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O'Shaughnessy KL, Sasser AL, Bell KS, Riutta C, Ford JL, Grindstaff RD, Gilbert ME. Bypassing the brain barriers: upregulation of serum miR-495 and miR-543-3p reflects thyroid-mediated developmental neurotoxicity in the rat. Toxicol Sci 2024; 198:128-140. [PMID: 38070162 DOI: 10.1093/toxsci/kfad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Evaluating the neurodevelopmental effects of thyroid-disrupting chemicals is challenging. Although some standardized developmental and reproductive toxicity studies recommend serum thyroxine (T4) measures in developing rats, extrapolating between a serum T4 reduction and neurodevelopmental outcomes is not straightforward. Previously, we showed that the blood-brain and blood-cerebrospinal fluid barriers may be affected by developmental hypothyroidism in newborn rats. Here, we hypothesized that if the brain barriers were functionally disturbed by abnormal thyroid action, then small molecules may escape from the brain tissue and into general circulation. These small molecules could then be identified in blood samples, serving as a direct readout of thyroid-mediated developmental neurotoxicity. To address these hypotheses, pregnant rats were exposed to propylthiouracil (PTU, 0 or 3 ppm) to induce thyroid hormone insufficiency, and dams were permitted to give birth. PTU significantly reduced serum T4 in postnatal offspring. Consistent with our hypothesis, we show that tight junctions of the brain barriers were abnormal in PTU-exposed pups, and the blood-brain barrier exhibited increased permeability. Next, we performed serum microRNA Sequencing (miRNA-Seq) to identify noncoding RNAs that may reflect these neurodevelopmental disturbances. Of the differentially expressed miRNAs identified, 7 were upregulated in PTU-exposed pups. Validation by qRT-PCR shows that miR-495 and miR-543-3p were similarly upregulated in males and females. Interestingly, these miRNAs have been linked to cell junction dysfunction in other models, paralleling the identified abnormalities in the rat brain. Taken together, these data show that miR-495 and miR-543-3p may be novel in vivo biomarkers of thyroid-mediated developmental neurotoxicity.
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Affiliation(s)
- Katherine L O'Shaughnessy
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Aubrey L Sasser
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, USA
| | - Kiersten S Bell
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, USA
| | - Cal Riutta
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, USA
| | - Jermaine L Ford
- Chemical Characterization and Exposure Division, Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Rachel D Grindstaff
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Mary E Gilbert
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
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MicroRNAs miR-584-5p and miR-425-3p Are Up-Regulated in Plasma of Colorectal Cancer (CRC) Patients: Targeting with Inhibitor Peptide Nucleic Acids Is Associated with Induction of Apoptosis in Colon Cancer Cell Lines. Cancers (Basel) 2022; 15:cancers15010128. [PMID: 36612125 PMCID: PMC9817681 DOI: 10.3390/cancers15010128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Liquid biopsy has dramatically changed cancer management in the last decade; however, despite the huge number of miRNA signatures available for diagnostic or prognostic purposes, it is still unclear if dysregulated miRNAs in the bloodstream could be used to develop miRNA-based therapeutic approaches. In one author's previous work, nine miRNAs were found to be dysregulated in early-stage colon cancer (CRC) patients by NGS analysis followed by RT-dd-PCR validation. In the present study, the biological effects of the targeting of the most relevant dysregulated miRNAs with anti-miRNA peptide nucleic acids (PNAs) were verified, and their anticancer activity in terms of apoptosis induction was evaluated. Our data demonstrate that targeting bloodstream up-regulated miRNAs using anti-miRNA PNAs leads to the down-regulation of target miRNAs associated with inhibition of the activation of the pro-apoptotic pathway in CRC cellular models. Moreover, very high percentages of apoptotic cells were found when the anti-miRNA PNAs were associated with other pro-apoptotic agents, such as sulforaphane (SFN). The presented data sustain the idea that the targeting of miRNAs up-regulated in the bloodstream with a known role in tumor pathology might be a tool for the design of protocols for anti-tumor therapy based on miRNA-targeting molecules.
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Affiliation(s)
- Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
| | | | | | | | | | | | | | | | | | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
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4
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Ultrahigh sensitive and selective detection of single nucleotide polymorphism using peptide nucleic acid and ribonuclease H assembled DNA amplification (PRADA). Anal Chim Acta 2022; 1233:340423. [DOI: 10.1016/j.aca.2022.340423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/06/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
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Basic Science with Preclinical Models to Investigate and Develop Liquid Biopsy: What Are the Available Data and Is It a Fruitful Approach? Int J Mol Sci 2022; 23:ijms23105343. [PMID: 35628154 PMCID: PMC9141279 DOI: 10.3390/ijms23105343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular analysis of circulating analytes (circulating tumor-DNA (ctDNA), -cells (CTCs) and -RNA (ctRNA)/exosomes) deriving from solid tumors and detected in the bloodstream—referred as liquid biopsy—has emerged as one of the most promising concepts in cancer management. Compelling data have evidenced its pivotal contribution and unique polyvalence through multiple applications. These data essentially derived from translational research. Therewith, data on liquid biopsy in basic research with preclinical models are scarce, a concerning lack that has been widely acknowledged in the field. This report aimed to comprehensively review the available data on the topic, for each analyte. Only 17, 17 and 2 studies in basic research investigated ctDNA, CTCs and ctRNA/exosomes, respectively. Albeit rare, these studies displayed noteworthy relevance, demonstrating the capacity to investigate questions related to the biology underlying analytes release that could not be explored via translational research with human samples. Translational, clinical and technological sectors of liquid biopsy may benefit from basic research and should take note of some important findings generated by these studies. Overall, results underscored the need to intensify the efforts to conduct future studies on liquid biopsy in basic research with new preclinical models.
