterials.2c00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blood-compatible and cell-adhering polymer materials are extremely useful for regenerative medicine and disease diagnosis. (Meth)acryl polymers with high hydrophilicity have been widely used in industries, and attempts to apply these polymers in the medical field are frequently reported. We focused on crosslinked polymer films prepared using bifunctional monomers, which are widely used as coating materials, and attempted to alter the cell adhesion behavior while maintaining blood compatibility by changing the chemical structure of the crosslinker. Four bifunctional monomers were studied, three of which were found to be blood-compatible polymers and to suppress platelet adhesion. The adhesion behavior of cancer cells to polymer films varied; moreover, the cancer model cells MCF-7 [EpCAM(+)] and MDA-MB-231 [EpCAM (-)], with different expression levels of epithelial cell adhesion molecule (EpCAM), showed distinct adhesion behavior for each material. We suggest that a combination of these materials has the potential to selectively capture and enrich highly metastatic cancer cells.
Collapse
Affiliation(s)
- Shingo Kobayashi
- Institute for Materials Chemistry and Engineering, Kyushu University, CE41 744 Motooka, Nishi-ku, Fukuoka819-0395, Japan
| | - Atsushi Sugasaki
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 4000 Kawashiri, Yoshida-cho, Haibara-gun, Shizuoka421-0396, Japan
| | - Yosuke Yamamoto
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa258-0022, Japan
| | - Yuta Shigenoi
- Electronic Materials Research Laboratories, FUJIFILM Corporation, 4000 Kawashiri, Yoshida-cho, Haibara-gun, Shizuoka421-0396, Japan
| | - Airi Udaka
- Institute for Materials Chemistry and Engineering, Kyushu University, CE41 744 Motooka, Nishi-ku, Fukuoka819-0395, Japan
| | - Aki Yamamoto
- Institute for Materials Chemistry and Engineering, Kyushu University, CE41 744 Motooka, Nishi-ku, Fukuoka819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, CE41 744 Motooka, Nishi-ku, Fukuoka819-0395, Japan
| |
Collapse
|
23
|
Hirotsu A, Kikuchi H, Yamada H, Ozaki Y, Haneda R, Kawata S, Murakami T, Matsumoto T, Hiramatsu Y, Kamiya K, Yamashita D, Fujimori Y, Ueda Y, Okazaki S, Kitagawa M, Konno H, Takeuchi H. Artificial intelligence-based classification of peripheral blood nucleated cells using label-free imaging flow cytometry. LAB ON A CHIP 2022; 22:3464-3474. [PMID: 35942978 DOI: 10.1039/d2lc00166g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Label-free image identification of circulating rare cells, such as circulating tumor cells within peripheral blood nucleated cells (PBNCs), the vast majority of which are white blood cells (WBCs), remains challenging. We previously described developing label-free image cytometry for classifying live cells using computer vision technology for pattern recognition, based on the subcellular structure of the quantitative phase microscopy images. We applied our image recognition methods to cells flowing in a flow cytometer microfluidic channel, and differentiated WBCs from cancer cell lines (area under receiver operating characteristic curve = 0.957). We then applied this method to healthy volunteers' and advanced cancer patients' blood samples and found that the non-WBC fraction rates (NWBC-FRs), defined as the percentage of cells classified as non-WBCs of the total PBNCs, were significantly higher in cancer patients than in healthy volunteers. Furthermore, we monitored NWBC-FRs over the therapeutic courses in cancer patients, which revealed the potential ability in monitoring the clinical status during therapy. Our image recognition system has the potential to provide a morphological diagnostic tool for circulating rare cells as non-WBC fractions.
Collapse
Affiliation(s)
- Amane Hirotsu
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Hirotoshi Kikuchi
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Hidenao Yamada
- Central Research Laboratory, Hamamatsu Photonics K.K, Hamamatsu, Shizuoka, Japan
| | - Yusuke Ozaki
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Ryoma Haneda
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Sanshiro Kawata
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Tomohiro Murakami
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Tomohiro Matsumoto
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Yoshihiro Hiramatsu
- Department Perioperative Functioning Care and Support, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Kinji Kamiya
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| | - Daisuke Yamashita
- Central Research Laboratory, Hamamatsu Photonics K.K, Hamamatsu, Shizuoka, Japan
| | - Yuki Fujimori
- Central Research Laboratory, Hamamatsu Photonics K.K, Hamamatsu, Shizuoka, Japan
| | - Yukio Ueda
- Central Research Laboratory, Hamamatsu Photonics K.K, Hamamatsu, Shizuoka, Japan
| | - Shigetoshi Okazaki
- HAMAMATSU BioPhotonics Innovation Chair, Institute for Medical Photonics Research, Preeminent Medical Photonics Education and Research Centre, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Centre, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Hiroyuki Konno
- Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Hiroya Takeuchi
- Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan.
| |
Collapse
|
24
|
New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
Collapse
|
25
|
García-Pardo M, Makarem M, Li JJN, Kelly D, Leighl NB. Integrating circulating-free DNA (cfDNA) analysis into clinical practice: opportunities and challenges. Br J Cancer 2022; 127:592-602. [PMID: 35347327 PMCID: PMC9381753 DOI: 10.1038/s41416-022-01776-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/12/2022] Open
Abstract
In the current era of precision medicine, the identification of genomic alterations has revolutionised the management of patients with solid tumours. Recent advances in the detection and characterisation of circulating tumour DNA (ctDNA) have enabled the integration of liquid biopsy into clinical practice for molecular profiling. ctDNA has also emerged as a promising biomarker for prognostication, monitoring disease response, detection of minimal residual disease and early diagnosis. In this Review, we discuss current and future clinical applications of ctDNA primarily in non-small cell lung cancer in addition to other solid tumours.
