1
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Tu X, Zhang T. A commentary on 'Association between plasma circulating tumor DNA and the prognosis of esophageal cancer patients: a meta-analysis'. Int J Surg 2024; 110:5885-5886. [PMID: 39275775 PMCID: PMC11392062 DOI: 10.1097/js9.0000000000001649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 09/16/2024]
Affiliation(s)
- Xiaolong Tu
- Department of Oncology, Ningbo Hospital of Traditional Chinese Medicine, Zhejiang, People's Republic of China
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2
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Duranti E, Villa C. Insights into Dysregulated Neurological Biomarkers in Cancer. Cancers (Basel) 2024; 16:2680. [PMID: 39123408 PMCID: PMC11312413 DOI: 10.3390/cancers16152680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
The link between neurodegenerative diseases (NDs) and cancer has generated greater interest in biomedical research, with decades of global studies investigating neurodegenerative biomarkers in cancer to better understand possible connections. Tau, amyloid-β, α-synuclein, SOD1, TDP-43, and other proteins associated with nervous system diseases have also been identified in various types of solid and malignant tumors, suggesting a potential overlap in pathological processes. In this review, we aim to provide an overview of current evidence on the role of these proteins in cancer, specifically examining their effects on cell proliferation, apoptosis, chemoresistance, and tumor progression. Additionally, we discuss the diagnostic and therapeutic implications of this interconnection, emphasizing the importance of further research to completely comprehend the clinical implications of these proteins in tumors. Finally, we explore the challenges and opportunities in targeting these proteins for the development of new targeted anticancer therapies, providing insight into how to integrate knowledge of NDs in oncology research.
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Affiliation(s)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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3
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Beech C, Hechtman JF. Molecular Approach to Colorectal Carcinoma: Current Evidence and Clinical Application. Clin Lab Med 2024; 44:221-238. [PMID: 38821642 DOI: 10.1016/j.cll.2023.08.011] [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: 06/02/2024]
Abstract
Colorectal carcinoma is one of the most common cancer types in men and women, responsible for both the third highest incidence of new cancer cases and the third highest cause of cancer deaths. In the last several decades, the molecular mechanisms surrounding colorectal carcinoma's tumorigenesis have become clearer through research, providing new avenues for diagnostic testing and novel approaches to therapeutics. Laboratories are tasked with providing the most current information to help guide clinical decisions. In this review, we summarize the current knowledge surrounding colorectal carcinoma tumorigenesis and highlight clinically relevant molecular testing.
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Affiliation(s)
- Cameron Beech
- Department of Pathology, Yale New Haven Hospital, New Haven, CT, USA
| | - Jaclyn F Hechtman
- Molecular and GI Pathologist, NeoGenomics Laboratories, Fort Myers, FL, USA.
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4
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Scaini MC, Catoni C, Poggiana C, Pigozzo J, Piccin L, Leone K, Scarabello I, Facchinetti A, Menin C, Elefanti L, Pellegrini S, Aleotti V, Vidotto R, Schiavi F, Fabozzi A, Chiarion-Sileni V, Rosato A. A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance. NPJ Precis Oncol 2024; 8:78. [PMID: 38548846 PMCID: PMC10978909 DOI: 10.1038/s41698-024-00567-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Melanoma heterogeneity is a hurdle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcomes, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker for the real-time tracing of disease evolution. Thus, we aimed to correlate liquid biopsy dynamics with treatment response and progression by devising a multiplatform approach applied to longitudinal melanoma patient monitoring. We conceived an approach that exploits Next Generation Sequencing (NGS) and droplet digital PCR, as well as the FDA-cleared platform CellSearch, to analyze circulating tumor DNA (ctDNA) trend and circulating melanoma cell (CMC) count, together with their customized genetic and copy number variation analysis. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, followed for up to 28 months. BRAF mutations were detected in the plasma of 82% of patients. Single nucleotide variants known or suspected to confer resistance were identified in 70% of patients. Moreover, the amount of ctDNA, both at baseline and during response, correlated with the type and duration of the response itself, and the CMC count was confirmed to be a prognostic biomarker. This work provides proof of principle of the power of this approach and paves the way for a validation study aimed at evaluating early ctDNA-guided treatment decisions in stage IV melanoma. The NGS-based molecular profile complemented the analysis of ctDNA trend and, together with CMC analysis, revealed to be useful in capturing tumor evolution.
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Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Jacopo Pigozzo
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Luisa Piccin
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Kevin Leone
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Ilaria Scarabello
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Stefania Pellegrini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Riccardo Vidotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Francesca Schiavi
- Familial Cancer Clinic, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Oncology Unit 3, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | | | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
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5
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Wang HY, Lin WY, Zhou C, Yang ZA, Kalpana S, Lebowitz MS. Integrating Artificial Intelligence for Advancing Multiple-Cancer Early Detection via Serum Biomarkers: A Narrative Review. Cancers (Basel) 2024; 16:862. [PMID: 38473224 DOI: 10.3390/cancers16050862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The concept and policies of multicancer early detection (MCED) have gained significant attention from governments worldwide in recent years. In the era of burgeoning artificial intelligence (AI) technology, the integration of MCED with AI has become a prevailing trend, giving rise to a plethora of MCED AI products. However, due to the heterogeneity of both the detection targets and the AI technologies, the overall diversity of MCED AI products remains considerable. The types of detection targets encompass protein biomarkers, cell-free DNA, or combinations of these biomarkers. In the development of AI models, different model training approaches are employed, including datasets of case-control studies or real-world cancer screening datasets. Various validation techniques, such as cross-validation, location-wise validation, and time-wise validation, are used. All of the factors show significant impacts on the predictive efficacy of MCED AIs. After the completion of AI model development, deploying the MCED AIs in clinical practice presents numerous challenges, including presenting the predictive reports, identifying the potential locations and types of tumors, and addressing cancer-related information, such as clinical follow-up and treatment. This study reviews several mature MCED AI products currently available in the market, detecting their composing factors from serum biomarker detection, MCED AI training/validation, and the clinical application. This review illuminates the challenges encountered by existing MCED AI products across these stages, offering insights into the continued development and obstacles within the field of MCED AI.
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Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu 300044, Taiwan
- 20/20 GeneSystems, Gaithersburg, MD 20877, USA
| | - Wan-Ying Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | | | - Zih-Ang Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | - Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
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6
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Fawaz A, Ferraresi A, Isidoro C. Systems Biology in Cancer Diagnosis Integrating Omics Technologies and Artificial Intelligence to Support Physician Decision Making. J Pers Med 2023; 13:1590. [PMID: 38003905 PMCID: PMC10672164 DOI: 10.3390/jpm13111590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is the second major cause of disease-related death worldwide, and its accurate early diagnosis and therapeutic intervention are fundamental for saving the patient's life. Cancer, as a complex and heterogeneous disorder, results from the disruption and alteration of a wide variety of biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites, that eventually emerge as clinical symptoms. Traditionally, diagnosis is based on clinical examination, blood tests for biomarkers, the histopathology of a biopsy, and imaging (MRI, CT, PET, and US). Additionally, omics biotechnologies help to further characterize the genome, metabolome, microbiome traits of the patient that could have an impact on the prognosis and patient's response to the therapy. The integration of all these data relies on gathering of several experts and may require considerable time, and, unfortunately, it is not without the risk of error in the interpretation and therefore in the decision. Systems biology algorithms exploit Artificial Intelligence (AI) combined with omics technologies to perform a rapid and accurate analysis and integration of patient's big data, and support the physician in making diagnosis and tailoring the most appropriate therapeutic intervention. However, AI is not free from possible diagnostic and prognostic errors in the interpretation of images or biochemical-clinical data. Here, we first describe the methods used by systems biology for combining AI with omics and then discuss the potential, challenges, limitations, and critical issues in using AI in cancer research.
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Affiliation(s)
| | | | - Ciro Isidoro
- Laboratory of Molecular Pathology, Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (A.F.); (A.F.)
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7
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Wahab MRA, Palaniyandi T, Ravi M, Viswanathan S, Baskar G, Surendran H, Gangadharan SGD, Rajendran BK. Biomarkers and biosensors for early cancer diagnosis, monitoring and prognosis. Pathol Res Pract 2023; 250:154812. [PMID: 37741139 DOI: 10.1016/j.prp.2023.154812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/22/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023]
Abstract
Cancers continue to be of major concern due to their serious global socioeconomic impact, apart from the continued increase in the incidence of various cancer types. A major challenge that this disease poses is due to the low "early detection" rates which limit the therapeutic outcomes for the affected individuals. Current research has highlighted the discovering biomarkers that help in early cancer detection and the development of technologies for the detection and quantification of such biomarkers. Biomarkers range from proteins to nucleic acids, and can be specific to a particular cancer type. Detection and quantification of such biomarkers at low levels from biological samples is being made possible by the advent of developing biosensors and by using biomedical engineering technologies such as tumor-on-a-chip models. Here, we present biomarkers that can be helpful for the early detection of breast, colorectal, esophageal, lung, liver, ovarian, and prostate cancer. In addition, we discuss the potential of circulating tumor cell DNA (ctDNA) as an early diagnostic marker. Finally, biosensors available for the detection of cancer biomarkers, which is a recent advancement in this area of research, are discussed.
