1
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Dhamdhere MR, Spiegelman VS. Extracellular vesicles in neuroblastoma: role in progression, resistance to therapy and diagnostics. Front Immunol 2024; 15:1385875. [PMID: 38660306 PMCID: PMC11041043 DOI: 10.3389/fimmu.2024.1385875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid pediatric cancer, and is one of the leading causes of cancer-related deaths in children. Despite the current multi-modal treatment regimens, majority of patients with advanced-stage NBs develop therapeutic resistance and relapse, leading to poor disease outcomes. There is a large body of knowledge on pathophysiological role of small extracellular vesicles (EVs) in progression and metastasis of multiple cancer types, however, the importance of EVs in NB was until recently not well understood. Studies emerging in the last few years have demonstrated the involvement of EVs in various aspects of NB pathogenesis. In this review we summarize these recent findings and advances on the role EVs play in NB progression, such as tumor growth, metastasis and therapeutic resistance, that could be helpful for future investigations in NB EV research. We also discuss different strategies for therapeutic targeting of NB-EVs as well as utilization of NB-EVs as potential biomarkers.
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Affiliation(s)
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States
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2
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van Eijck CWF, Strijk G, Vietsch EE, van der Sijde F, Verheij M, Mustafa DAM, Vink M, Aerts JGJV, van Eijck CHJ, Willemsen M. FOLFIRINOX chemotherapy modulates the peripheral immune landscape in pancreatic cancer: Implications for combination therapies and early response prediction. Eur J Cancer 2024; 196:113440. [PMID: 37988843 DOI: 10.1016/j.ejca.2023.113440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND FOLFIRINOX chemotherapy has improved outcomes for pancreatic cancer patients, but poor long-term survival outcomes and high toxicity remain challenges. This study investigates the impact of FOLFIRINOX on plasma proteins and peripheral immune cells to guide immune-based combination therapies and, ideally, to identify a potential biomarker to predict early disease progression during FOLFIRINOX. METHODS Blood samples were collected from 86 pancreatic cancer patients before and two weeks after the first FOLFIRINOX cycle and subjected to comprehensive immune cell and proteome profiling. Principal Component Analysis and Linear Mixed Effect Regression models were used for data analysis. FOLFIRINOX efficacy was radiologically evaluated after the fourth cycle. RESULTS One cycle of FOLFIRINOX diminished tumour-cell-related pathways and enhanced pathways related to immune activation, illustrated by an increase in pro-inflammatory IL-18, IL-15, and TNFRSF4. Similarly, FOLFIRINOX promoted the activation of CD4 + and CD8 + T cells, the proliferation of NK(T), and the activation of antigen-presenting cells. Furthermore, high pre-treatment levels of VEGFA and PRDX3 and an elevation in FCRL3 levels after one cycle predicted early progression under FOLFIRINOX. Finally, patients with progressive disease exhibited high levels of inhibitory markers on B cells and CD8 + T cells, while responding patients exhibited high levels of activation markers on CD4 + and CD8 + T cell subsets. CONCLUSION FOLFIRINOX has immunomodulatory effects, providing a foundation for clinical trials exploring immune-based combination therapies that harness the immune system to treat pancreatic cancer. In addition, several plasma proteins hold potential as circulating predictive biomarkers for early prediction of FOLFIRINOX response in patients with pancreatic cancer.
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Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gaby Strijk
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Eveline E Vietsch
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Fleur van der Sijde
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maaike Verheij
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Madelief Vink
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Joachim G J V Aerts
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marcella Willemsen
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands.
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3
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Kiio LK, Onyatta JO, Ndangili PM, Oloo F, Santamaria C, Montuenga LM, Mbui DN. Ultrasensitive immunosensor for multiplex detection of cancer biomarkers carcinoembryonic antigen (CEA) and yamaguchi sarcoma viral oncogene homolog 1 (YES1) based on eco-friendly synthesized gold nanoparticles. Talanta 2024; 266:124934. [PMID: 37454512 DOI: 10.1016/j.talanta.2023.124934] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Cancer is one of the most extensive diseases with the highest mortality rate, accounting for almost 10 million deaths in 2020. The most common cancers are breast, lung, colon and rectum and prostate cancers. Of these, lung cancer, accounted for about 1.8 million of all cancer deaths (25%) in 2020. Detection of cancer relies on presence of biomarkers such as DNA molecules, proteins and metabolites released by cancerous cells into the circulation. Carcinoembryonic antigen (CEA) is one of the biomarkers that has been used for the detection of lung cancer. However, CEA is not specific to lung cancer since it is also manifested in gastric cancer, pancreatic cancer, colorectal cancer, and breast cancer. Recently, v-YES1 Yamaguchi sarcoma viral oncogene homolog 1 (YES1) was described as a specific biomarker for lung cancer. The detection of both CEA and YES1 would give more precise and authentic information for detecting lung cancer. This is because detection of a single tumor marker usually limits the precision in tumor diagnosis, due to the fact that several cancers have more than one marker linked with their prevalence. Whereas traditional methods have been used for the detection of CEA, electrochemical immunosensors have attracted considerable attention owing to their profound advantages, including fast response, miniaturization, high selectivity, low sample requirements and magnificent sensitivity. The fabrication of a multiplex and simultaneous immunosensor is met with challenge of preparation of distinguishable immunoprobes with different redox activities. This can be addressed by incorporation of electroactive Nano metals into the sensing platform. In this study, gold nanoparticles were used for the fabrication of an ultrasensitive sandwich electrochemical multiplex immunosensor for simultaneous detection of CEA and YES1. Under optimized conditions, the electrochemical immunosensor detection limit for YES1 and CEA was found to be 0.0022 and 0.0034 ng/mL respectively within a linear range of 0.1-50 ng/mL. The proposed immunosensor proved to be stable for up to 2 weeks and had negligible cross reactivity towards various interfering compounds in human plasma. This study reports that gold nanoparticles can be bio synthesized using shade dried Mangifera indica leaves extract. The bio-synthesized gold nanoparticles coupled with thiolated protein G can be used for fabrication of a multiplex immunosensor for detection of CEA and YES1. The proposed immunosensor can provide a new approach for early diagnosis of circulating cancer biomarkers and holds great promise for application in clinical diagnosis.
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Affiliation(s)
- Lucia K Kiio
- Program in Solid Tumors, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, 31008, Pamplona, Spain; Department of Chemistry, University of Nairobi, 30197-00100, Nairobi, Kenya; School of Chemistry and Material Science, The Technical University of Kenya, 52428-00200, Nairobi, Kenya.
| | - John O Onyatta
- Department of Chemistry, University of Nairobi, 30197-00100, Nairobi, Kenya.
| | - Peter M Ndangili
- School of Chemistry and Material Science, The Technical University of Kenya, 52428-00200, Nairobi, Kenya.
| | - Florence Oloo
- School of Chemistry and Material Science, The Technical University of Kenya, 52428-00200, Nairobi, Kenya.
| | - Carolina Santamaria
- BIOMA Center, Department of Chemistry, School of Sciences University of Navarra, 31008, Pamplona, Spain.
| | - Luis M Montuenga
- Program in Solid Tumors, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, 31008, Pamplona, Spain; Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain; Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Navarra Health Research Institute (IDISNA), Pamplona, Spain.
| | - Damaris N Mbui
- Department of Chemistry, University of Nairobi, 30197-00100, Nairobi, Kenya.
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Cisterna-García A, Beric A, Ali M, Pardo JA, Chen HH, Fernandez MV, Norton J, Gentsch J, Bergmann K, Budde J, Perlmutter JS, Morris JC, Cruchaga C, Botia JA, Ibanez L. Cell-free RNA signatures predict Alzheimer's disease. iScience 2023; 26:108534. [PMID: 38089583 PMCID: PMC10711471 DOI: 10.1016/j.isci.2023.108534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
There is a need for affordable, scalable, and specific blood-based biomarkers for Alzheimer's disease that can be applied to a population level. We have developed and validated disease-specific cell-free transcriptomic blood-based biomarkers composed by a scalable number of transcripts that capture AD pathobiology even in the presymptomatic stages of the disease. Accuracies are in the range of the current CSF and plasma biomarkers, and specificities are high against other neurodegenerative diseases.
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Affiliation(s)
- Alejandro Cisterna-García
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Jose Adrian Pardo
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joel S. Perlmutter
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Radiology, Neuroscience, Physical Therapy, and Occupational Therapy, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John C. Morris
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Juan A. Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
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5
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Amorrortu R, Garcia M, Zhao Y, El Naqa I, Balagurunathan Y, Chen DT, Thieu T, Schabath MB, Rollison DE. Overview of approaches to estimate real-world disease progression in lung cancer. JNCI Cancer Spectr 2023; 7:pkad074. [PMID: 37738580 PMCID: PMC10637832 DOI: 10.1093/jncics/pkad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Randomized clinical trials of novel treatments for solid tumors normally measure disease progression using the Response Evaluation Criteria in Solid Tumors. However, novel, scalable approaches to estimate disease progression using real-world data are needed to advance cancer outcomes research. The purpose of this narrative review is to summarize examples from the existing literature on approaches to estimate real-world disease progression and their relative strengths and limitations, using lung cancer as a case study. METHODS A narrative literature review was conducted in PubMed to identify articles that used approaches to estimate real-world disease progression in lung cancer patients. Data abstracted included data source, approach used to estimate real-world progression, and comparison to a selected gold standard (if applicable). RESULTS A total of 40 articles were identified from 2008 to 2022. Five approaches to estimate real-world disease progression were identified including manual abstraction of medical records, natural language processing of clinical notes and/or radiology reports, treatment-based algorithms, changes in tumor volume, and delta radiomics-based approaches. The accuracy of these progression approaches were assessed using different methods, including correlations between real-world endpoints and overall survival for manual abstraction (Spearman rank ρ = 0.61-0.84) and area under the curve for natural language processing approaches (area under the curve = 0.86-0.96). CONCLUSIONS Real-world disease progression has been measured in several observational studies of lung cancer. However, comparing the accuracy of methods across studies is challenging, in part, because of the lack of a gold standard and the different methods used to evaluate accuracy. Concerted efforts are needed to define a gold standard and quality metrics for real-world data.