Collapse
Affiliation(s)
- Miguel García-Pardo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maisam Makarem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Janice J N Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Deirdre Kelly
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Natasha B Leighl
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| |
Collapse
|
26
|
Perge P, Nyirő G, Vékony B, Igaz P. Liquid biopsy for the assessment of adrenal cancer heterogeneity: where do we stand? Endocrine 2022; 77:425-431. [PMID: 35552979 PMCID: PMC9385753 DOI: 10.1007/s12020-022-03066-z] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/27/2022] [Indexed: 02/06/2023]
Abstract
Almost 10 years have passed since the first attempts of liquid biopsy aimed at the characterisation of tumor cells present in the bloodstream from a regular sample of peripheral blood were performed. Liquid biopsy has been used to characterise tumor heterogeneity in various types of solid tumors including adrenocortical carcinoma. The development of molecular biology, genetics, and methodological advances such as digital PCR and next-generation sequencing allowed us to use besides circulating tumor cells a variety of circulating cell-free nucleic acids, DNAs, RNAs and microRNAs secreted by tumors into blood and other body fluids as specific molecular markers. These markers are used for diagnosis, to check tumor development, selecting efficient therapies, therapy monitoring and even possess prognostic power. In adrenocortical carcinoma, there are some studies reporting analysis of circulating tumor cells, circulating cell free DNA and microRNAs for assessing tumor heterogeneity. Among microRNAs, hsa-miR-483-5p seems to be the most important player. Combined with other microRNAs like hsa-miR-195, their expression correlates with recurrence-free survival. Most studies support the applicability of liquid biopsy for assessing temporal tumor heterogeneity (i.e. tumor progression) in adrenocortical cancer. In this mini-review, the available findings of liquid biopsy for assessing tumor heterogeneity in adrenocortical cancer are presented.
Collapse
Affiliation(s)
- Pál Perge
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, H-1083, Budapest, Hungary
| | - Gábor Nyirő
- Department of Endocrinology, ENS@T Research Center of Excellence, Faculty of Medicine, Semmelweis University, H-1083, Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, H-1083, Budapest, Hungary
- Institute of Laboratory Medicine, Faculty of Medicine, Semmelweis University, H-1089, Budapest, Hungary
| | - Bálint Vékony
- Department of Endocrinology, ENS@T Research Center of Excellence, Faculty of Medicine, Semmelweis University, H-1083, Budapest, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, H-1083, Budapest, Hungary.
- Department of Endocrinology, ENS@T Research Center of Excellence, Faculty of Medicine, Semmelweis University, H-1083, Budapest, Hungary.
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, H-1083, Budapest, Hungary.
| |
Collapse
|
27
|
Preanalytical Variables in the Analysis of Mitochondrial DNA in Whole Blood and Plasma from Pancreatic Cancer Patients. Diagnostics (Basel) 2022; 12:diagnostics12081905. [PMID: 36010255 PMCID: PMC9406772 DOI: 10.3390/diagnostics12081905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 02/07/2023] Open
Abstract
Given the crucial role of mitochondria as the main cellular energy provider and its contribution towards tumor growth, chemoresistance, and cancer cell plasticity, mitochondrial DNA (mtDNA) could serve as a relevant biomarker. Thus, the profiling of mtDNA mutations and copy number variations is receiving increasing attention for its possible role in the early diagnosis and monitoring therapies of human cancers. This applies particularly to highly aggressive pancreatic cancer, which is often diagnosed late and is associated with poor prognosis. As current diagnostic procedures are based on imaging, tissue histology, and protein biomarkers with rather low specificity, tumor-derived mtDNA mutations detected from whole blood represents a potential significant leap forward towards early cancer diagnosis. However, for future routine use in clinical settings it is essential that preanalytics related to the characterization of mtDNA in whole blood are thoroughly standardized, controlled, and subject to proper quality assurance, yet this is largely lacking. Therefore, in this study we carried out a comprehensive preanalytical workup comparing different mtDNA extraction methods and testing important preanalytical steps, such as the use of different blood collection tubes, different storage temperatures, length of storage time, and yields in plasma vs. whole blood. To identify analytical and preanalytical differences, all variables were tested in both healthy subjects and pancreatic carcinoma patients. Our results demonstrated a significant difference between cancer patients and healthy subjects for some preanalytical workflows, while other workflows failed to yield statistically significant differences. This underscores the importance of controlling and standardizing preanalytical procedures in the development of clinical assays based on the measurement of mtDNA.
Collapse
|
28
|
Qayyumi B, Bharde A, Aland G, D'Souza A, Jayant S, Singh N, Tripathi S, Badave R, Kale N, Singh B, Arora S, Gore I, Singh A, Vasudevan A, Prabhash K, Khandare J, Chaturvedi P. Circulating tumor cells as a predictor for poor prognostic factors and overall survival in treatment naïve oral squamous cell carcinoma patients. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 134:73-83. [PMID: 35595620 DOI: 10.1016/j.oooo.2022.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the presence of circulating tumor cells (CTCs) and their correlation with prognostic factors and clinical outcomes in treatment-naive patients with oral squamous cell carcinoma. STUDY DESIGN CTCs were isolated using OncoDiscover technique from presurgically obtained peripheral blood of 152 patients with treatment naïve oral squamous cell carcinoma. Sensitivity analysis was performed by including 40 healthy controls. CTCs cutoff values for clinicopathologic factors were obtained from receiver operating characteristic curves. Multivariate models determined the significance of CTC as independent variables. Kaplan-Meier analysis differentiated in overall survival between CTC values corresponding to the stage. RESULTS Sensitivity, specificity, and accuracy of CTC detection were 94.32%, 98%, and 95.17%, respectively. Platform differentiated true positives at >3.5 CTCs (P < .00001). CTCs above 20.5 were suggestive of nodal metastasis (P < .0001) with a linear trend for detecting occult metastasis (P = .061). Early and advanced stages could be differentiated by >13.5 CTCs (P < .0001). Elevated CTCs were significantly associated with extranodal extension (>21.45 CTCs, P = .025), perineural invasion (>19.35 CTCs, P = .049), and depth of invasion (>12.5 CTCs, P = .0038). Median survival was reduced by 19 months when CTCs were >13. CONCLUSIONS Preoperative CTC levels demonstrated a strong correlation with adverse clinicopathology factors and suggested its role as a sensitive prognostic marker to predict survival outcome and disease progress.
