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Zhang W, Pham TH, Wang DH. A "Clue" to Improving Liquid Biopsies for Cancer: Microfluidic Multiparametric Exosome Analysis. Clin Chem 2020; 67:335-337. [PMID: 33207364 DOI: 10.1093/clinchem/hvaa209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Wei Zhang
- Esophageal Diseases Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thai H Pham
- Esophageal Diseases Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA.,VA North Texas Health Care System, Dallas, TX, USA
| | - David H Wang
- Esophageal Diseases Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,VA North Texas Health Care System, Dallas, TX, USA
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Dalal S, Petersen J, Jhala D. Liquid Biopsies in a Veteran Patient Population With Advanced Prostate and Lung Non-Small Cell Carcinomas: A New Paradigm and Unique Challenge in Personalized Medicine. Fed Pract 2020; 38:8-14. [PMID: 33574643 DOI: 10.12788/fp.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Liquid biopsy in solid tumors is a major milestone in the field of precision oncology by analyzing circulating tumor cells in peripheral blood and genomic alterations. DNA damage repair gene (DDR) mutations have been reported in 25 to 40% of prostatic cancers and > 50% of non-small cell lung cancers (NSCLC). Tp53 mutation has been found to be associated with a poor prognosis and increased germline mutations. We herein present a quality assurance study for the utility of liquid biopsies with frequency of DDR, Tp53, and androgen receptor (AR) mutations and the clinical impact in advanced lung and prostate cancers in the veteran patient population; these quality assurance observations are the study endpoints. Methods We reviewed documentation from advanced cancer biomarker tests on liquid biopsies performed at the Corporal Michael J. Crescenz Veteran Affairs Medical Center in Philadelphia, Pennsylvania, from May 2019 to April 15, 2020. Results Mutations were detected in 29 of 31 (93.5%) liquid biopsies, hence, 29 liquid biopsies had sufficient ctDNA for analysis. Notable mutations were found in 23 cases (79.3%), irrespective of the cancer type showed. Of 21 prostate cancers biopsies 4 (19.0%) biomarker test directed the targeted therapy to driver mutations of the AR gene. Gene mutations from the DDR gene family were detected in 8 of 23 (34.7%) advanced prostate and lung cancer liquid biopsies, and in 6 of 21 (28.5%) prostate cancer cases indicating poor outcome and possible resistance to the current therapy. Irrespective of the cancer type, 15 of 23 (65.2%) patients harbored Tp53 mutations, which is much more frequent than is documented in the literature. Of 31 patients, 15 (48.4%) were Vietnam era veterans with the potential of Agent Orange exposure and, 20 of 31 (64.5%) had a smoking history. Seven (46.6%) of the Vietnam era veterans with potential exposure to Agent Orange were positive for Tp53 mutations irrespective of the cancer type. Conclusion The minimally invasive liquid biopsy shows a great promise as a diagnostic and prognostic tool in the personalized clinical management of advanced prostate and NSCLC in veteran patient population with unique demographic characteristics. Difference in frequency of the genetic mutations (DDR, TP53, AR) in this cohort provides valuable information for disease progression, lack of response, mechanism of resistance to the implemented therapy and clinical decision making. Precision oncology can be further tailored for this cohort by focusing on DNA repair genes and Tp53 mutations in future for personalized targeted therapy.
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Affiliation(s)
- Sharvari Dalal
- and are Staff Pathologists and is Chief, Pathology and Laboratory Medicine, all at Corporal Michael J. Crescenz Veteran Affairs Medical Center in Philadelphia, Pennsylvania. Sharvari Dalal is Adjunct Assistant Professor of Clinical Pathology and Laboratory Medicine, Jeffrey Petersen is Assistant Professor of Clinical Pathology and Laboratory Medicine, and Darshana Jhala is Professor of Clinical Pathology and Laboratory Medicine, all at the University of Pennsylvania Perelman School of Medicine
| | - Jeffrey Petersen
- and are Staff Pathologists and is Chief, Pathology and Laboratory Medicine, all at Corporal Michael J. Crescenz Veteran Affairs Medical Center in Philadelphia, Pennsylvania. Sharvari Dalal is Adjunct Assistant Professor of Clinical Pathology and Laboratory Medicine, Jeffrey Petersen is Assistant Professor of Clinical Pathology and Laboratory Medicine, and Darshana Jhala is Professor of Clinical Pathology and Laboratory Medicine, all at the University of Pennsylvania Perelman School of Medicine
| | - Darshana Jhala
- and are Staff Pathologists and is Chief, Pathology and Laboratory Medicine, all at Corporal Michael J. Crescenz Veteran Affairs Medical Center in Philadelphia, Pennsylvania. Sharvari Dalal is Adjunct Assistant Professor of Clinical Pathology and Laboratory Medicine, Jeffrey Petersen is Assistant Professor of Clinical Pathology and Laboratory Medicine, and Darshana Jhala is Professor of Clinical Pathology and Laboratory Medicine, all at the University of Pennsylvania Perelman School of Medicine
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Lim HK, Jeffrey GP, Ramm GA, Soekmadji C. Pathogenesis of Viral Hepatitis-Induced Chronic Liver Disease: Role of Extracellular Vesicles. Front Cell Infect Microbiol 2020; 10:587628. [PMID: 33240824 PMCID: PMC7683521 DOI: 10.3389/fcimb.2020.587628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles are encapsulated lipid nanoparticles secreted by a variety of cell types in living organisms. They are known to carry proteins, metabolites, nucleic acids, and lipids as their cargoes and are important mediators of intercellular communication. The role of extracellular vesicles in chronic liver disease has been reported. Chronic liver disease such as viral hepatitis accounts for a significant mortality and morbidity burden worldwide. Hepatic fibrosis has been commonly associated with the chronic form of viral hepatitis, which results in end-stage liver disease, including cirrhosis, liver failure, and carcinoma in some patients. In this review, we discuss the potential role of extracellular vesicles in mediating communication between infectious agents (hepatitis B and C viruses) and host cells, and how these complex cell-cell interactions may facilitate the development of chronic liver disease. We will further discuss how understanding their biological mechanism of action might be beneficial for developing therapeutic strategies to treat chronic liver disease.
