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Qin S, Wu H, Li C, Yang J, Yan W, He Z, Xing X, Zhang J, Xu X, Zhao L, Su X. Detection of Naturally occurring abortive transcripts by Base-Stacking Hybridization Assisted Ligation and PCR amplification. Biosens Bioelectron 2024; 251:116099. [PMID: 38330773 DOI: 10.1016/j.bios.2024.116099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Abortive transcripts (ATs) refer to nascent 2-10 nucleotides (nt) RNAs released by RNA polymerases before synthesizing productive RNAs. The quantitative detection of ATs is important for studying transcription initiation and the biological function of ATs; however, no method is available for the qualitative and quantitative assessment of such ultra-short oligonucleotides (typically shorter than 11 nt) in vivo at present, even with the LNA probes, the detection limit can only reach 11 nt. Here, we demonstrated the base stacking hybridization assisted ligation (BSHAL) technique, combined with TaqMan-MGB qPCR, can detect 4-10 nt ATs with a specificity of nucleotide resolution and a sensitivity of approximately 10 pM. By this technique, we detected endogenous ATs in cell lines, mice plasmas, and mice liver tissues, respectively, and proved that naturally occurring ATs do exist. We found that the 8 nt ATs of HMSB and Gapdh could be used as reference ATs for data normalization in Homo and mouse respectively, and 8 nt ATs of Afp and Gpc3 were suitable for use as plasma biomarkers of Hepatocellular carcinoma in mouse, indicate ATs are promising biomarkers. This study offers opportunities to study ATs and other ultra-short oligonucleotides in biological samples.
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Affiliation(s)
- Shaowei Qin
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Haizhu Wu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Cailin Li
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Jiarui Yang
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, 21218, USA
| | - Weiwei Yan
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Zhigui He
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Xuekun Xing
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Jiayang Zhang
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Xianglin Xu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Lifeng Zhao
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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2
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Shi H, Ge Q, Pan M, Sheng Y, Qi T, Zhou Y, Sun Y, Bai Y, Cai L. Agarose amplification based sequencing characterization cell-free RNA in preimplantation spent embryo medium. Anal Chim Acta 2024; 1296:342331. [PMID: 38401939 DOI: 10.1016/j.aca.2024.342331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The cell-free RNA (cf-RNA) of spent embryo medium (SEM) has aroused a concern of academic and clinical researchers for its potential use in non-invasive embryo screening. However, comprehensive characterization of cf-RNA from SEM still presents significant technical challenges, primarily due to the limited volume of SEM. Hence, there is urgently need to a small input liquid volume and ultralow amount of cf-RNA library preparation method to unbiased cf-RNA sequencing from SEM. (75) RESULT: Here, we report a high sensitivity agarose amplification-based cf-RNA sequencing method (SEM-Acf) for human preimplantation SEM cf-RNA analysis. It is a cf-RNA sequencing library preparation method by adding agarose amplification. The agarose amplification sensitivity (0.005 pg) and efficiency (105.35 %) were increased than that of without agarose addition (0.45 pg and 96.06 %) by ∼ 90 fold and 9.29 %, respectively. Compared with SMART sequencing (SMART-seq), the correlation of gene expression was stronger in different SEM samples by using SEM-Acf. The cf-RNA number of detected and coverage uniformity of 3' end were significantly increased. The proportion of 5' end adenine, alternative splicing events and short fragments (<400 bp) were increased. It is also found that 4-mer end motifs of cf-RNA fragments was significantly differences between different embryonic stage by day3 spent cleavage medium and day5/6 spent blastocyst medium. (141) SIGNIFICANCE: This study established an efficient SEM amplification and library preparation method. Additionally, we successfully described the characterizations of SEM cf-RNA in preimplantation embryo using SEM-Acf, including expression features and fragment lengths. SEM-Acf facilitates the exploration of cf-RNA as a noninvasive embryo screening biomarker, and opens up potential clinical utilities of small input liquid volume and ultralow amount cf-RNA sequencing. (59).
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Affiliation(s)
- Huajuan Shi
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, 210097, China
| | - Yuqi Sheng
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ting Qi
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Zhou
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yuqing Sun
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Lingbo Cai
- Clinical Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
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3
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Foster JB, Koptyra MP, Bagley SJ. Recent Developments in Blood Biomarkers in Neuro-oncology. Curr Neurol Neurosci Rep 2023; 23:857-867. [PMID: 37943477 DOI: 10.1007/s11910-023-01321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE OF REVIEW Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system (CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors. RECENT FINDINGS We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier. Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz P Koptyra
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, 10th Floor Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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4
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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5
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Mokhtari F, Kaboosi H, Mohebbi SR, Asadzadeh Aghdaei H, Zali MR. Circulating Plasma miR-122 and miR-583 Levels Are Involved in Chronic Hepatitis B Virus Pathogenesis and Serve As Novel Diagnostic Biomarkers. Genet Test Mol Biomarkers 2023; 27:232-238. [PMID: 37643324 DOI: 10.1089/gtmb.2023.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Background: MicroRNAs regulate many biological processes and are involved in the pathogenesis of many diseases including chronic hepatitis B (CHB). Moreover, besides investigation of their roles in hepatitis B virus (HBV) infection, a noninvasive, sensitive, and specific biomarker is essential in the diagnosis of liver diseases. This study was designed to evaluate the role of miR-122, miR-583, and miR-24 in the pathogenesis of CHB both in active chronic hepatitis (ACH) patients and in inactive carriers (IC). Materials and Methods: Plasma samples and all relevant clinical features were collected from 43 patients with CHB (28 ACH and 15 IC) and 43 healthy controls. Quantitative real-time PCR was performed to detect the plasma levels of miR-122, miR-583, and miR-24. Results: Results show miR-122 (p = 0.0001) and miR-583 (p = 0.006) but not miR-24 (p = 0.65) were upregulated in patients with CHB versus the control group. Interestingly, there was a significant increase in the plasma expression of miR-583 in IC versus ACH. Moreover, receiver operating characteristic curve analysis determined plasma levels of miR-122 (area under the ROC curve [AUC] = 0.89, p < 0.0001, sensitivity: 100%, specificity: 62.5%) and miR-583 (AUC = 0.71, p = 0.0007, sensitivity: 90%, specificity: 47.62%) as sensitive biomarkers to discriminate CHB patients from controls. Conclusion: Our data showed an increase in the plasma levels of miR-583 in IC versus ACH patients. Moreover, we demonstrated that miR-122 and miR-583 may serve as potential biomarkers for CHB diagnosis and activity.
