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Thakur S, Rathor A, Jain S, Nambirajan A, Khurana S, Malik PS, Jain D. Pleural effusion supernatant: a reliable resource for cell-free DNA in molecular testing of lung cancer. J Am Soc Cytopathol 2024; 13:291-302. [PMID: 38704351 DOI: 10.1016/j.jasc.2024.03.006] [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: 01/03/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 05/06/2024]
Abstract
INTRODUCTION DNA extracted from malignant pleural effusion (PE) sediments is the traditional source of tumor DNA for predictive biomarker molecular testing (MT). Few recent studies have proposed the utility of cell-free DNA (cfDNA) extracted from effusion cytology centrifuged supernatants (CCS) in MT. The aim of this study was to assess the feasibility and utility of molecular testing on cfDNA extracted from PE CCS in lung cancer patients. MATERIALS AND METHODS The study was of prospective design. All PE CCS were collected and stored. Subsequently, in patients confirmed as primary lung adenocarcinoma (LUAD) and where patient matched effusion sediment/tissue biopsy/plasma was being tested for EGFR mutations, cfDNA extraction and EGFR MT by real-time polymerase chain reaction (qPCR) were performed. Custom panel targeted next-generation sequencing (NGS) (Ion Torrent; Thermo Fisher, Carlsbad, CA) was also performed wherever feasible. RESULTS Out of 299 PE CCS collected, 20 CCS samples were included in the study. Concordant EGFR mutations were detected in pleural effusion CCS of 10 of 11 (91%) EGFR mutant cases as per qPCR performed on the matched sediment DNA (n = 8), lung biopsy (n = 2), and plasma (n = 1) samples. In 1 positive sample, CCS detected additional EGFR T790M mutation. Among 10 CCS samples also tested by NGS, additional EGFR mutations missed by qPCR were picked up in 2 (2 of 10). Success of mutation detection in CCS cfDNA did not correlate with cfDNA quantity or tumor fraction in sediment. CONCLUSIONS cfDNA from effusion CCS is a reliable and independent source of tumor DNA highly amenable for MT and complement results from other tumor DNA sources for comprehensive mutation profiling in LUAD patients.
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Affiliation(s)
- Shilpi Thakur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Amber Rathor
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Surabhi Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Khurana
- Department of Medical Oncology, Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat Singh Malik
- Department of Medical Oncology, Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.
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Pastò B, Buzzatti G, Schettino C, Malapelle U, Bergamini A, De Angelis C, Musacchio L, Dieci MV, Kuhn E, Lambertini M, Passarelli A, Toss A, Farolfi A, Roncato R, Capoluongo E, Vida R, Pignata S, Callari M, Baldassarre G, Bartoletti M, Gerratana L, Puglisi F. Unlocking the potential of Molecular Tumor Boards: from cutting-edge data interpretation to innovative clinical pathways. Crit Rev Oncol Hematol 2024; 199:104379. [PMID: 38718940 DOI: 10.1016/j.critrevonc.2024.104379] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The emerging era of precision medicine is characterized by an increasing availability of targeted anticancer therapies and by the parallel development of techniques to obtain more refined molecular data, whose interpretation may not always be straightforward. Molecular tumor boards gather various professional figures, in order to leverage the analysis of molecular data and provide prognostic and predictive insights for clinicians. In addition to healthcare development, they could also become a tool to promote knowledge and research spreading. A growing body of evidence on the application of molecular tumor boards to clinical practice is forming and positive signals are emerging, although a certain degree of heterogeneity exists. This work analyzes molecular tumor boards' potential workflows, figures involved, data sources, sample matrices and eligible patients, as well as available evidence and learning examples. The emerging concept of multi-institutional, disease-specific molecular tumor boards is also considered by presenting two ongoing nationwide experiences.
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Affiliation(s)
- Brenno Pastò
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Giulia Buzzatti
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
| | - Clorinda Schettino
- Clinical Trials Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli 80131, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Napoli 80131, Italy
| | - Alice Bergamini
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milano 20132, Italy; Unit of Obstetrics and Gynaecology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - Carmine De Angelis
- Oncology Unit - Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoli 80131, Italy
| | - Lucia Musacchio
- Department of Women and Child Health, Division of Gynaecologic Oncology, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma 00168, Italy
| | - Maria Vittoria Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova 35122, Italy; Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova 35128, Italy
| | - Elisabetta Kuhn
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milano 20122, Italy; Pathology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano 20122, Italy
| | - Matteo Lambertini
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy; Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova 16132, Italy
| | - Anna Passarelli
- Department of Urology and Gynaecology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli 80131, Italy
| | - Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena 41124, Italy; Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena 41124, Italy
| | - Alberto Farolfi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola 47014, Italy
| | - Rossana Roncato
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano 33081, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli 80131, Italy; Clinical Pathology Unit, Azienda Ospedaliera San Giovanni Addolorata, Roma 00184, Italy
| | - Riccardo Vida
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Sandro Pignata
- Department of Urology and Gynaecology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli 80131, Italy
| | | | - Gustavo Baldassarre
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano 33081, Italy
| | - Michele Bartoletti
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy.