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Affiliation(s)
- Hong Kiat Lim
- Hepatic Fibrosis Group, Department of Cellular and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gary P Jeffrey
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia.,Sir Charles Gairdner Hospital, Nedlands, Hepatology Department and Liver Transplant Service, Perth, WA, Australia
| | - Grant A Ramm
- Hepatic Fibrosis Group, Department of Cellular and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Carolina Soekmadji
- Hepatic Fibrosis Group, Department of Cellular and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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Raos D, Krasic J, Masic S, Abramovic I, Coric M, Kruslin B, Katusic Bojanac A, Bulic-Jakus F, Jezek D, Ulamec M, Sincic N. In Search of TGCT Biomarkers: A Comprehensive In Silico and Histopathological Analysis. DISEASE MARKERS 2020; 2020:8841880. [PMID: 33224314 PMCID: PMC7666710 DOI: 10.1155/2020/8841880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/10/2020] [Accepted: 07/31/2020] [Indexed: 01/22/2023]
Abstract
Testicular germ cell tumors (TGCTs) are ever more affecting the young male population. Germ cell neoplasia in situ (GCNIS) is the origin of TGCTs, namely, seminomas (SE) and a heterogeneous group of nonseminomas (NS) comprising embryonal carcinoma, teratoma, yolk sac tumor, and choriocarcinoma. Response to the treatment and prognosis, especially of NS, depend on precise diagnosis with a necessity for discovery of new biomarkers. We aimed to perform comprehensive in silico analysis at the DNA, RNA, and protein levels of six prospective (HOXA9, MGMT, CFC1, PRSS21, RASSF1A, and MAGEC2) and six known TGCT biomarkers (OCT4, SOX17, SOX2, SALL4, NANOG, and KIT) and assess its congruence with histopathological analysis in all forms of TGCTs. Cancer Hallmarks Analytics Tool, the Search Tool for the Retrieval of Interacting Genes/Proteins database, and UALCAN, an interactive web resource for analyzing cancer OMICS data, were used. In 108 TGCT and 48 tumor-free testicular samples, the immunoreactivity score (IRS) was calculated. SE showed higher frequency in DNA alteration, while DNA methylation was significantly higher for all prospective biomarkers in NS. In GCNIS, we assessed the clinical positivity of RASSF1 and PRSS21 in 52% and 62% of samples, respectively, in contrast to low or nil positivity in healthy seminiferous tubules, TGTCs as a group, SE, NS, or all NS components. Although present in approximately 80% of healthy seminiferous tubules (HT) and GCNIS, HOXA9 was diagnostically positive in 64% of TGCTs, while it was positive in 82% of NS versus 29% of SE. Results at the DNA, mRNA, and protein levels on putative and already known biomarkers were included in the suggested panels that may prove to be important for better diagnostics of various forms of TGCTs.
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Affiliation(s)
- Dora Raos
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Jure Krasic
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Silvija Masic
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Vinogradska Cesta 29, 10000 Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Marijana Coric
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Department of Pathology and Cytology, University Hospital Centre Zagreb, Kišpatićeva Ulica 12, 10000 Zagreb, Croatia
| | - Bozo Kruslin
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Vinogradska Cesta 29, 10000 Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Floriana Bulic-Jakus
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Davor Jezek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Department of Histology and Embryology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Vinogradska Cesta 29, 10000 Zagreb, Croatia
- Department of Pathology, University of Zagreb School of Dental Medicine and School of Medicine, Gundulićeva Ulica 5, 10000 Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 3, 10000 Zagreb, Croatia
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Adeoye J, Wan CCJ, Thomson P. Mock clinical testing in the validation of fluid-phase biomarkers for head and neck carcinoma diagnosis: Scoping review. Head Neck 2020; 43:691-704. [PMID: 33151603 DOI: 10.1002/hed.26526] [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: 08/25/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
This review sought to determine the range and nature of prospective-sampling and blinding methods for validating nonviral biofluid markers diagnostic of head and neck carcinomas. Electronic database searching was conducted to identify studies published in English from January 1, 2009 to August 1, 2020. Sixteen studies from 17 articles published between 2011 and 2020 were included in this review. We found that about 3 out of 100 studies utilized at least one of the mock testing approaches for biomarker validation. Protein, mRNA, and metabolomic markers also represented the only groups whose validation has been attempted using these methods. Furthermore, studies that utilized both methods were found to have lower bias concerns on the quality assessment of diagnostic accuracy studies (QUADAS-2) tool. Overall, there is a need to include these protocols in research endeavours verifying diagnostic biomarkers for head and neck carcinomas following the preliminary establishment of their classification accuracy.
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Affiliation(s)
- John Adeoye
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.,Oral Cancer Research Group, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Chi Ching Joan Wan
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Peter Thomson
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.,Oral Cancer Research Group, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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106
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Davey M, Benzina S, Savoie M, Breault G, Ghosh A, Ouellette RJ. Affinity Captured Urinary Extracellular Vesicles Provide mRNA and miRNA Biomarkers for Improved Accuracy of Prostate Cancer Detection: A Pilot Study. Int J Mol Sci 2020; 21:ijms21218330. [PMID: 33172003 PMCID: PMC7664192 DOI: 10.3390/ijms21218330] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
Serum prostate-specific antigen (sPSA) testing has helped to increase early detection of and decrease mortality from prostate cancer. However, since sPSA lacks specificity, an invasive prostate tissue biopsy is required to confirm cancer diagnosis. Using urinary extracellular vesicles (EVs) as a minimally invasive biomarker source, our goal was to develop a biomarker panel able to distinguish prostate cancer from benign conditions with high accuracy. We enrolled 56 patients in our study, 28 negative and 28 positive for cancer based on tissue biopsy results. Using our Vn96 peptide affinity method, we isolated EVs from post-digital rectal exam urines and used quantitative polymerase chain reaction to measure several mRNA and miRNA targets. We identified a panel of seven mRNA biomarkers whose expression ratio discriminated non-cancer from cancer with an area under the curve (AUC) of 0.825, sensitivity of 75% and specificity of 84%. We also identified two miRNAs whose combined score yielded an AUC of 0.744. A model pairing the seven mRNA and two miRNA panels yielded an AUC of 0.843, sensitivity of 79% and specificity of 89%. Addition of EV-derived PCA3 levels and clinical characteristics to the biomarker model further improved test accuracy. An AUC of 0.955, sensitivity of 86% and specificity of 93% were obtained. Hence, Vn96-isolated urinary EVs are a clinically applicable and minimally invasive source of mRNA and miRNA biomarkers with potential to improve on the accuracy of prostate cancer screening and diagnosis.