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de Freitas AJA, Causin RL, Varuzza MB, Hidalgo Filho CMT, da Silva VD, Souza CDP, Marques MMC. Molecular Biomarkers Predict Pathological Complete Response of Neoadjuvant Chemotherapy in Breast Cancer Patients: Review. Cancers (Basel) 2021; 13:cancers13215477. [PMID: 34771640 PMCID: PMC8582511 DOI: 10.3390/cancers13215477] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Breast cancer is the most common cancer in women worldwide. Although many studies have aimed to understand the genetic basis of breast cancer, leading to increasingly accurate diagnoses, only a few molecular biomarkers are used in clinical practice to predict response to therapy. Current studies aim to develop more personalized therapies to decrease the adverse effects of chemotherapy. Personalized medicine not only requires clinical, but also molecular characterization of tumors, which allows the use of more effective drugs for each patient. The aim of this study was to identify potential molecular biomarkers that can predict the response to therapy after neoadjuvant chemotherapy in patients with breast cancer. In this review, we summarize genomic, transcriptomic, and proteomic biomarkers that can help predict the response to therapy. Abstract Neoadjuvant chemotherapy (NAC) is often used to treat locally advanced disease for tumor downstaging, thus improving the chances of breast-conserving surgery. From the NAC response, it is possible to obtain prognostic information as patients may reach a pathological complete response (pCR). Those who do might have significant advantages in terms of survival rates. Breast cancer (BC) is a heterogeneous disease that requires personalized treatment strategies. The development of targeted therapies depends on identifying biomarkers that can be used to assess treatment efficacy as well as the discovery of new and more accurate therapeutic agents. With the development of new “OMICS” technologies, i.e., genomics, transcriptomics, and proteomics, among others, the discovery of new biomarkers is increasingly being used in the context of clinical practice, bringing us closer to personalized management of BC treatment. The aim of this review is to compile the main biomarkers that predict pCR in BC after NAC.
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Affiliation(s)
- Ana Julia Aguiar de Freitas
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, SP, Brazil; (A.J.A.d.F.); (R.L.C.); (M.B.V.)
| | - Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, SP, Brazil; (A.J.A.d.F.); (R.L.C.); (M.B.V.)
| | - Muriele Bertagna Varuzza
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, SP, Brazil; (A.J.A.d.F.); (R.L.C.); (M.B.V.)
| | | | | | | | - Márcia Maria Chiquitelli Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, SP, Brazil; (A.J.A.d.F.); (R.L.C.); (M.B.V.)
- Barretos School of Health Sciences, Dr. Paulo Prata–FACISB, Barretos 14785-002, SP, Brazil
- Correspondence: ; Tel.: +55-17-3321-6600 (ext. 7057)
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Selvaraj M, Greco P, Sensi M, Saygin GD, Bellassai N, D'Agata R, Spoto G, Biscarini F. Label free detection of miRNA-21 with electrolyte gated organic field effect transistors (EGOFETs). Biosens Bioelectron 2021; 182:113144. [PMID: 33799026 DOI: 10.1016/j.bios.2021.113144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 10/21/2022]
Abstract
We report a dual gate/common channel organic transistor architecture designed for quantifying the concentration of one of the strands of miRNA-21 in solution. The device allows one to measure the differential response between two gate electrodes, viz. one sensing and one reference, both immersed in the electrolyte above the transistor channel. Hybridization with oligonucleotide in the picomolar regime induces a sizable reduction of the current flowing through the transistor channel. The device signal is reported at various gate voltages, showing maximum sensitivity in the sublinear regime, with a limit of detection as low as 35 pM. We describe the dose curves with an analytical function derived from a thermodynamic model of the reaction equilibria relevant in our experiment and device configuration, and we show that the apparent Hill dependence on analyte concentration, whose exponent lies between 0.5 and 1, emerges from the interplay of the different equilibria. The binding free energy characteristic of the hybridization on the device surface is found to be approximately 20% lower with respect to the reaction in solution, hinting to partially inhibiting effect of the surface and presence of competing reactions. Impedance spectroscopy and surface plasmon resonance (SPR) performed on the same oligonucleotide pair were correlated to the electronic current transduced by the EGOFET, and confirmed the selectivity of the biorecognition probe covalently bound on the gold surface.