| | - Fabio Puglisi
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
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Sementsov M, Ott L, Kött J, Sartori A, Lusque A, Degenhardt S, Segier B, Heidrich I, Volkmer B, Greinert R, Mohr P, Simon R, Stadler JC, Irwin D, Koch C, Andreas A, Deitert B, Thewes V, Trumpp A, Schneeweiss A, Belloum Y, Peine S, Wikman H, Riethdorf S, Schneider SW, Gebhardt C, Pantel K, Keller L. Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma. EMBO Mol Med 2024:10.1038/s44321-024-00082-6. [PMID: 38898234 DOI: 10.1038/s44321-024-00082-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating tumor DNA (ctDNA) is the cornerstone of liquid biopsy diagnostics, revealing clinically relevant genomic aberrations from blood of cancer patients. Genomic analysis of single circulating tumor cells (CTCs) could provide additional insights into intra-patient heterogeneity, but it requires whole-genome amplification (WGA) of DNA, which might introduce bias. Here, we describe a novel approach based on mass spectrometry for mutation detection from individual CTCs not requiring WGA and complex bioinformatics pipelines. After establishment of our protocol on tumor cell line-derived single cells, it was validated on CTCs of 33 metastatic melanoma patients and the mutations were compared to those obtained from tumor tissue and ctDNA. Although concordance with tumor tissue was superior for ctDNA over CTC analysis, a larger number of mutations were found within CTCs compared to ctDNA (p = 0.039), including mutations in melanoma driver genes, or those associated with resistance to therapy or metastasis. Thus, our results demonstrate proof-of-principle data that CTC analysis can provide clinically relevant genomic information that is not redundant to tumor tissue or ctDNA analysis.
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Affiliation(s)
- Mark Sementsov
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Ott
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Kött
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Amelie Lusque
- Biostatistics & Health Data Science Unit, Institut Claudius-Regaud, IUCT-Oncopole, Toulouse, France
| | - Sarah Degenhardt
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Bertille Segier
- Biostatistics & Health Data Science Unit, Institut Claudius-Regaud, IUCT-Oncopole, Toulouse, France
| | - Isabel Heidrich
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Beate Volkmer
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Rüdiger Greinert
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Peter Mohr
- Department of Dermatology, Elbe Kliniken Buxtehude, 21614, Buxtehude, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia-Christina Stadler
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Claudia Koch
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antje Andreas
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Deitert
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Verena Thewes
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harriett Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan W Schneider
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoffer Gebhardt
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Laura Keller
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.
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Huang X, Leo P, Jones L, Duijf PHG, Hartel G, Kenny L, Vasani S, Punyadeera C. A comparison between mutational profiles in tumour tissue DNA and circulating tumour DNA in head and neck squamous cell carcinoma - A systematic review. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108477. [PMID: 37977279 DOI: 10.1016/j.mrrev.2023.108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Head and neck cancer is the seventh most common malignancy globally. Head and neck squamous cell carcinoma (HNSCC) originates from squamous cells and 90% of HNC are HNSCC. The gold standard for diagnosing HNSCC is tissue biopsy. However, given tumour heterogeneity, biopsies may miss important cancer-associated molecular signatures, and more importantly, after the tumour is excised, there is no means of tracking response to treatment in patients. Captured under liquid biopsy, circulating tumour DNA (ctDNA), may identify in vivo molecular genotypes and complements tumour tissue analysis in cancer management. A systematic search was conducted in PubMed, Embase, Scopus and the Cochran Library between 2012 to early 2023 on ctDNA in HNSCC using publications written in English. We summarise 20 studies that compared mutational profiles between tumour tissue DNA (tDNA) and ctDNA, using a cohort of 631 HNSCC patients and 139 controls. Among these studies, the concordance rates varied greatly and the most mutated and the most concordant gene was TP53, followed by PIK3CA, CDKN2A, NOTCH1 and FAT1. Concordant variants were mainly found in Stage IV tumours, and the mutation type is mostly single nucleotide variants (SNV). We conclude that, as a biomarker for HNSCC, ctDNA demonstrates great promise as it recapitulates tumour genotypes, however additional multi-central trials are needed.
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Affiliation(s)
- Xiaomin Huang
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, The School of Environment and Science, Griffith University, Brisbane, QLD, Australia
| | - Paul Leo
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia; Center for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia; Australian Translational Genomics Center, Brisbane, QLD, Australia
| | - Lee Jones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Research Methods Group, School of Public Health and Social Work, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, Australia
| | - Pascal H G Duijf
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia; Center for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia & SA Pathology, Adelaide, SA, Australia; Department of Medical Genetics, Oslo University Hospital, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lizbeth Kenny
- School of Medicine, University of Queensland, Brisbane, QLD, Australia; Cancer Care Service, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
| | - Sarju Vasani
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Otolaryngology, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, The School of Environment and Science, Griffith University, Brisbane, QLD, Australia; Menzies Health Institute Queensland, Griffith University, QLD, Australia.