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Affiliation(s)
- Fedra Mokhtari
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Hami Kaboosi
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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6
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Patel BY, Bhome R, Liu DSK, Giovannetti E, Merali N, Primrose JN, Mirnezami AH, Rockall TA, Annels N, Frampton AE. Cancer cell-derived extracellular vesicles activate hepatic stellate cells in colorectal cancer. Expert Rev Mol Diagn 2023; 23:843-849. [PMID: 37599564 DOI: 10.1080/14737159.2023.2246893] [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: 01/03/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
Colorectal cancer (CRC) is the 2nd leading cause of cancer-related deaths worldwide, primarily due to the development of metastatic disease. The liver is the most frequently affected site. The metastatic cascade relies on a complex interaction between the immune system, tumor, and distant organs. Communication between the tumor and the metastatic site can be mediated by tumor-derived extracellular vesicles (EVs) and their cargo. The mechanisms underlying this process are starting to be understood through research that has rapidly expanded over the past 15 years. One crucial aspect is the remodeling of the microenvironment at the site of metastasis, which is essential for the formation of a premetastatic niche and the subsequent establishment of metastatic deposits. In the evaluated study, the authors use cellular experiments and a mouse model to investigate how tumour derived extracellular vesicles and their microRNA contents interact with hepatic stellate cells (HSCs). They demonstrate how this may lead to remodelling of the microenvironment and the formation of colorectal liver metastasis using their experimental model. In this mini review, we examine the current evidence surrounding tumour derived EVs and their effect on the tumour microenvironment to highlight potential areas for future research in CRC and other malignancies.
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Affiliation(s)
- Bhavik Y Patel
- Section of Oncology, Dept. of Clinical & Experimental Medicine, University of Surrey, Guildford, Surrey, UK
- Minimal Access Therapy Training Unit (MATTU), Leggett Building, University of Surrey, Guildford, UK
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, Guildford, UK
| | - Rahul Bhome
- Cancer Sciences, University of Southampton, Southampton, UK
| | - Daniel S K Liu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per La Scienza, San Giuliano, Italy
| | - Nabeel Merali
- Section of Oncology, Dept. of Clinical & Experimental Medicine, University of Surrey, Guildford, Surrey, UK
- Minimal Access Therapy Training Unit (MATTU), Leggett Building, University of Surrey, Guildford, UK
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, Guildford, UK
| | - John N Primrose
- Department of Surgery, University of Southampton, Southampton, UK
| | - Alex H Mirnezami
- Department of Surgery, University of Southampton, Southampton, UK
| | - Timothy A Rockall
- Minimal Access Therapy Training Unit (MATTU), Leggett Building, University of Surrey, Guildford, UK
| | - Nicola Annels
- Section of Oncology, Dept. of Clinical & Experimental Medicine, University of Surrey, Guildford, Surrey, UK
| | - Adam E Frampton
- Section of Oncology, Dept. of Clinical & Experimental Medicine, University of Surrey, Guildford, Surrey, UK
- Minimal Access Therapy Training Unit (MATTU), Leggett Building, University of Surrey, Guildford, UK
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, Guildford, UK
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7
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Munguía-Ramírez B, Armenta-Leyva B, Henao-Díaz A, Cheng TY, Zhang J, Rawal G, Ye F, Giménez-Lirola L, Zimmerman JJ. Effect of extrinsic factors on the detection of PRRSV and a porcine-specific internal sample control in serum, oral fluid, and fecal specimens tested by RT-rtPCR. J Vet Diagn Invest 2023; 35:374-383. [PMID: 37166086 PMCID: PMC10331379 DOI: 10.1177/10406387231174556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
We characterized the effect of 1) temperature × time, 2) freeze-thaw cycles, and 3) high porcine reproductive and respiratory syndrome virus (PRRSV) RNA concentrations on the detection of PRRSV and a porcine-specific internal sample control (ISC) in serum, oral fluid, and fecal samples using a commercial PRRSV RT-rtPCR assay (Idexx). In study 1, the effect of temperature × time on PRRSV and ISC detection was shown to be specimen dependent. In serum stored at 4, 10, or 20°C, PRRSV detection was consistent for up to 168 h, but storage at 30°C reduced detectable PRRSV RNA. ISC RNA was stable in serum held at 4 and 10°C, but not at 20 and 30°C. In contrast, PRRSV and ISC RNAs in oral fluid and fecal samples continuously decreased at all temperature × time treatments. Based on these data, serum samples should be stored at ≤ 20°C to optimize PRRSV RNA detection. Oral fluid and fecal samples should be frozen in a non-self-defrosting freezer until tested. In study 2, freeze-thaw cycles had little impact on PRRSV and ISC detection, but more so in oral fluids than serum or fecal samples. Thus, freeze-thaw cycles in oral fluids should be minimized before RT-rtPCR testing. In study 3, the ISC was not affected by high concentrations of PRRSV RNA in serum, oral fluid, or fecal samples. It should not be assumed that data from our PRRSV study are applicable to other pathogens; additional pathogen-specific studies are required.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Luis Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J. Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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8
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Paluschinski M, Loosen S, Kordes C, Keitel V, Kuebart A, Brandenburger T, Schöler D, Wammers M, Neumann UP, Luedde T, Castoldi M. Extracellular Vesicles as Markers of Liver Function: Optimized Workflow for Biomarker Identification in Liver Disease. Int J Mol Sci 2023; 24:9631. [PMID: 37298585 PMCID: PMC10253831 DOI: 10.3390/ijms24119631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Liver diseases represent a significant global health burden, necessitating the development of reliable biomarkers for early detection, prognosis, and therapeutic monitoring. Extracellular vesicles (EVs) have emerged as promising candidates for liver disease biomarkers due to their unique cargo composition, stability, and accessibility in various biological fluids. In this study, we present an optimized workflow for the identification of EVs-based biomarkers in liver disease, encompassing EVs isolation, characterization, cargo analysis, and biomarker validation. Here we show that the levels of microRNAs miR-10a, miR-21, miR-142-3p, miR-150, and miR-223 were different among EVs isolated from patients with nonalcoholic fatty liver disease and autoimmune hepatitis. In addition, IL2, IL8, and interferon-gamma were found to be increased in EVs isolated from patients with cholangiocarcinoma compared with healthy controls. By implementing this optimized workflow, researchers and clinicians can improve the identification and utilization of EVs-based biomarkers, ultimately enhancing liver disease diagnosis, prognosis, and personalized treatment strategies.
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Affiliation(s)
- Martha Paluschinski
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Sven Loosen
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Claus Kordes
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Anne Kuebart
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (A.K.); (T.B.)
| | - Timo Brandenburger
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (A.K.); (T.B.)
| | - David Schöler
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Marianne Wammers
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Ulf P. Neumann
- Visceral and Transplant Surgery, University Hospital RWTH Aachen, 52074 Aachen, Germany;
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
| | - Mirco Castoldi
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (M.P.); (S.L.); (C.K.); (V.K.); (D.S.); (M.W.); (T.L.)