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Affiliation(s)
| | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, Tamil Nadu, India.
| | - Maddaly Ravi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, Tamil Nadu, India
| | - Sandhiya Viswanathan
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - S G D Gangadharan
- Department of Medical Oncology, Madras Medical College, R. G. G. G. H., Chennai, Tamil Nadu, India
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8
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Bittla P, Kaur S, Sojitra V, Zahra A, Hutchinson J, Folawemi O, Khan S. Exploring Circulating Tumor DNA (CtDNA) and Its Role in Early Detection of Cancer: A Systematic Review. Cureus 2023; 15:e45784. [PMID: 37745752 PMCID: PMC10516512 DOI: 10.7759/cureus.45784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023] Open
Abstract
There is a significant increase in the need for an efficient screening method that might identify cancer at an early stage and could improve patients' long-term survival due to the continued rise in cancer incidence and associated mortality. One such effort involved using circulating tumor DNA (ctDNA) as a rescue agent for a non-invasive blood test that may identify many tumors. A tumor marker called ctDNA is created by cells with the same DNA alterations. Due to its shorter half-life, it may be useful for both early cancer detection and real-time monitoring of tumor development, therapeutic response, and tumor outcomes. We obtained 156 papers from PUBMED using the MeSH approach in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) criteria and ten articles from additional online resources. After removing articles with irrelevant titles and screening the abstract and full text of the articles that contained information unrelated to or not specific to the title query using inclusion and exclusion criteria, 18 out of 166 articles were chosen for the quality check. Fourteen medium to high-quality papers were chosen out of the 18 publications to be included in the study design. The reviewed literature showed no significant utility of ctDNA in detecting early-stage tumors of size less than 1 cm diameter. Still, the ideal screening test would require the assay to detect a size <5 mm tumor, which is nearly impossible with the current data. The sensitivity and specificity of the assay ranged from 69% to 98% and 99%, respectively. Furthermore, CancerSEEK achieves tumor origin localization in 83% of cases, while targeted error correction sequencing (TEC-Seq) assays demonstrate a cancer detection rate ranging from 59% to 71%, depending on the type of cancer. However, it could be of great value as a prognostic indicator, and the levels are associated with progression-free survival (PFS) and overall survival (OS) rates, wherein the positive detection of ctDNA is associated with worse OS compared to the tumors detected through standard procedures, with an odds ratio (OS) of 4.83. We conclude that ctDNA could be better applied in cancer patients for prognosis, disease progression monitoring, and treatment outcomes compared to its use in early cancer detection. Due to its specific feature of recognizing the tumor-related mutations, it could be implemented as a supplemental tool to assess the nature of the tumor, grade, and size of the tumor and for predicting the outcomes by pre-operative and post-operative evaluation of the tumor marker, ctDNA, and thereby estimating PFS and OS depending on the level of marker present. A vast amount of research is required in early detection to determine the sensitivity, specificity, false positive rates, and false negative rates in evaluating its true potential as a screening tool. Even if the test could detect the mutations, an extensive workup for the search of tumor is required as the assay could only detect but cannot localize the disease. Establishing the clinical validity and utility of ctDNA is imperative for its implementation in future clinical practice.
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Affiliation(s)
- Parikshit Bittla
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Simran Kaur
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Vani Sojitra
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Anam Zahra
- Surgery, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Jhenelle Hutchinson
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Oluwa Folawemi
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Safeera Khan
- Internal Medicine, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
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9
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Al-Obeidi E, Riess JW, Malapelle U, Rolfo C, Gandara DR. Convergence of Precision Oncology and Liquid Biopsy in Non-Small Cell Lung Cancer. Hematol Oncol Clin North Am 2023; 37:475-487. [PMID: 37024388 DOI: 10.1016/j.hoc.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
This review article illuminates the role of liquid biopsy in the continuum of care for non-small cell lung cancer (NSCLC). We discuss its current application in advanced-stage NSCLC at the time of diagnosis and at progression. We highlight research showing that concurrent testing of blood and tissue yields faster, more informative, and cheaper answers than the standard stepwise approach. We also describe future applications for liquid biopsy including treatment response monitoring and testing for minimal residual disease. Lastly, we discuss the emerging role of liquid biopsy for screening and early detection.
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Affiliation(s)
- Ebaa Al-Obeidi
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA.
| | - Jonathan W Riess
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy. https://twitter.com/UmbertoMalapel1
| | - Christian Rolfo
- Center for Thoracic Oncology at the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, Box 1079, New York, NY 10029, USA. https://twitter.com/ChristianRolfo
| | - David R Gandara
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA. https://twitter.com/drgandara
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10
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Schmidt MK, Kelly JE, Brédart A, Cameron DA, de Boniface J, Easton DF, Offersen BV, Poulakaki F, Rubio IT, Sardanelli F, Schmutzler R, Spanic T, Weigelt B, Rutgers EJT. EBCC-13 manifesto: Balancing pros and cons for contralateral prophylactic mastectomy. Eur J Cancer 2023; 181:79-91. [PMID: 36641897 PMCID: PMC10326619 DOI: 10.1016/j.ejca.2022.11.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022]
Abstract
After a diagnosis of unilateral breast cancer, increasing numbers of patients are requesting contralateral prophylactic mastectomy (CPM), the surgical removal of the healthy breast after diagnosis of unilateral breast cancer. It is important for the community of breast cancer specialists to provide meaningful guidance to women considering CPM. This manifesto discusses the issues and challenges of CPM and provides recommendations to improve oncological, surgical, physical and psychological outcomes for women presenting with unilateral breast cancer: (1) Communicate best available risks in manageable timeframes to prioritise actions; better risk stratification and implementation of risk-assessment tools combining family history, genetic and genomic information, and treatment and prognosis of the first breast cancer are required; (2) Reserve CPM for specific situations; in women not at high risk of contralateral breast cancer (CBC), ipsilateral breast-conserving surgery is the recommended option; (3) Encourage patients at low or intermediate risk of CBC to delay decisions on CPM until treatment for the primary cancer is complete, to focus on treating the existing disease first; (4) Provide patients with personalised information about the risk:benefit balance of CPM in manageable timeframes; (5) Ensure patients have an informed understanding of the competing risks for CBC and that there is a realistic plan for the patient; (6) Ensure patients understand the short- and long-term physical effects of CPM; (7) In patients considering CPM, offer psychological and surgical counselling before surgery; anxiety alone is not an indication for CPM; (8) Eliminate inequality between countries in reimbursement strategies; CPM should be reimbursed if it is considered a reasonable option resulting from multidisciplinary tumour board assessment; (9) Treat breast cancer patients at specialist breast units providing the entire patient-centred pathway.
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Affiliation(s)
- Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | | | - Anne Brédart
- Institut Curie, Paris, France; Psychology Institute, Psychopathology and Health Process Laboratory UR4057, Paris City University, Paris, France
| | - David A Cameron
- Edinburgh University Cancer Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jana de Boniface
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Surgery, Breast Unit, Capio St. Göran's Hospital, Stockholm, Sweden
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Birgitte V Offersen
- Department of Experimental Clinical Oncology, Aarhus University Hospital - Aarhus University, Aarhus N, Denmark
| | - Fiorita Poulakaki
- Breast Surgery Department, Athens Medical Center, Athens, Greece; Europa Donna - The European Breast Cancer Coalition, Milan, Italy
| | - Isabel T Rubio
- Breast Surgical Oncology, Clinica Universidad de Navarra, Madrid, Spain
| | - Francesco Sardanelli
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy; Unit of Radiology, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Rita Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University Hospital Cologne, Cologne, Germany
| | - Tanja Spanic
- Europa Donna - The European Breast Cancer Coalition, Milan, Italy; Europa Donna Slovenia, Ljubljana, Slovenia
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emiel J T Rutgers
- Department of Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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11
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Circulating Tumor DNA Methylation Biomarkers for Characterization and Determination of the Cancer Origin in Malignant Liver Tumors. Cancers (Basel) 2023; 15:cancers15030859. [PMID: 36765815 PMCID: PMC9913861 DOI: 10.3390/cancers15030859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Malignant liver tumors include primary malignant liver tumors and liver metastases. They are among the most common malignancies worldwide. The disease has a poor prognosis and poor overall survival, especially with liver metastases. Therefore, early detection and differentiation between malignant liver tumors are critical for patient treatment selection. The detection of cancer and the prediction of its origin is possible with a DNA methylation profile of the tumor DNA compared to that of normal cells, which reflects tissue differentiation and malignant transformation. New technologies enable the characterization of the tumor methylome in circulating tumor DNA (ctDNA), providing a variety of new ctDNA methylation biomarkers, which can provide additional information to clinical decision-making. Our review of the literature provides insight into methylation changes in ctDNA from patients with common malignant liver tumors and can serve as a starting point for further research.
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12
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Dholariya S, Singh RD, Sonagra A, Yadav D, Vajaria BN, Parchwani D. Integrating Cutting-Edge Methods to Oral Cancer Screening, Analysis, and Prognosis. Crit Rev Oncog 2023; 28:11-44. [PMID: 37830214 DOI: 10.1615/critrevoncog.2023047772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Oral cancer (OC) has become a significant barrier to health worldwide due to its high morbidity and mortality rates. OC is among the most prevalent types of cancer that affect the head and neck region, and the overall survival rate at 5 years is still around 50%. Moreover, it is a multifactorial malignancy instigated by genetic and epigenetic variabilities, and molecular heterogeneity makes it a complex malignancy. Oral potentially malignant disorders (OPMDs) are often the first warning signs of OC, although it is challenging to predict which cases will develop into malignancies. Visual oral examination and histological examination are still the standard initial steps in diagnosing oral lesions; however, these approaches have limitations that might lead to late diagnosis of OC or missed diagnosis of OPMDs in high-risk individuals. The objective of this review is to present a comprehensive overview of the currently used novel techniques viz., liquid biopsy, next-generation sequencing (NGS), microarray, nanotechnology, lab-on-a-chip (LOC) or microfluidics, and artificial intelligence (AI) for the clinical diagnostics and management of this malignancy. The potential of these novel techniques in expanding OC diagnostics and clinical management is also reviewed.