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Huang X, Duijf PHG, Sriram S, Perera G, Vasani S, Kenny L, Leo P, Punyadeera C. Circulating tumour DNA alterations: emerging biomarker in head and neck squamous cell carcinoma. J Biomed Sci 2023; 30:65. [PMID: 37559138 PMCID: PMC10413618 DOI: 10.1186/s12929-023-00953-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023] Open
Abstract
Head and Neck cancers (HNC) are a heterogeneous group of upper aero-digestive tract cancer and account for 931,922 new cases and 467,125 deaths worldwide. About 90% of these cancers are of squamous cell origin (HNSCC). HNSCC is associated with excessive tobacco and alcohol consumption and infection with oncogenic viruses. Genotyping tumour tissue to guide clinical decision-making is becoming common practice in modern oncology, but in the management of patients with HNSCC, cytopathology or histopathology of tumour tissue remains the mainstream for diagnosis and treatment planning. Due to tumour heterogeneity and the lack of access to tumour due to its anatomical location, alternative methods to evaluate tumour activities are urgently needed. Liquid biopsy approaches can overcome issues such as tumour heterogeneity, which is associated with the analysis of small tissue biopsy. In addition, liquid biopsy offers repeat biopsy sampling, even for patients with tumours with access limitations. Liquid biopsy refers to biomarkers found in body fluids, traditionally blood, that can be sampled to provide clinically valuable information on both the patient and their underlying malignancy. To date, the majority of liquid biopsy research has focused on blood-based biomarkers, such as circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), and circulating microRNA. In this review, we will focus on ctDNA as a biomarker in HNSCC because of its robustness, its presence in many body fluids, adaptability to existing clinical laboratory-based technology platforms, and ease of collection and transportation. We will discuss mechanisms of ctDNA release into circulation, technological advances in the analysis of ctDNA, ctDNA as a biomarker in HNSCC management, and some of the challenges associated with translating ctDNA into clinical and future perspectives. ctDNA provides a minimally invasive method for HNSCC prognosis and disease surveillance and will pave the way in the future for personalized medicine, thereby significantly improving outcomes and reducing healthcare costs.
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Affiliation(s)
- Xiaomin Huang
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- University Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Ganganath Perera
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Sarju Vasani
- Department of Otolaryngology, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Lizbeth Kenny
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Paul Leo
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia.
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold coast, QLD, Australia.
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Zanganeh S, Abbasgholinejad E, Doroudian M, Esmaelizad N, Farjadian F, Benhabbour SR. The Current Landscape of Glioblastoma Biomarkers in Body Fluids. Cancers (Basel) 2023; 15:3804. [PMID: 37568620 PMCID: PMC10416862 DOI: 10.3390/cancers15153804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Glioblastoma (GBM) is a highly aggressive and lethal primary brain cancer that necessitates early detection and accurate diagnosis for effective treatment and improved patient outcomes. Traditional diagnostic methods, such as imaging techniques and tissue biopsies, have limitations in providing real-time information and distinguishing treatment-related changes from tumor progression. Liquid biopsies, used to analyze biomarkers in body fluids, offer a non-invasive and dynamic approach to detecting and monitoring GBM. This article provides an overview of GBM biomarkers in body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), cell-free RNA (cfRNA), microRNA (miRNA), and extracellular vesicles. It explores the clinical utility of these biomarkers for GBM detection, monitoring, and prognosis. Challenges and limitations in implementing liquid biopsy strategies in clinical practice are also discussed. The article highlights the potential of liquid biopsies as valuable tools for personalized GBM management but underscores the need for standardized protocols and further research to optimize their clinical utility.
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Affiliation(s)
- Saba Zanganeh
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Elham Abbasgholinejad
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran; (E.A.); (N.E.)
| | - Mohammad Doroudian
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran; (E.A.); (N.E.)
| | - Nazanin Esmaelizad
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran; (E.A.); (N.E.)
| | - Fatemeh Farjadian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran;
| | - Soumya Rahima Benhabbour
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Division of Pharmacoengineering and Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Huber LT, Kraus JM, Ezić J, Wanli A, Groth M, Laban S, Hoffmann TK, Wollenberg B, Kestler HA, Brunner C. Liquid biopsy: an examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for predictive molecular tumor markers. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:422-446. [PMID: 37455825 PMCID: PMC10344902 DOI: 10.37349/etat.2023.00143] [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: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 07/18/2023] Open
Abstract
Aim Recently, a tumor cell-platelet interaction was identified in different tumor entities, resulting in a transfer of tumor-derived RNA into platelets, named further "tumor-educated platelets (TEP)". The present pilot study aims to investigate whether such a tumor-platelet transfer of RNA occurs also in patients suffering from head and neck squamous cell carcinoma (HNSCC). Methods Sequencing analysis of RNA derived from platelets of tumor patients (TPs) and healthy donors (HDs) were performed. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used for verification of differentially expressed genes in platelets from TPs and HDs in a second cohort of patients and HDs. Data were analyzed by applying bioinformatic tools. Results Sequencing of RNA derived from the tumor as well as from platelets of TPs and HDs revealed 426 significantly differentially existing RNA, at which 406 RNA were more and 20 RNA less abundant in platelets from TPs in comparison to that of HDs. In TPs' platelets, abundantly existing RNA coding for 49 genes were detected, characteristically expressed in epithelial cells and RNA, the products of which are involved in tumor progression. Applying bioinformatic tools and verification on a second TP/HD cohort, collagen type I alpha 1 chain (COL1A1) and zinc finger protein 750 (ZNF750) were identified as the strongest potentially platelet-RNA-sequencing (RNA-seq)-based biomarkers for HNSCC. Conclusions These results indicate a transfer of tumor-derived messenger RNA (mRNA) into platelets of HNSCC patients. Therefore, analyses of a patient's platelet RNA could be an efficient option for liquid biopsy in order to diagnose HNSCC or to monitor tumorigenesis as well as therapeutic responses at any time and in real time.