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9
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Korotkaja K, Zajakina A. Recombinant Virus Quantification Using Single-Cell Droplet Digital PCR: A Method for Infectious Titer Quantification. Viruses 2023; 15:v15051060. [PMID: 37243145 DOI: 10.3390/v15051060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The quantification of viruses is necessary for both research and clinical applications. The methods available for RNA virus quantification possess several drawbacks, including sensitivity to inhibitors and the necessity of a standard curve generation. The main purpose of this study was to develop and validate a method for the quantification of recombinant, replication-deficient Semliki Forest virus (SFV) vectors using droplet digital PCR (ddPCR). This technique demonstrated stability and reproducibility using various sets of primers that targeted inserted transgenes, as well as the nsP1 and nsP4 genes of the SFV genome. Furthermore, the genome titers in the mixture of two types of replication-deficient recombinant virus particles were successfully measured after optimizing the annealing/extension temperature and virus:virus ratios. To measure the infectious units, we developed a single-cell ddPCR, adding the whole infected cells to the droplet PCR mixture. Cell distribution in the droplets was investigated, and β-actin primers were used to normalize the quantification. As a result, the number of infected cells and the virus infectious units were quantified. Potentially, the proposed single-cell ddPCR approach could be used to quantify infected cells for clinical applications.
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Affiliation(s)
- Ksenija Korotkaja
- Cancer Gene Therapy Group, Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k.1, LV-1067 Riga, Latvia
| | - Anna Zajakina
- Cancer Gene Therapy Group, Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k.1, LV-1067 Riga, Latvia
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10
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de Los Reyes-García AM, Zapata-Martínez L, Águila S, Lozano ML, Martínez C, González-Conejero R. microRNAs as biomarkers of risk of major adverse cardiovascular events in atrial fibrillation. Front Cardiovasc Med 2023; 10:1135127. [PMID: 36895835 PMCID: PMC9988920 DOI: 10.3389/fcvm.2023.1135127] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Atrial fibrillation is a complex and multifactorial disease. Although prophylactic anticoagulation has great benefits in avoiding comorbidities, adverse cardiovascular events still occur and thus in recent decades, many resources have been invested in the identification of useful markers in the prevention of the risk of MACE in these patients. As such, microRNAs, that are small non-coding RNAs whose function is to regulate gene expression post-transcriptionally, have a relevant role in the development of MACE. miRNAs, have been investigated for many years as potential non-invasive biomarkers of several diseases. Different studies have shown their utility in the diagnosis and prognosis of cardiovascular diseases. In particular, some studies have associated the presence of certain miRNAs in plasma with the development of MACE in AF. Despite these results, there are still many efforts to be done to allow the clinical use of miRNAs. The lack of standardization concerning the methodology in purifying and detecting miRNAs, still provides contradictory results. miRNAs also have a functional impact in MACE in AF through the dysregulation of immunothrombosis. Indeed, miRNAs may be a link between MACE and inflammation, through the regulation of neutrophil extracellular traps that are a key element in the establishment and evolution of thrombotic events. The use of miRNAs as therapy against thromboinflammatory processes should also be a future approach to avoid the occurrence of MACE in atrial fibrillation.
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Affiliation(s)
- Ascensión M de Los Reyes-García
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Laura Zapata-Martínez
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Sonia Águila
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Constantino Martínez
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Rocío González-Conejero
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
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11
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Khan FB, Uddin S, Elderdery AY, Goh KW, Ming LC, Ardianto C, Palakot AR, Anwar I, Khan M, Owais M, Huang CY, Daddam JR, Khan MA, Shoaib S, Khursheed M, Reshadat S, Khayat Kashani HR, Mirza S, Khaleel AA, Ayoub MA. Illuminating the Molecular Intricacies of Exosomes and ncRNAs in Cardiovascular Diseases: Prospective Therapeutic and Biomarker Potential. Cells 2022; 11:cells11223664. [PMID: 36429092 PMCID: PMC9688392 DOI: 10.3390/cells11223664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022] Open
Abstract
Cardiovascular diseases (CVDs) are one of the leading causes of death worldwide. Accumulating evidences have highlighted the importance of exosomes and non-coding RNAs (ncRNAs) in cardiac physiology and pathology. It is in general consensus that exosomes and ncRNAs play a crucial role in the maintenance of normal cellular function; and interestingly it is envisaged that their potential as prospective therapeutic candidates and biomarkers are increasing rapidly. Considering all these aspects, this review provides a comprehensive overview of the recent understanding of exosomes and ncRNAs in CVDs. We provide a great deal of discussion regarding their role in the cardiovascular system, together with providing a glimpse of ideas regarding strategies exploited to harness their potential as a therapeutic intervention and prospective biomarker against CVDs. Thus, it could be envisaged that a thorough understanding of the intricacies related to exosomes and ncRNA would seemingly allow their full exploration and may lead clinical settings to become a reality in near future.
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Affiliation(s)
- Farheen Badrealam Khan
- Department of Biology, College of Science, The United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Correspondence: (F.B.K.); (M.A.A.); (C.A.)
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
- Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Abozer Y. Elderdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Khang Wen Goh
- Faculty of Data Sciences and Information Technology, INTI International University, Nilai 78100, Malaysia
| | - Long Chiau Ming
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong BE1410, Brunei
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Chrismawan Ardianto
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
- Correspondence: (F.B.K.); (M.A.A.); (C.A.)
| | - Abdul Rasheed Palakot
- Department of Biology, College of Science, The United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Irfa Anwar
- Department of Biology, College of Science, The United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Mohsina Khan
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Chih-Yang Huang
- Department of Biotechnology, Asia University, Taichung 404, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
- Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 970, Taiwan
- Centre of General Education, Buddhist Tzu Chi Medical Foundation, Tzu Chi University of Science and Technology, Hualien 970, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan
| | - Jayasimha Rayalu Daddam
- Department of Ruminant Science, Institute of Animal Sciences, Agriculture Research Organization, Volcani Center, Rishon Lezion 7505101, Israel
| | - Meraj Alam Khan
- Program in Translational Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children & DigiBiomics Inc, Toronto, ON M51X8, Canada
| | - Shoaib Shoaib
- Department Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Md Khursheed
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Sara Reshadat
- Department of Internal Medicine, Semnan University of Medical Sciences, Semnan 3513119111, Iran
| | | | - Sameer Mirza
- Department of Chemistry, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Abbas A. Khaleel
- Department of Chemistry, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Mohammed Akli Ayoub
- Department of Biology, College of Science, The United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Department of Biology, College of Arts and Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Correspondence: (F.B.K.); (M.A.A.); (C.A.)