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Affiliation(s)
- Sagar Dholariya
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Ragini D Singh
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Amit Sonagra
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | | | | | - Deepak Parchwani
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
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13
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Malapelle U, Pisapia P, Pepe F, Russo G, Buono M, Russo A, Gomez J, Khorshid O, Mack PC, Rolfo C, Troncone G. The evolving role of liquid biopsy in lung cancer. Lung Cancer 2022; 172:53-64. [PMID: 35998482 DOI: 10.1016/j.lungcan.2022.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022]
Abstract
Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Jorge Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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14
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Savage R, Messenger M, Neal RD, Ferguson R, Johnston C, Lloyd KL, Neal MD, Sansom N, Selby P, Sharma N, Shinkins B, Skinner JR, Tully G, Duffy S, Hall G. Development and validation of multivariable machine learning algorithms to predict risk of cancer in symptomatic patients referred urgently from primary care: a diagnostic accuracy study. BMJ Open 2022; 12:e053590. [PMID: 35365520 PMCID: PMC8977764 DOI: 10.1136/bmjopen-2021-053590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 03/04/2022] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To develop and validate tests to assess the risk of any cancer for patients referred to the NHS Urgent Suspected Cancer (2-week wait, 2WW) clinical pathways. SETTING Primary and secondary care, one participating regional centre. PARTICIPANTS Retrospective analysis of data from 371 799 consecutive 2WW referrals in the Leeds region from 2011 to 2019. The development cohort was composed of 224 669 consecutive patients with an urgent suspected cancer referral in Leeds between January 2011 and December 2016. The diagnostic algorithms developed were then externally validated on a similar consecutive sample of 147 130 patients (between January 2017 and December 2019). All such patients over the age of 18 with a minimum set of blood counts and biochemistry measurements available were included in the cohort. PRIMARY AND SECONDARY OUTCOME MEASURES sensitivity, specificity, negative predictive value, positive predictive value, Receiver Operating Characteristic (ROC) curve Area Under Curve (AUC), calibration curves RESULTS: We present results for two clinical use-cases. In use-case 1, the algorithms identify 20% of patients who do not have cancer and may not need an urgent 2WW referral. In use-case 2, they identify 90% of cancer cases with a high probability of cancer that could be prioritised for review. CONCLUSIONS Combining a panel of widely available blood markers produces effective blood tests for cancer for NHS 2WW patients. The tests are affordable, and can be deployed rapidly to any NHS pathology laboratory with no additional hardware requirements.
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Affiliation(s)
| | - Mike Messenger
- University of Leeds, Leeds, UK
- NIHR MedTech and In Vitro Diagnostic Co-Operative, Leeds, UK
| | - Richard D Neal
- University of Leeds, Leeds, UK
- NIHR MedTech and In Vitro Diagnostic Co-Operative, Leeds, UK
- University of Exeter, Exeter, UK
| | | | | | | | | | | | - Peter Selby
- University of Leeds, Leeds, UK
- NIHR MedTech and In Vitro Diagnostic Co-Operative, Leeds, UK
- Chair of the PinPoint Scientific Advisory Board, Leeds, UK
| | | | | | | | | | - Sean Duffy
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Geoff Hall
- University of Leeds, Leeds, UK
- NIHR MedTech and In Vitro Diagnostic Co-Operative, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
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15
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Ozturk EA, Caner A. Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections. Acta Parasitol 2022; 67:1-17. [PMID: 34176040 DOI: 10.1007/s11686-021-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections. METHODS In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature. RESULTS Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo. CONCLUSION In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.
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Affiliation(s)
- Eylem Akdur Ozturk
- Department of Parasitology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Faculty of Medicine, 35100, Izmir, Turkey.
- Cancer Research Center, Ege University, Izmir, Turkey.
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16
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Doubeni CA, Lau YK, Lin JS, Pennello GA, Carlson RW. Development and evaluation of safety and effectiveness of novel cancer screening tests for routine clinical use with applications to multicancer detection technologies. Cancer 2022; 128 Suppl 4:883-891. [PMID: 35133658 PMCID: PMC11296691 DOI: 10.1002/cncr.33954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/22/2021] [Accepted: 08/30/2021] [Indexed: 12/19/2022]
Abstract
Multicancer screening is a promising approach to improving the detection of preclinical disease, but current technologies have limited ability to identify precursor or early stage lesions, and approaches for developing the evidentiary chain are unclear. Frameworks to enable development and evaluation from discovery through evidence of clinical effectiveness are discussed.
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Affiliation(s)
- Chyke A. Doubeni
- Center for Health Equity and Community Engagement Research, Mayo Clinic, Rochester, Minnesota
- Department of Family Medicine, Mayo Clinic, Rochester, Minnesota
- Department of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Family Medicine, Mayo Clinic, Phoenix, Arizona
| | - Yan Kwan Lau
- Center for Health Equity and Community Engagement Research, Mayo Clinic, Rochester, Minnesota
- Department of Family Medicine, Mayo Clinic, Rochester, Minnesota
- Department of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jennifer S. Lin
- Kaiser Permanente Evidence-Based Practice Center, Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Gene A. Pennello
- Division of Imaging, Diagnostics, and Software Reliability, US Food and Drug Administration, Silver Spring, Maryland
| | - Robert W. Carlson
- National Comprehensive Cancer Network, Plymouth Meeting, Pennsylvania
- Department of Medicine, Division of Medical Oncology, Stanford University Medical Center, Stanford, California
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17
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Refining risk stratification in HR-positive/HER2-negative early breast cancer: how to select patients for treatment escalation? Breast Cancer Res Treat 2022; 192:465-484. [DOI: 10.1007/s10549-022-06535-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/23/2022] [Indexed: 12/13/2022]
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18
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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19
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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20
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Jafarpour S, Saberi F, Yazdi M, Nedaeinia R, Amini G, Ferns GA, Salehi R. Association between colorectal cancer and the degree of ITGA4 promoter methylation in peripheral blood mononuclear cells. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Chalasani NP, Porter K, Bhattacharya A, Book AJ, Neis BM, Xiong KM, Ramasubramanian TS, Edwards DK, Chen I, Johnson S, Roberts LR, Kisiel JB, Reddy KR, Singal AG, Olson MC, Bruinsma JJ. Validation of a Novel Multitarget Blood Test Shows High Sensitivity to Detect Early Stage Hepatocellular Carcinoma. Clin Gastroenterol Hepatol 2022; 20:173-182.e7. [PMID: 34391922 DOI: 10.1016/j.cgh.2021.08.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 08/09/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Although biannual ultrasound surveillance with or without α-fetoprotein (AFP) testing is recommended for at-risk patients, sensitivity for early stage HCC, for which potentially curative treatments exist, is suboptimal. We conducted studies to establish the multitarget HCC blood test (mt-HBT) algorithm and cut-off values and to validate test performance in patients with chronic liver disease. METHODS Algorithm development and clinical validation studies were conducted with participants in an international, multicenter, case-control study. Study subjects had underlying cirrhosis or chronic hepatitis B virus; HCC cases were diagnosed per the American Association for the Study of Liver Diseases criteria and controls were matched for age and liver disease etiology. Whole blood and serum were shipped to a central laboratory and processed while blinded to case/control status. An algorithm was developed for the mt-HBT, which incorporates methylation biomarkers (HOXA1, TSPYL5, and B3GALT6), AFP, and sex. RESULTS In algorithm development, with 136 HCC cases (60% early stage) and 404 controls, the mt-HBT showed 72% sensitivity for early stage HCC at 88% specificity. Test performance was validated in an independent cohort of 156 HCC cases (50% early stage) and 245 controls, showing 88% overall sensitivity, 82% early stage sensitivity, and 87% specificity. Early stage sensitivity in clinical validation was significantly higher than AFP at 20 ng/mL or greater (40%; P < .0001) and GALAD (gender, age, Lens culinaris agglutinin-reactive AFP, AFP, and des-γ-carboxy-prothrombin score) of -0.63 or greater (71%; P = .03), although AFP and GALAD at these cut-off values had higher specificities (100% and 93%, respectively). CONCLUSIONS The mt-HBT may significantly improve early stage HCC detection for patients undergoing HCC surveillance, a critical step to increasing curative treatment opportunities and reducing mortality. ClinicalTrials.gov number NCT03628651.
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Affiliation(s)
- Naga P Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Kyle Porter
- Exact Sciences Corporation, Madison, Wisconsin
| | | | - Adam J Book
- Exact Sciences Development Corporation, Madison, Wisconsin
| | - Brenda M Neis
- Exact Sciences Development Corporation, Madison, Wisconsin
| | - Kong M Xiong
- Exact Sciences Development Corporation, Madison, Wisconsin
| | | | | | - Irene Chen
- Exact Sciences Corporation, Madison, Wisconsin
| | | | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amit G Singal
- Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas
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22
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Beheshti Namdar A, Kabiri M, Mosanan Mozaffari H, Aminifar E, Mehrad-Majd H. Circulating Clusterin Levels and Cancer Risk: A Systematic Review and Meta-Analysis. Cancer Control 2022; 29:10732748211038437. [PMID: 35465749 PMCID: PMC9047800 DOI: 10.1177/10732748211038437] [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] [Indexed: 12/03/2022] Open
Abstract
Introduction The previous reports on clusterin (CLU) levels in various types of cancer
have been controversial and heterogeneous. The present meta-analysis has
aimed to evaluate the association between soluble CLU levels and the risk of
different human cancers based on observational studies. Methods A systematic literature review was conducted to determine the relevant
eligible studies in English language from health-related electronic
databases up to January 2021. Random effects models were used to calculate
the summary standard mean difference (SMD) with 95% confidence intervals
(CIs) to identify the correlation between CLU levels and cancer risk. The
meta-regression, sensitivity, Galbraith, and subgroup analyses were
performed to explore the source of between-study heterogeneity. Furthermore,
the funnel plot and Egger’s linear regression tests were carried out to
evaluate the risk of publication bias. Results According to 16 eligible articles, 3331 patients and 839 healthy controls
were included in our meta-analysis. Overall, the CLU levels were
significantly higher in various cancer cases compared to the healthy groups
(SMD = 1.50, 95% CI = 0.47–2.53). Moreover, subgroup analysis based on types
of cancer showed a significant correlation between CLU levels and the risk
of digestive system cancers (SMD = 1.54, 95% CI = 0.91–2.18,
P <0.001), especially in HCC (SMD = 1.89, 95% CI =
0.76–3.03, P = 0.001), and CRC (SMD = 1.63, 95% CI =
0.0–3.23, P = 0.048). Conclusion The present meta-analysis indicates a significant association of CLU levels
with the risk of digestive system cancers such as hepatocellular carcinoma
and colorectal cancer. Therefore, CLU can be monitored as a novel molecular
biomarker for the prognosis and diagnosis of various types of cancers
particularly in the digestive system.