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Affiliation(s)
- Lisa T. Huber
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Jasmin Ezić
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Amin Wanli
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Marco Groth
- Leibniz Institute of Aging – Fritz Lipmann Institute, CF DNA sequencing, 07745 Jena, Germany
| | - Simon Laban
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Thomas K. Hoffmann
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Barbara Wollenberg
- Clinic for Otorhinolaryngology, Head and Neck Surgery, Technical University of Munich, 80333 Munich, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
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8
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Lin LH, Chang KW, Cheng HW, Liu CJ. Identification of Somatic Mutations in Plasma Cell-Free DNA from Patients with Metastatic Oral Squamous Cell Carcinoma. Int J Mol Sci 2023; 24:10408. [PMID: 37373553 DOI: 10.3390/ijms241210408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The accurate diagnosis and treatment of oral squamous cell carcinoma (OSCC) requires an understanding of its genomic alterations. Liquid biopsies, especially cell-free DNA (cfDNA) analysis, are a minimally invasive technique used for genomic profiling. We conducted comprehensive whole-exome sequencing (WES) of 50 paired OSCC cell-free plasma with whole blood samples using multiple mutation calling pipelines and filtering criteria. Integrative Genomics Viewer (IGV) was used to validate somatic mutations. Mutation burden and mutant genes were correlated to clinico-pathological parameters. The plasma mutation burden of cfDNA was significantly associated with clinical staging and distant metastasis status. The genes TTN, PLEC, SYNE1, and USH2A were most frequently mutated in OSCC, and known driver genes, including KMT2D, LRP1B, TRRAP, and FLNA, were also significantly and frequently mutated. Additionally, the novel mutated genes CCDC168, HMCN2, STARD9, and CRAMP1 were significantly and frequently present in patients with OSCC. The mutated genes most frequently found in patients with metastatic OSCC were RORC, SLC49A3, and NUMBL. Further analysis revealed that branched-chain amino acid (BCAA) catabolism, extracellular matrix-receptor interaction, and the hypoxia-related pathway were associated with OSCC prognosis. Choline metabolism in cancer, O-glycan biosynthesis, and protein processing in the endoplasmic reticulum pathway were associated with distant metastatic status. About 20% of tumors carried at least one aberrant event in BCAA catabolism signaling that could possibly be targeted by an approved therapeutic agent. We identified molecular-level OSCC that were correlated with etiology and prognosis while defining the landscape of major altered events of the OSCC plasma genome. These findings will be useful in the design of clinical trials for targeted therapies and the stratification of patients with OSCC according to therapeutic efficacy.
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Affiliation(s)
- Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 11121, Taiwan
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
| | - Chung-Ji Liu
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Oral and Maxillofacial Surgery, Taipei MacKay Memorial Hospital, Taipei 10449, Taiwan
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9
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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10
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Patterns of Somatic Variants in Colorectal Adenoma and Carcinoma Tissue and Matched Plasma Samples from the Hungarian Oncogenome Program. Cancers (Basel) 2023; 15:cancers15030907. [PMID: 36765865 PMCID: PMC9913259 DOI: 10.3390/cancers15030907] [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: 09/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
Analysis of circulating cell-free DNA (cfDNA) of colorectal adenoma (AD) and cancer (CRC) patients provides a minimally invasive approach that is able to explore genetic alterations. It is unknown whether there are specific genetic variants that could explain the high prevalence of CRC in Hungary. Whole-exome sequencing (WES) was performed on colon tissues (27 AD, 51 CRC) and matched cfDNAs (17 AD, 33 CRC); furthermore, targeted panel sequencing was performed on a subset of cfDNA samples. The most frequently mutated genes were APC, KRAS, and FBN3 in AD, while APC, TP53, TTN, and KRAS were the most frequently mutated in CRC tissue. Variants in KRAS codons 12 (AD: 8/27, CRC: 11/51 (0.216)) and 13 (CRC: 3/51 (0.06)) were the most frequent in our sample set, with G12V (5/27) dominance in ADs and G12D (5/51 (0.098)) in CRCs. In terms of the cfDNA WES results, tumor somatic variants were found in 6/33 of CRC cases. Panel sequencing revealed somatic variants in 8 out of the 12 enrolled patients, identifying 12/20 tumor somatic variants falling on its targeted regions, while WES recovered only 20% in the respective regions in cfDNA of the same patients. In liquid biopsy analyses, WES is less efficient compared to the targeted panel sequencing with a higher coverage depth that can hold a relevant clinical potential to be applied in everyday practice in the future.
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11
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Saproo S, Sarkar SS, Gautam V, Konyak CW, Dass G, Karmakar A, Sharma M, Ahuja G, Gupta A, Tayal J, Mehta A, Naidu S. Salivary protein kinase C alpha and novel microRNAs as diagnostic and therapeutic resistance markers for oral squamous cell carcinoma in Indian cohorts. Front Mol Biosci 2023; 9:1106963. [PMID: 36703917 PMCID: PMC9871261 DOI: 10.3389/fmolb.2022.1106963] [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: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the second leading cause of cancer-related morbidity and mortality in India. Tobacco, alcohol, poor oral hygiene, and socio-economic factors remain causative for this high prevalence. Identification of non-invasive diagnostic markers tailored for Indian population can facilitate mass screening to reduce overall disease burden. Saliva offers non-invasive sampling and hosts a plethora of markers for OSCC diagnosis. Here, to capture the OSCC-specific salivary RNA markers suitable for Indian population, we performed RNA-sequencing of saliva from OSCC patients (n = 9) and normal controls (n = 5). Differential gene expression analysis detected an array of salivary RNAs including mRNAs, long non-coding RNAs, transfer-RNAs, and microRNAs specific to OSCC. Computational analysis and functional predictions identified protein kinase c alpha (PRKCA), miR-6087, miR-449b-5p, miR-3656, miR-326, miR-146b-5p, and miR-497-5p as potential salivary indicators of OSCC. Notably, higher expression of PRKCA, miR-6087 and miR-449b-5p were found to be associated with therapeutic resistance and poor survival, indicating their prognostic potential. In addition, sequencing reads that did not map to the human genome, showed alignments with microbial reference genomes. Metagenomic and statistical analysis of these microbial reads revealed a remarkable microbial dysbiosis between OSCC patients and normal controls. Moreover, the differentially abundant microbial taxa showed a significant association with tumor promoting pathways including inflammation and oxidative stress. Summarily, we provide an integrated landscape of OSCC-specific salivary RNAs relevant to Indian population which can be instrumental in devising non-invasive diagnostics for OSCC.