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Affiliation(s)
- Michelle Davey
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (M.D.); (S.B.); (A.G.)
| | - Sami Benzina
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (M.D.); (S.B.); (A.G.)
| | - Marc Savoie
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB E1C 2Z3, Canada; (M.S.); (G.B.)
| | - Guy Breault
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB E1C 2Z3, Canada; (M.S.); (G.B.)
| | - Anirban Ghosh
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (M.D.); (S.B.); (A.G.)
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (M.D.); (S.B.); (A.G.)
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB E1C 2Z3, Canada; (M.S.); (G.B.)
- Correspondence:
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107
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Lakshminarayanan H, Rutishauser D, Schraml P, Moch H, Bolck HA. Liquid Biopsies in Renal Cell Carcinoma-Recent Advances and Promising New Technologies for the Early Detection of Metastatic Disease. Front Oncol 2020; 10:582843. [PMID: 33194717 PMCID: PMC7656014 DOI: 10.3389/fonc.2020.582843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) displays a highly varying clinical progression, from slow growing localized tumors to very aggressive metastatic disease (mRCC). Almost a third of all patients with ccRCC show metastatic dissemination at presentation while another third develop metastasis during the course of the disease. Survival rates of mRCC patients remain low despite the development of novel targeted treatment regimens. Biomarkers indicating disease progression could help to define its aggressive potential and thus guide patient management. However, molecular markers that can reliably assess metastatic dissemination and disease recurrence in ccRCC have not been recommended for clinical practice to date. Liquid biopsies could provide an attractive and non-invasive method to determine the risk of recurrence or metastatic dissemination during follow-up and thus assist the search for surveillance biomarkers in ccRCC tumors. A wide spectrum of circulating molecules have already shown considerable potential for ccRCC diagnosis and prognostication. In this review, we outline state of the art of the key circulating analytes such as cfDNA, cfRNA, proteins, and exosomes that may serve as biomarkers for the longitudinal monitoring of ccRCC progression to metastasis. Moreover, we address some of the prevailing limitations in the past approaches and present promising adoptable technologies that could help to pursue the implementation of liquid biopsies as a prognostic tool for mRCC.
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Affiliation(s)
| | | | | | - Holger Moch
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Hella A. Bolck
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
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108
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Das T, Andrieux G, Ahmed M, Chakraborty S. Integration of Online Omics-Data Resources for Cancer Research. Front Genet 2020; 11:578345. [PMID: 33193699 PMCID: PMC7645150 DOI: 10.3389/fgene.2020.578345] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
The manifestations of cancerous phenotypes necessitate alterations at different levels of information-flow from genome to proteome. The molecular alterations at different information processing levels serve as the basis for the cancer phenotype to emerge. To understand the underlying mechanisms that drive the acquisition of cancer hallmarks it is required to interrogate cancer cells using multiple levels of information flow represented by different omics - such as genomics, epigenomics, transcriptomics, and proteomics. The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to integrate the omics-data in a biologically meaningful manner. The plethora of cancer-specific online omics-data resources, if able to be integrated efficiently and systematically, may facilitate the generation of new biological insights for cancer research. In this review, we provide a comprehensive overview of the online single- and multi-omics resources that are dedicated to cancer. We catalog various online omics-data resources such as The Cancer Genome Atlas (TCGA) along with various TCGA-associated data portals and tools for multi-omics analysis and visualization, the International Cancer Genome Consortium (ICGC), Catalogue of Somatic Mutations in Cancer (COSMIC), The Pathology Atlas, Gene Expression Omnibus (GEO), and PRoteomics IDEntifications (PRIDE). By comparing the strengths and limitations of the respective online resources, we aim to highlight the current biological and technological challenges and possible strategies to overcome these challenges. We outline the available schemes for the integration of the multi-omics dimensions for stratifying cancer patients and biomarker prediction based on the integrated molecular-signatures of cancer. Finally, we propose the multi-omics driven systems-biology approaches to realize the potential of precision onco-medicine as the future of cancer research. We believe this systematic review will encourage scientists and clinicians worldwide to utilize the online resources to explore and integrate the available omics datasets that may provide a window of opportunity to generate new biological insights and contribute to the advancement of the field of cancer research.
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Affiliation(s)
- Tonmoy Das
- Molecular Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Geoffroy Andrieux
- Medical Center - University of Freiburg, Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Freiburg, Freiburg, Germany
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sajib Chakraborty
- Molecular Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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109
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Arechederra M, Ávila MA, Berasain C. Liquid biopsy for cancer management: a revolutionary but still limited new tool for precision medicine. ADVANCES IN LABORATORY MEDICINE 2020; 1:20200009. [PMID: 37361495 PMCID: PMC10197281 DOI: 10.1515/almed-2020-0009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 06/28/2023]
Abstract
The term liquid biopsy is used in contraposition to the traditional "solid" tissue biopsy. In the oncology field it has opened a new plethora of clinical opportunities as tumor-derived material is shedded into the different biofluids from where it can be isolated and analyzed. Common biofluids include blood, urine, saliva, cerebrospinal fluid (CSF), pleural effusion or bile. Starting from these biological specimens several analytes can be isolated, among which we will review the most widely used: circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), proteins, metabolites, and exosomes. Regarding the nature of the biomarkers it will depend on the analyte, the type of tumor and the clinical application of the liquid biopsy and it includes, somatic point mutations, deletions, amplifications, gene-fusions, DNA-methylated marks, tumor-specific miRNAs, proteins or metabolites. Here we review the characteristics of the analytes and the methodologies used for their isolation. We also describe the applications of the liquid biopsy in the management of patients with cancer, from the early detection of cancers to treatment guidance in patients with advanced tumors. Finally, we also discuss some current limitations and still open questions.