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Affiliation(s)
| | - Melany Garcia
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Yayi Zhao
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Issam El Naqa
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Dung-Tsa Chen
- Department of Biostatistics and Bionformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Thanh Thieu
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
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6
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McNamara ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain SS, Martinez Roth S, McDeed AP, Shahrour N, Ballew E, Lin YT, Li HH, Deslattes Mays A, Rudra S, Riegel AT, Unger K, Kaplan T, Wellstein A. Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment. JCI Insight 2023; 8:e156529. [PMID: 37318863 PMCID: PMC10443812 DOI: 10.1172/jci.insight.156529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type-specific reference DNA methylation atlases. We found that cell-type-specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer undergoing radiation treatment revealed distinct dose-dependent and tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation, indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type-specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.
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Affiliation(s)
- Megan E. McNamara
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Marcel O. Schmidt
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sidharth S. Jain
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sarah Martinez Roth
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - A. Patrick McDeed
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Nesreen Shahrour
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Yun-Tien Lin
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Heng-Hong Li
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Sonali Rudra
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Anna T. Riegel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Keith Unger
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
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7
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Xin J, Gu D, Chen S, Ben S, Li H, Zhang Z, Du M, Wang M. SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival. Nucleic Acids Res 2023; 51:D1160-D1167. [PMID: 35947748 PMCID: PMC9825440 DOI: 10.1093/nar/gkac677] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains unestablished. Here, we systematically evaluated genetic effects at the genome-wide level on cancer survival that included overall survival (OS) and cancer-specific survival (CSS), leveraging data deposited in the UK Biobank cohort of a total of 19 628 incident patients across 17 cancer types. Furthermore, we assessed the causal effects of risk factors and circulating biomarkers on cancer prognosis via a Mendelian randomization (MR) analytic framework, which integrated cancer survival GWAS dataset, along with phenome-wide association study (PheWAS) and blood genome-wide gene expression/DNA methylation quantitative trait loci (eQTL/meQTL) datasets. On average, more than 10 traits, 700 genes, and 4,500 CpG sites were prone to cancer prognosis. Finally, we developed a user-friendly online database, SUrvival related cancer Multi-omics database via MEndelian Randomization (SUMMER; http://njmu-edu.cn:3838/SUMMER/), to help users query, browse, and download cancer survival results. In conclusion, SUMMER provides an important resource to assist the research community in understanding the genetic mechanisms of cancer survival.
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Affiliation(s)
- Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Silu Chen
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huiqin Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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8
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Premachandran S, Haldavnekar R, Das S, Venkatakrishnan K, Tan B. DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy. ACS NANO 2022; 16:17948-17964. [PMID: 36112671 DOI: 10.1021/acsnano.2c04187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Brain cancers, one of the most fatal malignancies, require accurate diagnosis for guided therapeutic intervention. However, conventional methods for brain cancer prognosis (imaging and tissue biopsy) face challenges due to the complex nature and inaccessible anatomy of the brain. Therefore, deep analysis of brain cancer is necessary to (i) detect the presence of a malignant tumor, (ii) identify primary or secondary origin, and (iii) find where the tumor is housed. In order to provide a diagnostic technique with such exhaustive information here, we attempted a liquid biopsy-based deep surveillance of brain cancer using a very minimal amount of blood serum (5 μL) in real time. We hypothesize that holistic analysis of serum can act as a reliable source for deep brain cancer surveillance. To identify minute amounts of tumor-derived material in circulation, we synthesized an ultrasensitive 3D nanosensor, adopted SERS as a diagnostic methodology, and undertook a DEEP neural network-based brain cancer surveillance. Detection of primary and secondary tumor achieved 100% accuracy. Prediction of intracranial tumor location achieved 96% accuracy. This modality of using patient sera for deep surveillance is a promising noninvasive liquid biopsy tool with the potential to complement current brain cancer diagnostic methodologies.
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Affiliation(s)
- Srilakshmi Premachandran
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Sunit Das
- Scientist, St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Institute of Medical Sciences, Neurosurgery, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University (formerly Ryerson University) and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Nano Characterization Laboratory, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface facility, Faculty of Engineering and Architectural Sciences, Toronto Metropolitan University (formerly Ryerson University), 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
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9
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Ebrahimi N, Faghihkhorasani F, Fakhr SS, Moghaddam PR, Yazdani E, Kheradmand Z, Rezaei-Tazangi F, Adelian S, Mobarak H, Hamblin MR, Aref AR. Tumor-derived exosomal non-coding RNAs as diagnostic biomarkers in cancer. Cell Mol Life Sci 2022; 79:572. [DOI: 10.1007/s00018-022-04552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 12/24/2022]
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10
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Styk J, Buglyó G, Pös O, Csók Á, Soltész B, Lukasz P, Repiská V, Nagy B, Szemes T. Extracellular Nucleic Acids in the Diagnosis and Progression of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14153712. [PMID: 35954375 PMCID: PMC9367600 DOI: 10.3390/cancers14153712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is a disease that usually shows no evident clinical symptoms in the early stages, often leading to late diagnosis. Over the past few years, a new approach based on liquid biopsy has gained far-reaching applications in less-invasive CRC diagnosis and management, allowing for the use of extracellular nucleic acids as promising biomarkers to detect CRC at an early stage and monitor disease recurrence. That is why an up-to-date review and discussion of in-depth liquid biopsy-derived DNA and RNA biomarkers is essential. We hereby offer an overview of known predisposing genetic factors for developing sporadic and hereditary CRC, and an extensive repertoire of available extracellular DNA/RNA molecules with their potential clinical applications and shortcomings. Our review may be of value to experts dealing with CRC at the molecular level as well as to clinical professionals aiming for a better understanding of state-of-the-art techniques in CRC diagnosis and management. Abstract Colorectal cancer (CRC) is the 3rd most common malignant neoplasm worldwide, with more than two million new cases diagnosed yearly. Despite increasing efforts in screening, many cases are still diagnosed at a late stage, when mortality is high. This paper briefly reviews known genetic causes of CRC (distinguishing between sporadic and familial forms) and discusses potential and confirmed nucleic acid biomarkers obtainable from liquid biopsies, classified by their molecular features, focusing on clinical relevance. We comment on advantageous aspects such as better patient compliance due to blood sampling being minimally invasive, the possibility to monitor mutation characteristics of sporadic and hereditary CRC in a disease showing genetic heterogeneity, and using up- or down-regulated circulating RNA markers to reveal metastasis or disease recurrence. Current difficulties and thoughts on some possible future directions are also discussed. We explore current evidence in the field pointing towards the introduction of personalized CRC management.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Correspondence:
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Ondrej Pös
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Peter Lukasz
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, 1082 Budapest, Hungary;
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Medirex Group Academy, n.p.o., 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Tomáš Szemes
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
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11
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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12
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New Insights into the Multivariate Analysis of SER Spectra Collected on Blood Samples for Prostate Cancer Detection: Towards a Better Understanding of the Role Played by Different Biomolecules on Cancer Screening: A Preliminary Study. Cancers (Basel) 2022; 14:cancers14133227. [PMID: 35804993 PMCID: PMC9264810 DOI: 10.3390/cancers14133227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In recent years, research on biofluids using Raman and SERS has expanded dramatically, indicating the enormous promise of this technology as a high-throughput tool for identifying cancer and other disorders. In the investigations thus far, researchers have concentrated on a specific illness or condition, but the techniques employed to acquire experimental spectra prevent direct comparison of the data. This necessitates comparative research of a variety of diseases and an increase in scientific cooperation to standardize experimental conditions. In our study, positive results were reached by applying a combined SERS multivariate analysis (MVA) to the urgent problem of prostate cancer diagnosis that was directly linked to real-world settings in healthcare. Moreover, in comparison to the prostate-specific antigen (PSA) test, which has a high sensitivity but limited specificity, our combined SERS-MVA method has greater specificity, which may assist in preventing the overtreatment of patients. Abstract It is possible to obtain diagnostically relevant data on the changes in biochemical elements brought on by cancer via the use of multivariate analysis of vibrational spectra recorded on biological fluids. Prostate cancer and control groups included in this research generated almost similar SERS spectra, which means that the values of peak intensities present in SERS spectra can only give unspecific and limited information for distinguishing between the two groups. Our diagnostic algorithm for prostate cancer (PCa) differentiation was built using principal component analysis and linear discriminant analysis (PCA-LDA) analysis of spectral data, which has been widely used in spectral data management in many studies and has shown promising results so far. In order to fully utilize the entire SERS spectrum and automatically determine the most meaningful spectral features that can be used to differentiate PCa from healthy patients, we perform a multivariate analysis on both the entire and specific spectral intervals. Using the PCA-LDA model, the prostate cancer and control groups are clearly distinguished in our investigation. The separability of the following two data sets is also evaluated using two alternative discrimination techniques: principal least squares discriminant analysis (PLS-DA) and principal component analysis—support vector machine (PCA-SVM).