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12
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Jayasinghe R, Jayarajah U, Seneviratne S. Circulating Biomarkers in Predicting Pathological Response to Neoadjuvant Therapy for Colorectal Cancer. Biomark Med 2022. [DOI: 10.2174/9789815040463122010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Circulating biomarkers show promise in the management of many cancers.
They have become the novel non-invasive approach to complement the current
strategies in colorectal cancer (CRC) management. Their ability in guiding diagnosis,
evaluating response to treatment, screening and prognosis is phenomenal, especially
when it comes to their minimally invasive nature. These “liquid biopsies,” which show
potential for replacing invasive surgical biopsies, provide useful information on the
primary and metastatic disease by providing an insight into cancer biology. Analysis of
blood and body fluids for circulating tumour DNA (ctDNA), carcinoembryonic antigen
(CEA), circulating tumour cells (CTC), or circulating micro RNA (miRNA) shows
potential for improving CRC management. Recognizing a predictive model to assess
response to neoadjuvant chemotherapy would help in better patient selection. This
review was conducted with the aim of outlining the use of circulatory biomarkers in
current practice and their effectiveness in the management of patients having CRC with
a focus on response to neoadjuvant therapy.
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Affiliation(s)
- Ravindri Jayasinghe
- Department of Surgery, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Umesh Jayarajah
- Department of Surgery, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sanjeewa Seneviratne
- Department of Surgery, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
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13
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Uslu-Beşli L. Circulating Biomarkers in Thyroid Cancer. Biomark Med 2022. [DOI: 10.2174/9789815040463122010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thyroid cancer is the most important endocrine cancer with increasing
incidence. While thyroid cancers, especially papillary thyroid cancers, are known to
exhibit generally a favorable outcome with excellent survival rates, some thyroid
cancers are more aggressive with a poor prognosis. Several different biomarkers have
been introduced for the diagnosis of disease, identification of tumor load, assessment of
therapy response, and the detection of recurrence during follow-up of the thyroid
cancer patients. This chapter gives a brief overview of the circulating biomarkers used
in thyroid cancer patients.
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Affiliation(s)
- Lebriz Uslu-Beşli
- Department of Nuclear Medicine, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa,
Istanbul, Turkey
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14
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Sun J, Yang X, Wang T, Xing Y, Chen H, Zhu S, Zeng J, Zhou Q, Chen F, Zhang X, Wang WJ. Evaluating the Effects of Storage Conditions on Multiple Cell-Free RNAs in Plasma by High-Throughput Sequencing. Biopreserv Biobank 2022. [PMID: 36006659 DOI: 10.1089/bio.2022.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Plasma cell-free RNAs (cfRNAs) can serve as noninvasive biomarkers for the diagnosis and monitoring of diseases. However, the delay in blood processing may lead to unreliable results. Therefore, an unbiased evaluation based on the whole transcriptome under different storage conditions is needed. Methods: Here, blood samples were collected in ethylenediaminetetraacetic acid tubes and processed immediately (0 hour), or stored at room temperature (RT) or 4°C for different time intervals (2, 6, and 24 hours) before plasma separation. High-throughput sequencing was applied to assess the effects of storage conditions on the transcript profiles and fragment characteristics of plasma cell-free mRNA, long noncoding RNA (lncRNA), and small RNAs. Results: More genes changed their expression levels with time when blood was stored at RT compared with those at 4°C. Cell-free mRNA and lncRNA were relatively stable in blood preserved at 4°C for 6 hours, while cell-free microRNA (miRNA) and piwi-interacting RNA (piRNA) remained stable at 4°C for 24 hours. After 24 hours, more contamination of the leukocyte-derived RNAs occurred at RT, possibly due to apoptosis. Meanwhile, significant changes were also observed regarding the characteristics of the RNA fragments, including fragment size, the proportion of intron, and the pyrimidine frequency of the fragmented 3' end. Fifteen tissue-enriched genes were detected in the plasma but not expressed in leukocytes. The expression level and fragment length of these genes gradually decreased during storage, suggesting the degradation of the cfRNA and the dilution of leukocyte-derived RNA with other tissue-derived cfRNA. Conclusions: Our results suggest that the contamination of leukocyte-derived RNA and the degradation of original cfRNA contribute to the changes in the cfRNA expression profiles and the fragment characteristics during short-term storage. The storage of blood at 4°C for 6 hours allows plasma cfRNA to remain relatively stable, which will be useful for further studies or clinical applications where adequate quantification or the fragment signature of cfRNA is required.
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Affiliation(s)
- Jinghua Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China
| | - Xi Yang
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | | | | | | | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China
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15
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Henriques DG, Lamback EB, Dezonne RS, Kasuki L, Gadelha MR. MicroRNA in Acromegaly: Involvement in the Pathogenesis and in the Response to First-Generation Somatostatin Receptor Ligands. Int J Mol Sci 2022; 23:ijms23158653. [PMID: 35955787 PMCID: PMC9368811 DOI: 10.3390/ijms23158653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Acromegaly is a chronic and systemic disease due to excessive growth hormone and insulin-like growth factor type I caused, in the vast majority of cases, by a GH-secreting pituitary adenoma. About 40% of these tumors have somatic mutations in the stimulatory G protein alpha-subunit 1 gene. The pathogenesis of the remaining tumors, however, is still not fully comprehended. Surgery is the first-line therapy for these tumors, and first-generation somatostatin receptor ligands (fg-SRL) are the most prescribed medications in patients who are not cured by surgery. MicroRNAs are small, non-coding RNAs that control the translation of many mRNAs, and are involved in the post-transcriptional regulation of gene expression. Differentially expressed miRNAs can explain differences in the pathogenesis of acromegaly and tumor resistance. In this review, we focus on the most validated miRNAs, which are mainly involved in acromegaly’s tumorigenesis and fg-SRL resistance, as well as in circulating miRNAs in acromegaly.