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Affiliation(s)
- María Arechederra
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
- Hepatology Program, CIMA, University of Navarra, Avda. Pio XII, n55, 31008, Pamplona, Spain
| | - Matías A. Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Berasain
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Hepatology Program, CIMA, University of Navarra, Avda. Pio XII, n55, 31008, Pamplona, Spain
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Moccia M, Caratelli V, Cinti S, Pede B, Avitabile C, Saviano M, Imbriani AL, Moscone D, Arduini F. Paper-based electrochemical peptide nucleic acid (PNA) biosensor for detection of miRNA-492: a pancreatic ductal adenocarcinoma biomarker. Biosens Bioelectron 2020; 165:112371. [PMID: 32729503 DOI: 10.1016/j.bios.2020.112371] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/28/2020] [Accepted: 06/06/2020] [Indexed: 12/29/2022]
Abstract
Pancreatic ductal adenocarcinoma is the predominant neoplastic disease of the pancreas and it represents the fourth most frequent cause of death in cancer-related disease, with only 8% of survivors after 5-year to the diagnosis. The main issues of this type of cancer rely on fast progress (i.e. 14 months from T1 to a T4 stage), nonspecific symptoms with delay in diagnosis, and the absence of effective screening strategies. To address the lack of early diagnosis, we report a cost-effective paper-based biosensor for the detection of miRNA-492, which is recognised as a biomarker for pancreatic ductal adenocarcinoma. To design a miniaturised, sensitive, and robust paper-based platform, an electrochemical sensor was screen-printed on office paper previously wax-patterned via wax-printing technique. The paper-based sensor was then engineered with a novel and highly specific peptide nucleic acid (PNA) as the recognition element. The formation of PNA/miRNA-492 adduct was evaluated by monitoring the interaction between the positively charged ruthenium (III) hexamine with uncharged PNA and/or negatively charged PNA/miRNA-492 duplex by differential pulse voltammetry. The paper-based biosensor provided a linear range up to 100 nM, with a LOD of 6 nM. Excellent selectivity towards one- and two-base mismatches (1MM, 2MM) or scrambled (SCR) sequences was highlighted and the applicability for biomedical analyses was demonstrated, measuring miRNA-492 in undiluted serum samples.
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Affiliation(s)
- Maria Moccia
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technology, Via G. Amendola 122/O, 70126, Bari, Italy.
| | - Veronica Caratelli
- Tor Vergata University, Department of Chemical Science and Technologies, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Stefano Cinti
- University of Naples "Federico II", Department of Pharmacy, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Biagio Pede
- Tor Vergata University, Department of Chemical Science and Technologies, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Concetta Avitabile
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technology, Via G. Amendola 122/O, 70126, Bari, Italy
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technology, Via G. Amendola 122/O, 70126, Bari, Italy
| | - Anna Lisa Imbriani
- Biochemical Systems International S.p.A. Loc, Palazzo del Pero, 23, 52100, Arezzo, Italy
| | - Danila Moscone
- Tor Vergata University, Department of Chemical Science and Technologies, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Fabiana Arduini
- Tor Vergata University, Department of Chemical Science and Technologies, Via Della Ricerca Scientifica, 00133, Rome, Italy; SENSE4MED, Via Renato Rascel 30, 00133, Rome, Italy.
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Mahshid SS, Dabdoub A. Development of a novel electrochemical immuno-biosensor for circulating biomarkers of the inner ear. Biosens Bioelectron 2020; 165:112369. [PMID: 32729501 DOI: 10.1016/j.bios.2020.112369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022]
Abstract
Current approaches for diagnosis of hearing or vestibular disorders are mostly based on physical examinations that cannot provide information about the exact location of cellular damage inside the inner ear. Therefore, there is a need for new diagnostic methods capable of identifying the sites of damage through the detection of inner ear blood-circulating biomarkers. Here, we developed the first biosensor platform for rapid detection of otolin-1 and prestin, blood-circulating proteins specifically expressed in the vestibule and cochlea, respectively. The platform was designed on a DNA-based immunoassay that employed conjugated antibodies for target protein recognition, which when bound, altered the DNA-DNA hybridization on the surface, resulting in generation of a concentration-dependent signal. The signal was recorded when the redox moiety brought to the surface by the target enabled a selective electrochemical output directly in whole blood. Signal amplification was acquired by employing high-curvature nanostructured electrodes for sensitive sample analysis at picomolar concentrations with a three-fold quantitative range. The combination of nanostructuring and optimum density of the probes on the surface provided low-picomolar detection limits while utilizing small 10 μL sample volume with a 10-min response time. The proposed immuno-biosensor is highly selective and quantitative and can easily be adapted for rapid detection of any blood-circulating protein using their specific antibodies as recognition elements.
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Affiliation(s)
- Sahar S Mahshid
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada.
| | - Alain Dabdoub
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada; Department of Otolaryngology-Head & Neck Surgery, University of Toronto, Toronto, ON, M5S 3H2, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada.