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Affiliation(s)
- Ali Beheshti Namdar
- Department of Gastroenterology and Hepatology, Faculty of Medicine, 37552Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Kabiri
- School of Pharmacy, 37552Mashhad University of Medical Sciences, Mashhad, Iran.,Clinical Research Development Unit, Ghaem Hospital, 37552Mashhad University of Medical Sciences, Mashhad, Iran
| | - Homan Mosanan Mozaffari
- Department of Gastroenterology and Hepatology, Faculty of Medicine, 37552Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Aminifar
- Student Research Committee, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Hassan Mehrad-Majd
- Cancer Molecular Pathology Research Center, 37552Mashhad University of Medical Sciences, Mashhad, Iran
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23
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Xie L, Du X, Wang S, Shi P, Qian Y, Zhang W, Tang X, Lin Y, Chen J, Peng L, Yu CC, Qian B. Development and evaluation of cancer differentiation analysis technology: a novel biophysics-based cancer screening method. Expert Rev Mol Diagn 2021; 22:111-117. [PMID: 34846233 DOI: 10.1080/14737159.2021.2013201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Routine health checkup is an essential strategy for monitoring population health and maintaining healthy workforces. However, there was a lack of cancer screening tests among routine health checkups due to high costs and unreliable methods. METHODS We conducted a two-stage study to evaluate the value of a blood test, Cancer Differentiation Analysis (CDATM), which is developed to differentiate the blood samples of healthy individuals from those of cancer patients through measuring and analyzing multiple biophysical properties. RESULTS The first stage of a cross-sectional study included 75,942 healthy individuals in routine health checkup, and the second stage of a prospective population-based cohort included 1,957 healthy community members. Forty-eight and ten cancer cases were identified among cross-sectional study and prospective population-based cohort, respectively. Using a pre-determined cutoff, we found that the CDA™ test could differentiate blood samples between healthy and cancer individuals with >93% specificity and >55% sensitivity in both studies. CONCLUSIONS With high specificity and moderate sensitivity of CDA™ test, our study indicates that we can analyze biophysical properties in the blood to rapidly and reliably screen healthy individuals from cancer patients in a health checkup setting where most individuals are healthy or with average risk of cancer.
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Affiliation(s)
- Li Xie
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuedong Du
- AnPac Bio-Medical Science Co., Ltd, Shanghai, China
| | - Suna Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Shi
- Department of Statistics and Data Management, Children's Hospital of Fudan University, Shanghai, China
| | - Ying Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weituo Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Tang
- AnPac Bio-Medical Science Co., Ltd, Shanghai, China
| | - Yue Lin
- AnPac Bio-Medical Science Co., Ltd, Shanghai, China
| | - Jie Chen
- AnPac Bio-Medical Science Co., Ltd, Shanghai, China
| | - Lan Peng
- AnPac Bio-Medical Science Co., Ltd, Shanghai, China
| | | | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Clinical Research Promotion and Development Center, Shanghai Hospital Development Center, Shanghai, China
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24
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Aleotti V, Catoni C, Poggiana C, Rosato A, Facchinetti A, Scaini MC. Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. Cancers (Basel) 2021; 13:6217. [PMID: 34944843 PMCID: PMC8699653 DOI: 10.3390/cancers13246217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023] Open
Abstract
Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
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Affiliation(s)
- Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
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25
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Wu Y, Chen Q, Zhang Q, Li M, Li H, Jia L, Huang Y, Zhang J. Analysis of whole-exome data of cfDNA and the tumor tissue of non-small cell lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1453. [PMID: 34734005 PMCID: PMC8506706 DOI: 10.21037/atm-21-4117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022]
Abstract
Background Non-small cell lung cancer (NSCLC) has the highest cancer mortality rate in the world, but currently there is no effective method of dynamic monitoring. Gene mutation is an important factor in tumorigenesis and can be detected using high-throughput sequencing technology. This study aimed to analyze the driving genes in the tumor of NSCLC patients by whole exon sequencing, and to compare and analyze the subclones of the tumor at different time points. Methods We collected 87 cases of NSCLC tumor tissues, para-cancer tissues, and peripheral blood samples for detecting cell-free DNAs (cfDNAs) from January 2016 to December 2018, and whole-exome sequencing was performed. The gene mutation map of NSCLC was drawn in detail by second-generation sequencing data analysis and new driver genes were found. In addition, we performed a subclonal analysis of tumors from different stages of the same patient to further describe the tumor heterogeneity. Results We found that the clonal analysis obtained by cfDNA detection was similar to the clonal analysis of the tissue samples, so real-time monitoring of tumor changes can be carried out through monitoring cfDNA. Conclusions This study provides evidence for studying the gene mutation information of NSCLC and shows the importance of cfDNA in the analysis of tumor subcloning information.
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Affiliation(s)
- Yuanzhou Wu
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qunqing Chen
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | | | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Li
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Longfei Jia
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Huang
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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26
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Beech C, Hechtman JF. Molecular Approach to Colorectal Carcinoma: Current Evidence and Clinical Application. Surg Pathol Clin 2021; 14:429-441. [PMID: 34373094 DOI: 10.1016/j.path.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Colorectal carcinoma is one of the most common cancer types in men and women, responsible for both the third highest incidence of new cancer cases and the third highest cause of cancer deaths. In the last several decades, the molecular mechanisms surrounding colorectal carcinoma's tumorigenesis have become clearer through research, providing new avenues for diagnostic testing and novel approaches to therapeutics. Laboratories are tasked with providing the most current information to help guide clinical decisions. In this review, we summarize the current knowledge surrounding colorectal carcinoma tumorigenesis and highlight clinically relevant molecular testing.
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Affiliation(s)
- Cameron Beech
- Department of Pathology, Yale New Haven Hospital, New Haven, CT, USA
| | - Jaclyn F Hechtman
- Molecular and GI Pathologist, NeoGenomics Laboratories, Fort Myers, FL, USA.
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27
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Liquid Biopsy for Biomarker Testing in Non-Small Cell Lung Cancer: A European Perspective. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2030022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The development of targeted therapies has improved survival rates for patients with advanced non-small cell lung cancer (NSCLC). However, tissue biopsy is unfeasible or inadequate in many patients, limiting biomarker testing and access to targeted therapies. The increasing numbers of established and emerging biomarkers with available targeted treatments highlights the challenges associated with sequential single-gene testing and limited tissue availability. Multiplex next-generation sequencing (NGS) offers an attractive alternative and represents a logical next step, and in cases where the tumour is inaccessible, tissue biopsy yields insufficient tumour content, or when the patient’s performance status does not allow a tissue biopsy, liquid biopsy can provide valuable material for molecular diagnosis. Here, we explore the role of liquid biopsy (i.e., circulating cell-free DNA analysis) in Europe. Liquid biopsies could be used as a complementary approach to increase rates of molecular diagnosis, with the ultimate aim of improving patient access to appropriate targeted therapies. Expert opinion is also provided on potential future applications of liquid biopsy in NSCLC, including for cancer prevention, detection of early stage and minimum residual disease, monitoring of response to therapy, selection of patients for immunotherapy, and monitoring of tumour evolution to enable optimal adaptation/combination of drug therapies.
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28
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Bruschini R, Maffini F, Chiesa F, Lepanto D, De Berardinis R, Chu F, Tagliabue M, Giugliano G, Ansarin M. Oral cancer: changing the aim of the biopsy in the age of precision medicine. A review. ACTA ACUST UNITED AC 2021; 41:108-119. [PMID: 34028455 PMCID: PMC8142729 DOI: 10.14639/0392-100x-n1056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/03/2021] [Indexed: 01/15/2023]
Abstract
Oral cancer is a heterogeneous disease that develops through a complex, multi-step process. Precision medicine should help to better understand its molecular basis, integrate traditional classifications and have a positive impact on cancer management. To apply this information in clinical practice, we need to define its histology and identify biomarkers expressed by the tumour that provide useful information for planning tailored treatment. The most reliable information currently derives from evaluation of biomarkers on post-operative samples. To plan personalised treatment, oncologists need to assess these markers on biopsy samples. We reviewed the recent literature and identified 6 of 184 publications that compared markers measured on biopsy and post-operative samples or assessed their predictivity for the development of lymph node metastases. Data from these studies suggest that markers measured on biopsy samples can provide useful indications for tailoring treatments. However, due to their heterogeneity and low level of evidence, these results need to be confirmed by clinical studies on a large population to standardise and validate biomarkers in biopsies and to assess their reliability in other diagnostic mini-invasive procedures such as radiomics and liquid biopsy.
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Affiliation(s)
- Roberto Bruschini
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Fausto Maffini
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Fausto Chiesa
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Daniela Lepanto
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Rita De Berardinis
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Chu
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Marta Tagliabue
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Gioacchino Giugliano
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
| | - Mohssen Ansarin
- Division of Otolaryngology and Head & Neck Surgery, European Institute of Oncology IRCCS, Milan, Italy
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29
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Liu L, Chen X, Petinrin OO, Zhang W, Rahaman S, Tang ZR, Wong KC. Machine Learning Protocols in Early Cancer Detection Based on Liquid Biopsy: A Survey. Life (Basel) 2021; 11:638. [PMID: 34209249 PMCID: PMC8308091 DOI: 10.3390/life11070638] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
With the advances of liquid biopsy technology, there is increasing evidence that body fluid such as blood, urine, and saliva could harbor the potential biomarkers associated with tumor origin. Traditional correlation analysis methods are no longer sufficient to capture the high-resolution complex relationships between biomarkers and cancer subtype heterogeneity. To address the challenge, researchers proposed machine learning techniques with liquid biopsy data to explore the essence of tumor origin together. In this survey, we review the machine learning protocols and provide corresponding code demos for the approaches mentioned. We discuss algorithmic principles and frameworks extensively developed to reveal cancer mechanisms and consider the future prospects in biomarker exploration and cancer diagnostics.