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13
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Babu M, Pavithran K. Therapeutic Drug Monitoring as a Tool for Therapy Optimization. Drug Metab Lett 2022; 15:DML-EPUB-122284. [PMID: 35382721 DOI: 10.2174/1872312815666220405122021] [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: 11/26/2021] [Revised: 01/21/2022] [Accepted: 02/09/2022] [Indexed: 11/22/2022]
Abstract
The use of pharmacotherapy for improving healthcare in society is increasing. A vast majority of patients have either received subtherapeutic treatment (which could result from low pharmacokinetic) or experienced adverse effects due to the toxic levels of the drug. The medicines used to treat chronic conditions, such as epilepsy; cardiovascular diseases; and oncological, neurological, and psychiatric disorders, require routine monitoring. New targeted therapies suggest an individualized treatment that can slowly move practitioners away from the concept of a one-size-fits-all-fixed-dosing approach. Therapeutic drug use can be monitored based on pharmacokinetic, pharmacodynamic, and pharmacometric methods. Based on the experiences of therapeutic drug monitoring of various agents across the globe, we can look ahead to the possible developments of therapeutic drug monitoring in India.
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Affiliation(s)
- Merin Babu
- Department of Medical Oncology, Amrita Institute of Medical Sciences and Research Centre Amrita Vishwa Vidyapeetham, Ponekkara P.O, Kochi, Kerala, India
| | - Keechilat Pavithran
- Department of Medical Oncology, Amrita Institute of Medical Sciences and Research Centre Amrita Vishwa Vidyapeetham, Ponekkara P.O, Kochi, Kerala, India
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14
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Metastasis prevention: targeting causes and roots. Clin Exp Metastasis 2022; 39:505-519. [PMID: 35347574 DOI: 10.1007/s10585-022-10162-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
The spread of tumor cells from the primary focus, metastasis, is the main cause of cancer mortality. Therefore, anticancer therapy should be focused on the prevention of metastatic disease. Key targets can be conditions in the primary tumor that are favorable for the appearance of metastatic cells and the first steps of the metastatic cascade. Here, we discuss different approaches for targeting metastasis causes (hypoxia, metabolism changes, and tumor microenvironment) and roots (angiogenesis, epithelial-mesenchymal transition, migration, and invasion). Also, we emphasize the challenges of the existing approaches for metastasis prevention and suggest opportunities to overcome them. In conclusion, we highlight the importance of clinical evaluation of the agents showing antimetastatic effects in vivo, especially in patients with early-stage cancers, the identification of metastatic seeds, and the development of therapeutics for their eradication.
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15
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Pothipor C, Bamrungsap S, Jakmunee J, Ounnunkad K. A gold nanoparticle-dye/poly(3-aminobenzylamine)/two dimensional MoSe 2/graphene oxide electrode towards label-free electrochemical biosensor for simultaneous dual-mode detection of cancer antigen 15-3 and microRNA-21. Colloids Surf B Biointerfaces 2021; 210:112260. [PMID: 34894598 DOI: 10.1016/j.colsurfb.2021.112260] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022]
Abstract
A dual-mode electrochemical biosensor is successfully developed for simultaneous detection of two different kinds of breast cancer biomarkers, namely cancer antigen 15-3 (CA 15-3) and microRNA-21 (miRNA-21), for the first time. The sensor composes of a poly(3-aminobenzylamine)/two-dimensional (2D) molybdenum selenide/graphene oxide nanocomposite modified two-screen-printed carbon electrode array (dual electrode), functionalized individually with 2,3-diaminophenazine-gold nanoparticles and toluidine blue-gold nanoparticles. Both kinds of the redox probe-gold nanoparticles are employed as signaling molecules and supports for immobilization of anti-CA 15-3 antibodies and capture DNA-21 probes, respectively. Due to the good conductivity and high surface-to-volume ratio of the nanocomposite, high amount of the antibodies and capture probes can be immobilized on the modified dual-electrode, giving the efficient duplex detection. Consequently, the biosensor provides good selectivity, and high sensitivity for the dual target analyte detection. The experimental results show that this label-free biosensor exhibits good linear responses to the concentrations of both target analytes with the limits of detection (LODs) of 0.14 U mL-1 and 1.2 fM for CA 15-3 and miRNA-21, respectively. This assay strategy has a great potential to be further developed for the simultaneous detection of a variety of miRNAs and protein biomarkers for point-of-care (POC) diagnostic applications.
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Affiliation(s)
- Chammari Pothipor
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; The Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Suwussa Bamrungsap
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Jaroon Jakmunee
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kontad Ounnunkad
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai 50200, Thailand.
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16
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Teixeira AL, Patrão AS, Dias F, Silva C, Vieira I, Silva JF, Ferreira M, Morais A, Maurício J, Medeiros R. AGO2 expression levels and related genetic polymorphisms: influence in renal cell progression and aggressive phenotypes. Pharmacogenomics 2021; 22:1069-1079. [PMID: 34672687 DOI: 10.2217/pgs-2021-0072] [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] [Indexed: 11/21/2022] Open
Abstract
Aim: Renal cell carcinoma (RCC) is the most lethal urological cancer and up to 40% of patients submitted to surgery will relapse. Thus, the study aim was to analyze the associations of AGO2 SNPs with RCC patients' prognosis, and evaluate their effect on AGO2 mRNA levels. Materials & methods: The AGO2 rs4961280, rs3928672 and rs11996715 polymorphisms and the relative quantification of AGO2 mRNA levels were analyzed by real-time PCR. Results: We observed that AGO2 rs4961280 AC + AA genotypes carriers presented a higher cancer progression risk (odds ratio= 3.13, p < 0.001), a reduced progression-free survival (log rank test, p = 0.003) and an increased risk of an early relapse (hazard ratio= 2.26, p = 0.008). In fact, these patients also presented higher circulating levels of AGO2 mRNA (p = 0.043), with the high levels being associated with more aggressive tumors. Conclusion: The AGO2 rs4961280 AA/AC genotypes are unfavorable RCC prognostic biomarkers, with the AGO2 levels being a useful RCC aggressive phenotype biomarker.
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Affiliation(s)
- Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto CCC)
| | - Ana Sofia Patrão
- Medical Oncology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Francisca Dias
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISECI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto CCC)
| | - Carlos Silva
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISECI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto CCC)
| | - Isabel Vieira
- Urology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - José Fernando Silva
- Urology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Marta Ferreira
- Medical Oncology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - António Morais
- Urology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Joaquina Maurício
- Medical Oncology Department of The Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISECI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto CCC).,ICBAS, Abel Salazar Institute for The Biomedical Sciences, University of Porto, Portugal.,FMUP, Faculty of Medicine, University of Porto, Portugal.,Research Department, LPCC- Portuguese League Against Cancer (NR Norte), Porto, Portugal.,Faculty of Health Sciences, Fernando Pessoa University, Porto, Portugal
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17
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Velmanickam L, Jayasooriya V, Vemuri MS, Tida UR, Nawarathna D. Recent advances in dielectrophoresis toward biomarker detection: A summary of studies published between 2014 and 2021. Electrophoresis 2021; 43:212-231. [PMID: 34453855 DOI: 10.1002/elps.202100194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/22/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022]
Abstract
Dielectrophoresis is a well-understood phenomenon that has been widely utilized in biomedical applications. Recent advancements in miniaturization have contributed to the development of dielectrophoretic-based devices for a wide variety of biomedical applications. In particular, the integration of dielectrophoresis with microfluidics, fluorescence, and electrical impedance has produced devices and techniques that are attractive for screening and diagnosing diseases. This review article summarizes the recent utility of dielectrophoresis in assays of biomarker detection. Common screening and diagnostic biomarkers, such as cellular, protein, and nucleic acid, are discussed. Finally, the potential use of recent developments in machine learning approaches toward improving biomarker detection performance is discussed. This review article will be useful for researchers interested in the recent utility of dielectrophoresis in the detection of biomarkers and for those developing new devices to address current gaps in dielectrophoretic biomarker detection.
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Affiliation(s)
| | - Vidura Jayasooriya
- Department of Electrical and Electronic Engineering, University of SriJayewardenepura, Jayewardenepura, Sri Lanka
| | - Madhava Sarma Vemuri
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, North Dakota, USA
| | - Umamaheswara Rao Tida
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, North Dakota, USA
| | - Dharmakeerthi Nawarathna
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, North Dakota, USA.,Biomedical Engineering Program, North Dakota State University, Fargo, North Dakota, USA
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18
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Liquid Biopsy in Cervical Cancer: Hopes and Pitfalls. Cancers (Basel) 2021; 13:cancers13163968. [PMID: 34439120 PMCID: PMC8394398 DOI: 10.3390/cancers13163968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cervical cancer is the fourth most common cancer in women worldwide, and its incidence is variably distributed between developed and less-resourced countries, in which socio-economic issues and religious beliefs often limit the widespread diffusion and the access to screening campaigns. In the “liquid biopsy” era, the application of non-invasive and repeatable techniques to the identification of diagnostic, prognostic, and predictive biomarkers might facilitate the management of this disease and, hopefully, improve its outcome. The purpose of this review is to explore the progress status of liquid biopsy in cervical cancer patients. Several methods are described, which include the analysis of circulating tumor cells, the search for pathogenic mutations on circulating tumor DNA, as well as the identification of circulating RNAs, focusing on their potential clinical applications and current limitations. Abstract Cervical cancer (CC) is the fourth most common cancer in women worldwide, with about 90% of cancer-related deaths occurring in developing countries. The geographical influence on disease evolution reflects differences in the prevalence of human papilloma virus (HPV) infection, which is the main cause of CC, as well as in the access and quality of services for CC prevention and diagnosis. At present, the most diffused screening and diagnostic tools for CC are Papanicolaou test and the more sensitive HPV-DNA test, even if both methods require gynecological practices whose acceptance relies on the woman’s cultural and religious background. An alternative (or complimentary) tool for CC screening, diagnosis, and follow-up might be represented by liquid biopsy. Here, we summarize the main methodologies developed in this context, including circulating tumor cell detection and isolation, cell tumor DNA sequencing, coding and non-coding RNA detection, and exosomal miRNA identification. Moreover, the pros and cons of each method are discussed, and their potential applications in diagnosis and prognosis of CC, as well as their role in treatment monitoring, are explored. In conclusion, it is evident that despite many advances obtained in this field, further effort is needed to validate and standardize the proposed methodologies before any clinical use.