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112
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Mentis AFA, Grivas PD, Dardiotis E, Romas NA, Papavassiliou AG. Circulating tumor cells as Trojan Horse for understanding, preventing, and treating cancer: a critical appraisal. Cell Mol Life Sci 2020; 77:3671-3690. [PMID: 32333084 PMCID: PMC11104835 DOI: 10.1007/s00018-020-03529-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/29/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Circulating tumor cells (CTCs) are regarded as harbingers of metastases. Their ability to predict response to therapy, relapse, and resistance to treatment has proposed their value as putative diagnostic and prognostic indicators. CTCs represent one of the zeniths of cancer evolution in terms of cell survival; however, the triggers of CTC generation, the identification of potentially metastatic CTCs, and the mechanisms contributing to their heterogeneity and aggressiveness represent issues not yet fully deciphered. Thus, prior to enabling liquid biopsy applications to reach clinical prime time, understanding how the above mechanistic information can be applied to improve treatment decisions is a key challenge. Here, we provide our perspective on how CTCs can provide mechanistic insights into tumor pathogenesis, as well as on CTC clinical value. In doing so, we aim to (a) describe how CTCs disseminate from the primary tumor, and their link to epithelial-mesenchymal transition (EMT); (b) trace the route of CTCs through the circulation, focusing on tumor self-seeding and the possibility of tertiary metastasis; (c) describe possible mechanisms underlying the enhanced metastatic potential of CTCs; (d) discuss how CTC could provide further information on the tissue of origin, especially in cancer of unknown primary origin. We also provide a comprehensive review of meta-analyses assessing the prognostic significance of CTCs, to highlight the emerging role of CTCs in clinical oncology. We also explore how cell-free circulating tumor DNA (ctDNA) analysis, using a combination of genomic and phylogenetic analysis, can offer insights into CTC biology, including our understanding of CTC heterogeneity and tumor evolution. Last, we discuss emerging technologies, such as high-throughput quantitative imaging, radiogenomics, machine learning approaches, and the emerging breath biopsy. These technologies could compliment CTC and ctDNA analyses, and they collectively represent major future steps in cancer detection, monitoring, and management.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
- Department of Microbiology, University Hospital of Thessaly, Larissa, Greece
| | - Petros D Grivas
- Division of Oncology, Department of Medicine, University of Washington School of Medicine, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Nicholas A Romas
- Department of Urology, Columbia University Medical Center, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street-Bldg. 16, 11527, Athens, Greece.
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113
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Eslami-S Z, Cortés-Hernández LE, Alix-Panabières C. The Metastatic Cascade as the Basis for Liquid Biopsy Development. Front Oncol 2020; 10:1055. [PMID: 32850309 PMCID: PMC7396546 DOI: 10.3389/fonc.2020.01055] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
The metastatic cascade describes the process whereby aggressive cancer cells leave the primary tumor, travel through the bloodstream, and eventually reach distant organs to develop one or several metastases. During the last decade, innovative technologies have exploited the recent biological knowledge to identify new circulating biomarkers for the screening and early detection of cancer, real-time monitoring of treatment response, assessment of tumor relapse risk (prognosis), identification of new therapeutic targets and resistance mechanisms, patient stratification, and therapeutic decision-making. These techniques are broadly described using the term of Liquid Biopsy. This field is in constant progression and is based on the detection of circulating tumor cells, circulating free nucleic acids (e.g., circulating tumor DNA), circulating tumor-derived extracellular vesicles, and tumor-educated platelets. The aim of this review is to describe the biological principles underlying the liquid biopsy concept and to discuss how functional studies can expand the clinical applications of these circulating biomarkers.
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Affiliation(s)
- Zahra Eslami-S
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, UPRES EA2415, Montpellier, France
| | - Luis Enrique Cortés-Hernández
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, UPRES EA2415, Montpellier, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, UPRES EA2415, Montpellier, France
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114
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Palermo G, Lio GE, Esposito M, Ricciardi L, Manoccio M, Tasco V, Passaseo A, De Luca A, Strangi G. Biomolecular Sensing at the Interface between Chiral Metasurfaces and Hyperbolic Metamaterials. ACS APPLIED MATERIALS & INTERFACES 2020; 12:30181-30188. [PMID: 32551524 DOI: 10.1021/acsami.0c07415] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In recent times, biomolecular sensing to recognize genetic fragments and proteins is spurring unprecedented interest as a diagnostic protocol for cancer and infectious diseases. Significant efforts have been made to design nanomaterials able to control the light-matter interaction at the single nanometer scale, where genes and proteins bind specifically to receptors. Here, we numerically show how the interface between a chiral metasurface and hyperbolic metamaterials can enable both high sensitivity and specificity for low-molecular-weight nucleic acids and proteins. As we have recently reported, hyperbolic dispersion metamaterials allow molecular biorecognition with extreme sensitivity because of coupled and highly confined plasmon polaritons. Specificity is almost exclusively achieved by receptor-ligand interaction at the in-plane sensing surface. Interestingly, an adapted out-of-plane chiral metasurface enables three key functionalities of the hyperbolic metamaterial sensor. Computational effort reveals that helicoidal metasurfaces can act as (i) efficient diffractive elements to excite surface and bulk plasmon polaritons; (ii) out-of-plane sensing branches to reduce the diffusion limit and increase the sensing surface; and (iii) biorecognition assay also via circular dichroism and chiral selectivity.