Collapse
Affiliation(s)
- Burhanuddin Qayyumi
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Atul Bharde
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | | | - Alain D'Souza
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Sreeja Jayant
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Nitin Singh
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Swati Tripathi
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Reecha Badave
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Narendra Kale
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Balram Singh
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Smriti Arora
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Isha Gore
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Arjun Singh
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | | | - Kumar Prabhash
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Jayant Khandare
- Actorius Innovations and Research Pvt. Ltd., Pune, India; Actorius Innovations and Research Co, Simi Valley, CA, USA; OneCell Diagnostics Inc, Cupertino, CA, USA; OneCell Diagnostics Pvt. Ltd., Pune, India.
| | - Pankaj Chaturvedi
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India.
| |
Collapse
|
29
|
Temraz S, Nasr R, Mukherji D, Kreidieh F, Shamseddine A. Liquid Biopsy Derived Circulating Tumor Cells and Circulating Tumor DNA as Novel Biomarkers in Hepatocellular Carcinoma. Expert Rev Mol Diagn 2022; 22:507-518. [PMID: 35758097 DOI: 10.1080/14737159.2022.2094706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The diagnosis of hepatocellular carcinoma (HCC) is made at a relatively advanced stage resulting in poor prognosis. Alpha-fetoprotein and liver ultrasound have limited accuracy as biomarkers in HCC. Liver biopsy provides information on tumor biology; however, it is invasive and holds high threat of tumor seeding. Thus, more accurate and less invasive approaches are needed. AREAS COVERED Highly sensitive liquid biopsy assays have made possible the detection and analysis of cells or organelles such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and tumor-derived exosomes. Here, we focus on CTCs and ctDNA components of liquid biopsy and their clinical application as diagnostic, prognostic and predictive biomarkers in HCC. Unlike tissue biopsy, liquid biopsy involves attaining a sample at several time frames in an easy and a non-invasive manner. They have been efficacious in detecting and classifying cancer, in predicting treatment response, in monitoring disease relapse and in identifying mechanisms of resistance to targeted therapies. EXPERT OPINION Although interesting and highly promising, liquid biopsy techniques still have many obstacles to overcome before their wide spread clinical application sees the light. It is expected that these techniques will be incorporated into traditional methodologies for better diagnostic, predictive and prognostic results.
Collapse
Affiliation(s)
- Sally Temraz
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiology, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Deborah Mukherji
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Firas Kreidieh
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Ali Shamseddine
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| |
Collapse
|
30
|
Aulakh SS, Silverman DA, Young K, Dennis SK, Birkeland AC. The Promise of Circulating Tumor DNA in Head and Neck Cancer. Cancers (Basel) 2022; 14:cancers14122968. [PMID: 35740633 PMCID: PMC9221491 DOI: 10.3390/cancers14122968] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 12/17/2022] Open
Abstract
As the seventh most common cancer globally, head and neck cancers (HNC) exert considerable disease burden, with an estimated 277,597 deaths worldwide in 2020 alone. Traditional risk factors for HNC include tobacco, alcohol, and betel nut; more recently, human papillomavirus has emerged as a distinct driver of disease. Currently, limitations of cancer screening and surveillance methods often lead to identifying HNC in more advanced stages, with associated poor outcomes. Liquid biopsies, in particular circulating tumor DNA (ctDNA), offer the potential for enhancing screening, early diagnosis, and surveillance in HNC patients, with potential improvements in HNC patient outcomes. In this review, we examine current methodologies for detecting ctDNA and highlight current research illustrating viral and non-viral ctDNA biomarker utilities in HNC screening, diagnosis, treatment response, and prognosis. We also summarize current challenges and future directions for ctDNA testing in HNC patients.
Collapse
Affiliation(s)
| | - Dustin A. Silverman
- Department of Otolaryngology—Head and Neck Surgery, University of California, Davis, CA 95817, USA; (D.A.S.); (S.K.D.)
| | - Kurtis Young
- John A. Burns School of Medicine, Honolulu, HI 96813, USA;
| | - Steven K. Dennis
- Department of Otolaryngology—Head and Neck Surgery, University of California, Davis, CA 95817, USA; (D.A.S.); (S.K.D.)
| | - Andrew C. Birkeland
- Department of Otolaryngology—Head and Neck Surgery, University of California, Davis, CA 95817, USA; (D.A.S.); (S.K.D.)
- Correspondence:
| |
Collapse
|
31
|
Al Abir F, Shovan SM, Hasan MAM, Sayeed A, Shin J. Biomarker identification by reversing the learning mechanism of an autoencoder and recursive feature elimination. Mol Omics 2022; 18:652-661. [PMID: 35616228 DOI: 10.1039/d1mo00467k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA-Seq has made significant contributions to various fields, particularly in cancer research. Recent studies on differential gene expression analysis and the discovery of novel cancer biomarkers have extensively used RNA-Seq data. New biomarker identification is essential for moving cancer research forward, and early cancer diagnosis improves patients' chances of recovery and increases life expectancy. There is an urgency and scope of improvement in both sections. In this paper, we developed an autoencoder-based biomarker identification method by reversing the learning mechanism of the trained encoders. We devised an explainable post hoc methodology for identifying influential genes with a high likelihood of becoming biomarkers. We applied recursive feature elimination to shorten the list further and presented a list of 17 potential biomarkers that are 99.93% accurate in identifying cancer types using support vector machine for the UCI gene expression cancer RNA-Seq dataset consisting of five cancerous tumor types. Our methodology outperforms all of the state-of-the-art methods, confirming the potential of the newly identified biomarkers as well as the efficacy of the biomarker identification procedure. Moreover, we have evaluated the performance of our methodology using six independent RNA-Seq gene expression datasets for several tasks, i.e., classification of tumors from non-tumors, detecting the origin of circulating tumor cells (CTCs), and predicting if metastasis occurs or not. Our methodology achieved stimulating results for these tasks as well. The source code of this project is available at https://github.com/fuad021/biomarker-identification.