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Affiliation(s)
- Sheetanshu Saproo
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Shashanka S. Sarkar
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Vishakha Gautam
- Department of Computational Biology, Indraprastha Institute of Information Technology- Delhi (IIIT-Delhi), New Delhi, India
| | - Chingmei W. Konyak
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Gouri Dass
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Arpita Karmakar
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Mansi Sharma
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology- Delhi (IIIT-Delhi), New Delhi, India
| | - Anand Gupta
- Department of Dentistry, Government Medical College and Hospital, Chandigarh, India
| | - Juhi Tayal
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Anurag Mehta
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Srivatsava Naidu
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India,*Correspondence: Srivatsava Naidu,
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12
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Ma J, Teng Y, Youming H, Tao X, Fan Y. The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases. Methods Mol Biol 2023; 2695:247-262. [PMID: 37450124 DOI: 10.1007/978-1-0716-3346-5_17] [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] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.
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Affiliation(s)
- Jingwen Ma
- Medical Cosmetic Center, Shanghai Skin Disease Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yan Teng
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huang Youming
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xiaohua Tao
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yibin Fan
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China.
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13
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Horgan D, Čufer T, Gatto F, Lugowska I, Verbanac D, Carvalho Â, Lal JA, Kozaric M, Toomey S, Ivanov HY, Longshore J, Malapelle U, Hasenleithner S, Hofman P, Alix-Panabières C. Accelerating the Development and Validation of Liquid Biopsy for Early Cancer Screening and Treatment Tailoring. Healthcare (Basel) 2022; 10:1714. [PMID: 36141326 PMCID: PMC9498805 DOI: 10.3390/healthcare10091714] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 11/26/2022] Open
Abstract
Liquid biopsy (LB) is a minimally invasive method which aims to detect circulating tumor-derived components in body fluids. It provides an alternative to current cancer screening methods that use tissue biopsies for the confirmation of diagnosis. This paper attempts to determine how far the regulatory, policy, and governance framework provide support to LB implementation into healthcare systems and how the situation can be improved. For that reason, the European Alliance for Personalised Medicine (EAPM) organized series of expert panels including different key stakeholders to identify different steps, challenges, and opportunities that need to be taken to effectively implement LB technology at the country level across Europe. To accomplish a change of patient care with an LB approach, it is required to establish collaboration between multiple stakeholders, including payers, policymakers, the medical and scientific community, and patient organizations, both at the national and international level. Regulators, pharma companies, and payers could have a major impact in their own domain. Linking national efforts to EU efforts and vice versa could help in implementation of LB across Europe, while patients, scientists, physicians, and kit manufacturers can generate a pull by undertaking more research into biomarkers.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Faculty of Engineering and Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Tanja Čufer
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Francesco Gatto
- Department of Oncology-Pathology, Karolinska Institute, 171 64 Stockholm, Sweden
| | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute and Oncology Centre (MSCI), 02781 Warsaw, Poland
| | - Donatella Verbanac
- Department of Medical Biochemistry and Hematology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Ângela Carvalho
- i3S—nstituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Faculty of Engineering and Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, GROW School of Oncology and Developmental Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Marta Kozaric
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
| | - Sinead Toomey
- Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Smurfit Building, D09 Dublin, Ireland
| | - Hristo Y. Ivanov
- Department of Paediatric and Medical Genetics, Medical University, 4000 Plovdiv, Bulgaria
| | - John Longshore
- Astra Zeneca, 1800 Concord Pike, Wilmington, DE 19803, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80137 Naples, Italy
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8036 Graz, Austria
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Pasteur Hospital, University Côte d’Azur, CEDEX 01, 06001 Nice, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 641 Avenue du Doyen Gaston Giraud, CEDEX 5, 34093 Montpellier, France
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14
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Mack M, Broche J, George S, Hajjari Z, Janke F, Ranganathan L, Ashouri M, Bleul S, Desuki A, Engels C, Fliedner SM, Hartmann N, Hummel M, Janning M, Kiel A, Köhler T, Koschade S, Lablans M, Lambarki M, Loges S, Lueong S, Meyer S, Ossowski S, Scherer F, Schroeder C, Skowronek P, Thiede C, Uhl B, Vehreschild JJ, von Bubnoff N, Wagner S, Werner TV, Westphalen CB, Fresser P, Sültmann H, Tinhofer I, Winter C. The DKTK EXLIQUID consortium – exploiting liquid biopsies to advance cancer precision medicine for molecular tumor board patients. J LAB MED 2022. [DOI: 10.1515/labmed-2022-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Testing for genetic alterations in tumor tissue allows clinicians to identify patients who most likely will benefit from molecular targeted treatment. EXLIQUID – exploiting liquid biopsies to advance cancer precision medicine – investigates the potential of additional non-invasive tools for guiding therapy decisions and monitoring of advanced cancer patients. The term “liquid biopsy” (LB) refers to non-invasive analysis of tumor-derived circulating material such as cell-free DNA in blood samples from cancer patients. Although recent technological advances allow sensitive and specific detection of LB biomarkers, only few LB assays