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19
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Cardiomyocyte-Specific Circulating Cell-Free Methylated DNA in Esophageal Cancer Patients Treated with Chemoradiation. GASTROINTESTINAL DISORDERS 2021; 3:100-112. [PMID: 35531260 PMCID: PMC9074856 DOI: 10.3390/gidisord3030011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Thoracic high-dose radiation therapy (RT) for cancer has been associated with early and late cardiac toxicity. To assess altered rates of cardiomyocyte cell death due to RT we monitored changes in cardiomyocyte-specific, cell-free methylated DNA (cfDNA) shed into the circulation. Eleven patients with distal esophageal cancer treated with neoadjuvant chemoradiation to 50.4 Gy (RT) and concurrent carboplatin and paclitaxel were enrolled. Subjects underwent fasting blood draws prior to the initiation and after completion of RT as well as 4–6 months following RT. An island of six unmethylated CpGs in the FAM101A locus was used to identify cardiomyocyte-specific cfDNA in serum. After bisulfite treatment this specific cfDNA was quantified by amplicon sequencing at a depth of >35,000 reads/molecule. Cardiomyocyte-specific cfDNA was detectable before RT in the majority of patient samples and showed some distinct changes during the course of treatment and recovery. We propose that patient-specific cardiac damages in response to the treatment are indicated by these changes although co-morbidities may obscure treatment-specific events.
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20
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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21
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Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are regulatory small non-coding RNAs that participate in transposon inactivation, chromatin regulation, and endogenous gene regulation. Numerous genetic and epigenetic factors regulate cell proliferation and tumor metastasis. PIWI proteins and piRNAs have been revealed to function in regulating upstream or downstream of oncogenes or tumor-suppressor genes in cancer tissues. In the present review, we summarize major recent findings in uncovering the regulation and role of PIWI proteins and piRNAs in tumorigenesis and highlight some of the promising applications of specific piRNAs in cancer therapeutics and as cancer biomarkers.
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Yang W, Qian Y, Gao K, Zheng W, Wu G, He Q, Chen Q, Song Y, Wang L, Wang Y, Gu P, Chen B, Zhai R. LncRNA BRCAT54 inhibits the tumorigenesis of non-small cell lung cancer by binding to RPS9 to transcriptionally regulate JAK-STAT and calcium pathway genes. Carcinogenesis 2021; 42:80-92. [PMID: 32459848 DOI: 10.1093/carcin/bgaa051] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/12/2020] [Accepted: 05/24/2020] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Increasing evidence suggest that long non-coding RNAs (lncRNAs) play critical roles in cancers. However, the expression pattern and underlying mechanisms of lncRNAs in non-small cell lung cancer (NSCLC) remain incompletely understood. This study aimed to elucidate the functions and molecular mechanisms of a certain lncRNA in NSCLC. METHODS LncRNA microarray was performed to identify differential expressed lncRNAs between pre- and postoperation plasma in NSCLC patients. The expression level of candidate lncRNA in NSCLC tissues, plasma and cells was determined by quantitative real-time PCR (qRT-PCR) and in situ hybridization. The functional roles of lncRNA were assessed in vitro and in vivo. Furthermore, RNA pull-down, RNA immunoprecipitation, microarray, qRT-PCR and rescue assays were conducted to explore the mechanism action of lncRNA in NSCLC cells. RESULTS We identified a novel lncRNA (BRCAT54), which was significantly upregulated in preoperative plasma, NSCLC tissues and NSCLC cells, and its higher expression was associated with better prognosis in patients with NSCLC. Overexpression of BRCAT54 inhibited proliferation, migration and activated apoptosis in NSCLC cells. Conversely, knockdown of BRCAT54 reversed the suppressive effects of BRCAT54. Moreover, overexpression of BRCAT54 repressed NSCLC cell growth in vivo. Mechanistically, BRCAT54 directly bound to RPS9. Knockdown of RPS9 substantially reversed the promoting effects of si-BRCAT54 on cell proliferation and enhanced the inhibitive effect of si-BRCAT54 on BRCAT54 expression. In addition, silencing of RPS9 activated JAK-STAT pathway and suppressed calcium signaling pathway gene expressions. CONCLUSION This study identified BRCAT54 as a tumor suppressor in NSCLC. Targeting the BRCAT54 and RPS9 feedback loop might be a novel therapeutic strategy for NSCLC.
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Affiliation(s)
- Wenhan Yang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Youhui Qian
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Kaiping Gao
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Wenjing Zheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Guodong Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qihan He
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Qianqian Chen
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yi Song
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Liang Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yejun Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Peigui Gu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Bin Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Rihong Zhai
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
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Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:cancers13112652. [PMID: 34071230 PMCID: PMC8199052 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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Mokánszki A, Bádon ES, Mónus A, Tóth L, Bittner N, Méhes G. Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma? Pathol Oncol Res 2021; 27:613071. [PMID: 34257581 PMCID: PMC8262152 DOI: 10.3389/pore.2021.613071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pathogenic molecular features gained specific significance in therapeutic decisions in lung carcinoma in the past decade. Initial and follow up genetic testing requres appropriate amounts and quality of tumor derived DNA, but tumor sampling, especially for disease monitoring is generally limited. Further to the peripheral blood (PB), samples from pleural fluid, accumulating in diverse lung processes might serve as an alternative source for cell-free DNA (cfDNA) for genetic profiling. In our study, cfDNA isolated from the pleural effusion and from the PB, and genomic DNA (gDNA) obtained from tissue/cellular samples were analyzed and compared from altogether 65 patients with pulmonary disease, including 36 lung adenocarcinomas. The quantity of effusion cfDNA yield appeared to be significantly higher compared to that from simultaneously collected PB plasma (23.2 vs. 4.8 ng/μl, p < 0.05). Gene mutations could be safely demonstrated from the effusion cfDNA fraction obtained from adenocarcinoma patients, 3/36 EGFR, 9/36 KRAS and 1/36 BRAF gene variants were detected. In this series, 9/13 samples showed an effusion+/plasma-mutational status, while only 1/13 samples presented with the opposite findings (effusion-/plasma+). gDNA analysis from sediment cell blocks from the identical effusion sample was surprisingly ineffective for lung adenocarcinoma profiling due to the low DNA yield. In conclusion, the cell free supernatant of pleural effusions appears to concentrate cancer derived cfDNA and seems to be particularly suitable for serial genotyping of pulmonary adenocarcinoma.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nóra Bittner
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Identification of key genes of papillary thyroid carcinoma by integrated bioinformatics analysis. Biosci Rep 2021; 40:226004. [PMID: 32766727 PMCID: PMC7433002 DOI: 10.1042/bsr20201555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is one of the fastest-growing malignant tumor types of thyroid cancer. Therefore, identifying the interaction of genes in PTC is crucial for elucidating its pathogenesis and finding more specific molecular biomarkers. METHODS Four pairs of PTC tissues and adjacent tissues were sequenced using RNA-Seq, and 3745 differentially expressed genes were screened (P<0.05, |logFC|>1). The enrichment analysis indicated that the vast majority of differentially expressed genes (DEGs) may play a positive role in the development of cancer. Then, the significant modules were analyzed using Cytoscape software in the protein-protein interaction network. Survival analysis, TNM analysis, and immune infiltration analysis of key genes were analyzed. And the expression of ADORA1, APOE, and LPAR5 genes were verified by qPCR in PTC compared with matching adjacent tissues. RESULTS Twenty-five genes were identified as hub genes with nodes greater than 10. The expression of 25 genes were verified by the GEPIA database, and the overall survival and disease-free survival analyses were conducted with Kaplan-Meier plotter. We found only three genes were confirmed with our validation and were statistically significant in PTC, namely ADORA1, APOE, and LPAR5. Further analysis found that the mRNA levels and methylation degree of these three genes were significantly correlated with the TNM staging of PTC. And these three genes were related to PTC immune infiltration. Verification of the expression of these three genes by RT-qPCR and Western blot further confirmed the reliability of our results. CONCLUSION Our study identified three genes that may play key regulatory roles in the development, metastasis, and immune infiltration of papillary thyroid carcinoma.
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Mitroshina IY, Sirota NP, Prokofiev VN, Kuznetsova EA. Levels of Circulating DNA in Blood Serum and DNA Damage in Leukocytes of Healthy Donors of Different Genders and Ages. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Data Integration Reveals the Potential Biomarkers of Circulating MicroRNAs in Osteoarthritis. Diagnostics (Basel) 2021; 11:diagnostics11030412. [PMID: 33670901 PMCID: PMC7997238 DOI: 10.3390/diagnostics11030412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
The abnormal expression of circulating miRNAs (c-miRNAs) has become an emerging field in the development of miRNAs-based diagnostic and therapeutic tools for human diseases, including osteoarthritis (OA). OA is the most common form of arthritis leading to disability and a major socioeconomic burden. The abnormal expression of miRNAs plays important roles in the pathogenesis of OA. Unraveling the role of miRNAs in the pathogenesis of OA will throw light on the potential for the development of miRNAs-based diagnostic and therapeutic tools for OA. This article reviews and highlights recent advances in the study of miRNAs in OA, with specific demonstration of the functions of miRNA, especially c-miRNA, in OA pathogenesis as well as its potential implication in the treatment of OA. Based on a systematic literature search using online databases, we figured out the following main points: (1) the integrative systematic review of c-mRNAs and its target genes related to OA pathogenesis; (2) the potential use of c-miRNAs for OA diagnosis purposes as potential biomarkers; and (3) for therapeutic purposes, and we also highlight certain remedies that regulate microRNA expression based on its target genes.