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Affiliation(s)
- Meenu Selvaraj
- Scriba Nanotecnologie s.r.l., Via di Corticella 183/8, I-40128, Bologna, Italy; Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Pierpaolo Greco
- Department of Life Sciences, Università, Degli Studi di Modena e Reggio Emilia, Via Campi 103, I-41125, Modena, Italy.
| | - Matteo Sensi
- Department of Life Sciences, Università, Degli Studi di Modena e Reggio Emilia, Via Campi 103, I-41125, Modena, Italy
| | - Gulseren Deniz Saygin
- Scriba Nanotecnologie s.r.l., Via di Corticella 183/8, I-40128, Bologna, Italy; Department of Physics, Informatics and Mathematics, Università, Degli Studi di Modena e Reggio Emilia, Via Campi 103, I-41125, Modena, Italy
| | - Noemi Bellassai
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Roberta D'Agata
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Giuseppe Spoto
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, I-95125, Catania, Italy
| | - Fabio Biscarini
- Department of Life Sciences, Università, Degli Studi di Modena e Reggio Emilia, Via Campi 103, I-41125, Modena, Italy; Center for Translational Neurophysiology - Istituto Italiano di Tecnologia, Via Fossato di Mortara 17-19, I-44100, Ferrara, Italy
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8
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Labgaa I, von Felden J, Craig AJ, Martins-Filho SN, Villacorta-Martin C, Demartines N, Dormond O, D'Avola D, Villanueva A. Experimental Models of Liquid Biopsy in Hepatocellular Carcinoma Reveal Clone-Dependent Release of Circulating Tumor DNA. Hepatol Commun 2021; 5:1095-1105. [PMID: 34141992 PMCID: PMC8183169 DOI: 10.1002/hep4.1692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 01/12/2023] Open
Abstract
Liquid biopsy, the molecular analysis of tumor components released into the bloodstream, has emerged as a noninvasive and resourceful means to access genomic information from cancers. Most data derived from translational studies showcase its numerous potential clinical applications. However, data from experimental models are scarce, and little is known about the underlying mechanisms and factors controlling the release of circulating tumor DNA (ctDNA) and cells (CTCs). This study aimed to model liquid biopsy in hepatocellular carcinoma xenografts and to study the dynamics of release of ctDNA and CTCs; this included models of intratumoral heterogeneity (ITH) and metastatic disease. We quantified ctDNA by quantitative polymerase chain reaction (PCR) targeting human long interspersed nuclear element group 1; targeted mutation analysis was performed with digital droplet PCR. CTCs were traced by flow cytometry. Results demonstrated the feasibility of detecting ctDNA, including clone-specific mutations, as well as CTCs in blood samples of mice. In addition, the concentration of ctDNA and presence of tumor-specific mutations reflected tumor progression, and detection of CTCs was associated with metastases. Our ITH model suggested differences in the release of DNA fragments impacted by the cell-clone origin and the treatment. Conclusion: These data present new models to study liquid biopsy and its underlying mechanisms and highlighted a clone-dependent release of ctDNA into the bloodstream.
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Affiliation(s)
- Ismail Labgaa
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Department of Visceral SurgeryLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Johann von Felden
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,1. Department of Internal MedicineUniversity Medical Center Hamburg EppendorfHamburgGermany
| | - Amanda J Craig
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Liver Cancer ProgramCenter for Cancer ResearchNational Cancer InstituteBethesdaMDUSA
| | - Sebastiao N Martins-Filho
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Department of Pathology and Laboratory MedicineUniversity Health NetworkUniversity of TorontoTorontoONCanada.,Departamento de PatologiaFaculdade de Medicina da Universidade de São PauloUniversidade de São PauloSão PauloBrazil
| | - Carlos Villacorta-Martin
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Center for Regenerative MedicineBoston University and Boston Medical CenterBostonMAUSA
| | - Nicolas Demartines
- Department of Visceral SurgeryLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Olivier Dormond
- Department of Visceral SurgeryLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Delia D'Avola
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Liver UnitClinica Universidad de NavarraPamplonaSpain.,Liver UnitClinica Universidad de NavarraMadridSpain.,Centro de Investigacion Biomédica en Red de Enfermedades Hepáticas y DigestivasPamplonaSpain
| | - Augusto Villanueva
- Division of Liver DiseasesLiver Cancer ProgramTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNYUSA.,Division of Hematology/OncologyDepartment of MedicineIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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9
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Labgaa I, Villanueva A, Dormond O, Demartines N, Melloul E. The Role of Liquid Biopsy in Hepatocellular Carcinoma Prognostication. Cancers (Basel) 2021; 13:cancers13040659. [PMID: 33562173 PMCID: PMC7914891 DOI: 10.3390/cancers13040659] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is one of the deadliest cancer. Clinical guidelines for the management of HCC endorse algorithms deriving from clinical variables whose performances to prognosticate HCC is limited. Liquid biopsy is the molecular analysis of tumor by-products released into the bloodstream. It offers minimally-invasive access to circulating analytes like DNA, RNA, exosomes and cells. This technology demonstrated promising results for various applications in cancers, including prognostication. This review aimed to provide a comprehensive overview of the contribution of liquid biopsy in HCC prognostication. The results suggested that liquid biopsy may be a polyvalent and valuable tool to prognosticate HCC. Abstract Showing a steadily increasing cancer-related mortality, the epidemiological evolution of hepatocellular carcinoma (HCC) is concerning. Numerous strategies have attempted to prognosticate HCC but their performance is modest; this is partially due to the heterogeneous biology of this cancer. Current clinical guidelines endorse classifications and scores that use clinical variables, such as the Barcelona Clinic Liver Cancer (BCLC) classification. These algorithms are unlikely to fully recapitulate the genomic complexity of HCC. Integrating molecular readouts on a patient-basis, following a precision-medicine perspective, might be an option to refine prognostic systems. The limited access to HCC tissue samples is an important limitation to these approaches but it could be partially circumvented by using liquid biopsy. This concept consists of the molecular analysis of products derived from a solid tumor and released into biological fluids, mostly into the bloodstream. It offers an easy and minimally-invasive access to DNA, RNA, extracellular vesicles and cells that can be analyzed with next-generation sequencing (NGS) technologies. This review aims to investigate the potential contributions of liquid biopsy in HCC prognostication. The results identified prognostic values for each of the components of liquid biopsy, suggesting that this technology may help refine HCC prognostication.