Collapse
Affiliation(s)
- Fuad Al Abir
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh.
| | - S M Shovan
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh. .,Department of Computer Science, Missouri University of Science & Technology, MO, USA
| | - Md Al Mehedi Hasan
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh. .,School of Computer Science and Engineering, University of Aizu, Aizuwakamatsu, Japan
| | - Abu Sayeed
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh.
| | - Jungpil Shin
- School of Computer Science and Engineering, University of Aizu, Aizuwakamatsu, Japan
| |
Collapse
|
32
|
Concentration of circulating tumour DNA in patients with metastatic gastric cancer and its prognostic significance. FORUM OF CLINICAL ONCOLOGY 2022. [DOI: 10.2478/fco-2021-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Abstract
Gastric cancer is one of the most common cancers worldwide. The amount of cell-free DNA (cfDNA) in the blood of patients with gastric cancer was found to be higher than that of healthy controls (69.1 ng/μL vs. 34.8 ng/μL). Patients with cfDNA ≤ 50 ng/μL were found to have an increased overall survival (OS) and progression free survival (PFS) than in patients with cfDNA > 50 ng/μL.
Collapse
|
33
|
Stiefel J, Freese C, Sriram A, Alebrand S, Srinivas N, Sproll C, Wandrey M, Gül D, Hagemann J, Becker JC, Baßler M. Characterization of a novel microfluidic platform for the isolation of rare single cells to enable CTC analysis from head and neck squamous cell carcinoma patients. Eng Life Sci 2022; 22:391-406. [PMID: 35573135 PMCID: PMC9077830 DOI: 10.1002/elsc.202100133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/14/2021] [Accepted: 12/24/2021] [Indexed: 12/20/2022] Open
Abstract
Detailed examination of tumor components is leading‐edge to establish personalized cancer therapy. Accompanying research on cell‐free DNA, the cell count of circulating tumor cells (CTCs) in patient blood is seen as a crucial prognostic factor. The potential of CTC analysis is further not limited to the determination of the overall survival rate but sheds light on understanding inter‐ and intratumoral heterogeneity. In this regard, commercial CTC isolation devices combining an efficient enrichment of rare cells with a droplet deposition of single cells for downstream analysis are highly appreciated. The Liquid biopsy platform CTCelect was developed to realize a fully‐automated enrichment and single cell dispensing of CTCs from whole blood without pre‐processing. We characterized each process step with two different carcinoma cell lines demonstrating up to 87 % enrichment (n = 10) with EpCAM coupled immunomagnetic beads, 73 % optical detection and dispensing efficiency (n = 5). 40 to 56.7 % of cells were recovered after complete isolation from 7.5 ml untreated whole blood (n = 6). In this study, CTCelect enabled automated dispensing of single circulating tumor cells from HNSCC patient samples, qPCR‐based confirmation of tumor‐related biomarkers and immunostaining. Finally, the platform was compared to commercial CTC isolation technologies to highlight advantages and limitations of CTCelect. This system offers new possibilities for single cell screening in cancer diagnostics, individual therapy approaches and real‐time monitoring.
Collapse
Affiliation(s)
- Janis Stiefel
- Fraunhofer Institute for Microengineering and Microsystems IMM Mainz Germany
| | - Christian Freese
- Fraunhofer Institute for Microengineering and Microsystems IMM Mainz Germany
| | - Ashwin Sriram
- Translational Skin Cancer Research DKTK Partner Site Essen/Düsseldorf West German Cancer Center Dermatology University Duisburg‐Essen, Essen, Germany; German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Sabine Alebrand
- Fraunhofer Institute for Microengineering and Microsystems IMM Mainz Germany
| | - Nalini Srinivas
- Translational Skin Cancer Research DKTK Partner Site Essen/Düsseldorf West German Cancer Center Dermatology University Duisburg‐Essen, Essen, Germany; German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Christoph Sproll
- Clinic for Oral and Maxilofacial Surgery Düsseldorf University Hospital Heinrich‐Heine‐University Düsseldorf Germany
| | - Madita Wandrey
- Department of Otorhinolaryngology/ENT University Medical Center Mainz Germany
| | - Désirée Gül
- Department of Otorhinolaryngology/ENT University Medical Center Mainz Germany
| | - Jan Hagemann
- Department of Otorhinolaryngology/ENT University Medical Center Mainz Germany
| | - Jürgen C. Becker
- Translational Skin Cancer Research DKTK Partner Site Essen/Düsseldorf West German Cancer Center Dermatology University Duisburg‐Essen, Essen, Germany; German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Michael Baßler
- Fraunhofer Institute for Microengineering and Microsystems IMM Mainz Germany
| |
Collapse
|
34
|
Gunderson CC, Radhakrishnan R, Gomathinayagam R, Husain S, Aravindan S, Moore KM, Dhanasekaran DN, Jayaraman M. Circulating Tumor Cell-Free DNA Genes as Prognostic Gene Signature for Platinum Resistant Ovarian Cancer Diagnosis. Biomark Insights 2022; 17:11772719221088404. [PMID: 35370397 PMCID: PMC8966103 DOI: 10.1177/11772719221088404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Clinical management of gynecological cancer begins by optimal debulking with first-line platinum-based chemotherapy. However, in ~80% patients, ovarian cancer will recur and is lethal. Prognostic gene signature panel identifying platinum-resistance enables better patient stratification for precision therapy. Retrospectively collected serum from 11 "poor" (<6 months progression free interval [PFI]) and 22 "favorable" (>24 months PFI) prognosis patients, were evaluated using circulating cell-free DNA (cfDNA). DNA from both groups showed 50 to 10 000 bp fragments. Pairwise analysis of sequenced cfDNA from patients showed that gene dosages were higher for 29 genes and lower for 64 genes in poor than favorable prognosis patients. Gene ontology analysis of higher dose genes predominantly grouped into cytoskeletal proteins, while lower dose genes, as hydrolases and receptors. Higher dosage genes searched for cancer-relatedness in Reactome database indicated 15 genes were referenced with cancer. Among them 3 genes, TGFBR2, ZMIZ2, and NRG2, were interacting with more than 4 cancer-associated genes. Protein expression analysis of tumor samples indicated that TGFBR2 was downregulated and ZMIZ2 was upregulated in poor prognosis patients. Our results indicate that the cfDNA gene dosage combined with protein expression in tumor samples can serve as gene signature panel for prognosis determination amongst ovarian cancer patients.