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Affiliation(s)
- Linjing Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Olutomilayo Olayemi Petinrin
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Weitong Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Saifur Rahaman
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Zhi-Ri Tang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
- Hong Kong Institute for Data Science, City University of Hong Kong, Hong Kong, China
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30
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Yalchin M, Baker AM, Graham TA, Hart A. Predicting Colorectal Cancer Occurrence in IBD. Cancers (Basel) 2021; 13:2908. [PMID: 34200768 PMCID: PMC8230430 DOI: 10.3390/cancers13122908] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with colonic inflammatory bowel disease (IBD) are at an increased risk of developing colorectal cancer (CRC), and are therefore enrolled into a surveillance programme aimed at detecting dysplasia or early cancer. Current surveillance programmes are guided by clinical, endoscopic or histological predictors of colitis-associated CRC (CA-CRC). We have seen great progress in our understanding of these predictors of disease progression, and advances in endoscopic technique and management, along with improved medical care, has been mirrored by the falling incidence of CA-CRC over the last 50 years. However, more could be done to improve our molecular understanding of CA-CRC progression and enable better risk stratification for patients with IBD. This review summarises the known risk factors associated with CA-CRC and explores the molecular landscape that has the potential to complement and optimise the existing IBD surveillance programme.
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Affiliation(s)
- Mehmet Yalchin
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ann-Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Trevor A. Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ailsa Hart
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
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31
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Del Corvo M, Lazzari B, Capra E, Zavarez L, Milanesi M, Utsunomiya YT, Utsunomiya ATH, Stella A, de Paula Nogueira G, Garcia JF, Ajmone-Marsan P. Methylome Patterns of Cattle Adaptation to Heat Stress. Front Genet 2021; 12:633132. [PMID: 34122501 PMCID: PMC8194315 DOI: 10.3389/fgene.2021.633132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperature at the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 819 genes. Among these, 351 were only seen in Angus, 366 were specific to Nellore, and 102 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were under methylated during heat stress, whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Ludmilla Zavarez
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Yuri Tani Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Adam Taiti Harth Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Guilherme de Paula Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil
| | - Josè Fernando Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
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32
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Siddiqui AS, Alshehri FA, Yaqinuddin A. Aberrant DNA Methylation in Bladder Cancer among Saudi Arabia Population. JOURNAL OF HEALTH AND ALLIED SCIENCES NU 2021. [DOI: 10.1055/s-0041-1726685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractTumor biomarkers developed based on the aberrant deoxyribonucleic acid (DNA) methylation patterns in bladder cancer (BC) hold great promise due to their stability, specificity, and known associations with the disease. No study has investigated DNA methylation patterns in BC patients from Saudi population. We analyzed DNA methylation levels of 48 tumor suppressor genes loci in 24 bladder tissues (19 BC and 5 control samples) using Human Tumour Suppressor Genes EpiTect Methyl II Complete PCR Array (Qiagen, Hilden, Germany). We identified significant difference in DNA hypermethylation levels at E2F1, ERBB2, HIC1, OPCML, SFN, SFRP1, SFRP2, SPARC, and TERT gene loci between controls and cancerous samples. SCGB3A1 was differentially methylated in nonmuscle invasive versus muscle invasive BC samples. Results suggest that these aberrant DNA methylation patterns in BC are disease and population specific and can be developed as distinct DNA methylation-based biomarkers for BC detection.
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Affiliation(s)
- Amna Shoaib Siddiqui
- Department of Anatomy and Genetics, College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Faizah A Alshehri
- Office of Research and Innovation ORI, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | - Ahmed Yaqinuddin
- Department of Anatomy and Genetics, College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
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33
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Liquid biopsy genotyping by a simple lateral flow strip assay with visual detection. Anal Chim Acta 2021; 1163:338470. [PMID: 34024417 DOI: 10.1016/j.aca.2021.338470] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
Liquid biopsy, as a minimally invasive method that allows real-time monitoring of the tumor genome, represents a competing approach for cancer diagnosis, prognosis and therapy decision making. Liquid biopsy in cancer patients mainly includes analysis of circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). ctDNA is the tumor-derived fraction of the cell-free DNA present in the blood. ctDNA is detected based on cancer-specific genomic aberrations (mainly mutations) and represents a challenging analyte due to high fragmentation and low concentration. Several methodologies have been developed for ctDNA analysis in cancer patients but many of these technologies are too time-intensive, complicated and expensive for implementation in diagnostic testing. Herein, we developed a novel lateral flow strip assay for mutational analysis of ctDNA in blood samples and visual detection that is based on gold nanoparticles as reporters. As a model, common single-point mutations of the KRAS gene, related to colorectal cancer (CRC), have been selected for method development. The proposed DNA biosensor has been successfully applied for the detection of three KRAS mutations (KRAS G12D/A/V), along with the wild-type KRAS gene in synthetic DNA targets, cancer cell lines and cfDNA from blood samples of healthy individuals and CRC patients. The main advantages of the proposed lateral flow assay are simplicity, rapid analysis time (∼10 min) and visual detection without the requirement of special instrumentation. The assay is also cost-effective with high detectability, specificity and reproducibility and has the potential to be used as a portable and universal device. In conclusion, the proposed assay offers a rapid diagnostic strip test for visual genotyping, as an alternative approach for liquid biopsy applications.
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34
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Robichaud PP, Arseneault M, O'Connell C, Ouellette RJ, Morin PJ. Circulating cell-free DNA as potential diagnostic tools for amyotrophic lateral sclerosis. Neurosci Lett 2021; 750:135813. [PMID: 33705931 DOI: 10.1016/j.neulet.2021.135813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
DNA methylation has garnered much attention in recent years for its diagnostic potential in multiple conditions including cancer and neurodegenerative diseases. Conversely, advances regarding the potential diagnostic relevance of DNA methylation status have been sparse in the field of amyotrophic lateral sclerosis (ALS) even though patients diagnosed with this condition would significantly benefit from improved molecular assays aimed at furthering the current diagnostic and therapeutic options available. This review will provide an overview of the current diagnostic approaches available for ALS diagnosis and discuss the potential clinical usefulness of DNA methylation. We will also present examples of DNA methylation as a diagnostic tool in various types of cancer and neurodegenerative conditions and expand on how circulating cfDNA methylation may be leveraged for the early detection of ALS. In general, this article will reinforce the importance of cfDNA methylation as diagnostic tools and will further highlight its clinical relevance for persons diagnosed with ALS.
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Affiliation(s)
- Philippe-Pierre Robichaud
- Vitalité Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Department of Genetic Services, 330 Université Ave, Moncton, New Brunswick, E1C 2Z3, Canada; Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, New Brunswick, E1C 8X3, Canada; Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Michael Arseneault
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Colleen O'Connell
- Stan Cassidy Centre for Rehabilitation, 800 Priestman Street, Fredericton, New Brunswick, E3B 0C7, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, New Brunswick, E1C 8X3, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada.
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35
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Ottaviano M, Giuliano M, Tortora M, La Civita E, Liotti A, Longo M, Bruzzese D, Cennamo M, Riccio V, De Placido P, Picozzi F, Parola S, Daniele B, Botti G, Formisano P, Beguinot F, De Placido S, Terracciano D, Palmieri G. A New Horizon of Liquid Biopsy in Thymic Epithelial Tumors: The Potential Utility of Circulating Cell-Free DNA. Front Oncol 2021; 10:602153. [PMID: 33634024 PMCID: PMC7902074 DOI: 10.3389/fonc.2020.602153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Thymic epithelial tumors (TETs) are rare thoracic malignancies, commonly divided into two different histopathological entities, thymoma (T) and thymic carcinoma (TC). To date, there are no specific biomarkers for monitoring the biological course of these rare tumors. We carried out a single center study aiming at the detection of circulating cell-free DNA (ccfDNA) and the correlation of its levels with metastatic dissemination and histological subtype in patients with TETs. METHODS From July 2018 to January 2020, 5-ml blood samples from 26 patients with advanced TET (aTET) (11 patients with TC and 15 patients with T) and from six patients with completely resected TET (cr-TET), were prospectively obtained before the initiation of systemic therapy. Blood samples from 10 healthy donors were used as control. The QIAamp MinElute ccfDNA Kits was used for ccfDNA isolation from plasma; real-time PCR was used for cfDNA quantification. RESULTS We found significantly higher ccfDNA amount in patients with T and TC compared to controls, with median ccfDNA level of 3.3 ng/µl, 11.4 ng/µl and 25.6 ng/µl, for healthy donors, T and TC patients, respectively (p<0.001). No significant difference was found between cr-TET and controls (p = 0.175). ccfDNA concentrations were higher in metastatic (M1a and M1b) compared to non-metastatic (M0) TETs (25.6 ng/µl versus 7.2 ng/µl; p= 0.037). No significant correlation was found either between ccfDNA and disease stage, according to both the Masaoka-Koga (p= 0.854) and the TNM 8th edition staging systems (p = 0.66), or between ccfDNA levels and overall tumor burden, estimated according RECIST 1.1 criteria (r = 0.07, p = 0.725). CONCLUSIONS To the best of our knowledge, this is the first study that prospectively explores detection and quantification of ccfDNA in TETs. Higher baseline cfDNA levels have been observed in both advanced T and TC comparing to the control group.