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Abstract
Non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancer cases. The pathogenesis of NSCLC involves complex gene networks that include different types of non-coding RNAs, such as long non-coding RNAs (lncRNAs). The role of lncRNAs in NSCLC is gaining an increasing interest as their function is being explored in various human cancers. Recently, a new oncogenic lncRNA, LINC00152 (cytoskeleton regulator RNA (CYTOR)), has been identified in different tumor types. In NSCLC, the high expression of LINC00152 in tumor tissue and peripheral blood samples has been shown to be associated with worse prognoses of NSCLC patients. Overexpression of LINC00152 has been confirmed to promote the proliferation, invasion, and migration of NSCLC cells in vitro, as well as increase tumor growth in vivo. This review discusses the role of LINC00152 in NSCLC.
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Affiliation(s)
- Hong Yu
- Cell Biology Laboratory, Jilin Province Institute of Cancer Prevention and Treatment, Jilin Cancer Hospital, Changchun 130012, China
| | - Shu-Bin Li
- Department of Internal Medicine, Southern Branch of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 102600, China
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Yu Y, Shen L, Ji W, Lu S. Standardization of pleural effusion-based tumor mutation burden (TMB) estimation using capture-based targeted sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:140. [PMID: 33569442 PMCID: PMC7867960 DOI: 10.21037/atm-20-7702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Tumor mutation burden (TMB) has received considerable attention as a potential predictive biomarker for response to anticancer treatment with immune checkpoint inhibitors (ICIs), and has been increasingly incorporated into clinical practice. Currently, TMB is often determined with tissue biopsies using whole-exome sequencing (WES) or panel-based targeted sequencing. Meanwhile, liquid biopsies such as blood are actively investigated as alternative media, although there is currently no report of the performance of targeted sequencing in assessing TMB using pleural effusion (PE) specimens. Methods Thirty-two patients diagnosed with advanced non-small cell lung cancer (NSCLC) with associated PE were prospectively enrolled (NCT03546452). Cell-free DNA (cfDNA) from the supernatant of PE was subjected to both WES and capture-based targeted sequencing using various commercially-available panels. Results All five panels assessed in this study demonstrated a good correlation with WES-derived TMB, with correlation coefficients ranging from 0.68-0.81. Two- and three-tier classification systems built on the TMB estimates achieved respective concordance rates of 74% and 63% between classifications based on WES- and panel-derived TMB levels. Conclusions This study provides real-world evidence that all panels assessed in this study can be used for TMB evaluation based on PE samples. We also demonstrated that PE can serve as an alternative medium for TMB evaluation. To the best of our knowledge, this is the first study evaluating the potential of PE samples for TMB estimation, thereby providing a basis for establishing future standard protocols.
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Affiliation(s)
- Yongfeng Yu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Shen
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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Barefoot ME, Lindberg MR, Wellstein A. Decoding the Tissue of Origin of Cellular Damage from Cell-Free DNA in Liquid Biopsies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11669-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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王 闫, 梁 震, 刘 勇, 寇 芙, 姜 丹, 郑 艳, 刘 巍, 朱 步. [A Method for Isolating Tumor Cells from Large Volume of Malignant Pleural
Effusion and Its Efficacy Evaluation]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:1080-1086. [PMID: 33357315 PMCID: PMC7786232 DOI: 10.3779/j.issn.1009-3419.2020.103.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 11/05/2022]
Abstract
BACKGROUND Malignant plural effusion (MPE) is one of the most common specimen for liquid biopsy gene detection. This study aims to explore a method for isolating tumor cells from large volume of MPE and evaluate its efficacy and application prospect in gene detection. METHODS Pleural effusions (>500 mL) from 20 advanced lung cancer patients were obtained by effusion drainage and used to isolate tumor cells with cell separation media Percoll and Ficoll. Cell number and purity were calculated. DNA was extracted from the supernatant (etDNA), total cells and isolated tumor cells of pleural effusion (ETC-DNA) to detect the mutation of tumor-related genes by next-generation sequencing. RESULTS The median number of cells isolated from malignant pleural effusion was 8.50×10⁴ (interquel range: 9.25×10³-3.75×10⁵), 85.50%±5.80% of the cells were identified as tumor cells. The detection rates of epidermal growth factor receptor (EGFR) gene mutation of etDNA, total cell DNA and ETC-DNA were 70.00%, 50.00% and 70.00%, reseparately, while the median EGFR mutation abundance in 3 components was 16.05% (4.78%-43.06%), 1.09% (0.00%-2.39%), and 33.02% (18.50%-76.70%), respectively. ETC-DNA had good consistency with tissue DNA (P>0.999, kappa=1.000) and etDNA (P>0.999, kappa=1.000). ETC-DNA inclined to have higher EGFR mutation than etDNA, but the result was not statistically significant. CONCLUSIONS Our method can isolate large amount of tumor cells from a large volume of malignant pleural effusion with high purity. Using ETC-DNA as specimen improves the efficacy of gene detection, thus is worth further study.
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Affiliation(s)
- 闫飞 王
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 震 梁
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,胸外一科Department of Thoracic Surgery I, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 勇 刘
- 102206 北京,康为世纪生物科技有限公司ComWin Biotech Co., Ltd, Beijing 102206, China
| | - 芙蓉 寇
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 丹凤 姜
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 艳群 郑
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 巍 刘
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - 步东 朱
- 100142 北京,北京大学肿瘤医院暨北京市肿瘤防治研究所,恶性肿瘤发病机制及转化研究教育部重点实验室,日间病房Daycare Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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Hirschfeld M, Ge I, Rücker G, Waldschmidt J, Mayer S, Jäger M, Voigt M, Kammerer B, Nöthling C, Berner K, Weiss D, Asberger J, Erbes T. Mutually distinguishing microRNA signatures of breast, ovarian and endometrial cancers in vitro. Mol Med Rep 2020; 22:4048-4060. [PMID: 33000259 DOI: 10.3892/mmr.2020.11466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/06/2020] [Indexed: 11/05/2022] Open
Abstract
Early diagnosis and therapy in the first stages of a malignant disease is the most crucial factor for successful cancer treatment and recovery. Currently, there is a high demand for novel diagnostic tools that indicate neoplasms in the first or pre‑malignant stages. MicroRNAs (miRNA or miR) are small non‑coding RNAs that may act as oncogenes and downregulate tumor‑suppressor genes. The detection and mutual discrimination of the three common female malignant neoplasia types breast (BC), ovarian (OC) and endometrial cancer (EC) could be enabled by identification of tumor entity‑specific miRNA expression differences. In the present study, the relative expression levels of 25 BC, EC and OC‑related miRNAs were assessed by reverse transcription‑quantitative PCR and determined using the 2‑ΔΔCq method for normalization against the mean of four housekeeping genes. Expression levels of all miRNAs were analyzed by regression against cell line as a factor. An expression level‑based discrimination between BC and OC cell types was obtained for a subgroup of ten different miRNA types. miR‑30 family genes, as well as three other miRNAs, were found to be uniformly upregulated in OC cells compared with BC cells. BC and EC cells could be distinguished by the expression profiles of six specific miRNAs. In addition, four miRNAs were differentially expressed between EC and OC cells. In conclusion, miRNAs were identified as a potential novel tool to detect and mutually discriminate between BC, OC and EC. Based on a subset of 25 clinically relevant human miRNA types, the present study could significantly discriminate between these three female cancer types by means of their expression levels. For further verification and validation of miRNA‑based biomarker expression signatures that enable valuable tumor detection and characterization in routine screening or potential therapy monitoring, additional and extended in vitro analyses, followed by translational studies utilizing patients' tissue and liquid biopsy materials, are required.
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Affiliation(s)
- Marc Hirschfeld
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Isabel Ge
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79104 Freiburg, Germany
| | - Julia Waldschmidt
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Sebastian Mayer
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Markus Jäger
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Matthias Voigt
- Praxis of Plastic and Aesthetic Surgery and Evangelian Deaconry Hospital, D‑79110 Freiburg, Germany
| | - Bernd Kammerer
- Center for Biological Systems Analysis, University of Freiburg, D‑79104 Freiburg, Germany
| | - Claudia Nöthling
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Kai Berner
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Daniela Weiss
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Jasmin Asberger
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
| | - Thalia Erbes
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, D‑79106 Freiburg, Germany
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Gowthami J, Gururaj N, Mahalakshmi V, Sathya R, Sabarinath TR, Doss DM. Genetic predisposition and prediction protocol for epithelial neoplasms in disease-free individuals: A systematic review. J Oral Maxillofac Pathol 2020; 24:293-307. [PMID: 33456239 PMCID: PMC7802851 DOI: 10.4103/jomfp.jomfp_348_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Background Epithelial neoplasm is an important global health-care problem, with high morbidity and mortality rates. Early diagnosis and appropriate treatment are essential for increased life survival. Prediction of occurrence of malignancy in a disease-free individual by any means will be a great breakthrough for healthy living. Aims and Objectives The aims and objectives were to predict the genetic predisposition and propose a prediction protocol for epithelial malignancy of various systems in our body, in a disease-free individual. Methods We have searched databases both manually and electronically, published in English language in Cochrane group, Google search, MEDLINE and PubMed from 2000 to 2019. We have included all the published, peer-reviewed, narrative reviews; randomized controlled trials; case-control studies; and cohort studies and excluded the abstract-only articles and duplicates. Specific words such as "etiological factors," "pathology and mutations," "signs and symptoms," "genetics and IHC marker," and "treatment outcome" were used for the search. A total of 1032 citations were taken, and only 141 citations met the inclusion criteria and were analyzed. Results After analyzing various articles, the etiological factors, clinical signs and symptoms, genes and the pathology involved and the commonly used blood and tissue markers were analyzed. A basic investigation strategy using immunohistochemistry markers was established. Conclusion The set of proposed biomarkers should be studied in future to predict genetic predisposition in disease-free individuals.