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Affiliation(s)
- Daniel G. Henriques
- Neuroendocrinology Research Center, Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Elisa B. Lamback
- Neuroendocrinology Research Center, Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Romulo S. Dezonne
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Leandro Kasuki
- Neuroendocrinology Research Center, Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Endocrinology Division, Hospital Federal de Bonsucesso, Rio de Janeiro 21041-020, Brazil
| | - Monica R. Gadelha
- Neuroendocrinology Research Center, Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Correspondence:
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16
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Studying Epigenetics of Cardiovascular Diseases on Chip Guide. CARDIOGENETICS 2022. [DOI: 10.3390/cardiogenetics12030021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Epigenetics is defined as the study of inheritable changes in the gene expressions and phenotypes that occurs without altering the normal DNA sequence. These changes are mainly due to an alteration in chromatin or its packaging, which changes the DNA accessibility. DNA methylation, histone modification, and noncoding or microRNAs can best explain the mechanism of epigenetics. There are various DNA methylated enzymes, histone-modifying enzymes, and microRNAs involved in the cause of various CVDs (cardiovascular diseases) such as cardiac hypertrophy, heart failure, and hypertension. Moreover, various CVD risk factors such as diabetes mellitus, hypoxia, aging, dyslipidemia, and their epigenetics are also discussed together with CVDs such as CHD (coronary heart disease) and PAH (pulmonary arterial hypertension). Furthermore, different techniques involved in epigenetic chromatin mapping are explained. Among these techniques, the ChIP-on-chip guide is explained with regard to its role in cardiac hypertrophy, a final form of heart failure. This review focuses on different epigenetic factors that are involved in causing cardiovascular diseases.
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17
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Butz H. Circulating Noncoding RNAs in Pituitary Neuroendocrine Tumors-Two Sides of the Same Coin. Int J Mol Sci 2022; 23:ijms23095122. [PMID: 35563510 PMCID: PMC9101693 DOI: 10.3390/ijms23095122] [Citation(s) in RCA: 9] [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: 04/04/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 01/27/2023] Open
Abstract
Pituitary neuroendocrine tumors (PitNET) are common intracranial neoplasms. While in case of hormone secreting tumors pituitary hormone measurements can be used for monitoring the disease, in non-functional tumors there is a need to discover non-invasive biomarkers. Non-coding RNAs (ncRNAs) are popular biomarker candidates due to their stability and tissue specificity. Among ncRNAs, miRNAs, lncRNAs and circRNAs have been investigated the most in pituitary tumor tissues and in circulation. However, it is still not known whether ncRNAs are originated from the pituitary, or whether they are casually involved in the pathophysiology. Additionally, there is strong diversity among different studies reporting ncRNAs in PitNET. Therefore, to provide an overview of the discrepancies between published studies and to uncover the reasons why despite encouraging experimental data application of ncRNAs in clinical routine has not yet taken hold, in this review available data are summarized on circulating ncRNAs in PitNET. The data on circulating miRNAs, lncRNAs and circRNAs are organized according to different PitNET subtypes. Biological (physiological and pathophysiological) factors behind intra- and interindividual variability and technical aspects of detecting these markers, including preanalytical and analytical parameters, sample acquisition (venipuncture) and type, storage, nucleic acid extraction, quantification and normalization, which reveal the two sides of the same coin are discussed.
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Affiliation(s)
- Henriett Butz
- Hereditary Tumours Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
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18
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Factors influencing degradation kinetics of mRNAs and half-lives of microRNAs, circRNAs, lncRNAs in blood in vitro using quantitative PCR. Sci Rep 2022; 12:7259. [PMID: 35508612 PMCID: PMC9068688 DOI: 10.1038/s41598-022-11339-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
RNAs are rapidly degraded in samples and during collection, processing and testing. In this study, we used the same method to explore the half-lives of different RNAs and the influencing factors, and compared the degradation kinetics and characteristics of different RNAs in whole blood and experimental samples. Fresh anticoagulant blood samples were incubated at room temperature for different durations, RNAs were extracted, and genes, including internal references, were amplified by real-time quantitative PCR. A linear half-life model was established according to cycle threshold (Ct) values. The effects of experimental operations on RNA degradation before and after RNA extraction were explored. Quantitative analysis of mRNA degradation in samples and during experimental processes were explored using an orthogonal experimental design. The storage duration of blood samples at room temperature had the greatest influence on RNA degradation. The half-lives of messenger RNAs (mRNAs) was 16.4 h. The half-lives of circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were 24.56 ± 5.2 h, 17.46 ± 3.0 h and 16.42 ± 4.2 h, respectively. RNA degradation occurred mainly in blood samples. The half-life of mRNAs was the shortest among the four kinds of RNAs. Quantitative experiments related to mRNAs should be completed within 2 h. The half-lives of circRNAs and lncRNAs were longer than those of the former two.
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19
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Yeoh S, Warner WS, Merchant SS, Hsu EW, Agoston DV, Mahan MA. Incorporating Blood Flow in Nerve Injury and Regeneration Assessment. Front Surg 2022; 9:862478. [PMID: 35529911 PMCID: PMC9069240 DOI: 10.3389/fsurg.2022.862478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/04/2022] [Indexed: 01/22/2023] Open
Abstract
Peripheral nerve injury is a significant public health challenge, with limited treatment options and potential lifelong impact on function. More than just an intrinsic part of nerve anatomy, the vascular network of nerves impact regeneration, including perfusion for metabolic demands, appropriate signaling and growth factors, and structural scaffolding for Schwann cell and axonal migration. However, the established nerve injury classification paradigm proposed by Sydney Sunderland in 1951 is based solely on hierarchical disruption to gross anatomical nerve structures and lacks further information regarding the state of cellular, metabolic, or inflammatory processes that are critical in determining regenerative outcomes. This review covers the anatomical structure of nerve-associated vasculature, and describes the biological processes that makes these vessels critical to successful end-organ reinnervation after severe nerve injuries. We then propose a theoretical framework that incorporates measurements of blood vessel perfusion and inflammation to unify perspectives on all mechanisms of nerve injury.