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Affiliation(s)
- Giovanna Palermo
- Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende, CS, Italy
- CNR NANOTEC-Istituto di Nanotecnologia, UOS Cosenza, 87036 Rende, CS, Italy
| | - Giuseppe E Lio
- Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende, CS, Italy
- CNR NANOTEC-Istituto di Nanotecnologia, UOS Cosenza, 87036 Rende, CS, Italy
| | - Marco Esposito
- CNR NANOTEC-Istituto di Nanotecnologia, Polo di Nanotecnologia, Campus Ecotekne, Lecce, Italy
| | - Loredana Ricciardi
- CNR NANOTEC-Istituto di Nanotecnologia, UOS Cosenza, 87036 Rende, CS, Italy
| | - Mariachiara Manoccio
- CNR NANOTEC-Istituto di Nanotecnologia, Polo di Nanotecnologia, Campus Ecotekne, Lecce, Italy
| | - Vittorianna Tasco
- CNR NANOTEC-Istituto di Nanotecnologia, Polo di Nanotecnologia, Campus Ecotekne, Lecce, Italy
| | - Adriana Passaseo
- CNR NANOTEC-Istituto di Nanotecnologia, Polo di Nanotecnologia, Campus Ecotekne, Lecce, Italy
| | - Antonio De Luca
- Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende, CS, Italy
- CNR NANOTEC-Istituto di Nanotecnologia, UOS Cosenza, 87036 Rende, CS, Italy
| | - Giuseppe Strangi
- Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende, CS, Italy
- CNR NANOTEC-Istituto di Nanotecnologia, UOS Cosenza, 87036 Rende, CS, Italy
- Department of Physics, Case Western Reserve University, 10600 Euclid Avenue, Cleveland, Ohio 44106, United States
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115
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Lennon AM, Buchanan AH, Kinde I, Warren A, Honushefsky A, Cohain AT, Ledbetter DH, Sanfilippo F, Sheridan K, Rosica D, Adonizio CS, Hwang HJ, Lahouel K, Cohen JD, Douville C, Patel AA, Hagmann LN, Rolston DD, Malani N, Zhou S, Bettegowda C, Diehl DL, Urban B, Still CD, Kann L, Woods JI, Salvati ZM, Vadakara J, Leeming R, Bhattacharya P, Walter C, Parker A, Lengauer C, Klein A, Tomasetti C, Fishman EK, Hruban RH, Kinzler KW, Vogelstein B, Papadopoulos N. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science 2020; 369:eabb9601. [PMID: 32345712 PMCID: PMC7509949 DOI: 10.1126/science.abb9601] [Citation(s) in RCA: 327] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer treatments are often more successful when the disease is detected early. We evaluated the feasibility and safety of multicancer blood testing coupled with positron emission tomography-computed tomography (PET-CT) imaging to detect cancer in a prospective, interventional study of 10,006 women not previously known to have cancer. Positive blood tests were independently confirmed by a diagnostic PET-CT, which also localized the cancer. Twenty-six cancers were detected by blood testing. Of these, 15 underwent PET-CT imaging and nine (60%) were surgically excised. Twenty-four additional cancers were detected by standard-of-care screening and 46 by neither approach. One percent of participants underwent PET-CT imaging based on false-positive blood tests, and 0.22% underwent a futile invasive diagnostic procedure. These data demonstrate that multicancer blood testing combined with PET-CT can be safely incorporated into routine clinical care, in some cases leading to surgery with intent to cure.
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Affiliation(s)
- Anne Marie Lennon
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Medicine Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Isaac Kinde
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Andrew Warren
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | | | - Ariella T Cohain
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Fred Sanfilippo
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 100 Woodruff Circle Atlanta, GA 30322, USA
| | | | | | - Christian S Adonizio
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
- Geisinger Cancer Institute, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Hee Jung Hwang
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Kamel Lahouel
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Joshua D Cohen
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Aalpen A Patel
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Leonardo N Hagmann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Nirav Malani
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Shibin Zhou
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - David L Diehl
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Bobbi Urban
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Lisa Kann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Julie I Woods
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | | | | | | | | | - Carroll Walter
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Alex Parker
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Christoph Lengauer
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | - Alison Klein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biostatistics, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Elliot K Fishman
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Radiology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Ralph H Hruban
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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116
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Marples B, Kerns S. Oncology Scan: Radiation Biology and Genomic Predictors of Response. Int J Radiat Oncol Biol Phys 2020; 107:393-397. [PMID: 32531379 DOI: 10.1016/j.ijrobp.2020.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brian Marples
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York.
| | - Sarah Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York
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117
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Iliuk A, Wu X, Li L, Sun J, Hadisurya M, Boris RS, Tao WA. Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification. J Proteome Res 2020; 19:2563-2574. [PMID: 32396726 DOI: 10.1021/acs.jproteome.0c00151] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The invasive nature and the pain caused to patients inhibit the routine use of tissue biopsy-based procedures for cancer diagnosis and surveillance. The analysis of extracellular vesicles (EVs) from biofluids has recently gained significant traction in the liquid biopsy field. EVs offer an essential "snapshot" of their precursor cells in real time and contain an information-rich collection of nucleic acids, proteins, lipids, and so on. The analysis of protein phosphorylation, as a direct marker of cellular signaling and disease progression could be an important stepping stone to successful liquid biopsy applications. Here we introduce a rapid EV isolation method based on chemical affinity called EVtrap (extracellular vesicle total recovery and purification) for the EV phosphoproteomics analysis of human plasma. By incorporating EVtrap with high-performance mass spectrometry (MS), we were able to identify over 16 000 unique peptides representing 2238 unique EV proteins from just 5 μL of plasma sample, including most known EV markers, with substantially higher recovery levels compared with ultracentrifugation. Most importantly, more than 5500 unique phosphopeptides representing almost 1600 phosphoproteins in EVs were identified using only 1 mL of plasma. Finally, we carried out a quantitative EV phosphoproteomics analysis of plasma samples from patients diagnosed with chronic kidney disease or kidney cancer, identifying dozens of phosphoproteins capable of distinguishing disease states from healthy controls. The study demonstrates the potential feasibility of our robust analytical pipeline for cancer signaling monitoring by tracking plasma EV phosphorylation.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Jie Sun
- College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ronald S Boris
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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118
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Shang L, Wang Y, Cai L, Shu Y, Zhao Y. Structural color barcodes for biodiagnostics. VIEW 2020. [DOI: 10.1002/viw2.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Luoran Shang
- Zhongshan∼Xuhui Hospital, Institutes of Biomedical SciencesFudan University Shanghai China
- ENT Institute and Otorhinolaryngology Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyFudan University Shanghai China
- The Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical SciencesFudan University Shanghai China
- NHC Key Laboratory of Hearing MedicineFudan University Shanghai China
| | - Yuetong Wang
- Department of Clinical LaboratoryThe Affiliated Drum Tower Hospital of Nanjing University Medical School Nanjing China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast University Nanjing China
| | - Lijun Cai
- Department of Clinical LaboratoryThe Affiliated Drum Tower Hospital of Nanjing University Medical School Nanjing China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast University Nanjing China
| | - Yilai Shu
- ENT Institute and Otorhinolaryngology Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyFudan University Shanghai China
- NHC Key Laboratory of Hearing MedicineFudan University Shanghai China
| | - Yuanjin Zhao
- Department of Clinical LaboratoryThe Affiliated Drum Tower Hospital of Nanjing University Medical School Nanjing China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast University Nanjing China
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119
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Amini M, Ghorban K, Mokhtarzadeh A, Dadmanesh M, Baradaran B. CD40 DNA hypermethylation in primary gastric tumors; as a novel diagnostic biomarker. Life Sci 2020; 254:117774. [PMID: 32407843 DOI: 10.1016/j.lfs.2020.117774] [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: 04/08/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
AIMS Gastric cancer (GC) remains one of the deadliest malignancies worldwide due to its poor prognosis. DNA methylation changes, as an early event during tumor progression, constitute attractive markers for cancer diagnostics. In the current study, CD40 DNA methylation was investigated in GC as a novel epigenetic biomarker. MAIN METHODS We first analyzed DNA methylation microarrays from the Gene Expression Omnibus database on GC samples to evaluate the potential diagnostic value of CD40 methylation. Moreover, using q-MSP, in a set of internal samples including GC primary tumors and adjacent normal specimens, CD40 DNA methylation levels were determined. The Cancer Genome Atlas (TCGA) data on GC was also analyzed for further validation. KEY FINDINGS Our results illustrated significant CD40 hypermethylation in GC samples compared to normal specimens which was significantly correlated with the clinical stage of malignancy. Besides, the high accuracy of CD40 methylation as a diagnostic biomarker in GC was confirmed using the ROC curve analysis with an AUC value of 0.9089. Also, gene set enrichment analysis showed that CD40 is mainly involved in biological processes regulating immune response activation in GC. Further analysis of other prevalent cancer entities in TCGA showed that CD40 hypermethylation is a common event during tumor progression and could be considered as a potential biomarker for the detection of breast, colorectal, and prostate cancers as well. SIGNIFICANCE The finding of this study suggests that CD40 methylation as a potential pan biomarker could be a valuable target for liquid biopsy application of human cancers.