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Affiliation(s)
- J Gowthami
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - N Gururaj
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - V Mahalakshmi
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - R Sathya
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - T R Sabarinath
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - Daffney Mano Doss
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
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Yao J, Wu DC, Nottingham RM, Lambowitz AM. Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. eLife 2020; 9:e60743. [PMID: 32876046 PMCID: PMC7518892 DOI: 10.7554/elife.60743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.
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Affiliation(s)
- Jun Yao
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
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Bruno DCF, Donatti A, Martin M, Almeida VS, Geraldis JC, Oliveira FS, Dogini DB, Lopes-Cendes I. Circulating nucleic acids in the plasma and serum as potential biomarkers in neurological disorders. ACTA ACUST UNITED AC 2020; 53:e9881. [PMID: 32813850 PMCID: PMC7446710 DOI: 10.1590/1414-431x20209881] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
Neurological diseases are responsible for approximately 6.8 million deaths every year. They affect up to 1 billion people worldwide and cause significant disability and reduced quality of life. In most neurological disorders, the diagnosis can be challenging; it frequently requires long-term investigation. Thus, the discovery of better diagnostic methods to help in the accurate and fast diagnosis of neurological disorders is crucial. Circulating nucleic acids (CNAs) are defined as any type of DNA or RNA that is present in body biofluids. They can be found within extracellular vesicles or as cell-free DNA and RNA. Currently, CNAs are being explored as potential biomarkers for diseases because they can be obtained using non-invasive methods and may reflect unique characteristics of the biological processes involved in several diseases. CNAs can be especially useful as biomarkers for conditions that involve organs or structures that are difficult to assess, such as the central nervous system. This review presents a critical assessment of the most current literature about the use of plasma and serum CNAs as biomarkers for several aspects of neurological disorders: defining a diagnosis, establishing a prognosis, and monitoring the disease progression and response to therapy. We explored the biological origin, types, and general mechanisms involved in the generation of CNAs in physiological and pathological processes, with specific attention to neurological disorders. In addition, we present some of the future applications of CNAs as non-invasive biomarkers for these diseases.
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Affiliation(s)
- D C F Bruno
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - A Donatti
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - M Martin
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - V S Almeida
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - J C Geraldis
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - F S Oliveira
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - D B Dogini
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - I Lopes-Cendes
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
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Tran VT, Phan TT, Nguyen ST, Tran BT, Ho TT, Pho SP, Nguyen TB, Pham TTB, Le AT, Le VT, Nguyen HT. Smoking habit and chemo-radiotherapy and/or surgery affect the sensitivity of EGFR plasma test in non-small cell lung cancer. BMC Res Notes 2020; 13:367. [PMID: 32746896 PMCID: PMC7398354 DOI: 10.1186/s13104-020-05209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE This study aimed to identify the influential factors for the sensitivity of epidermal growth factor receptor (EGFR) plasma test in non-small cell lung cancer (NSCLC). The mutations were detected in tumor tissue and matched plasma samples from 125 newly diagnosed adenocarcinoma, clinical-stage IIIB-IV patients, and compared the diagnostic values of EGFR plasma test between groups of clinical characteristics. The influential factors for the sensitivity were identified and assessed by logistic regression. RESULTS EGFR mutations were detected in 65 (52.0%) tumor tissue and 50 (40.0%) matched plasma samples (P = 0.028). Compared to the tissue method, the concordance rate, sensitivity, and specificity of the EGFR plasma test were 86.4%, 75.4%, and 98.3%, respectively. Notably, we found that sensitivity of the test is higher in non-smokers (84.1%) compared to smokers (57.1%, P = 0.018), and in treatment naïve subjects (85.7%) compared to whom undergone chemo-radiotherapy with/without surgery before testing (56.5%, P = 0.009). Furthermore, the highest sensitivity was attained in patients without these two factors (90.3%), whilst the lowest value was noted in those with both factors (40.0%, P = 0.004). The multivariable analysis confirmed that smoking habit and treatment history have independently negative impacts on sensitivity (OR = 0.24, P = 0.019, and OR = 0.36, P = 0.047, respectively).
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Affiliation(s)
- Vinh Thanh Tran
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Thang Thanh Phan
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam.
- Faculty of Biology-Biotechnology, University of Science, VNU-HCM, Ho Chi Minh City, 700000, Vietnam.
| | - Son Truong Nguyen
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
- Department of the Vice Minister, Ministry of Health, Hanoi City, 100000, Vietnam
| | - Bich-Thu Tran
- Faculty of Biology-Biotechnology, University of Science, VNU-HCM, Ho Chi Minh City, 700000, Vietnam
| | - Toan Trong Ho
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Suong Phuoc Pho
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Tran Bao Nguyen
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Tuyen Thi Bich Pham
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Anh Tuan Le
- Department of Chemo-Radiotherapy, Clinical Cancer Center, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
| | - Vu Thuong Le
- Department of Thoracic Disease, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
| | - Hang Thuy Nguyen
- Department of Clinical Pathology, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
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Medipally DKR, Cullen D, Untereiner V, Sockalingum GD, Maguire A, Nguyen TNQ, Bryant J, Noone E, Bradshaw S, Finn M, Dunne M, Shannon AM, Armstrong J, Meade AD, Lyng FM. Vibrational spectroscopy of liquid biopsies for prostate cancer diagnosis. Ther Adv Med Oncol 2020; 12:1758835920918499. [PMID: 32821294 PMCID: PMC7412923 DOI: 10.1177/1758835920918499] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/18/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Screening for prostate cancer with prostate specific antigen and digital rectal examination allows early diagnosis of prostate malignancy but has been associated with poor sensitivity and specificity. There is also a considerable risk of over-diagnosis and over-treatment, which highlights the need for better tools for diagnosis of prostate cancer. This study investigates the potential of high throughput Raman and Fourier Transform Infrared (FTIR) spectroscopy of liquid biopsies for rapid and accurate diagnosis of prostate cancer. Methods: Blood samples (plasma and lymphocytes) were obtained from healthy control subjects and prostate cancer patients. FTIR and Raman spectra were recorded from plasma samples, while Raman spectra were recorded from the lymphocytes. The acquired spectral data was analysed with various multivariate statistical methods, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and classical least squares (CLS) fitting analysis. Results: Discrimination was observed between the infrared and Raman spectra of plasma and lymphocytes from healthy donors and prostate cancer patients using PCA. In addition, plasma and lymphocytes displayed differentiating signatures in patients exhibiting different Gleason scores. A PLS-DA model was able to discriminate these groups with sensitivity and specificity rates ranging from 90% to 99%. CLS fitting analysis identified key analytes that are involved in the development and progression of prostate cancer. Conclusions: This technology may have potential as an alternative first stage diagnostic triage for prostate cancer. This technology can be easily adaptable to many other bodily fluids and could be useful for translation of liquid biopsy-based diagnostics into the clinic.
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Affiliation(s)
- Dinesh K R Medipally
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Ireland
| | - Daniel Cullen
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Ireland
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, BioSpecT EA 7506, UFR Pharmacie, Reims, France
| | - Ganesh D Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT EA 7506, UFR Pharmacie, Reims, France
| | - Adrian Maguire
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Ireland
| | - Thi Nguyet Que Nguyen
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Ireland
| | - Jane Bryant
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Ireland
| | - Emma Noone
- Clinical Trials Unit, St Luke's Radiation Oncology Network, St Luke's Hospital, Dublin, Ireland
| | - Shirley Bradshaw
- Clinical Trials Unit, St Luke's Radiation Oncology Network, St Luke's Hospital, Dublin, Ireland
| | - Marie Finn
- Clinical Trials Unit, St Luke's Radiation Oncology Network, St Luke's Hospital, Dublin, Ireland
| | - Mary Dunne
- Clinical Trials Unit, St Luke's Radiation Oncology Network, St Luke's Hospital, Dublin, Ireland
| | | | | | - Aidan D Meade
- School of Physics & Clinical & Optometric Sciences, Technological University Dublin, Kevin Street, Dublin, Dublin D08 NF82, Ireland
| | - Fiona M Lyng
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Dublin, Dublin D08 NF82, Ireland
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Vad-Nielsen J, Meldgaard P, Sorensen BS, Nielsen AL. Cell-free Chromatin Immunoprecipitation (cfChIP) from blood plasma can determine gene-expression in tumors from non-small-cell lung cancer patients. Lung Cancer 2020; 147:244-251. [PMID: 32759018 DOI: 10.1016/j.lungcan.2020.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Lung cancer is the leading cause of cancer related death worldwide. Accurate molecular diagnostics from a tumor biopsy is paramount for correct diagnosis, treatment strategy, and prediction of outcome. However, a tumor biopsy can be misleading due to tumor heterogeneity and consecutive biopsies are rarely achievable. Importantly, tumor-specific genetic information concerning mutations and translocations, can also be obtained from liquid biopsies, e.g. blood plasma, containing cell-free DNA (cfDNA) with both systemic and tumor origin. Tumor-specific gene-expression information can also be determined from liquid biopsies using cfDNA methylation and cell-free RNA analyses. However, supplementary methodologies that can determine gene-expression patterns in lung tumors from liquid biopsies could also have diagnostic impact. MATERIALS AND METHODS We here present the method cell-free chromatin Immunoprecipitation (cfChIP), which for genes having high expression specifically in the tumor, can determine such gene-expression from blood plasma. In cfChIP cell-free nucleosomes modified with histone H3 lysine 36 tri-methylation (H3K36me3), a mark quantitatively correlated with the transcription of the underlying gene, are isolated, and associated cfDNA quantified. RESULTS We demonstrate that cfChIP from lung cancer patient blood plasma can successfully quantify the level of H3K36me3 associated with circulating cell-free nucleosomes and thereby quantify the transcriptional level of genes associated with these nucleosomes. Moreover, as a proof-of-principle we show that in blood plasma from 14 lung cancer patients, H3K36me3 cfChIP can replicate the expected higher expression of KRT6 in lung squamous cell carcinoma relative to adenocarcinoma. CONCLUSION This work shows that for genes with a high expression specifically in tumor, cfChIP can determine this gene-expression pattern from blood plasma. cfChIP is a method that determine gene-expression at the transcriptional level and accordingly can supplement cfDNA methylation and cell-free RNA analyses.