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Affiliation(s)
- Stewart Yeoh
- Department of Neurosurgery, University of Utah, Salt Lake City, Utah, United States
| | - Wesley S. Warner
- Department of Neurosurgery, University of Utah, Salt Lake City, Utah, United States
| | - Samer S. Merchant
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, United States
| | - Edward W. Hsu
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, United States
| | - Denes v. Agoston
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States
| | - Mark A. Mahan
- Department of Neurosurgery, University of Utah, Salt Lake City, Utah, United States
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20
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Meza CA, Amador M, McAinch AJ, Begum K, Roy S, Bajpeyi S. Eight weeks of combined exercise training do not alter circulating microRNAs-29a, -133a, -133b, and -155 in young, healthy men. Eur J Appl Physiol 2022; 122:921-933. [PMID: 35015112 DOI: 10.1007/s00421-022-04886-7] [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: 09/03/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Individuals with a family history of type 2 diabetes (FH +) have an increased risk of developing type 2 diabetes. Circulating microRNAs (miRNAs) have been implicated as biomarkers of type 2 diabetes risk. Here, we investigated if four circulating miRNAs related to glucose metabolism were altered in men with a FH + and we conducted a preliminary analysis to determine if miRNA expressions were responsive to 8 weeks of combined exercise training. METHODS Sixteen young healthy men (mean ± SD; age 22.5 ± 2.5; BMI 26.4 ± 4.0) with FH + or without a family history of type 2 diabetes (FH -) underweight 8 weeks of combined endurance and resistance exercise training (n = 8 FH -; n = 8 FH +). The expression of miR-29a, miR-133a, miR-133b, and miR-155 were measured in serum before and after exercise training. QIAGEN's Ingenuity® Pathway Analysis was used to examine miRNA target genes and their involvement in glucose metabolism signaling pathways. RESULTS There were no differences in miRNA expressions between FH - and FH + . Exercise training did not alter miRNA expressions in either FH - or FH + despite improvements in insulin sensitivity, aerobic capacity, and muscular strength. miR-29a and miR-155 were inversely related to fasting glucose, and miR-133a and miR-133b were negatively correlated with glucose tolerance; however, correlations were not observed with insulin sensitivity. CONCLUSIONS The circulating miRNAs- miR-29a, miR-133a, miR-133b, and miR-155 are related to measures of glucose metabolism in healthy, normoglycemic men, but do not reflect peripheral insulin sensitivity or improvements in metabolic health following 8 weeks of combined exercise training.
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Affiliation(s)
- Cesar A Meza
- Metabolic, Nutrition and Exercise Research (MiNER) Laboratory, Department of Kinesiology, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79902, USA
| | - Manuel Amador
- Metabolic, Nutrition and Exercise Research (MiNER) Laboratory, Department of Kinesiology, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79902, USA
| | - Andrew J McAinch
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia.,Australian Institute for Musculoskeletal Science (AIMSS), Victoria University, St. Albans, VIC, Australia
| | - Khodeza Begum
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79902, USA
| | - Sourav Roy
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79902, USA
| | - Sudip Bajpeyi
- Metabolic, Nutrition and Exercise Research (MiNER) Laboratory, Department of Kinesiology, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79902, USA.
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21
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Kim J, Cho S, Park Y, Lee J, Park J. Evaluation of micro-RNA in extracellular vesicles from blood of patients with prostate cancer. PLoS One 2021; 16:e0262017. [PMID: 34972164 PMCID: PMC8719659 DOI: 10.1371/journal.pone.0262017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) contain various types of molecules including micro-RNAs, so isolating EVs can be an effective way to analyze and diagnose diseases. A lot of micro-RNAs have been known in relation to prostate cancer (PCa), and we evaluate miR-21, miR-141, and miR-221 in EVs and compare them with prostate-specific antigen (PSA). EVs were isolated from plasma of 38 patients with prostate cancer and 8 patients with benign prostatic hyperplasia (BPH), using a method that showed the highest recovery of RNA. Isolation of EVs concentrated micro-RNAs, reducing the cycle threshold (Ct) value of RT-qPCR amplification of micro-RNA such as miR-16 by 5.12 and miR-191 by 4.65, compared to the values before EV isolation. Normalization of target micro-RNAs was done using miR-191. For miR-221, the mean expression level of patients with localized PCa was significantly higher than that of the control group, having 33.45 times higher expression than the control group (p < 0.01). Area under curve (AUC) between BPH and PCa for miR-221 was 0.98 (p < 0.0001), which was better than AUC for prostate-specific antigen (PSA) level in serum for the same patients. The levels of miR-21 and miR-141 in EVs did not show significant changes in patients with PCa compared to the control group in this study. This study suggests isolating EVs can be a helpful approach in analyzing micro-RNAs with regard to disease.
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Affiliation(s)
- Jiyoon Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
| | - Siwoo Cho
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
| | - Yonghyun Park
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jiyoul Lee
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaesung Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
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22
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Oh-Hohenhorst SJ, Lange T. Role of Metastasis-Related microRNAs in Prostate Cancer Progression and Treatment. Cancers (Basel) 2021; 13:cancers13174492. [PMID: 34503302 PMCID: PMC8431208 DOI: 10.3390/cancers13174492] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In this review article we summarize the current literature on the pro- and anti-metastatic roles of distinct microRNAs in prostate cancer with a particular focus on their impact on invasion, migration and epithelial-to-mesenchymal transition. Moreover, we give a brief overview on how this knowledge developed so far into novel therapeutic approaches to target metastatic prostate cancer. Abstract Prostate cancer (PCa) is one of the most prevalent cancer types in males and the consequences of its distant metastatic deposits are the leading cause of PCa mortality. Therefore, identifying the causes and molecular mechanisms of hematogenous metastasis formation is of considerable clinical importance for the future development of improved therapeutic approaches. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level by targeting messenger RNAs. Numerous studies have identified miRNAs as promotors or inhibitors of metastasis and revealed, in part, their targeting pathways in PCa. Because miRNAs are remarkably stable and can be detected in both tissue and body fluid, its potential as specific biomarkers for metastasis and therapeutic response is also currently under preclinical evaluation. In the present review, we focus on miRNAs that are supposed to initiate or suppress metastasis by targeting several key mRNAs in PCa. Metastasis-suppressing miRNAs include miR-33a-5p, miR-34, miR-132 and miR-212, miR-145, the miR-200 family (incl. miR-141-3p), miR-204-5p, miR-532-3p, miR-335, miR-543, miR-505-3p, miR 19a 3p, miR-802, miR-940, and miR-3622a. Metastasis-promoting RNAs, such as miR-9, miR-181a, miR-210-3, miR-454, miR-671-5p, have been shown to increase the metastatic potential of PCa cells. Other metastasis-related miRNAs with conflicting reports in the literature are also discussed (miR-21 and miR-186). Finally, we summarize the recent developments of miRNA-based therapeutic approaches, as well as current limitations in PCa. Taken together, the metastasis-controlling miRNAs provide the potential to be integrated in the strategy of diagnosis, prognosis, and treatment of metastatic PCa. Nevertheless, there is still a lack of consistency between certain miRNA signatures and reproducibility, which impedes clinical implementation.