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Affiliation(s)
- Mohammad Amini
- Department of Immunology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
| | - Khodayar Ghorban
- Department of Immunology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Dadmanesh
- Department of Infectious Diseases, School of Medicine, Aja University of Medical Sciences, Tehran, Iran.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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120
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Faulkner E, Holtorf AP, Walton S, Liu CY, Lin H, Biltaj E, Brixner D, Barr C, Oberg J, Shandhu G, Siebert U, Snyder SR, Tiwana S, Watkins J, IJzerman MJ, Payne K. Being Precise About Precision Medicine: What Should Value Frameworks Incorporate to Address Precision Medicine? A Report of the Personalized Precision Medicine Special Interest Group. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2020; 23:529-539. [PMID: 32389217 DOI: 10.1016/j.jval.2019.11.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 06/11/2023]
Abstract
Precision medicine is a dynamic area embracing a diverse and increasing type of approaches that allow the targeting of new medicines, screening programs or preventive healthcare strategies, which include the use of biologic markers or complex tests driven by algorithms also potentially taking account of patient preferences. The International Society for Pharmacoeconomics and Outcome Research expanded its current work around precision medicine to (1) describe the evolving paradigm of precision medicine with examples of current and evolving applications, (2) describe key stakeholders perspectives on the value of precision medicine in their respective domains, and (3) define the core factors that should be considered in a value assessment framework for precision medicine. With the ultimate goal of improving health of well-defined patient groups, precision medicine will affect all stakeholders in the healthcare system at multiple levels spanning the individual perspective to the societal perspective. For an efficient, timely and practical precision medicine value assessment framework, it will be important to address these multiple perspectives through building consensus among the stakeholders for robust procedures and measures of value aspects, including performance of precision mechanism; aligned reimbursement processes of precision mechanism and subsequent treatment; transparent expectations for evidence requirements and study designs adequately matched to the intended use of the precision mechanism and to the smaller target patient populations; recognizing the potential range of value-generation such as ruling-in and ruling-out decisions.
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Affiliation(s)
- Eric Faulkner
- Evidera, Bethesda, MD, USA; University of North Carolina at Chapel Hill, Chapel Hill, NC; National Association of Managed Care Physicians, Glen Allen, VA, USA.
| | | | - Surrey Walton
- University of Illinois at Chicago, Chicago, IL, USA; Second City Outcomes Research, LLC, Chicago, IL, USA
| | | | - Hwee Lin
- National University of Singapore, Singapore
| | | | | | | | | | | | - Uwe Siebert
- University for Health Sciences, Medical Informatics, and Technology, Hall in Tirol, Austria; Harvard School of Public Health and Harvard Medical School, Boston, MA, USA; ONCOTYROL Center for Personalized Cancer Medicine, Innsbruck, Austria
| | | | | | | | - Maarten J IJzerman
- University of Melbourne Centre for Cancer Research, Parkville, Australia
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121
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Freeman S, Craddock C. Less Is Not Necessarily More: Toward a Rational Selection of the Conditioning Regimen in Acute Myeloid Leukemia. J Clin Oncol 2020; 38:1249-1251. [DOI: 10.1200/jco.19.03161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sylvie Freeman
- Institute of Infection and Immunity University of Birmingham, Edgbaston, Birmingham, United Kingdom
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Charles Craddock
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, United Kingdom
- Cancer Research UK Cancer Trials Unit, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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122
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Koo KM, Mainwaring PN. The role of circulating tumor DNA testing in breast cancer liquid biopsies: getting ready for prime time. BREAST CANCER MANAGEMENT 2020. [DOI: 10.2217/bmt-2020-0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Kevin M Koo
- XING Technologies Pty Ltd, 4073, Brisbane, QLD, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), 4072, Brisbane, QLD, Australia
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123
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Rashed WM, Maher E, Adel M, Saber O, Zaghloul MS. Pediatric diffuse intrinsic pontine glioma: where do we stand? Cancer Metastasis Rev 2020; 38:759-770. [PMID: 31802357 DOI: 10.1007/s10555-019-09824-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pediatric diffuse intrinsic pontine glioma (DIPG) represents approximately 20% of all pediatric CNS tumors. However, disease outcomes are dismal with a median survival of less than 1 year and a 2-year overall survival rate of less than 10%. Despite extensive efforts to improve survival outcomes, progress towards clinical improvement has been largely stagnant throughout the last 4 decades. Focal radiotherapy remains the standard of care with no promising single-agent alternatives and no evidence for improvement with the addition of a long list of systemic therapies. A better understanding of the biology of DIPG, though not easy due to obstacles in obtaining pathological material to study, is promising for the development of specific individualized treatment for this fatal disease. Recent studies have found epigenetic mutations to be successful predictors and prognostic factors for developing future management policies. The aim of this review is to give a global overview about the epidemiology, diagnosis, and treatment of DIPG. We further examine the controversial biopsy and autopsy issue that is unique to DIPG and assess the subsequent impact this issue has on the research efforts and clinical management of DIPG.