Collapse
Affiliation(s)
- Camille C Gunderson
- Section of Gynecologic Oncology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Rohini Gomathinayagam
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sanam Husain
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sheeja Aravindan
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kathleen M Moore
- Section of Gynecologic Oncology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Danny N Dhanasekaran
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Muralidharan Jayaraman
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Muralidharan Jayaraman, Department of Cell Biology, University of Oklahoma Health Sciences Center, Stephenson Cancer Center, 975 NE 10th Street, BRC416, Oklahoma City, OK 73104, USA.
| |
Collapse
|
35
|
Ginghina O, Hudita A, Zamfir M, Spanu A, Mardare M, Bondoc I, Buburuzan L, Georgescu SE, Costache M, Negrei C, Nitipir C, Galateanu B. Liquid Biopsy and Artificial Intelligence as Tools to Detect Signatures of Colorectal Malignancies: A Modern Approach in Patient's Stratification. Front Oncol 2022; 12:856575. [PMID: 35356214 PMCID: PMC8959149 DOI: 10.3389/fonc.2022.856575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 01/19/2023] Open
Abstract
Colorectal cancer (CRC) is the second most frequently diagnosed type of cancer and a major worldwide public health concern. Despite the global efforts in the development of modern therapeutic strategies, CRC prognosis is strongly correlated with the stage of the disease at diagnosis. Early detection of CRC has a huge impact in decreasing mortality while pre-lesion detection significantly reduces the incidence of the pathology. Even though the management of CRC patients is based on robust diagnostic methods such as serum tumor markers analysis, colonoscopy, histopathological analysis of tumor tissue, and imaging methods (computer tomography or magnetic resonance), these strategies still have many limitations and do not fully satisfy clinical needs due to their lack of sensitivity and/or specificity. Therefore, improvements of the current practice would substantially impact the management of CRC patients. In this view, liquid biopsy is a promising approach that could help clinicians screen for disease, stratify patients to the best treatment, and monitor treatment response and resistance mechanisms in the tumor in a regular and minimally invasive manner. Liquid biopsies allow the detection and analysis of different tumor-derived circulating markers such as cell-free nucleic acids (cfNA), circulating tumor cells (CTCs), and extracellular vesicles (EVs) in the bloodstream. The major advantage of this approach is its ability to trace and monitor the molecular profile of the patient's tumor and to predict personalized treatment in real-time. On the other hand, the prospective use of artificial intelligence (AI) in medicine holds great promise in oncology, for the diagnosis, treatment, and prognosis prediction of disease. AI has two main branches in the medical field: (i) a virtual branch that includes medical imaging, clinical assisted diagnosis, and treatment, as well as drug research, and (ii) a physical branch that includes surgical robots. This review summarizes findings relevant to liquid biopsy and AI in CRC for better management and stratification of CRC patients.
Collapse
Affiliation(s)
- Octav Ginghina
- Department II, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Ariana Hudita
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Marius Zamfir
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Andrada Spanu
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Mara Mardare
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | - Irina Bondoc
- Department of Surgery, “Sf. Ioan” Clinical Emergency Hospital, Bucharest, Romania
| | | | - Sergiu Emil Georgescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| | - Carolina Negrei
- Department of Toxicology, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
| | - Cornelia Nitipir
- Department II, University of Medicine and Pharmacy “Carol Davila” Bucharest, Bucharest, Romania
- Department of Oncology, Elias University Emergency Hospital, Bucharest, Romania
| | - Bianca Galateanu
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
| |
Collapse
|
36
|
Colmenares R, Álvarez N, Barrio S, Martínez-López J, Ayala R. The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies. Cancers (Basel) 2022; 14:cancers14051310. [PMID: 35267616 PMCID: PMC8909350 DOI: 10.3390/cancers14051310] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Monitoring the response to treatment in hematologic malignancies is essential in defining the best way to optimize patient management. In general, achieving a deeper response has been shown to lead to a better prognosis, and the techniques used to study the minimal residual disease (MRD) are becoming more precise. The use of liquid biopsies, that is, analyzing the presence of alterations in nucleic acids, usually in peripheral blood or other biological fluids, is being studied and optimized with increasingly innovative molecular techniques, such as next-generation sequencing (NGS) in the monitoring of the MRD, avoiding, in many cases, more invasive tests in different hematological neoplasms. Currently, liquid biopsies are not standardized for the MRD monitoring, but there is increasing evidence of its correlation with other techniques to measure responses to treatments and patient outcomes. Abstract The study of cell-free DNA (cfDNA) and other peripheral blood components (known as “liquid biopsies”) is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.
Collapse
Affiliation(s)
- Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
| | - Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-9-1779-2788
| |
Collapse
|
37
|
Yang JC, Hu JJ, Li YX, Luo W, Liu JZ, Ye DW. Clinical Applications of Liquid Biopsy in Hepatocellular Carcinoma. Front Oncol 2022; 12:781820. [PMID: 35211399 PMCID: PMC8860830 DOI: 10.3389/fonc.2022.781820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor with high mortality and poor prognosis in the world. The low rate of early diagnosis, as well as the high risk of postoperative metastasis and recurrence, led to the poor clinical prognosis of HCC patients. Currently, it mainly depends on serum markers, imaging examination, and tissue biopsy to diagnose and determine the recurrence and metastasis of HCC after treatments. Nevertheless, the accuracy and sensitivity of serum markers and imaging for early HCC diagnosis are suboptimal. Tissue biopsy, containing limited tissue samples, is insufficient to reveal comprehensive tumor biology information and is inappropriate to monitor dynamic tumor progression due to its invasiveness. Thus, low invasive diagnostic methods and novel biomarkers with high sensitivity and reliability must be found to improve HCC detection and prediction. As a non-invasive, dynamic, and repeatable detection method, “liquid biopsy”, has attracted much attention to early diagnosis and monitoring of treatment response, which promotes the progress of precision medicine. This review summarizes the clinical applications of liquid biopsy in HCC, including circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosome in early diagnosis, prognostic evaluation, disease monitoring, and guiding personalized treatment.