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Wang Y, Li G, Guo W, Ji B, Aisikeerbayi A, Boratibai Y, Cao L. LncRNA PlncRNA-1 participates in rheumatoid arthritis by regulating transforming growth factor β1. Autoimmunity 2020; 53:297-302. [PMID: 32543888 DOI: 10.1080/08916934.2020.1750010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
LncRNA PlncRNA-1(PlncRNA-1) participates in breast cancer by upregulating TGF-β1. It is known that TGF-β1 plays an inhibitory role in the inflammatory responses in rheumatoid arthritis (RA). Therefore, PlncRNA-1 may also participate in RA. Serum and synovial fibroblasts were obtained from 34 patients with active RA (persistent symptoms), 36 patients with inactive RA (long term of no or few symptoms after active RA) and 40 healthy controls. Expression levels of PlncRNA-1 and TGF-β1 in active RA patients, inactive RA patients and healthy controls were measured by RT-qPCR and ELISA, respectively. Pearson Correlation Coefficient was used to determine the correlation between the expression levels of PlncRNA-1 and TGF-β1. Diagnostic value of PlncRNA-1 for active RA was detected by ROC curve analysis. PlncRNA-1 and TGF-β1 were downregulated in serum of active RA patients but not in inactive RA patients compared to the healthy controls. Expression of PlncRNA-1 and TGF-β1 were positively correlated only in RA patients, and altered expression levels of PlncRNA-1 distinguished the active RA patients from inactive RA patients and healthy controls. PlncRNA-1 and TGF-β1 were also downregulated in synovial fibroblasts derived from RA patients in comparison to inactive RA patients and healthy controls. Overexpression of PlncRNA-1 mediated upregulation of TGF-β1 in synovial fibroblasts derived from RA patients, while exogenous TGF-β1 treatment showed no significant effect on the expression of PlncRNA-1. Therefore, PlncRNA-1 participated in RA possibly by regulating TGF-β1.
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Affiliation(s)
- Yang Wang
- Department of Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
| | - Guoqing Li
- Department of Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
| | - Wentao Guo
- Department of Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
| | - Baochao Ji
- Department of Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
| | | | - Yelborati Boratibai
- Department of orthopedics, People's Hospital of Xinyuan County, YiLi, Xinjiang Province, P. R. China
| | - Li Cao
- Department of Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
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Mauriz E. Low-Fouling Substrates for Plasmonic Sensing of Circulating Biomarkers in Biological Fluids. BIOSENSORS-BASEL 2020; 10:bios10060063. [PMID: 32531908 PMCID: PMC7345924 DOI: 10.3390/bios10060063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
Abstract
The monitoring of biomarkers in body fluids provides valuable prognostic information regarding disease onset and progression. Most biosensing approaches use noninvasive screening tools and are conducted in order to improve early clinical diagnosis. However, biofouling of the sensing surface may disturb the quantification of circulating biomarkers in complex biological fluids. Thus, there is a great need for antifouling interfaces to be designed in order to reduce nonspecific adsorption and prevent inactivation of biological receptors and loss of sensitivity. To address these limitations and enable their application in clinical practice, a variety of plasmonic platforms have been recently developed for biomarker analysis in easily accessible biological fluids. This review presents an overview of the latest advances in the design of antifouling strategies for the detection of clinically relevant biomarkers on the basis of the characteristics of biological samples. The impact of nanoplasmonic biosensors as point-of-care devices has been examined for a wide range of biomarkers associated with cancer, inflammatory, infectious and neurodegenerative diseases. Clinical applications in readily obtainable biofluids such as blood, saliva, urine, tears and cerebrospinal and synovial fluids, covering almost the whole range of plasmonic applications, from surface plasmon resonance (SPR) to surface-enhanced Raman scattering (SERS), are also discussed.
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Affiliation(s)
- Elba Mauriz
- Department of Nursing and Physiotherapy, Universidad de León, Campus de Vegazana, s/n, 24071 León, Spain;
- Institute of Food Science and Technology (ICTAL), La Serna 58, 24007 León, Spain
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Detection of Microsatellite Instability from Circulating Tumor DNA by Targeted Deep Sequencing. J Mol Diagn 2020; 22:860-870. [PMID: 32428677 DOI: 10.1016/j.jmoldx.2020.04.210] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/17/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, microsatellite instability (MSI) detection is limited to tissue samples with sufficient tumor content. Detection of MSI from blood has been explored but confounded by low sensitivity due to limited circulating tumor DNA (ctDNA). We developed a next-generation sequencing-based algorithm, blood MSI signature enrichment analysis, to detect MSI from blood. Blood MSI signature enrichment analysis development involved three major steps. First, marker sites that can effectively distinguish high MSI (MSI-H) from microsatellite stable tumors were extracted. Second, MSI signature enrichment analysis was performed based on hypergeometric probability, under the null hypothesis that plasma samples have similar MSI-H and microsatellite stable read coverage patterns for particular marker sites as the white blood cells from the training data set. Finally, enrichment scores of marker sites were normalized, and all markers were collectively considered to determine the MSI status of a plasma sample. In vitro dilution experiments with cell lines and in silico simulation experiments based on mixtures of MSI-H plasma and paired white blood cell DNA demonstrated 98% sensitivity and 100% specificity at a minimum of 1% ctDNA and 91.8% sensitivity and 100% specificity with 0.4% ctDNA. An independent validation cohort of 87 colorectal cancer patients with orthogonal confirmation of MSI status of tissues confirmed performance, achieving 94.1% sensitivity (16/17) and 100% specificity (27/27) for samples with ctDNA >0.4%.
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De Michino S, Aparnathi M, Rostami A, Lok BH, Bratman SV. The Utility of Liquid Biopsies in Radiation Oncology. Int J Radiat Oncol Biol Phys 2020; 107:873-886. [PMID: 32417410 DOI: 10.1016/j.ijrobp.2020.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022]
Abstract
The use of therapeutic radiation is primarily guided by clinicopathologic factors and medical imaging, whereas molecular biomarkers currently play a comparatively minor role in most settings. Liquid biopsies provide a rich source of noninvasive tumor-specific biomarkers and are amenable to repeated and noninvasive assessment. Here, we review the current status of liquid biopsies and their potential impact on the field of radiation oncology. We focus on established and emerging approaches to analyze circulating tumor DNA and circulating tumor cells from peripheral blood. These promising classes of biomarkers could have an outsized impact on cancer management by meaningfully stratifying patients into risk groups, tracking radiation therapy efficacy during and after treatment, and identifying patients with radiosensitive or radioresistant disease. Finally, we highlight opportunities for future investigation including the need for prospective interventional studies employing liquid biopsies to guide the management of radiation therapy-treated patients.
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Affiliation(s)
- Steven De Michino
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mansi Aparnathi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ariana Rostami
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin H Lok
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.
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Circulating miRNAs as Biomarkers for Prostate Cancer Diagnosis in Subjects with Benign Prostatic Hyperplasia. J Immunol Res 2020; 2020:5873056. [PMID: 32455140 PMCID: PMC7230987 DOI: 10.1155/2020/5873056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
Body fluids often contain freely circulating nucleic acids, many of which can be exploited as noninvasive tools for the diagnosis of cancer as well as for clinical prognostication. Identifying microRNAs (miRNAs) in subjects' blood with various malignancies means that they can serve as novel biomarkers for prostate cancer (PCa) diagnosis. This study analyzed serum-circulating miRNAs as a noninvasive biomarker in subjects with PCa and subjects with benign prostatic hyperplasia (BPH). In total, 31 PCa subjects and 31 BPH subjects were included, with the BPH group serving as the control group. RT-qPCR was used to quantify the levels of 10 miRNAs, which included miR-18a, miR-34a, miR-106b, miR-183, miR-200a, miR-301a, miR-141, miR-182, miR-200b, and miR-375 in serum. Statistical tests were used to assess the relationship between the levels of miRNAs and the clinicopathological data. A significant increase was observed in the relative expression ratios of miR-141, miR-182, miR-200b, and miR-375 (1.89-, 2.09-, 2.41-, and 2.27-folds, respectively) in the PCa group when compared to the BPH group. Based on the receiver operating characteristic (ROC) analysis, the largest area under the curve (AUC), 0.923, was associated with the miR-200b group, indicating effective diagnostic properties for this biomarker. A correlation was observed between total prostate-specific antigen (TPSA) and the relative levels of miR-141, miR-182, miR-200b, and miR-375. The Gleason score and the miR-200b expression level were also correlated. These results are consistent with previous studies regarding the possibility of differentiating between PCa subjects and healthy controls based on the detection of miRNA. The findings attest to a distinctive expression profile of miRNA that is detectable in the blood of PCa subjects, thereby confirming the role of miRNAs as diagnostic biomarkers for PCa.