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Affiliation(s)
- Ismail Labgaa
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
| | - Augusto Villanueva
- Division of Liver Diseases, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olivier Dormond
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
| | - Nicolas Demartines
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
- Correspondence:
| | - Emmanuel Melloul
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
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10
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Shenoy GN, Greene CJ, Bhatta M, Baroja ML, Loyall JL, Balu‐Iyer SV, Kelleher RJ, Carreno BM, Linette GP, Shultz LD, Bankert RB. Preclinical evaluation of cancer immune therapy using patient-derived tumor antigen-specific T cells in a novel xenograft platform. Clin Transl Immunology 2021; 10:e1246. [PMID: 33552509 PMCID: PMC7853904 DOI: 10.1002/cti2.1246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/16/2020] [Accepted: 01/09/2021] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES With a rapidly growing list of candidate immune-based cancer therapeutics, there is a critical need to generate highly reliable animal models to preclinically evaluate the efficacy of emerging immune-based therapies, facilitating successful clinical translation. Our aim was to design and validate a novel in vivo model (called Xenomimetic or 'X' mouse) that allows monitoring of the ability of human tumor-specific T cells to suppress tumor growth following their entry into the tumor. METHODS Tumor xenografts are established rapidly in the greater omentum of globally immunodeficient NOD-scid IL2Rγnull (NSG) mice following an intraperitoneal injection of melanoma target cells expressing tumor neoantigen peptides, as well as green fluorescent protein and/or luciferase. Changes in tumor burden, as well as in the number and phenotype of adoptively transferred patient-derived tumor neoantigen-specific T cells in response to immunotherapy, are measured by imaging to detect fluorescence/luminescence and flow cytometry, respectively. RESULTS The tumors progress rapidly and disseminate in the mice unless patient-derived tumor-specific T cells are introduced. An initial T cell-mediated tumor arrest is later followed by a tumor escape, which correlates with the upregulation of the checkpoint molecules programmed cell death-1 (PD-1) and lymphocyte-activation gene 3 (LAG3) on T cells. Treatment with immune-based therapies that target these checkpoints, such as anti-PD-1 antibody (nivolumab) or interleukin-12 (IL-12), prevented or delayed the tumor escape. Furthermore, IL-12 treatment suppressed PD-1 and LAG3 upregulation on T cells. CONCLUSION Together, these results validate the X-mouse model and establish its potential to preclinically evaluate the therapeutic efficacy of immune-based therapies.
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Affiliation(s)
- Gautam N Shenoy
- Department of Microbiology and Immunology at the Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNYUSA
| | - Christopher J Greene
- Department of Microbiology and Immunology at the Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNYUSA,Present address:
Hodgson Russ LLP.BuffaloNYUSA
| | - Maulasri Bhatta
- Immune Modulatory Therapies, LLCEdenNYUSA,Present address:
Roswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Miren L Baroja
- Center for Cellular ImmunotherapiesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Jenni L Loyall
- Department of Microbiology and Immunology at the Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNYUSA
| | - Sathy V Balu‐Iyer
- Department of Pharmaceutical SciencesUniversity at BuffaloBuffaloNYUSA
| | - Raymond J Kelleher
- Department of Microbiology and Immunology at the Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNYUSA
| | - Beatriz M Carreno
- Center for Cellular ImmunotherapiesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Gerald P Linette
- Center for Cellular ImmunotherapiesPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | | | - Richard B Bankert
- Department of Microbiology and Immunology at the Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNYUSA
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11
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Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients. Biosens Bioelectron 2020; 170:112648. [PMID: 33010708 DOI: 10.1016/j.bios.2020.112648] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/01/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
RAS mutations in the blood of colorectal cancer (CRC) patients are emerging as biomarkers of acquired resistance to Epidermal Growth Factor Receptor therapy. Unfortunately, reliable assays granting fast, real-time monitoring of treatment response, capable of refining retrospective, tissue-based analysis, are still needed. Recently, several methods for detecting blood RAS mutations have been proposed, generally relying on multi-step and PCR-based, time-consuming and cost-ineffective procedures. By exploiting a liquid biopsy approach, we developed an ultrasensitive nanoparticle-enhanced plasmonic method for detecting ~1 aM RAS single nucleotide variants (SNVs) in the plasma of CRC patients. The assay does not require the extraction of tumor DNA from plasma and detects it in volumes as low as 40 μL of plasma, which is at least an order of magnitude smaller than that required by state of the art liquid biopsy technologies. The most prevalent RAS mutations are detected in DNA from tumor tissue with 100% sensitivity and 83.33% specificity. Spike-in experiments in human plasma further encouraged assay application on clinical specimens. The assay was proven in plasma from CRC patients and healthy donors, and full discrimination between mutated DNA from patients over wild-type DNA from healthy volunteers was obtained thus demonstrating its promising avenue for cancer monitoring based on liquid biopsy.