Collapse
Affiliation(s)
- Jin-Cui Yang
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun-Jie Hu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi-Xin Li
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Luo
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin-Zhou Liu
- Department of Pain Management, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Da-Wei Ye
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Pancreatic-Biliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| |
Collapse
|
38
|
Chen L, Luo S, Ge Z, Fan C, Yang Y, Li Q, Zhang Y. Unbiased Enrichment of Circulating Tumor Cells Via DNAzyme-Catalyzed Proximal Protein Biotinylation. NANO LETTERS 2022; 22:1618-1625. [PMID: 35156821 DOI: 10.1021/acs.nanolett.1c04583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Circulating tumor cells (CTCs) are noninvasive biomarkers with great potential for assessing neoplastic diseases. However, the enrichment bias toward heterogeneous CTCs remains to be minimized. Herein, a DNAzyme-catalyzed proximal protein biotinylation (DPPB) strategy is established for unbiased CTCs enrichment, employing DNA-framework-based, aptamer-coupled DNAzymes that bind to the surface marker of CTCs and subsequently biotinylated membrane proteins in situ. The DNA framework enables the construction of multivalent DNAzyme and serves as steric hindrance to avoid undesired interaction between DNAzymes and aptamer, leading to efficient binding and biotinylation. Compared with a biotinylated-aptamer strategy, fivefold lower bias of cell subpopulations was achieved by DPPB before and after capture, which enabled a 4.6-fold performance for CTCs analysis in clinic blood samples. DPPB is envisioned to offer a new solution for CTC-based cancer diagnostics.
Collapse
Affiliation(s)
- Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| |
Collapse
|
39
|
Investigating a clinically actionable BRAF mutation for monitoring low-grade serous ovarian cancer: A case report. Case Rep Womens Health 2022; 34:e00395. [PMID: 35198414 PMCID: PMC8851090 DOI: 10.1016/j.crwh.2022.e00395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 12/24/2022] Open
Abstract
Low-grade serous ovarian cancer (LGSOC) poses a specific clinical challenge due to advanced presentation at diagnosis and the lack of effective systemic treatments. The aim of this study was to use a precision medicine approach to identify clinically actionable mutations in a patient with recurrent LGSOC. Primary, metastatic and recurrence tissue, and blood samples were collected from a stage IV LGSOC patient. Single-gene testing for clinically actionable mutations (BRAF V600, KRAS and NRAS) and subsequent whole-exome sequencing (WES) were performed. Droplet digital PCR was used to evaluate the presence of an identified BRAF D594G mutation in the matched plasma cell-free DNA (cfDNA). No clinically actionable mutations were identified using single-gene testing. WES identified a BRAF D594G mutation in six of seven tumor samples. The patient was commenced on a MEK inhibitor, trametinib, but with minimal clinical response. A newly designed ddPCR assay detected the BRAF alteration in the matched tissues and liquid biopsy cfDNA. The identification and sensitive plasma detection of a common “druggable” target emphasises the impact of precision medicine on the management of rare tumors and its potential contribution to novel monitoring regimens in this field. First report of BRAF D594G mutation in multiple samples of a recurrent LGSOC patient. Discovery of a BRAF actionable mutation expands the range of LGSOC therapeutic options. ddPCR assay allows sensitive detection of the mutation in tissue and plasma samples.
Collapse
|
40
|
Nanomaterial-based biosensor developing as a route toward in vitro diagnosis of early ovarian cancer. Mater Today Bio 2022; 13:100218. [PMID: 35243293 PMCID: PMC8861407 DOI: 10.1016/j.mtbio.2022.100218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/13/2022] Open
Abstract
The grand challenges of ovarian cancer early diagnosis have led to an alarmingly high mortality rate from ovarian cancer (OC) in the past half century. In vitro diagnosis (IVD) has great potential in the early diagnosis of OC through non-invasive and dynamic analysis of biomarkers. However, common IVDs often fail to provide reliable test results due to lack of sensitivity, specificity, and convenience. In recent years, the discovery of new biomarkers and the progress of nanomaterials can solve the shortcomings of traditional IVD for early OC. These emerging biosensors based on nanomaterials offer great improvements in convenience, speed, selectivity, and sensitivity of IVD. In this review, we firstly systematically summarized the limits of commercial IVD biosensors of OC and the latest discovery of new biomarkers for OC. The representative optimization strategies for six potential ovarian cancer biomarkers are systematically discussed with emphasis on nanomaterial selection and the design of detection principles. Then, various strategies adopted by emerging biosensors based on nanomaterials are also introduced in detail, including optical, electrochemical, microfluidic, and surface plasmon sensors. Finally, current challenges of early OC IVD are proposed, and future research directions on this promising field are also discussed. Failure to diagnose OC early will lead to high mortality. The detection of OC-related biomarkers by IVD method will achieve early diagnosis of OC. The development of nanomaterials-based biosensors is expected to enhance efficiency of detection. Strategies and progress for nanomaterials-based biosensors are systematically reviewed.
Collapse
|
41
|
Zhang H, Zhao L, Jiang J, Zheng J, Yang L, Li Y, Zhou J, Liu T, Xu J, Lou W, Yang W, Tan L, Liu W, Yu Y, Ji M, Xu Y, Lu Y, Li X, Liu Z, Tian R, Hu C, Zhang S, Hu Q, Deng Y, Ying H, Zhong S, Zhang X, Wang Y, Wang H, Bai J, Li X, Duan X. Multiplexed nanomaterial-assisted laser desorption/ionization for pan-cancer diagnosis and classification. Nat Commun 2022; 13:617. [PMID: 35105875 PMCID: PMC8807648 DOI: 10.1038/s41467-021-26642-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
As cancer is increasingly considered a metabolic disorder, it is postulated that serum metabolite profiling can be a viable approach for detecting the presence of cancer. By multiplexing mass spectrometry fingerprints from two independent nanostructured matrixes through machine learning for highly sensitive detection and high throughput analysis, we report a laser desorption/ionization (LDI) mass spectrometry-based liquid biopsy for pan-cancer screening and classification. The Multiplexed Nanomaterial-Assisted LDI for Cancer Identification (MNALCI) is applied in 1,183 individuals that include 233 healthy controls and 950 patients with liver, lung, pancreatic, colorectal, gastric, thyroid cancers from two independent cohorts. MNALCI demonstrates 93% sensitivity at 91% specificity for distinguishing cancers from healthy controls in the internal validation cohort, and 84% sensitivity at 84% specificity in the external validation cohort, with up to eight metabolite biomarkers identified. In addition, across those six different cancers, the overall accuracy for identifying the tumor tissue of origin is 92% in the internal validation cohort and 85% in the external validation cohort. The excellent accuracy and minimum sample consumption make the high throughput assay a promising solution for non-invasive cancer diagnosis. As cancer is increasingly considered a metabolic disorder, it is postulated that serum metabolite profiling can be a viable approach for detecting the presence of cancer. Here, the authors report a machine learning model using mass spectrometry-based liquid biopsy data for pan-cancer screening and classification.