have entered clinical routine to date. EXLIQUID is a German Cancer Consortium (DKTK)-wide joint funding project that aims at establishing LBs as a minimally-invasive tool to analyze molecular changes in circulating tumor DNA (ctDNA). Here, we present the structure, clinical aim, and methodical approach of the new DKTK EXLIQUID consortium. Within EXLIQUID, we will set up a multicenter repository of high-quality LB samples from patients participating in DKTK MASTER and local molecular tumor boards, which use molecular profiles of tumor tissues to guide targeted therapies. We will develop LB assays for monitoring of therapy efficacy by the analysis of tumor mutant variants and tumor-specific DNA methylation patterns in ctDNA from these patients. By bringing together LB experts from all DKTK partner sites and exploiting the diversity of their particular expertise, complementary skills and technologies, the EXLIQUID consortium addresses the challenges of translating LBs into the clinic. The DKTK structure provides EXLIQUID a unique position for the identification of liquid biomarkers even in less common tumor types, thereby extending the group of patients benefitting from non-invasive LB testing. Besides its scientific aims, EXLIQUID is building a valuable precision oncology cohort and LB platform which will be available for future collaborative research studies within the DKTK and beyond.
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Affiliation(s)
- Matthias Mack
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Julian Broche
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephen George
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Zahra Hajjari
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Janke
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Lavanya Ranganathan
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohammadreza Ashouri
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sabine Bleul
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Desuki
- University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg-University Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Cecilia Engels
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephanie M.J. Fliedner
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Michael Hummel
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Melanie Janning
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Alexander Kiel
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Thomas Köhler
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sebastian Koschade
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Martin Lablans
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohamed Lambarki
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Smiths Lueong
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sandra Meyer
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Scherer
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrick Skowronek
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christian Thiede
- Department of Medicine I , University Hospital Carl Gustav Carus , Dresden , Germany
- German Cancer Consortium (DKTK), Partner Site Dresden , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Barbara Uhl
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Janne Vehreschild
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Sebastian Wagner
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Tamara V. Werner
- Medical Center, Medical Faculty , Institute for Surgical Pathology, University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - C. Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III , Ludwig Maximilian University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrizia Fresser
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Holger Sültmann
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christof Winter
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
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15
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Rahmanian M, Sartipzadeh Hematabad O, Askari E, Shokati F, Bakhshi A, Moghadam S, Olfatbakhsh A, Al Sadat Hashemi E, Khorsand Ahmadi M, Morteza Naghib S, Sinha N, Tel J, Eslami Amirabadi H, den Toonder JMJ, Majidzadeh-A K. A micropillar array-based microfluidic chip for label-free separation of circulating tumor cells: The best micropillar geometry? J Adv Res 2022; 47:105-121. [PMID: 35964874 PMCID: PMC10173300 DOI: 10.1016/j.jare.2022.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/22/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022] Open
Abstract
INTRODUCTION The information derived from the number and characteristics of circulating tumor cells (CTCs), is crucial to ensure appropriate cancer treatment monitoring. Currently, diverse microfluidic platforms have been developed for isolating CTCs from blood, but it remains a challenge to develop a low-cost, practical, and efficient strategy. OBJECTIVES This study aimed to isolate CTCs from the blood of cancer patients via introducing a new and efficient micropillar array-based microfluidic chip (MPA-Chip), as well as providing prognostic information and monitoring the treatment efficacy in cancer patients. METHODS We fabricated a microfluidic chip (MPA-Chip) containing arrays of micropillars with different geometries (lozenge, rectangle, circle, and triangle). We conducted numerical simulations to compare velocity and pressure profiles inside the micropillar arrays. Also, we experimentally evaluated the capture efficiency and purity of the geometries using breast and prostate cancer cell lines as well as a blood sample. Moreover, the device's performance was validated on 12 patients with breast cancer (BC) in different states. RESULTS The lozenge geometry was selected as the most effective and optimized micropillar design for CTCs isolation, providing high capture efficiency (>85 %), purity (>90 %), and viability (97 %). Furthermore, the lozenge MPA-chip was successfully validated by the detection of CTCs from 12 breast cancer (BC) patients, with non-metastatic (median number of 6 CTCs) and metastatic (median number of 25 CTCs) diseases, showing different prognoses. Also, increasing the chemotherapy period resulted in a decrease in the number of captured CTCs from 23 to 7 for the metastatic patient. The MPA-Chip size was only 0.25 cm2 and the throughput of a single chip was 0.5 ml/h, which can be increased by multiple MPA-Chips in parallel. CONCLUSION The lozenge MPA-Chip presented a novel micropillar geometry for on-chip CTC isolation, detection, and staining, and in the future, the possibilities can be extended to the culture of the CTCs.