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12
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Gasparello J, Papi C, Allegretti M, Giordani E, Carboni F, Zazza S, Pescarmona E, Romania P, Giacomini P, Scapoli C, Gambari R, Finotti A. A Distinctive microRNA (miRNA) Signature in the Blood of Colorectal Cancer (CRC) Patients at Surgery. Cancers (Basel) 2020; 12:cancers12092410. [PMID: 32854257 PMCID: PMC7564483 DOI: 10.3390/cancers12092410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Liquid biopsy (LB) provides an examination of the peripheral blood of cancer patients for circulating tumor cells, cell-free nucleic acids and microRNAs (miRNAs) and is an established tool of precision medicine. Unlike most previous LB studies that focused on advanced metastatic colorectal cancer (CRC), we assessed miRNA dysregulation in blood samples obtained on the day of surgery from patients with primary CRC lesions but no clinical evidence of extra-colonic diffusion. In this study, plasma preparation included miRNAs associated to exosomes, but excluded large macrovesicles from the preparation. Methods: The miRNA profile in plasma isolated from a cohort of 35 CRC patients at the day of surgery was analyzed by Next Generation Sequencing (NGS) and further confirmed by droplet digital RT-PCR (dd-RT-PCR). Results: A miR-141-3p/miR-221-3p/miR-222-3p upregulation signature previously described in advanced CRC did not discriminate the analyzed early-CRC cohort from six tumor-free donors (Tf-D). In contrast, NGS-based miRNome analysis of a training cohort of five CRC and three tumor-free donors identified a novel, distinct nine miRNA signature comprising five up-regulated and four down-regulated miRNAs, six of which could be confirmed in the full CRC and tumor-free donor validation dataset by dd-RT-PCR. Additionally, a KRAS (Kirsten Rat Sarcoma Viral Oncogene Homolog) mutant status was correlated with the plasma content of three identified miRNAs. Conclusions: When the data obtained were comparatively evaluated, at least one of the miRNAs belonging to the signature list was found to be dysregulated in 34/35 (97.1%) of our early-CRC plasma samples. The miRNA list provides diagnostic markers as well as possible molecular targets for protocols focusing on “microRNA therapeutics”.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Chiara Papi
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Matteo Allegretti
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Elena Giordani
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Fabio Carboni
- Digestive Surgery, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.C.); (S.Z.)
| | - Settimio Zazza
- Digestive Surgery, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.C.); (S.Z.)
| | - Edoardo Pescarmona
- Pathology, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Paolo Romania
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Patrizio Giacomini
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
- Correspondence: (R.G.); (A.F.); Tel.: +39-0532-974443 (R.G.); +39-0532-974510 (A.F.); Fax: +39-0532-974500 (R.G. & A.F.)
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
- Correspondence: (R.G.); (A.F.); Tel.: +39-0532-974443 (R.G.); +39-0532-974510 (A.F.); Fax: +39-0532-974500 (R.G. & A.F.)
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A self-powered bidirectional partition microfluidic chip with embedded microwells for highly sensitive detection of EGFR mutations in plasma of non-small cell lung cancer patients. Talanta 2020; 220:121426. [PMID: 32928434 DOI: 10.1016/j.talanta.2020.121426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker for tumor genotyping and therapy monitoring. Herein, we developed a digital PCR chip with embedded microwell and bidirectional partition network for highly sensitive ctDNA analysis. The embedded microwell contributes to increasing microreaction density (up to 7000 microwells/cm2) and reducing evaporation during amplification. The bidirectional partition network can achieve fast and random distribution of targets, ensuring the precise quantification of nucleic acid. We used plasmids, artificial samples and 32 clinical blood samples from non-small cell lung cancer patients to test the performance of this platform. The results demonstrated that our chip has not only comparable quantification performance to commercial counterpart but also the ability to detect EGFR mutations with as low as 0.01% mutation rate and 20 alter molecules in 27 ng genomic DNA. The identification of EGFR mutations in plasma using developed chip exhibited 85.71% sensitivity and 94.44% specificity for L858R mutation and 100% sensitivity and 86.96% specificity for T790 M mutation. Moreover, the monitoring of mutant allele in plasma was accomplished in this work. In conclusion, the developed chip has a potential in lung tumor genotyping and therapy monitoring for precision medicine, even other tumors.