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Affiliation(s)
- Margaret Ottaviano
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CRCTR Rare Tumors Coordinating Center of Campania Region, Naples, Italy
- Oncology Unit, Ospedale del Mare, Naples, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CRCTR Rare Tumors Coordinating Center of Campania Region, Naples, Italy
| | - Marianna Tortora
- CRCTR Rare Tumors Coordinating Center of Campania Region, Naples, Italy
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Antonietta Liotti
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Michele Longo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Michele Cennamo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Vittorio Riccio
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Pietro De Placido
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Fernanda Picozzi
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Sara Parola
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | | | - Gerardo Botti
- CRCTR Rare Tumors Coordinating Center of Campania Region, Naples, Italy
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Pietro Formisano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Francesco Beguinot
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CRCTR Rare Tumors Coordinating Center of Campania Region, Naples, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, Naples, Italy
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Cree IA, Indave Ruiz BI, Zavadil J, McKay J, Olivier M, Kozlakidis Z, Lazar AJ, Hyde C, Holdenrieder S, Hastings R, Rajpoot N, de la Fouchardiere A, Rous B, Zenklusen JC, Normanno N, Schilsky RL. The International Collaboration for Cancer Classification and Research. Int J Cancer 2021; 148:560-571. [PMID: 32818326 PMCID: PMC7756795 DOI: 10.1002/ijc.33260] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3 R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3 R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges.
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Affiliation(s)
- Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | | | - Jiri Zavadil
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - James McKay
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Magali Olivier
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Zisis Kozlakidis
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular PathologyThe University of Texas, MD Anderson Cancer CenterHoustonTexasUSA
| | - Chris Hyde
- Exeter Test GroupCollege of Medicine and Health, University of ExeterExeterUK
| | | | - Ros Hastings
- GenQA (Genomics External Quality Assessment)Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation TrustOxfordUK
| | - Nasir Rajpoot
- Department of Computer ScienceUniversity of WarwickCoventryUK
- Alan Turing InstituteLondonUK
- Department of PathologyUniversity Hospitals Coventry & Warwickshire NHS TrustCoventryUK
| | | | - Brian Rous
- National Cancer Registration Service (Eastern Office), Public Health England, Victoria HouseCambridgeUK
| | - Jean Claude Zenklusen
- Center for Cancer GenomicsNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Nicola Normanno
- Cell Biology and Biotherapy UnitIstituto Nazionale Tumori—IRCCS—“Fondazione G. Pascale,” Via M. SemmolaNaplesItaly
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Iftikhar MS, Talha GM, Aleem M, Shamim A. Bioinformatics–computer programming. NANOTECHNOLOGY IN CANCER MANAGEMENT 2021:125-148. [DOI: 10.1016/b978-0-12-818154-6.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Dasari A, Morris VK, Allegra CJ, Atreya C, Benson AB, Boland P, Chung K, Copur MS, Corcoran RB, Deming DA, Dwyer A, Diehn M, Eng C, George TJ, Gollub MJ, Goodwin RA, Hamilton SR, Hechtman JF, Hochster H, Hong TS, Innocenti F, Iqbal A, Jacobs SA, Kennecke HF, Lee JJ, Lieu CH, Lenz HJ, Lindwasser OW, Montagut C, Odisio B, Ou FS, Porter L, Raghav K, Schrag D, Scott AJ, Shi Q, Strickler JH, Venook A, Yaeger R, Yothers G, You YN, Zell JA, Kopetz S. ctDNA applications and integration in colorectal cancer: an NCI Colon and Rectal-Anal Task Forces whitepaper. Nat Rev Clin Oncol 2020; 17:757-770. [PMID: 32632268 PMCID: PMC7790747 DOI: 10.1038/s41571-020-0392-0] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
An increasing number of studies are describing potential uses of circulating tumour DNA (ctDNA) in the care of patients with colorectal cancer. Owing to this rapidly developing area of research, the Colon and Rectal-Anal Task Forces of the United States National Cancer Institute convened a panel of multidisciplinary experts to summarize current data on the utility of ctDNA in the management of colorectal cancer and to provide guidance in promoting the efficient development and integration of this technology into clinical care. The panel focused on four key areas in which ctDNA has the potential to change clinical practice, including the detection of minimal residual disease, the management of patients with rectal cancer, monitoring responses to therapy, and tracking clonal dynamics in response to targeted therapies and other systemic treatments. The panel also provides general guidelines with relevance for ctDNA-related research efforts, irrespective of indication.
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Affiliation(s)
- Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Chloe Atreya
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Al B Benson
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Patrick Boland
- Department of Medicine, Roswell Park Cancer Center, Buffalo, NY, USA
| | - Ki Chung
- Division of Hematology & Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Mehmet S Copur
- CHI Health St Francis Cancer Treatment Center, Grand Island, NE, USA
| | - Ryan B Corcoran
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dustin A Deming
- Division of Hematology, Medical Oncology and Palliative Care, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrea Dwyer
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas J George
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Marc J Gollub
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Stanley R Hamilton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard Hochster
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MD, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Atif Iqbal
- Section of Colorectal Surgery, Division of Surgery, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Samuel A Jacobs
- National Adjuvant Surgical and Bowel Project Foundation/NRG Oncology, Pittsburgh, PA, USA
| | - Hagen F Kennecke
- Department of Oncology, Virginia Mason Cancer Institute, Seattle, WA, USA
| | - James J Lee
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christopher H Lieu
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, CO, USA
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - O Wolf Lindwasser
- Coordinating Center for Clinical Trials, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Montagut
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bruno Odisio
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fang-Shu Ou
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Laura Porter
- Patient Advocate, NCI Colon Task Force, Boston, MA, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deborah Schrag
- Division of Population Sciences, Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aaron J Scott
- Division of Hematology and Oncology, Banner University of Arizona Cancer Center, Tucson, AZ, USA
| | - Qian Shi
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - John H Strickler
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alan Venook
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Greg Yothers
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Zell
- Department of Epidemiology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Gašperšič J, Videtič Paska A. Potential of modern circulating cell-free DNA diagnostic tools for detection of specific tumour cells in clinical practice. Biochem Med (Zagreb) 2020; 30:030504. [PMID: 32774122 PMCID: PMC7394254 DOI: 10.11613/bm.2020.030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
Personalized medicine is a developing field of medicine that has gained in importance in recent decades. New diagnostic tests based on the analysis of circulating cell-free DNA (cfDNA) were developed as a tool of diagnosing different cancer types. By detecting the subpopulation of mutated DNA from cancer cells, it is possible to detect the presence of a specific tumour in early stages of the disease. Mutation analysis is performed by quantitative polymerase chain reaction (qPCR) or the next generation sequencing (NGS), however, cfDNA protocols need to be modified carefully in preanalytical, analytical, and postanalytical stages. To further improve treatment of cancer the Food and Drug Administration approved more than 20 companion diagnostic tests that combine cancer drugs with highly efficient genetic diagnostic tools. Tools detect mutations in the DNA originating from cancer cells directly through the subpopulation of cfDNA, the circular tumour DNA (ctDNA) analysis or with visualization of cells through intracellular DNA probes. A large number of ctDNA tests in clinical studies demonstrate the importance of new findings in the field of cancer diagnosis. We describe the innovations in personalized medicine: techniques for detecting ctDNA and genomic DNA (gDNA) mutations approved Food and Drug Administration companion genetic diagnostics, candidate genes for assembling the cancer NGS panels, and a brief mention of the multitude of cfDNA currently in clinical trials. Additionally, an overview of the development steps of the diagnostic tools will refresh and expand the knowledge of clinics and geneticists for research opportunities beyond the development phases.
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Affiliation(s)
- Jernej Gašperšič
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Surface-enhanced Raman scattering (SERS)-based immunosystem for ultrasensitive detection of the 90K biomarker. Anal Bioanal Chem 2020; 412:7659-7667. [PMID: 32875368 PMCID: PMC7533257 DOI: 10.1007/s00216-020-02903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/07/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
The research and the individuation of tumour markers in biological fluids are currently one of the main tools to support diagnosis, prognosis, and monitoring of the therapeutic response in oncology. Although the identification of tumour markers in asymptomatic patients is crucial for early diagnosis, its application is still limited by the relatively low sensitivity and the complexity of existing methods (i.e. ELISA, mass spectrometry). We developed an easy, fast, and ultrasensitive surface-enhanced Raman scattering (SERS)-based system, for the detection and quantitation of the LGALS3BP (90K) biomarker that was used as a model, based on the development of antibody-functionalized nanostructured gold surfaces. The detection system was effective for the ultrasensitive detection and characterization of samples of different biochemical compositions. In conclusion, this work could provide the foundation for the development of a medical diagnostic device with the highest predictive power when compared with the methods currently used in cancer diagnostics.
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Chan HT, Chin YM, Nakamura Y, Low SK. Clonal Hematopoiesis in Liquid Biopsy: From Biological Noise to Valuable Clinical Implications. Cancers (Basel) 2020; 12:E2277. [PMID: 32823942 PMCID: PMC7463455 DOI: 10.3390/cancers12082277] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/06/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
The use of blood liquid biopsy is being gradually incorporated into the clinical setting of cancer management. The minimally invasive nature of the usage of cell-free DNA (cfDNA) and its ability to capture the molecular alterations of tumors are great advantages for their clinical applications. However, somatic mosaicism in plasma remains an immense challenge for accurate interpretation of liquid biopsy results. Clonal hematopoiesis (CH) is part of the normal process of aging with the accumulation of somatic mutations and clonal expansion of hematopoietic stem cells. The detection of these non-tumor derived CH-mutations has been repeatedly reported as a source of biological background noise of blood liquid biopsy. Incorrect classification of CH mutations as tumor-derived mutations could lead to inappropriate therapeutic management. CH has also been associated with an increased risk of developing cardiovascular disease and hematological malignancies. Cancer patients, who are CH carriers, are more prone to develop therapy-related myeloid neoplasms after chemotherapy than non-carriers. The detection of CH mutations from plasma cfDNA analysis should be cautiously evaluated for their potential pathological relevance. Although CH mutations are currently considered as "false-positives" in cfDNA analysis, future studies should evaluate their clinical significance in healthy individuals and cancer patients.