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Affiliation(s)
- Mehdi Rahmanian
- Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran; Microsystems Research Section, Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Omid Sartipzadeh Hematabad
- Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Esfandyar Askari
- Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Farhad Shokati
- Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Atin Bakhshi
- Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Shiva Moghadam
- Breast Diseases Group, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Asiie Olfatbakhsh
- Breast Diseases Group, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Esmat Al Sadat Hashemi
- Breast Diseases Group, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mohammad Khorsand Ahmadi
- Microsystems Research Section, Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology, Tehran, Iran
| | - Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Hossein Eslami Amirabadi
- Microsystems Research Section, Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; AZAR Innovations, Utrecht, the Netherlands
| | - Jaap M J den Toonder
- Microsystems Research Section, Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
| | - Keivan Majidzadeh-A
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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16
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Liu Z, Kong Y, Dang Q, Weng S, Zheng Y, Ren Y, Lv J, Li N, Han Y, Han X. Liquid Biopsy in Pre-Metastatic Niche: From Molecular Mechanism to Clinical Application. Front Immunol 2022; 13:958360. [PMID: 35911705 PMCID: PMC9334814 DOI: 10.3389/fimmu.2022.958360] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Metastatic dissemination represents a hallmark of cancer that is responsible for the high mortality rate. Recently, emerging evidence demonstrates a time-series event—pre-metastatic niche (PMN) has a profound impact on cancer metastasis. Exosomes, cell-free DNA (cfDNA), circulating tumor cells (CTC), and tumor microenvironment components, as critical components in PMN establishment, could be monitored by liquid biopsy. Intensive studies based on the molecular profile of liquid biopsy have made it a viable alternative to tissue biopsy. Meanwhile, the complex molecular mechanism and intercellular interaction are great challenges for applying liquid biopsy in clinical practice. This article reviews the cellular and molecular components involved in the establishment of the PMN and the promotion of metastasis, as well as the mechanisms of their interactions. Better knowledge of the characteristics of the PMN may facilitate the application of liquid biopsy for clinical diagnosis, prognosis, and treatment.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Ying Kong
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Youyang Zheng
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinxiang Lv
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Na Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yilin Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Interventional Institute of Zhengzhou University, Zhengzhou, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
- *Correspondence: Xinwei Han,
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17
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Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
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Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
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18
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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19
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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.
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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:
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20
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Fischer LE, Stintzing S, Heinemann V, Keilholz U, Keune D, Vollbrecht C, Burmeister T, Kind A, Weiss L, Horst D, Kirchner T, Klauschen F, Jung A, Westphalen CB, Jelas I. Liquid Biopsy in Colorectal Cancer: Quo Vadis? Implementation of Liquid Biopsies in Routine Clinical Patient Care in Two German Comprehensive Cancer Centers. Front Oncol 2022; 12:870411. [PMID: 35646657 PMCID: PMC9134071 DOI: 10.3389/fonc.2022.870411] [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: 02/06/2022] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Objectives The use of liquid biopsies (LB) in patients with solid malignancies enables comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) and has the potential to guide therapy stratification and support disease monitoring. To examine clinical uptake of LB in a real-world setting, LB implementation was analyzed at two German cancer centers (LMU Munich and Charité - Universitätsmedizin Berlin) between 2017 and 2021, with focus on colorectal cancer (CRC) patients. Methods In this retrospective analysis, all patients who received a LB between January 2017 and December 2021 as part of routine clinical management were included. To provide adequate context, we collected disease characteristics and technical specifications of the LB methods applied. Additionally, we examined the concordance of RAS status in tumor tissue and LB. Finally, we discuss the potential of LB as a diagnostic tool to drive personalized treatment in CRC patients and how to implement LB in clinical routine. Results In total, our cohort included 86 CRC patients and 161 LB conducted in these patients between 2017 and 2021. In 59 patients, comparison between tissue-based and liquid-based molecular diagnostics, revealed a divergence in 23 (39%) of the evaluable samples. Conclusion Our real-world data analysis indicates that the possibilities of LB are not yet exploited in everyday clinical practice. Currently, the variety of methods and lack of standardization, as well as restricted reimbursement for liquid based CGP hinder the use of LB in clinical routine. To overcome these issues, prospective clinical trials are needed to provide evidence driving the implementation of LB into the management of CRC patients and to support their implementation into clinical guidelines.