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García-Olmo D, Olmedillas-López S, Cortés-Guiral D, Villarejo P, López Rojo I, Guadalajara H, García Gómez-Heras S, García-Arranz M. The role of mucin cell-free DNA detection as a new marker for the study of acellular pseudomyxoma peritonei of appendicular origin by liquid biopsy. Ther Adv Med Oncol 2020; 12:1758835920928233. [PMID: 32636940 PMCID: PMC7318819 DOI: 10.1177/1758835920928233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Acellular pseudomyxoma peritonei (aPMP) is a rare peritoneal malignancy characterized by the accumulation of large amounts of mucin (lacking tumor cells) in the peritoneum. Many cases account for several kilograms of mucin to be screened by the pathologist. This is a comprehensive study of three patients with aPMP, whose tumors showed KRAS mutation, allowing for the tracking of this marker by liquid biopsy. Methods: Pre and post-surgery plasma, and mucin removed during cytoreductive surgery were collected from the patients. KRAS mutations were analyzed using droplet digital polymerase chain reaction (ddPCR). Mucin was injected in mice. KRAS and cytokine levels were measured in plasma of the mice using ddPCR and a magnetic bead-based assay. Mucin microbiome was analyzed by 16S rRNA sequencing. Results: KRAS mutations were detected in mucin cell-free DNA (cfDNA) from the three patients but not in the pre or post-surgery plasma. Electron microscopy detected microparticles (diameter <0.4 µm) in mucin. Mucin from one patient grew up inside the peritoneal cavity of mice and human KRAS was identified in mucin cfDNA, but not in plasma. All mucins showed the same bacterial profile. Cytokine levels were slightly altered in mice. Conclusions: The three aPMP patients included in this study shared some common aspects: the absence of tumor cells in mucin, the presence of KRAS mutated cfDNA in mucin, and the absence of this tumor-derived mutation in the bloodstream, providing additional information to the routine pathological examinations and suggesting that mucin cfDNA could potentially play a role in aPMP recurrence and prognosis.
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Affiliation(s)
- Damián García-Olmo
- Chief of the Department of Surgery, New Therapies Laboratory,Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, Madrid, 28040, Spain
| | - Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
| | - Delia Cortés-Guiral
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Pedro Villarejo
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Irene López Rojo
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Héctor Guadalajara
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | | | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
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Gasparello J, Gambari L, Papi C, Rozzi A, Manicardi A, Corradini R, Gambari R, Finotti A. High Levels of Apoptosis Are Induced in the Human Colon Cancer HT-29 Cell Line by Co-Administration of Sulforaphane and a Peptide Nucleic Acid Targeting miR-15b-5p. Nucleic Acid Ther 2020; 30:164-174. [DOI: 10.1089/nat.2019.0825] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Laura Gambari
- Laboratorio RAMSES, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Chiara Papi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Rozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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16
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Allegretti M, Cottone G, Carboni F, Cotroneo E, Casini B, Giordani E, Amoreo CA, Buglioni S, Diodoro M, Pescarmona E, Zazza S, Federici O, Zeuli M, Conti L, Cigliana G, Fiorentino F, Valle M, Giacomini P, Spinella F. Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:69. [PMID: 32312295 PMCID: PMC7168847 DOI: 10.1186/s13046-020-01569-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid biopsy (LB) in early-stage, non-metastatic colorectal cancer (CRC) must be sensitive enough to detect extremely low circulating tumor DNA (ctDNA) levels. This challenge has been seldom and non-systematically investigated. METHODS Next generation sequencing (NGS) and digital PCR (dPCR) were combined to test tumor DNAs (tDNAs) and paired ctDNAs collected at surgery from 39 patients, 12 of whom were also monitored during the immediate post-surgery follow up. Patients treated for metastatic disease (n = 14) were included as controls. RESULTS NGS and dPCR concordantly (100% agreement) called at least one single nucleotide variant (SNV) in 34 tDNAs, estimated differences in allelic frequencies being negligible (±1.4%). However, despite dPCR testing, SNVs were only detectable in 15/34 (44.1%) ctDNAs from patients at surgery, as opposed to 14/14 (100%) metastatic patients. This was likely due to striking differences (average 10 times, up to 500) in ctDNA levels between groups. NGS revealed blood-only SNVs, suggesting spatial heterogeneity since pre-surgery disease stages, and raising the combined NGS/dPCR sensitivity to 58.8%. ctDNA levels at surgery correlated with neither tumor size, stage, grade, or nodal status, nor with variant abundance in paired tDNA. LB sensitivity reached 63.6% when ctDNA was combined with CEA. Finally, persistence and absence of ctDNA on the first conventional (month 3) post-surgery follow-up were associated with fast relapse and a disease-free status in 3 and 7 patients, respectively. CONCLUSIONS A simple clinical NGS/dPCR/CEA combination effectively addresses the LB challenge in a fraction of non-metastatic CRC patients.
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Affiliation(s)
- Matteo Allegretti
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144, Rome, Italy
| | - Giuliano Cottone
- Oncogenomics Division, Eurofins Genoma Group, Via Castel Giubileo, 11, 00138, Rome, Italy
| | - Fabio Carboni
- Digestive Surgery, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Ettore Cotroneo
- Oncogenomics Division, Eurofins Genoma Group, Via Castel Giubileo, 11, 00138, Rome, Italy
| | - Beatrice Casini
- Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Elena Giordani
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144, Rome, Italy
| | | | | | - Maria Diodoro
- Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Settimio Zazza
- Digestive Surgery, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Orietta Federici
- Digestive Surgery, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Massimo Zeuli
- Medical Oncology 1, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Laura Conti
- Clinical Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Cigliana
- Clinical Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Fiorentino
- Oncogenomics Division, Eurofins Genoma Group, Via Castel Giubileo, 11, 00138, Rome, Italy
| | - Mario Valle
- Digestive Surgery, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144, Rome, Italy.
| | - Francesca Spinella
- Oncogenomics Division, Eurofins Genoma Group, Via Castel Giubileo, 11, 00138, Rome, Italy.