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Affiliation(s)
- Hiu Ting Chan
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (H.T.C.); (Y.M.C.); (Y.N.)
| | - Yoon Ming Chin
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (H.T.C.); (Y.M.C.); (Y.N.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (H.T.C.); (Y.M.C.); (Y.N.)
| | - Siew-Kee Low
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (H.T.C.); (Y.M.C.); (Y.N.)
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Chan HT, Nagayama S, Chin YM, Otaki M, Hayashi R, Kiyotani K, Fukunaga Y, Ueno M, Nakamura Y, Low S. Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy. Mol Oncol 2020; 14:1719-1730. [PMID: 32449983 PMCID: PMC7400786 DOI: 10.1002/1878-0261.12727] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
As the use of next-generation sequencing (NGS) for plasma cell-free DNA (cfDNA) continues to expand in clinical settings, accurate identification of circulating tumor DNA mutations is important to validate its use in the clinical management for cancer patients. Here, we aimed to characterize mutations including clonal hematopoiesis (CH)-related mutations in plasma cfDNA and tumor tissues using the same ultradeep NGS assay and evaluate the clinical significance of CH-related mutations on the interpretation of liquid biopsy results. Ultradeep targeted NGS using Oncomine Pan-Cancer Panel was performed on matched surgically resected tumor tissues, peripheral blood cells (PBCs), and 120 plasma cfDNA samples from 38 colorectal cancer patients. The clinical significance of the CH-related mutations in plasma cfDNA was evaluated by longitudinal monitoring of the postoperative plasma samples. Among the 38 patients, 74 nonsynonymous mutations were identified from tumor tissues and 64 mutations from the preoperative plasma samples. Eleven (17%) of the 64 mutations identified in plasma cfDNA were also detected in PBC DNA and were identified to be CH-related mutations. Overall, 11 of 38 (29%) patients in this cohort harbored at least one CH-related mutation in plasma cfDNA. These CH-related mutations were continuously detected in subsequent postoperative plasma samples from three patients which could be misinterpreted as the presence of residual disease or as lack of treatment response. Our results indicated that it is essential to integrate the mutational information of PBCs to differentiate tumor-derived from CH-related mutations in liquid biopsy analysis. This would prevent the misinterpretation of results to avoid misinformed clinical management for cancer patients.
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Affiliation(s)
- Hiu Ting Chan
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Satoshi Nagayama
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yoon Ming Chin
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Masumi Otaki
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Rie Hayashi
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Kazuma Kiyotani
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yosuke Fukunaga
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Masashi Ueno
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yusuke Nakamura
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Siew‐Kee Low
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
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Lampignano R, Neumann MHD, Weber S, Kloten V, Herdean A, Voss T, Groelz D, Babayan A, Tibbesma M, Schlumpberger M, Chemi F, Rothwell DG, Wikman H, Galizzi JP, Riise Bergheim I, Russnes H, Mussolin B, Bonin S, Voigt C, Musa H, Pinzani P, Lianidou E, Brady G, Speicher MR, Pantel K, Betsou F, Schuuring E, Kubista M, Ammerlaan W, Sprenger-Haussels M, Schlange T, Heitzer E. Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Clin Chem 2020; 66:149-160. [PMID: 31628139 DOI: 10.1373/clinchem.2019.306837] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making. METHODS We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites. RESULTS We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT. CONCLUSIONS This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.
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Affiliation(s)
| | | | - Sabrina Weber
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Vera Kloten
- Bayer AG, Biomarker Research, Wuppertal, Germany
| | | | | | | | - Anna Babayan
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marco Tibbesma
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Francesca Chemi
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Inger Riise Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hege Russnes
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Serena Bonin
- University of Trieste, DSM-Cattinara Hospital, Trieste, Italy
| | | | - Hanny Musa
- Boehringer-Ingelheim, Ingelheim am Rhein, Germany
| | | | | | - Ged Brady
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
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Shen H, Liu T, Cui J, Borole P, Benjamin A, Kording K, Issadore D. A web-based automated machine learning platform to analyze liquid biopsy data. LAB ON A CHIP 2020; 20:2166-2174. [PMID: 32420563 DOI: 10.1039/d0lc00096e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Liquid biopsy (LB) technologies continue to improve in sensitivity, specificity, and multiplexing and can measure an ever growing library of disease biomarkers. However, clinical interpretation of the increasingly large sets of data these technologies generate remains a challenge. Machine learning is a popular approach to discover and detect signatures of disease. However, limited machine learning expertise in the LB field has kept the discipline from fully leveraging these tools and risks improper analyses and irreproducible results. In this paper, we develop a web-based automated machine learning tool tailored specifically for LB, where machine learning models can be built without the user's input. We also incorporate a differential privacy algorithm, designed to limit the effects of overfitting that can arise from users iteratively developing a panel with feedback from our platform. We validate our approach by performing a meta-analysis on 11 published LB datasets, and found that we had similar or better performance compared to those reported in the literature. Moreover, we show that our platform's performance improved when incorporating information from prior LB datasets, suggesting that this approach can continue to improve with increased access to LB data. Finally, we show that by using our platform the results achieved in the literature can be matched using 40% of the number of subjects in the training set, potentially reducing study cost and time. This self-improving and overfitting-resistant automatic machine learning platform provides a new standard that can be used to validate machine learning works in the LB field.
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Affiliation(s)
- Hanfei Shen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Li B, Shen K, Zhang J, Jiang Y, Yang T, Sun X, Ma X, Zhu J. Serum netrin-1 as a biomarker for colorectal cancer detection. Cancer Biomark 2020; 28:391-396. [PMID: 32474463 DOI: 10.3233/cbm-190340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Recent evidence support that netrin-1 involves in colorectal carcinogenesis. OBJECTIVE This study was to evaluate the performance of serum netrin-1 for detection of colorectal cancer (CRC) in both clinical/screening sets. METHODS A total of 115 consecutive patients with CRC and matched healthy controls were included in Clinical Set. Fifty subjects with CRC, 50 subjects with advanced adenoma (AA), and 150 matched control participants free of neoplasia were included in Screening Set. RESULTS In Clinical set, subjects with CRC presented higher levels of serum netrin-1 (513.9 ± 22.6 pg/mL) than controls (347.8 ± 20.3 pg/mL, p< 0.0001). Similar in Screening set, serum netrin-1 was higher in CRC (644.5 ± 37.0 pg/mL, both p< 0.0001), compared with controls (407.7 ± 14.8 pg/mL) and AA (416.5 ± 18.5 pg/mL). However, there was no difference between controls and AA (p= 0.752). Compared with the low netrin-1 group, the high group presented increased risk of CRC (Clinical set: OR = 4.300, p< 0.001; Screening set: OR = 7.731, p< 0.001). ROC curve of netrin-1 was developed to detect CRC (Clinical set: AUC 0.703; Screening set: AUC 0.759). CONCLUSIONS It suggests netrin-1 as a potential biomarker for CRC detection.
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Affiliation(s)
- Bo Li
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Kexin Shen
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Jiayu Zhang
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yang Jiang
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Ting Yang
- Beihua University Attached Hospital, Jilin, Jilin, China
| | - Xiaoxu Sun
- The People's Hospital of Jilin Province, Changchun, Jilin, China
| | - Xiaoming Ma
- Suqian Affiliated Hospital of Xuzhou Medical University, Suqian, Jiangsu, China
| | - Jinzhou Zhu
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Shen R, Cheng T, Xu C, Yung RC, Bao J, Li X, Yu H, Lu S, Xu H, Wu H, Zhou J, Bu W, Wang X, Si H, Shi P, Zhao P, Liu Y, Deng Y, Zhu Y, Zeng S, Pineda JP, Lin C, Zhou N, Bai C. Novel visualized quantitative epigenetic imprinted gene biomarkers diagnose the malignancy of ten cancer types. Clin Epigenetics 2020; 12:71. [PMID: 32448196 PMCID: PMC7245932 DOI: 10.1186/s13148-020-00861-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Epigenetic alterations are involved in most cancers, but its application in cancer diagnosis is still limited. More practical and intuitive methods to detect the aberrant expressions from clinical samples using highly sensitive biomarkers are needed. In this study, we developed a novel approach in identifying, visualizing, and quantifying the biallelic and multiallelic expressions of an imprinted gene panel associated with cancer status. We evaluated the normal and aberrant expressions measured using the imprinted gene panel to formulate diagnostic models which could accurately distinguish the imprinting differences of normal and benign cases from cancerous tissues for each of the ten cancer types. Results The Quantitative Chromogenic Imprinted Gene In Situ Hybridization (QCIGISH) method developed from a 1013-case study which provides a visual and quantitative analysis of non-coding RNA allelic expressions identified the guanine nucleotide-binding protein, alpha-stimulating complex locus (GNAS), growth factor receptor-bound protein (GRB10), and small nuclear ribonucleoprotein polypeptide N (SNRPN) out of five tested imprinted genes as efficient epigenetic biomarkers for the early-stage detection of ten cancer types. A binary algorithm developed for cancer diagnosis showed that elevated biallelic expression (BAE), multiallelic expression (MAE), and total expression (TE) measurements for the imprinted gene panel were associated with cell carcinogenesis, with the formulated diagnostic models achieving consistently high sensitivities (91–98%) and specificities (86–98%) across the different cancer types. Conclusions The QCIGISH method provides an innovative way to visually assess and quantitatively analyze individual cells for cancer potential extending from hyperplasia and dysplasia until carcinoma in situ and invasion, which effectively supplements standard clinical cytologic and histopathologic diagnosis for early cancer detection. In addition, the diagnostic models developed from the BAE, MAE, and TE measurements of the imprinted gene panel GNAS, GRB10, and SNRPN could provide important predictive information which are useful in early-stage cancer detection and personalized cancer management.