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Affiliation(s)
- Laura E Fischer
- Department of Medicine III, University Hospital, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Stintzing
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany
| | - Volker Heinemann
- Department of Medicine III, University Hospital, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Munich, Germany
| | - Ulrich Keilholz
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany.,Charité Comprehensive Cancer Center, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dietmar Keune
- Charité Comprehensive Cancer Center, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Vollbrecht
- Institute of Pathology Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Burmeister
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Labor Berlin - Charité Vivantes, GmbH, Molekulardiagnostik - Hämatologie, Berlin, Germany
| | - Andreas Kind
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lena Weiss
- Department of Medicine III, University Hospital, Munich, Germany
| | - David Horst
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany.,Institute of Pathology Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Kirchner
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Munich, Germany.,Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, München, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Munich, Germany.,Institute of Pathology Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, München, Germany
| | - Andreas Jung
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Munich, Germany.,Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, München, Germany
| | - Christoph Benedikt Westphalen
- Department of Medicine III, University Hospital, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Munich, Germany
| | - Ivan Jelas
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany
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21
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Caterino M, Pirozzi M, Facchini S, Zotta A, Sica A, Lo Giudice G, Rauso R, Varriale E, Ciardiello F, Fasano M. Sorafenib in Metastatic Papillary Thyroid Carcinoma with BRAF K601E Mutation on Liquid Biopsy: A Case Report and Literature Review. Medicina (B Aires) 2022; 58:medicina58050666. [PMID: 35630083 PMCID: PMC9144761 DOI: 10.3390/medicina58050666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Differentiated thyroid cancer (DTC) includes papillary and follicular carcinomas and is the most common type of thyroid cancer. The incidence of this cancer has increased in the last few years, and even if its prognosis is generally good for a subset of patients that does not respond to radioactive iodine (RAI) therapy, the prognosis is much worse: the median overall survival (OS) from discovery of metastasis is 3–5 years and the 10-year survival rate is only 10%. Several mutations, including RAS or RET, as well as BRAF signaling, are associated with thyroid cancer. Liquid biopsy may be useful in selected patient to identify genomic alterations and thus allowing for a precision medicine approach with target therapy. Sorafenib, an oral multi-kinase inhibitor, can be used in the treatment of DTC. Case presentation: A 77 years old. man with diagnosis of metastatic DTC and evidence of presence of mutation of BRAF K601E on liquid biopsy was treated with sorafenib, showing a good response to the treatment and an improvement in the quality of life (QoL). Currently, this patient is still on treatment with sorafenib, gaining control of a multi-metastatic disease, generally characterized by a very poor prognosis. In conclusion, sorafenib has an active role in the treatment of DTC. It also has been considered the standard of care for patients with advanced unresectable hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC). In our case we observe the efficacy of using sorafenib in Papillary thyroid carcinoma (PTC) such as confirming both stable disease (SD) in the CT scan as clinical benefit with an increase in QoL. Therefore, use of sorafenib remains an important treatment option, even in case of BRAF mutation, despite a rapidly evolving treatment landscape. It also seems important to perform liquid biopsies, especially in patients in whom it is not possible to repeat a new tissue biopsy. Ongoing clinical trials continue to evaluate sorafenib in different settings, and in combination with other therapies in DTC and HCC.
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Affiliation(s)
- Marianna Caterino
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Mario Pirozzi
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Sergio Facchini
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Alessia Zotta
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Antonello Sica
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Giorgio Lo Giudice
- Maxillofacial Surgery Unit, Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Via Pansini, 5, 80131 Naples, Italy
| | - Raffaele Rauso
- Head and Neck Unit, Clinica Cobellis, 84078 Vallo della Lucania, Italy
| | - Elisa Varriale
- Division of Oncology, Fatebenefratelli Hospital, 80123 Naples, Italy
| | - Fortunato Ciardiello
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
| | - Morena Fasano
- Division of Oncology, Department of Precision Medicine, University of Campania, 80010 Naples, Italy
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22
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Circulating Cell-Free DNA Assessment in Biofluids from Children with Neuroblastoma Demonstrates Feasibility and Potential for Minimally Invasive Molecular Diagnostics. Cancers (Basel) 2022; 14:cancers14092080. [PMID: 35565208 PMCID: PMC9099910 DOI: 10.3390/cancers14092080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary The invasive nature of surgical biopsies prevents their sequential application to monitor disease. Single biopsies fail to reflect cancer dynamics, intratumor heterogeneity, and drug sensitivities that change over time. Detection and characterization of cell-free circulating tumor DNA in biofluids from patients with solid tumors may better support disease monitoring and provide advanced molecular information for clinical decision-making toward personalized medicine. Here, we investigated the cell-free DNA characteristics in blood, bone marrow, cerebrospinal fluid, and urine provided from 84 infants and children with low-, intermediate-, or high-risk neuroblastoma. We report characteristic size distribution and concentration patterns for each biofluid to provide information to support the development of successful liquid biopsy biobanking strategies. We investigate potential correlations between disease activity and cfDNA concentration and provide strong evidence that markers specific for neuroblastoma can be detected in very small blood volumes from infants. Abstract Liquid biopsy strategies in pediatric patients are challenging due to low body weight. This study investigated cfDNA size distribution and concentration in blood, bone marrow, cerebrospinal fluid, and urine from 84 patients with neuroblastoma classified as low (n = 28), intermediate (n = 6), or high risk (n = 50) to provide key data for liquid biopsy biobanking strategies. The average volume of blood and bone marrow plasma provided ranged between 1 and 2 mL. Analysis of 637 DNA electropherograms obtained by Agilent TapeStation measurement revealed five different major profiles and characteristic DNA size distribution patterns for each of the biofluids. The proportion of samples containing primarily cfDNA was, at 85.5%, the highest for blood plasma. The median cfDNA concentration amounted to 6.28 ng/mL (blood plasma), 58.2 ng/mL (bone marrow plasma), 0.08 ng/mL (cerebrospinal fluid), and 0.49 ng/mL (urine) in samples. Meta-analysis of the dataset demonstrated that multiple cfDNA-based assays employing the same biofluid sample optimally require sampling volumes of 1 mL for blood and bone marrow plasma, 2 mL for cerebrospinal fluid, and as large as possible for urine samples. A favorable response to treatment was associated with a rapid decrease in blood-based cfDNA concentration in patients with high-risk neuroblastoma. Blood-based cfDNA concentration was not sufficient as a single parameter to indicate high-risk disease recurrence. We provide proof of concept that monitoring neuroblastoma-specific markers in very small blood volumes from infants is feasible.
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