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17
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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18
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Wang YM, Trinh MP, Zheng Y, Guo K, Jimenez LA, Zhong W. Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner. Trends Analyt Chem 2019; 117:242-262. [PMID: 32292220 PMCID: PMC7156030 DOI: 10.1016/j.trac.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.
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Affiliation(s)
- Yu-Min Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, Guangdong 510006, P. R. China
| | - Michael Patrick Trinh
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Kaizhu Guo
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Luis A. Jimenez
- Program in Biomedical Sciences, University of California at Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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Garufi A, Traversi G, Gilardini Montani MS, D'Orazi V, Pistritto G, Cirone M, D'Orazi G. Reduced chemotherapeutic sensitivity in high glucose condition: implication of antioxidant response. Oncotarget 2019; 10:4691-4702. [PMID: 31384396 PMCID: PMC6659798 DOI: 10.18632/oncotarget.27087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Resistance to chemotherapy represents a major obstacle to successful treatment. The generation of reactive oxygen species (ROS) has been directly linked to the cytotoxic effects of several antitumor agents, including Adriamycin (ADR), and modulation of the oxidative balance has been implicated in the development and/or regulation of resistance to chemotherapeutic drugs. We recently showed that high glucose (HG) markedly diminished the cancer cell death induced by anticancer agents such as ADR. In the present study we attempted to evaluate the mechanism that impaired the cytotoxic effect of ADR in HG. We found that, in colon cancer cells, HG attenuated ADR-induced ROS production that consequently diminished ADR-induced H2AX phosphorylation and micronuclei (MN) formation. Mechanistically, HG attenuation of ADR-induced ROS production correlated with increased antioxidant response promoted by NRF2 activity. Thus, pharmacologic inhibition of NRF2 pathway by brusatol re-established the ADR cytotoxic effect impaired by HG. Together, the data provide new insights into chemotherapeutic-resistance mechanisms in HG condition dictated by increased NRF2-induced antioxidant response and how they may be overcome in order to restore chemosensitivity and ADR-induced cell death.
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Affiliation(s)
- Alessia Garufi
- IRCCS Regina Elena National Cancer Institute, Department of Research, Rome 00144, Italy.,University 'G. d'Annunzio', Department of Medical and Biotechnological Sciences, Chieti 66013, Italy
| | - Gianandrea Traversi
- IRCCS Regina Elena National Cancer Institute, Department of Research, Rome 00144, Italy.,University 'G. d'Annunzio', Department of Medical and Biotechnological Sciences, Chieti 66013, Italy
| | | | | | - Giuseppa Pistritto
- University Tor Vergata, Department of Systems Medicine, Rome 00133, Italy
| | - Mara Cirone
- Sapienza University, Department of Experimental Medicine, Rome 00161, Italy
| | - Gabriella D'Orazi
- IRCCS Regina Elena National Cancer Institute, Department of Research, Rome 00144, Italy.,University 'G. d'Annunzio', Department of Medical and Biotechnological Sciences, Chieti 66013, Italy
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Liang Z, Zhou J, Petti L, Shao L, Jiang T, Qing Y, Xie S, Wu G, Mormile P. SERS-based cascade amplification bioassay protocol of miRNA-21 by using sandwich structure with biotin-streptavidin system. Analyst 2019; 144:1741-1750. [PMID: 30663745 DOI: 10.1039/c8an02259c] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In our bioassay protocol, the Ag@4MBA@DNA-biotin probes were synthesized by linking biotin-modified DNA and 4-mercaptobenzoic acid-covered Ag nanoparticles, and the Si@Ag@anti-digoxin/digoxin-DNA substrate was fabricated by immune linking of digoxin-DNA and anti-digoxin immobilized on a Ag-coated wafer. Then, the probes, miRNA-21 and the substrate were constructed into a "sandwich structure" to detect the variation in the SERS signals with respect to miRNA-21 concentrations. Next, streptavidin and extra probes were alternately introduced to implement the cascade amplification of the SERS signal to increase the detection sensitivity. The results show that the limit of detection (LOD) with cascade amplification is remarkably improved from 97.81 pM to 38.02 fM, which is three orders of magnitude higher than the original data without cascade amplification. Furthermore, the SERS-based cascade amplification mechanism was analyzed and is attributed to the "hot spots effect" of the noble metal nanostructure. The biotin-streptavidin (B-S) system was introduced into the SERS detection platform, and the novel SERS-based cascade amplification bioassay protocol has significant creativity for the detection of nucleic acids.
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Affiliation(s)
- Zhaoheng Liang
- Institute of Photonics, Faculty of Science, Ningbo University, Ningbo 315211, Zhejiang, China.