Collapse
Affiliation(s)
- Hua Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Lin Zhao
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jie Zheng
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, 430079, China
| | - Li Yang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Yanyan Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Tianshu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Wenhui Lou
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Weige Yang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Weiren Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yiyi Yu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yaolin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yan Lu
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaomu Li
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhen Liu
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Rong Tian
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Cheng Hu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Shumang Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Qinsheng Hu
- Department of Orthopaedic Surgery, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yangdong Deng
- School of Software, Tsinghua University, 100084, Beijing, China
| | - Hao Ying
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sheng Zhong
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, 430079, China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China.
| | - Hua Wang
- Department of Oncology, the First Affiliated Hospital, Institute for Liver Diseases of Anhui Medical University, Hefei, 230032, China.
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China.
| | - Xiaoying Li
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Xiangfeng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| |
Collapse
|
42
|
Biosensors for circulating tumor cells (CTCs)-biomarker detection in lung and prostate cancer: Trends and prospects. Biosens Bioelectron 2022; 197:113770. [PMID: 34768065 DOI: 10.1016/j.bios.2021.113770] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023]
Abstract
Cancer is one of the leading cause of death worldwide. Lung cancer (LCa) and prostate cancer (PCa) are the two most common ones particularly among men with about 20% of aggressive metastatic form leading to shorter overall survival. In recent years, circulating tumor cells (CTCs) have been investigated extensively for their role in metastatic progression and their involvement in reduced overall survival and treatment responses. Analysis of these cells and their associated biomarkers as "liquid biopsy" can provide valuable real-time information regarding the disease state and can be a potential avenue for early-stage detection and possible selection of personalized treatments. This review focuses on the role of CTCs and their associated biomarkers in lung and prostate cancer, as well as the shortcomings of conventional methods for their isolation and analysis. To overcome these drawbacks, biosensors are an elegant alternative because they are capable of providing valuable multiplexed information in real-time and analyzing biomarkers at lower concentrations. A comparative analysis of different transducing elements specific for the analysis of cancer cell and cancer biomarkers have been compiled in this review.
Collapse
|
43
|
Unveiling the Potential of Liquid Biopsy in HER2-Positive Breast Cancer Management. Cancers (Basel) 2022; 14:cancers14030587. [PMID: 35158855 PMCID: PMC8833720 DOI: 10.3390/cancers14030587] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Breast cancer (BC) is the most prevailing cancer in women worldwide. Amongst the different BC subtypes, human epidermal growth factor receptor 2 (HER2)-positive tumours are characterised by an overexpression of the HER2 membrane receptor. Nowadays, HER2-status assessment relies on immunohistochemical methodologies in the tumour tissue, which could be complemented by novel methodologies to improve the clinical management of these patients. In this regard, liquid biopsy is an easy, rapid, and minimally invasive tool to obtain circulating tumour components from body fluids. Herein, by reviewing the published studies, we aim to decipher the clinical validity of liquid biopsy in both early and metastatic HER2-positive BC. Abstract Invasive breast cancer (BC) is the most common cancer in women with a slightly increasing yearly incidence. BC immunohistochemical characterisation is a crucial tool to define the intrinsic nature of each tumour and personalise BC patients’ clinical management. In this regard, the characterisation of human epidermal growth factor receptor 2 (HER2) status guides physicians to treat with therapies tailored to this membrane receptor. Standardly, a tumour solid biopsy is therefore required, which is an invasive procedure and has difficulties to provide the complete molecular picture of the tumour. To complement these standard-of-care approaches, liquid biopsy is a validated methodology to obtain circulating tumour components such as circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) from body fluids in an easy-to-perform minimal-invasive manner. However, its clinical validity in cancer is still to be demonstrated. This review focusses on the utilisation of both ctDNA and CTCs in early and metastatic HER2-positive BC tumours. We discuss recently published studies deciphering the capacity of liquid biopsy to determine the response to neoadjuvant and adjuvant therapies as well as to predict patients’ outcomes.
Collapse
|
44
|
Perrier A, Hainaut P, Guenoun A, Nguyen DP, Lamy PJ, Guerber F, Troalen F, Denis JA, Boissan M. En marche vers une oncologie personnalisée : l’apport des techniques génomiques et de l’intelligence artificielle dans l’usage des biomarqueurs tumoraux circulants. Bull Cancer 2022; 109:170-184. [DOI: 10.1016/j.bulcan.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/20/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022]
|
45
|
Zhu G, Liu W, Tang Z, Qu W, Fang Y, Jiang X, Song S, Wang H, Tao C, Zhou P, Huang R, Gao J, Sun H, Ding Z, Peng Y, Dai Z, Zhou J, Fan J, Shi Y. Serial circulating tumor DNA to predict early recurrence in patients with hepatocellular carcinoma: a prospective study. Mol Oncol 2022; 16:549-561. [PMID: 34543520 PMCID: PMC8763657 DOI: 10.1002/1878-0261.13105] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/25/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
We studied the value of circulating tumor DNA (ctDNA) in predicting early postoperative tumor recurrence and monitoring tumor burden in patients with hepatocellular carcinoma (HCC). Plasma-free DNA, germline DNA, and tissue DNA were isolated from 41 patients with HCC. Serial ctDNAs were analyzed by next-generation sequencing before and after operation. Whole-exome sequencing was used to detect the DNA of HCC and adjacent tissues. In total, 47 gene mutations were identified in the ctDNA of the 41 patients analyzed before surgery. ctDNA was detected in 63.4% and 46% of the patient plasma pre- and postoperation, respectively. The preoperative ctDNA positivity rate was significantly lower in the nonrecurrence group than in the recurrence group. With a median follow-up of 17.7 months, nine patients (22%) experienced tumor recurrence. ctDNA positivity at two time-points was associated with significantly shorter recurrence-free survival (RFS). Tumors with NRAS, NEF2L2, and MET mutations had significantly shorter times to recurrence than those without mutations and showed high recurrence prediction performance by machine learning. Multivariate analyses showed that the median variant allele frequency (VAF) of mutations in preoperative ctDNA was a strong independent predictor of RFS. ctDNA is a real-time monitoring indicator that can accurately reflect tumor burden. The median VAF of baseline ctDNA is a strong independent predictor of RFS in individuals with HCC.