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Affiliation(s)
- Su Jung Oh-Hohenhorst
- Martini-Klinik, Prostate Cancer Centre, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany;
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) et Institut du Cancer de Montréal (ICM), Montreal, QC H2X 0A9, Canada
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
- Correspondence:
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Prieto-Vila M, Yoshioka Y, Ochiya T. Biological Functions Driven by mRNAs Carried by Extracellular Vesicles in Cancer. Front Cell Dev Biol 2021; 9:620498. [PMID: 34527665 PMCID: PMC8435577 DOI: 10.3389/fcell.2021.620498] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs), including exosomes and microvesicles, are extracellular nanovesicles released by most cells. EVs play essential roles in intercellular communication via the transport of a large variety of lipids, proteins, and nucleic acids to recipient cells. Nucleic acids are the most commonly found molecules inside EVs, and due to their small size, microRNAs and other small RNAs are the most abundant nucleic acids. However, longer molecules, such as messenger RNAs (mRNAs), have also been found. mRNAs encapsulated within EVs have been shown to be transferred to recipient cells and translated into proteins, altering the behavior of the cells. Secretion of EVs is maintained not only through multiple normal physiological conditions but also during aberrant pathological conditions, including cancer. Recently, the mRNAs carried by EVs in cancer have attracted great interest due to their broad roles in tumor progression and microenvironmental remodeling. This review focuses on the biological functions driven by mRNAs carried in EVs in cancer, which include supporting tumor progression by activating cancer cell growth, migration, and invasion; inducing microenvironmental remodeling via hypoxia, angiogenesis, and immunosuppression; and promoting modulation of the microenvironment at distant sites for the generation of a premetastatic niche, collectively inducing metastasis. Furthermore, we describe the potential use of mRNAs carried by EVs as a noninvasive diagnostic tool and novel therapeutic approach.
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Affiliation(s)
| | | | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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24
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Role of microRNAs (MiRNAs) as biomarkers of cervical carcinogenesis: a systematic review. Obstet Gynecol Sci 2021; 64:419-436. [PMID: 34384196 PMCID: PMC8458608 DOI: 10.5468/ogs.21123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/26/2021] [Indexed: 12/24/2022] Open
Abstract
We performed a systematic review to identify the role of microRNAs (miRNAs) as biomarkers in the progression of cervical precancerous lesions. A comprehensive search of the Cochrane Controlled Register of Trials, PubMed, ScienceDirect, and Embase databases was performed for articles published between January 2010 and June 2020. The following Medical Subject Headings (MeSH) terms were searched: “microRNA” and “cervical” and “lesion.” All study designs that aimed to evaluate the correlation of miRNA expression with different precancerous cervical staging and/ or cervical cancer were included, except for case reports and case series. Approximately 82 individual miRNAs were found to be significant in differentiating the stages of cervical carcinogenesis. Among the miRNAs, miR-21 is the most prevalent, and it is consistently upregulated progressively from normal cervical to worsening cervical lesion stages in both cell and serum samples. miR-205 has been shown to have a higher specificity than human papilloma virus testing in predicting the absence of high-grade squamous intraepithelial lesions (HSILs) in exfoliated cell samples. The tumor suppressor miRNAs miR-34, let-7, miR-203 miR-29, and miR-375 were significantly downregulated in low-grade squamous intraepithelial lesions, HSILs, and cervical cancer. We found significant dysregulated miRNAs in cervical carcinogenesis with their dynamic expression changes and ability to detect viral persistency, risk prediction of low-grade lesions (cervical intraepithelial neoplasia [CIN] 2) to high-grade lesions (CIN 3), and progression of CIN 3 to cancer. Their ability to discriminate HSILs from non-dysplastic lesions has potential implications in early diagnosis and reducing overtreatment of otherwise regressive early preinvasive lesions.
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25
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Nganou-Makamdop K, Talla A, Sharma AA, Darko S, Ransier A, Laboune F, Chipman JG, Beilman GJ, Hoskuldsson T, Fourati S, Schmidt TE, Arumugam S, Lima NS, Moon D, Callisto S, Schoephoerster J, Tomalka J, Mugyenyi P, Ssali F, Muloma P, Ssengendo P, Leda AR, Cheu RK, Flynn JK, Morou A, Brunet-Ratnasingham E, Rodriguez B, Lederman MM, Kaufmann DE, Klatt NR, Kityo C, Brenchley JM, Schacker TW, Sekaly RP, Douek DC. Translocated microbiome composition determines immunological outcome in treated HIV infection. Cell 2021; 184:3899-3914.e16. [PMID: 34237254 DOI: 10.1016/j.cell.2021.05.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The impact of the microbiome on HIV disease is widely acknowledged although the mechanisms downstream of fluctuations in microbial composition remain speculative. We detected rapid, dynamic changes in translocated microbial constituents during two years after cART initiation. An unbiased systems biology approach revealed two distinct pathways driven by changes in the abundance ratio of Serratia to other bacterial genera. Increased CD4 T cell numbers over the first year were associated with high Serratia abundance, pro-inflammatory innate cytokines, and metabolites that drive Th17 gene expression signatures and restoration of mucosal integrity. Subsequently, decreased Serratia abundance and downregulation of innate cytokines allowed re-establishment of systemic T cell homeostasis promoting restoration of Th1 and Th2 gene expression signatures. Analyses of three other geographically distinct cohorts of treated HIV infection established a more generalized principle that changes in diversity and composition of translocated microbial species influence systemic inflammation and consequently CD4 T cell recovery.
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Affiliation(s)
- Krystelle Nganou-Makamdop
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Clinical and Molecular Virology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Aarthi Talla
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Ashish Arunkumar Sharma
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sam Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Farida Laboune
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey G Chipman
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gregory J Beilman
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Torfi Hoskuldsson
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Slim Fourati
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Thomas E Schmidt
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sahaana Arumugam
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noemia S Lima
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Damee Moon
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel Callisto
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Jeffery Tomalka
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | | | | | | | | | - Ana R Leda
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Ryan K Cheu
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID/NIH, Bethesda, MD 20892, USA
| | - Antigoni Morou
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada; Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Elsa Brunet-Ratnasingham
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Benigno Rodriguez
- Case Western Reserve University School of Medicine, Cleveland, OH 10900, USA
| | - Michael M Lederman
- Case Western Reserve University School of Medicine, Cleveland, OH 10900, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nichole R Klatt
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Cissy Kityo
- Joint Clinical Research Center, Kampala, Uganda
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID/NIH, Bethesda, MD 20892, USA
| | - Timothy W Schacker
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Rafick P Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA.
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Garcia A, Dunoyer-Geindre S, Fontana P. Do miRNAs Have a Role in Platelet Function Regulation? Hamostaseologie 2021; 41:217-224. [PMID: 34192780 DOI: 10.1055/a-1478-2105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs known to repress mRNA translation and subsequent protein production. miRNAs are predicted to modulate many targets and are involved in regulating various cellular processes. Identifying their role in cell function regulation may allow circulating miRNAs to be used as diagnostic or prognostic markers of various diseases. Increasing numbers of clinical studies have shown associations between circulating miRNA levels and platelet reactivity or the recurrence of cardiovascular events. However, these studies differed regarding population selection, sample types used, miRNA quantification procedures, and platelet function assays. Furthermore, they often lacked functional validation of the miRNA identified in such studies. The latter step is essential to identifying causal relationships and understanding if and how miRNAs regulate platelet function. This review describes recent advances in translational research dedicated to identifying miRNAs' roles in platelet function regulation.