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Affiliation(s)
- Wafaa M Rashed
- Research Department, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt.
| | - Eslam Maher
- Research Department, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
| | - Mohamed Adel
- Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Ossama Saber
- Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Mohamed Saad Zaghloul
- Radiotherapy Department, National Cancer Institute, Cairo University & Children's Cancer Hospital, Cairo, 57357, Egypt.
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124
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Elkrief A, Joubert P, Florescu M, Tehfe M, Blais N, Routy B. Therapeutic landscape of metastatic non-small-cell lung cancer in Canada in 2020. ACTA ACUST UNITED AC 2020; 27:52-60. [PMID: 32218661 DOI: 10.3747/co.27.5953] [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] [Indexed: 12/18/2022]
Abstract
Lung cancer is the most commonly diagnosed cancer in Canada and remains associated with high mortality. Nevertheless, recent advances in the fields of immuno-oncology and precision medicine have led to significant improvements in clinical outcome in metastatic non-small-cell lung cancer (nsclc). Those improvements were facilitated by a greater understanding of the biologic classification of nsclc, which catalyzed discoveries of novel therapies. Here, we present a comprehensive review of the recent avalanche of practice-changing trials in metastatic nsclc, and we offer an approach to the management of this disease from a Canadian perspective. We begin with an overview of the pathologic and molecular characterization of metastatic nsclc. Next, we review the indications for currently approved immune checkpoint inhibitors, and we provide an approach to the management of disease with a driver mutation. Finally, we address future avenues in both diagnostics and therapeutics for patients with advanced and metastatic nsclc.
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Affiliation(s)
- A Elkrief
- Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Montreal.,Cedars Cancer Centre, McGill University Health Centre, Montreal.,Centre de recherche du Centre hospitalier de l'Universtité de Montréal, Montreal
| | - P Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City
| | - M Florescu
- Centre de recherche du Centre hospitalier de l'Universtité de Montréal, Montreal.,Division of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC
| | - M Tehfe
- Centre de recherche du Centre hospitalier de l'Universtité de Montréal, Montreal.,Division of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC
| | - N Blais
- Centre de recherche du Centre hospitalier de l'Universtité de Montréal, Montreal.,Division of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC
| | - B Routy
- Centre de recherche du Centre hospitalier de l'Universtité de Montréal, Montreal.,Division of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC
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125
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Chatani PD, Agarwal SK, Sadowski SM. Molecular Signatures and Their Clinical Utility in Pancreatic Neuroendocrine Tumors. Front Endocrinol (Lausanne) 2020; 11:575620. [PMID: 33537001 PMCID: PMC7848028 DOI: 10.3389/fendo.2020.575620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022] Open
Abstract
Pancreatic neuroendocrine tumors (PNETs) are classified based on their histologic differentiation and proliferative indices, which have been used extensively to determine prognosis. Advances in next-generation sequencing and other high-throughput techniques have allowed researchers to objectively explore tumor specimens and learn about the genetic alterations associated with malignant transformation in PNETs. As a result, targeted, pathway-specific therapies have been emerging for the treatment of unresectable and metastatic disease. As we continue to trial various pharmaceutical products, evidence from studies using multi-omics approaches indicates that clinical aggressiveness stratifies along other genotypic and phenotypic demarcations, as well. In this review, we explore the clinically relevant and potentially targetable molecular signatures of PNETs, their associated trials, and the overall differences in reported prognoses and responses to existing therapies.
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Affiliation(s)
- Praveen Dilip Chatani
- Endocrine Surgery Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sunita Kishore Agarwal
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Samira Mercedes Sadowski
- Endocrine Surgery Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Samira Mercedes Sadowski,
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126
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Abstract
The concept of precision oncology is straightforward, but the actual results of treating advanced cancer patients with the targeted drug suggested by genomic analysis have been generally disappointing, indicating that this approach is not yet ready for routine clinical practice. A number of possible improvements can and will be tested by additional clinical trials.
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Affiliation(s)
- Bertrand Jordan
- UMR 7268 ADÉS, Aix-Marseille, Université/EFS/CNRS ; CoReBio PACA, case 901, Parc scientifique de Luminy, 13288 Marseille Cedex 09, France
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127
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Detecting TP53 mutations in diagnostic and archival liquid-based Pap samples from ovarian cancer patients using an ultra-sensitive ddPCR method. Sci Rep 2019; 9:15506. [PMID: 31664085 PMCID: PMC6820715 DOI: 10.1038/s41598-019-51697-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 10/07/2019] [Indexed: 12/14/2022] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is the most common subtype of epithelial ovarian cancer and early detection is challenging. TP53 mutations are a hallmark of HGSOC and detection of these mutations in liquid-based Pap samples could provide a method for early diagnosis. Here we evaluate the use of IBSAFE, an ultra-sensitive droplet digital PCR (ddPCR) method, for detecting TP53 mutations in liquid-based Pap samples collected from fifteen women at the time of diagnosis (diagnostic samples) and/or up to seven years prior to diagnosis (archival samples). We analysed tumours for somatic TP53 mutations with next generation sequencing and were able to detect the corresponding mutations in diagnostic samples from six of eight women, while one patient harboured a germline mutation. We further detected a mutation in an archival sample obtained 20 months prior to the ovarian cancer diagnosis. The custom designed IBSAFE assays detected minor allele frequencies (MAFs) with very high assay sensitivity (MAF = 0.0068%) and were successful despite low DNA abundance (0.17–206.14 ng, median: 17.27 ng). These results provide support for further evaluation of archival liquid-based Pap samples for diagnostic purposes and demonstrate that ultra-sensitive ddPCR should be evaluated for ovarian cancer screening in high-risk groups or in the recurrent setting.
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