Collapse
|
46
|
Aleotti V, Catoni C, Poggiana C, Rosato A, Facchinetti A, Scaini MC. Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. Cancers (Basel) 2021; 13:6217. [PMID: 34944843 PMCID: PMC8699653 DOI: 10.3390/cancers13246217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023] Open
Abstract
Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
Collapse
Affiliation(s)
- Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| |
Collapse
|
47
|
Pathak N, Chitikela S, Malik PS. Recent advances in lung cancer genomics: Application in targeted therapy. ADVANCES IN GENETICS 2021; 108:201-275. [PMID: 34844713 DOI: 10.1016/bs.adgen.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genomic characterization of lung cancer has not only improved our understanding of disease biology and carcinogenesis but also revealed several therapeutic opportunities. Targeting tumor dependencies on specific genomic alterations (oncogene addiction) has accelerated the therapeutic developments and significantly improved the outcomes even in advanced stage of disease. Identification of genomic alterations predicting response to specific targeted treatment is the key to success for this "personalized treatment" approach. Availability of multiple choices of therapeutic options for specific genomic alterations highlight the importance of optimum sequencing of drugs. Multiplex gene testing has become mandatory in view of constantly increasing number of therapeutic targets and effective treatment options. Influence of genomic characteristics on response to immunotherapy further makes comprehensive genomic profiling necessary before therapeutic decision making. A comprehensive elucidation of resistance mechanisms and directed treatments have made the continuum of care possible and transformed this deadly disease into a chronic condition. Liquid biopsy-based approach has made the dynamic monitoring of disease possible and enabled treatment optimizations accordingly. Current lung cancer management is the perfect example of "precision-medicine" in clinical oncology.
Collapse
Affiliation(s)
- Neha Pathak
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sindhura Chitikela
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat Singh Malik
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
48
|
Zhu Z, Li F, Wang X, Li C, Meng Q, Wang C, Huang J, Chen S, Wu X. Correlation of transrenal DNA with non-small-cell lung cancer in noninvasive disease monitoring. Biomark Med 2021; 15:1553-1562. [PMID: 34651512 DOI: 10.2217/bmm-2020-0651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: The study aims to use noninvasive transrenal DNA in advanced non-small-cell lung cancer (NSCLC) patients for treatment monitoring and prognosis. Methods: Urine specimens were collected longitudinally for 103 late-stage NSCLC patients. Detection of targetable mutations in transrenal DNA was achieved by digital droplet PCR. Patients' overall survival outcomes were correlated with levels of transrenal DNA. Results: Corresponding patients' matched tumor results demonstrated concordance rate of 95.6% with transrenal DNA. A significant decline in levels was observed after treatment initiation. We observed changes in transrenal DNA levels to be significantly associated with survival for patients (p < 0.0001). Conclusion: Our results demonstrated strong predictive values of transrenal DNA to better identify patients with poorer survival outcomes and may further complement disease management.
Collapse
Affiliation(s)
- Ziyang Zhu
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Fajiu Li
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Xiaojiang Wang
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Chenghong Li
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Qinghua Meng
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Chuanhai Wang
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Jie Huang
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Shi Chen
- Department of Respiratory Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| | - Xiaomu Wu
- Department of Internal Medicine, Wuhan No. 6 Hospital, Affiliated Hospital to Jianghan University, Wuhan, People's Republic of China
| |
Collapse
|
49
|
Gatto L, Franceschi E, Di Nunno V, Tosoni A, Lodi R, Brandes AA. Liquid Biopsy in Glioblastoma Management: From Current Research to Future Perspectives. Oncologist 2021; 26:865-878. [PMID: 34105205 PMCID: PMC8488799 DOI: 10.1002/onco.13858] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/02/2021] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary tumor of the central nervous system. Arising from neuroepithelial glial cells, GBM is characterized by invasive behavior, extensive angiogenesis, and genetic heterogeneity that contributes to poor prognosis and treatment failure. Currently, there are several molecular biomarkers available to aid in diagnosis, prognosis, and predicting treatment outcomes; however, all require the biopsy of tumor tissue. Nevertheless, a tissue sample from a single location has its own limitations, including the risk related to the procedure and the difficulty of obtaining longitudinal samples to monitor treatment response and to fully capture the intratumoral heterogeneity of GBM. To date, there are no biomarkers in blood or cerebrospinal fluid for detection, follow-up, or prognostication of GBM. Liquid biopsy offers an attractive and minimally invasive solution to support different stages of GBM management, assess the molecular biology of the tumor, identify early recurrence and longitudinal genomic evolution, predict both prognosis and potential resistance to chemotherapy or radiotherapy, and allow patient selection for targeted therapies. The aim of this review is to describe the current knowledge regarding the application of liquid biopsy in glioblastoma, highlighting both benefits and obstacles to translation into clinical care. IMPLICATIONS FOR PRACTICE: To translate liquid biopsy into clinical practice, further prospective studies are required with larger cohorts to increase specificity and sensitivity. With the ever-growing interest in RNA nanotechnology, microRNAs may have a therapeutic role in brain tumors.
Collapse
Affiliation(s)
- Lidia Gatto
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Enrico Franceschi
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Vincenzo Di Nunno
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Alicia Tosoni
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Raffaele Lodi
- Istituto delle Scienze Neurologiche di Bologna, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)BolognaItaly
| | - Alba Ariela Brandes
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| |
Collapse
|
50
|
Khan S, Burciu B, Filipe CDM, Li Y, Dellinger K, Didar TF. DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective. ACS NANO 2021; 15:13943-13969. [PMID: 34524790 DOI: 10.1021/acsnano.1c04327] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.
Collapse
Affiliation(s)
- Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Brenda Burciu
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Gate City Boulevard, Greensboro, North Carolina 27401, United States
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Gate City Boulevard, Greensboro, North Carolina 27401, United States
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| |
Collapse
|