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Predicting bipolar disorder and schizophrenia based on non-overlapping genetic phenotypes using deep neural network. EVOLUTIONARY INTELLIGENCE 2020. [DOI: 10.1007/s12065-019-00346-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Benešová L, Hálková T, Ptáčková R, Semyakina A, Menclová K, Pudil J, Ryska M, Levý M, Šimša J, Pazdírek F, Hoch J, Blaha M, Minárik M. Significance of postoperative follow-up of patients with metastatic colorectal cancer using circulating tumor DNA. World J Gastroenterol 2019; 25:6939-6948. [PMID: 31908397 PMCID: PMC6938726 DOI: 10.3748/wjg.v25.i48.6939] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/05/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the most notable applications for circulating tumor DNA (ctDNA) detection in peripheral blood of patients with metastatic colorectal cancer (mCRC) is a long-term postoperative follow-up. Sometimes referred to as a “liquid (re)biopsy” it is a minimally invasive procedure and can be performed repeatedly at relatively short intervals (months or even weeks). The presence of the disease and the actual extent of the tumor burden (tumor mass) within the patient’s body can be monitored. This is of particular importance, especially when evaluating radicality of surgical treatment as well as for early detection of disease progression or recurrence.
AIM To confirm the radicality of surgery using ctDNA and compare available methods for detection of recurrence in metastatic colorectal cancer.
METHODS A total of 47 patients with detected ctDNA and indications for resection of mCRC were enrolled in the multicenter study involving three surgical centers. Standard postoperative follow-ups using imaging techniques and the determination of tumor markers were supplemented by ctDNA sampling. In addition to the baseline ctDNA testing prior to surgery, a postoperative observation was conducted by evaluating ctDNA presence up to a week after surgery and subsequently at approximately three-month intervals. The presence of ctDNA was correlated with radicality of surgical treatment and the actual clinical status of the patient.
RESULTS Among the monitored patients, the R0 (curative) resection correlated with postoperative ctDNA negativity in 26 out of 28 cases of surgical procedures (26/28, 93%). In the remaining cases of R0 surgeries that displayed ctDNA, both patients were diagnosed with a recurrence of the disease after 6 months. In 7 patients who underwent an R1 resection, 4 ctDNA positivities (4/7, 57%) were detected after surgery and associated with the confirmation of early disease recurrence (after 3 to 7 months). All 15 patients (15/15, 100%) undergoing R2 resection remained constantly ctDNA positive during the entire follow-up period. In 22 cases of recurrence, ctDNA positivity was detected 22 times (22/22, 100%) compared to 16 positives (16/22, 73%) by imaging methods and 15 cases (15/22, 68%) of elevated tumor markers.
CONCLUSION ctDNA detection in patients with mCRC is a viable tool for early detection of disease recurrence as well as for confirmation of the radicality of surgical treatment.
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Affiliation(s)
- Lucie Benešová
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Tereza Hálková
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Renata Ptáčková
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Anastasiya Semyakina
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
| | - Kateřina Menclová
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Jiří Pudil
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Miroslav Ryska
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Military University Hospital, Prague CZ 169 02, Czech Republic
| | - Miroslav Levý
- Surgery Department, 1st Faculty of Medicine, Charles University Prague and Thomayer Hospital, Prague CZ 140 59, Czech Republic
| | - Jaromír Šimša
- Surgery Department, 1st Faculty of Medicine, Charles University Prague and Thomayer Hospital, Prague CZ 140 59, Czech Republic
| | - Filip Pazdírek
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Motol University Hospital, Prague CZ 150 06, Czech Republic
| | - Jiří Hoch
- Surgery Department, 2nd Faculty of Medicine of Charles University Prague and Motol University Hospital, Prague CZ 150 06, Czech Republic
| | - Milan Blaha
- Institute of Biostatistics and Analyses of the Masaryk University, Brno CZ 625 00, Czech Republic
| | - Marek Minárik
- Centre for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague CZ 161 00, Czech Republic
- Elphogene, Prague CZ 161 00, Czech Republic
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On the need for the development of a cancer early detection, diagnostic, prognosis, and treatment response system. Future Sci OA 2019; 6:FSO439. [PMID: 32025328 PMCID: PMC6997916 DOI: 10.2144/fsoa-2019-0028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cancer is the second leading cause of noncommunicable disease deaths in the world. In 2018, there were over 18 million new cancer cases and approximately 10 million people died from the disease globally. In 2019, almost two million new cases of cancer will be diagnosed in USA and over 600,000 people are expected to die from the disease. The incidence of cancer is expected to rise because of lifestyle changes and a rapidly aging population. Evidence suggests that early detection is critical to reducing cancer morbidity and mortality. In this paper, the development of an integrated smart wearable and biomarker detection system is proposed to help reduce cancer morbidity and mortality. The potential benefits and limitations of the system are discussed. Cancer is one of the leading causes of death in the world. Evidence suggests that its incidence will continue to rise in the future because of lifestyle changes and a rapidly aging population. There is currently no cure for the disease and the best way to reduce its incidence and morbidity is to detect it early. In this paper, an integrated smart wearable and biomarker detection system to help in the early detection, prognosis, diagnosis and treatment of cancer is proposed.
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Larijani B, Goodarzi P, Sheikh Hosseini M, M. Nejad S, Alavi-Moghadam S, Sarvari M, Abedi M, Arabi M, Rahim F, Foroughi Heravani N, Hadavandkhani M, Payab M. OMICs Profiling of Cancer Cells. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-27727-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Vietsch EE, Peran I, Suker M, van den Bosch TPP, van der Sijde F, Kros JM, van Eijck CHJ, Wellstein A. Immune-Related Circulating miR-125b-5p and miR-99a-5p Reveal a High Recurrence Risk Group of Pancreatic Cancer Patients after Tumor Resection. APPLIED SCIENCES (BASEL, SWITZERLAND) 2019; 9:4784. [PMID: 34484811 PMCID: PMC8415800 DOI: 10.3390/app9224784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Clinical follow-up aided by changes in the expression of circulating microRNAs (miRs) may improve prognostication of pancreatic ductal adenocarcinoma (PDAC) patients. Changes in 179 circulating miRs due to cancer progression in the transgenic Kras G12D/+; Trp53 R172H/+; P48-Cre (KPC) animal model of PDAC were analyzed for serum miRs that are altered in metastatic disease. In addition, expression levels of 250 miRs were profiled before and after pancreaticoduodenectomy in the serum of two patients with resectable PDAC with different progression free survival (PFS) and analyzed for changes indicative of PDAC recurrence after resection. Three miRs that were upregulated ≥3-fold in progressive PDAC in both mice and patients were selected for validation in 26 additional PDAC patients before and after resection. We found that high serum miR-125b-5p and miR-99a-5p levels after resection are significantly associated with shorter PFS (HR 1.34 and HR 1.73 respectively). In situ hybridization for miR detection in the paired resected human PDAC tissues showed that miR-125b-5p and miR-99a-5p are highly expressed in inflammatory cells in the tumor stroma, located in clusters of CD79A expressing cells of the B-lymphocyte lineage. In conclusion, we found that circulating miR-125b-5p and miR-99a-5p are potential immune-cell related prognostic biomarkers in PDAC patients after surgery.
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Affiliation(s)
- Eveline E. Vietsch
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, 3015GD Rotterdam, The Netherlands
| | - Ivana Peran
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Mustafa Suker
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, 3015GD Rotterdam, The Netherlands
| | | | - Fleur van der Sijde
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, 3015GD Rotterdam, The Netherlands
| | - Johan M. Kros
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, 3015GD Rotterdam, The Netherlands
| | - Casper H. J. van Eijck
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, 3015GD Rotterdam, The Netherlands
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
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Abstract
There is a clear and unmet need for biomarkers in hepatocellular carcinoma (HCC). Circulating cell free deoxyribonucleic acid (cfDNA) is a fragmented DNA subtype, found in the blood circulation. Circulating tumor DNA (ctDNA) is the fraction of total cfDNA, which originates from the primary tumor or metastases in patients with cancer. Earlier studies reported that quantitative measurement cfDNA has diagnostic and prognostic role for HCC. More recently, improvement in next-generation sequencing technology and better understanding of genetic or epigenetic alteration of HCC have allowed comprehensive analysis of mutational and methylation landscape of ctDNA. Hotspot mutation panels and methylation panels have both shown promising performance. None of these tests have yet been validated in longitudinal cohorts for preclinical detection of HCC. In this article, the authors discuss the currently available ctDNA detection technologies, their diagnostic and prognostic performance in HCC, and future research directions.
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Affiliation(s)
- Ju Dong Yang
- Division of Digestive and Liver Diseases, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, California
- Comprehensive Transplant Center, Cedars Sinai Medical Center, Los Angeles, California
- Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, California
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Minetta C. Liu
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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