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Affiliation(s)
- Rulong Shen
- Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Tong Cheng
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Navy Medical University, Shanghai, 200433, China
| | - Rex C Yung
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21207, USA
| | - Jiandong Bao
- Departments of Endocrinology, Ultrasound and Pathology, JiangYuan Hospital Affiliated to Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Xing Li
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Hongyu Yu
- Department of Pathology, Changzheng Hospital, Navy Medical University, Shanghai, 200003, China
| | - Shaohua Lu
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Tongji University School of Medicine, Shanghai, 200072, China
| | - Huixiong Xu
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Tongji University School of Medicine, Shanghai, 200072, China
| | - Hongxun Wu
- Departments of Endocrinology, Ultrasound and Pathology, JiangYuan Hospital Affiliated to Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Jian Zhou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Wenbo Bu
- Hospital for Skin Disease, Institute of Dermatology, Chinese Academy of Medical Science, Peking Union Medical College, Nanjing, 210042, China
| | - Xiaonan Wang
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Han Si
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Panying Shi
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Pengcheng Zhao
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Yun Liu
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Yongjie Deng
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Yun Zhu
- Departments of Endocrinology, Ultrasound and Pathology, JiangYuan Hospital Affiliated to Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Shuxiong Zeng
- Department of Urology, Changhai Hospital, Navy Medical University, Shanghai, 200433, China
| | - John P Pineda
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Chunlin Lin
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78245, USA
| | - Ning Zhou
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China.
| | - Chunxue Bai
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Misawa K, Imai A, Matsui H, Kanai A, Misawa Y, Mochizuki D, Mima M, Yamada S, Kurokawa T, Nakagawa T, Mineta H. Identification of novel methylation markers in HPV-associated oropharyngeal cancer: genome-wide discovery, tissue verification and validation testing in ctDNA. Oncogene 2020; 39:4741-4755. [PMID: 32415241 PMCID: PMC7286817 DOI: 10.1038/s41388-020-1327-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 12/03/2022]
Abstract
Human papilloma virus (HPV)-associated oropharyngeal cancer (OPC) is an independent tumour type with regard to cellular, biological, and clinical features. The use of non-invasive biomarkers such as circulating tumour DNA (ctDNA) may be relevant in early diagnosis and eventually improve the outcomes of patients with head and neck squamous cell carcinoma (HNSCC). Genome-wide discovery using RNA sequencing and reduced representation bisulfite sequencing yielded 21 candidates for methylation-targeted genes. A verification study (252 HNSCC patients) using quantitative methylation-specific PCR (Q-MSP) identified 10 genes (ATP2A1, CALML5, DNAJC5G, GNMT, GPT, LY6D, LYNX1, MAL, MGC16275, and MRGPRF) that showed a significant increase recurrence in methylation groups with OPC. Further study on ctDNA using Q-MSP in HPV-associated OPC showed that three genes (CALML5, DNAJC5G, and LY6D) had a high predictive ability as emerging biomarkers for a validation set, each capable of discriminating between the plasma of the patients from healthy individuals. Among the 42 ctDNA samples, methylated CALML5, DNAJC5G, and LY6D were observed in 31 (73.8%), 19 (45.2%), and 19 (45.2%) samples, respectively. Among pre-treatment ctDNA samples, methylated CALML5, DNAJC5G, and LY6D were observed in 8/8 (100%), 7/8 (87.5%), and 7/8 (87.5%) samples, respectively. Methylated CALML5, DNAJC5G, and LY6D were found in 2/8 (25.0%), 0/8 (0%), and 1/8 (12.5%) of the final samples in the series, respectively. Here, we present the relationship between the methylation status of three specific genes and cancer recurrence for risk classification of HPV-associated OPC cases. In conclusion, ctDNA analysis has the potential to aid in determining patient prognosis and real-time surveillance for disease recurrences and serves as an alternative method of screening for HPV-associated OPC.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan.
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akinori Kanai
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
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Pro-inflammatory modification of cancer cells microsurroundings increases the survival rates for rats with low differentiated malignant glioma of brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 151:253-279. [PMID: 32448611 DOI: 10.1016/bs.irn.2020.03.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RATIONALE Glioblastoma multiforme (GBM) is one of the most aggressive human brain tumors. The prognosis is unfavorable with a median survival of 15 months. GBM aggressive nature is associated with a special phenotype of cancer cells that develops because of the transforming growth factor β (TGF-β). The study was aimed at providing experimental justification in vivo of a possibility to suppress TGF-β production in a tumor via pro-inflammatory modification of cancer cell microenvironment, using CD45+ mononuclear cells of the red bone marrow. MATERIALS AND METHODS The experiment used animals with transplanted C6 glioma. The animals were divided into 4 groups: (I) control (N=60); (II) group of rats (N=30) that received granulocyte colony-stimulating factor (G-CSF) to recruit CD45+ bone marrow mononuclear cells into their systemic circulation (G-CSF group); (III) group of rats (N=30) that received pro-inflammatory therapy to trigger systemic inflammatory reaction by injecting bacterial lipopolysaccharides (LPS) and interferon-γ (IFNγ); (IV) rats (N=30), stimulated with G-CSF, followed by pro-inflammatory therapy. Stereotaxic modeling of a brain tumor in experimental animals, as well as a combination of morphological, immunocytochemical analyses and immunosorbent assay were used. RESULTS TGF-β1 production in the tumor tissue resulted being inversely proportional to the intensity of proliferation processes and directly proportional to the size of necrosis areas, peaking on the 28th day of the experiment. Stimulation of experimental animals with G-CSF recruits CD45+ mononuclear stem and progenitor cells into the systemic circulation of experimental animals with C6 glioma, accompanied by intensification of microglial proliferation in the tumor and infiltration of the tumor tissue with microglial cells. Pro-inflammatory therapy against G-CSF stimulation results in polarization of microglia/macrophages population together with intensified antigen presentation, lower production of TGF-β and IL10, increased synthesis of pro-inflammatory cytokines TNFα and IL1 in the tumor lesion and adjacent brain matter, remodeling of tumor matrix and higher survival rates for the experimental animals. CONCLUSIONS Pro-inflammatory inflammatory modification of cancer cell microenvironment suppresses TGFβ production in a tumor and increases survival rates of the rats with transplanted poorly differentiated malignant brain glioma.
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Xu T, Gao H. Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment? Hum Genomics 2020; 14:15. [PMID: 32375881 PMCID: PMC7201531 DOI: 10.1186/s40246-020-00265-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023] Open
Abstract
5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine bases of recent years. Unlike 5mC, global 5hmC levels vary from tissues that have differential distribution both in mammalian tissues and in the genome. DNA hydroxymethylation is the process that 5mC oxidates into 5hmC with the catalysis of TET (ten-eleven translocation) enzymes. It is an essential option of DNA demethylation, which modulates gene expression by adjusting the DNA methylation level. Various factors can regulate the demethylation of DNA, such as environmental toxins and mental stress. In this review, we summarize the progress in the formation of 5hmC, and obtaining 5hmC in a cell-free DNA sample presents multiple advantages and challenges for the subject. Furthermore, the clinical potential for 5hmC modification in dealing with cancer early diagnosis, prognostic evaluation, and prediction of therapeutic effect is also mentioned.
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Affiliation(s)
- Tianmin Xu
- The Second HospitaI of Jilin University, Changchun, Jilin, China.
| | - Haoyue Gao
- The Second HospitaI of Jilin University, Changchun, Jilin, China
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50
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Sarkisjan D, Julsing JR, El Hassouni B, Honeywell RJ, Kathmann I, Matherly LH, Lee YB, Kim DJ, Peters GJ. RX-3117 (Fluorocyclopentenyl-Cytosine)-Mediated Down-Regulation of DNA Methyltransferase 1 Leads to Protein Expression of Tumor-Suppressor Genes and Increased Functionality of the Proton-Coupled Folate Carrier. Int J Mol Sci 2020; 21:ijms21082717. [PMID: 32295203 PMCID: PMC7215832 DOI: 10.3390/ijms21082717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/31/2020] [Accepted: 04/10/2020] [Indexed: 12/31/2022] Open
Abstract
(1) Background: RX-3117 (fluorocyclopentenyl-cytosine) is a cytidine analog that inhibits DNA methyltransferase 1 (DNMT1). We investigated the mechanism and potential of RX-3117 as a demethylating agent in several in vitro models. (2) Methods: we used western blotting to measure expression of several proteins known to be down-regulated by DNA methylation: O6-methylguanine-DNA methyltransferase (MGMT) and the tumor-suppressor genes, p16 and E-cadherin. Transport of methotrexate (MTX) mediated by the proton-coupled folate transporter (PCFT) was used as a functional assay. (3) Results: RX-3117 treatment decreased total DNA-cytosine-methylation in A549 non-small cell lung cancer (NSCLC) cells, and induced protein expression of MGMT, p16 and E-cadherin in A549 and SW1573 NSCLC cells. Leukemic CCRF-CEM cells and the MTX-resistant variant (CEM/MTX, with a deficient reduced folate carrier) have a very low expression of PCFT due to promoter hypermethylation. In CEM/MTX cells, pre-treatment with RX-3117 increased PCFT-mediated MTX uptake 8-fold, and in CEM cells 4-fold. With the reference hypomethylating agent 5-aza-2′-deoxycytidine similar values were obtained. RX-3117 also increased PCFT gene expression and PCFT protein. (4) Conclusion: RX-3117 down-regulates DNMT1, leading to hypomethylation of DNA. From the increased protein expression of tumor-suppressor genes and functional activation of PCFT, we concluded that RX-3117 might have induced hypomethylation of the promotor.
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Affiliation(s)
- Dzjemma Sarkisjan
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Joris R. Julsing
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Btissame El Hassouni
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Richard J. Honeywell
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Ietje Kathmann
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Larry H. Matherly
- Department of Oncology, Wayne State University School of Medicine, Detroit, and Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201-1976, USA;
| | - Young B. Lee
- Rexahn Pharmaceuticals, Inc., Rockville, MD 20850, USA; (Y.B.L.); (D.J.K.)
| | - Deog J. Kim
- Rexahn Pharmaceuticals, Inc., Rockville, MD 20850, USA; (Y.B.L.); (D.J.K.)
| | - Godefridus J. Peters
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: ; Tel.: +31-20-4442633
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