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Gasparello J, Lamberti N, Papi C, Lampronti I, Cosenza LC, Fabbri E, Bianchi N, Zambon C, Dalla Corte F, Govoni M, Reverberi R, Manfredini F, Gambari R, Finotti A. Altered erythroid-related miRNA levels as a possible novel biomarker for detection of autologous blood transfusion misuse in sport. Transfusion 2019; 59:2709-2721. [PMID: 31148196 DOI: 10.1111/trf.15383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Autologous blood transfusion (ABT) is a performance-enhancing method prohibited in sport; its detection is a key issue in the field of anti-doping. Among novel markers enabling ABT detection, microRNAs (miRNAs) might be considered a promising analytical tool. STUDY DESIGN AND METHODS We studied the changes of erythroid-related microRNAs following ABT, to identify novel biomarkers. Fifteen healthy trained males were studied from a population of 24 subjects, enrolled and randomized into a Transfusion (T) and a Control (C) group. Seriated blood samples were obtained in the T group before and after the two ABT procedures (withdrawal, with blood refrigerated or cryopreserved, and reinfusion), and in the C group at the same time points. Traditional hematological parameters were assessed. Samples were tested by microarray analysis of a pre-identified set of erythroid-related miRNAs. RESULTS Hematological parameters showed moderate changes only in the T group, particularly following blood withdrawal. Among erythroid-related miRNAs tested, following ABT a pool of 7 miRNAs associated with fetal hemoglobin and regulating transcriptional repressors of gamma-globin gene was found stable in C and differently expressed in three out of six T subjects in the completed phase of ABT, independently from blood conservation. Particularly, two or more erythropoiesis-related miRNAs within the shortlist constituted of miR-126-3p, miR-144-3p, miR-191-3p, miR-197-3p, miR-486-3p, miR-486-5p, and miR-92a-3p were significantly upregulated in T subjects after reinfusion, with a person-to-person variability but with congruent changes. CONCLUSIONS This study describes a signature of potential interest for ABT detection in sports, based on the analysis of miRNAs associated with erythroid features.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Nicola Lamberti
- Department of Biomedical and Surgical Specialties Sciences, Section of Sport Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Papi
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Christel Zambon
- Department of Biomedical and Surgical Specialties Sciences, Section of Sport Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Dalla Corte
- Immunohematological and Transfusional Service, University Hospital of Ferrara, Ferrara, Italy
| | - Maurizio Govoni
- Immunohematological and Transfusional Service, University Hospital of Ferrara, Ferrara, Italy
| | - Roberto Reverberi
- Immunohematological and Transfusional Service, University Hospital of Ferrara, Ferrara, Italy
| | - Fabio Manfredini
- Department of Biomedical and Surgical Specialties Sciences, Section of Sport Sciences, University of Ferrara, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnologies, Section of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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22
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Advanced methods for microRNA biosensing: a problem-solving perspective. Anal Bioanal Chem 2019; 411:4425-4444. [PMID: 30710205 DOI: 10.1007/s00216-019-01621-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/07/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) present several features that make them more difficult to analyze than DNA and RNA. For this reason, efforts have been made in recent years to develop innovative platforms for the efficient detection of microRNAs. The aim of this review is to provide an overview of the sensing strategies able to deal with drawbacks and pitfalls related to microRNA detection. With a critical perspective of the field, we identify the main challenges to be overcome in microRNA sensing, and describe the areas where several innovative approaches are likely to come for managing those issues that put limits on improvement to the performances of the current methods. Then, in the following sections, we critically discuss the contribution of the most promising approaches based on the peculiar properties of nanomaterials or nanostructures and other hybrid strategies which are envisaged to support the adoption of these new methods useful for the detection of miRNA as biomarkers of practical clinical utility. Graphical abstract ᅟ.
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Finotti A, Allegretti M, Gasparello J, Giacomini P, Spandidos DA, Spoto G, Gambari R. Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review). Int J Oncol 2018; 53:1395-1434. [PMID: 30085333 PMCID: PMC6086621 DOI: 10.3892/ijo.2018.4516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
In oncology, liquid biopsy is used in the detection of next-generation analytes, such as tumor cells, cell-free nucleic acids and exosomes in peripheral blood and other body fluids from cancer patients. It is considered one of the most advanced non-invasive diagnostic systems to enable clinically relevant actions and implement precision medicine. Medical actions include, but are not limited to, early diagnosis, staging, prognosis, anticipation (lead time) and the prediction of therapy responses, as well as follow-up. Historically, the applications of liquid biopsy in cancer have focused on circulating tumor cells (CTCs). More recently, this analysis has been extended to circulating free DNA (cfDNA) and microRNAs (miRNAs or miRs) associated with cancer, with potential applications for development into multi-marker diagnostic, prognostic and therapeutic signatures. Liquid biopsies avoid some key limitations of conventional tumor tissue biopsies, including invasive tumor sampling, under-representation of tumor heterogeneity and poor description of clonal evolution during metastatic dissemination, strongly reducing the need for multiple sampling. On the other hand, this approach suffers from important drawbacks, i.e., the fragmentation of cfDNA, the instability of RNA, the low concentrations of certain analytes in body fluids and the confounding presence of normal, as well as aberrant DNAs and RNAs. For these reasons, the analysis of cfDNA has been mostly focused on mutations arising in, and pathognomonicity of, tumor DNA, while the analysis of cfRNA has been mostly focused on miRNA patterns strongly associated with neoplastic transformation/progression. This review lists some major applicative areas, briefly addresses how technology is bypassing liquid biopsy limitations, and places a particular emphasis on novel, PCR-free platforms. The ongoing collaborative efforts of major international consortia are reviewed. In addition to basic and applied research, we will consider technological transfer, including patents, patent applications and available information on clinical trials aimed at verifying the potential of liquid biopsy in cancer.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Giuseppe Spoto
- Department of Chemistry, Catania University, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
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