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Affiliation(s)
- A Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - P Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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27
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Takahashi H, Yasui T, Baba Y. Nanobiodevices for the Isolation of Circulating Nucleic Acid for Biomedical Applications. CHEM LETT 2021. [DOI: 10.1246/cl.210066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hiromi Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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28
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Tessier SN, Bookstaver LD, Angpraseuth C, Stannard CJ, Marques B, Ho UK, Muzikansky A, Aldikacti B, Reátegui E, Rabe DC, Toner M, Stott SL. Isolation of intact extracellular vesicles from cryopreserved samples. PLoS One 2021; 16:e0251290. [PMID: 33983964 PMCID: PMC8118530 DOI: 10.1371/journal.pone.0251290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/23/2021] [Indexed: 01/23/2023] Open
Abstract
Extracellular vesicles (EVs) have emerged as promising candidates in biomarker discovery and diagnostics. Protected by the lipid bilayer, the molecular content of EVs in diverse biofluids are protected from RNases and proteases in the surrounding environment that may rapidly degrade targets of interests. Nonetheless, cryopreservation of EV-containing samples to -80°C may expose the lipid bilayer to physical and biological stressors which may result in cryoinjury and contribute to changes in EV yield, function, or molecular cargo. In the present work, we systematically evaluate the effect of cryopreservation at -80°C for a relatively short duration of storage (up to 12 days) on plasma- and media-derived EV particle count and/or RNA yield/quality, as compared to paired fresh controls. On average, we found that the plasma-derived EV concentration of stored samples decreased to 23% of fresh samples. Further, this significant decrease in EV particle count was matched with a corresponding significant decrease in RNA yield whereby plasma-derived stored samples contained only 47-52% of the total RNA from fresh samples, depending on the extraction method used. Similarly, media-derived EVs showed a statistically significant decrease in RNA yield whereby stored samples were 58% of the total RNA from fresh samples. In contrast, we did not obtain clear evidence of decreased RNA quality through analysis of RNA traces. These results suggest that samples stored for up to 12 days can indeed produce high-quality RNA; however, we note that when directly comparing fresh versus cryopreserved samples without cryoprotective agents there are significant losses in total RNA. Finally, we demonstrate that the addition of the commonly used cryoprotectant agent, DMSO, alongside greater control of the rate of cooling/warming, can rescue EVs from damaging ice formation and improve RNA yield.
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Affiliation(s)
- Shannon N. Tessier
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Shriners Hospitals for Children—Boston, Boston, MA, United States of America
| | - Lauren D. Bookstaver
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Cindy Angpraseuth
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Cleo J. Stannard
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Beatriz Marques
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Uyen K. Ho
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Alona Muzikansky
- Biostatistics Center, Massachusetts General Hospital, Boston, MA, United States of America
| | - Berent Aldikacti
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Eduardo Reátegui
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Daniel C. Rabe
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Mehmet Toner
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Shriners Hospitals for Children—Boston, Boston, MA, United States of America
| | - Shannon L. Stott
- Department of Surgery, Center for Engineering in Medicine and BioMEMS Resource Center Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
- * E-mail:
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29
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Yuan F, Li Z, Chen L, Zeng T, Zhang YH, Ding S, Huang T, Cai YD. Identifying the Signatures and Rules of Circulating Extracellular MicroRNA for Distinguishing Cancer Subtypes. Front Genet 2021; 12:651610. [PMID: 33767734 PMCID: PMC7985347 DOI: 10.3389/fgene.2021.651610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/10/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the most threatening diseases to humans. It can invade multiple significant organs, including lung, liver, stomach, pancreas, and even brain. The identification of cancer biomarkers is one of the most significant components of cancer studies as the foundation of clinical cancer diagnosis and related drug development. During the large-scale screening for cancer prevention and early diagnosis, obtaining cancer-related tissues is impossible. Thus, the identification of cancer-associated circulating biomarkers from liquid biopsy targeting has been proposed and has become the most important direction for research on clinical cancer diagnosis. Here, we analyzed pan-cancer extracellular microRNA profiles by using multiple machine-learning models. The extracellular microRNA profiles on 11 cancer types and non-cancer were first analyzed by Boruta to extract important microRNAs. Selected microRNAs were then evaluated by the Max-Relevance and Min-Redundancy feature selection method, resulting in a feature list, which were fed into the incremental feature selection method to identify candidate circulating extracellular microRNA for cancer recognition and classification. A series of quantitative classification rules was also established for such cancer classification, thereby providing a solid research foundation for further biomarker exploration and functional analyses of tumorigenesis at the level of circulating extracellular microRNA.
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Affiliation(s)
- Fei Yuan
- School of Life Sciences, Shanghai University, Shanghai, China
- Department of Science and Technology, Binzhou Medical University Hospital, Binzhou, China
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Swellam M, Zahran RFK, Ghonem SA, Abdel-Malak C. Serum MiRNA-27a as potential diagnostic nucleic marker for breast cancer. Arch Physiol Biochem 2021; 127:90-96. [PMID: 31145011 DOI: 10.1080/13813455.2019.1616765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Accumulating evidence reveals that microRNA 27a (miR 27a) is implicated in the pathogenesis of cancer. However, its diagnostic role in breast cancer (BC) still needs investigation. MATERIALS AND METHODS MiR 27a expression was assessed in serum samples from patients with primary BC (n = 100), benign breast lesions (n = 30) and control group served as healthy volunteers (n = 20) using quantitative real-time PCR. RESULTS Both expression and mean rank of miR 27a and tumor markers among BC patients as compared to the other two groups. Clinicopathological characteristics showed significant relation with miRN 27a expression for clinical stage, histological grading, ER receptor and HER-2/neu. The diagnostic efficacy for miR 27a was superior to both tumor markers for early detection of BC especially high-risk BC groups. CONCLUSION Detection of miR 27a expression may serve as a potential sensitive minimally invasive molecular marker for early detection of primary BC.
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Affiliation(s)
- Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, Giza, Egypt
| | - Rasha F K Zahran
- Biochemistry Division, Faculty of Science, Damietta University, Damietta, Egypt
| | - Samar Ayman Ghonem
- Biochemistry Division, Faculty of Science, Damietta University, Damietta, Egypt
| | - Camelia Abdel-Malak
- Biochemistry Division, Faculty of Science, Damietta University, Damietta, Egypt
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31
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Clark ME, Rizos H, Pereira MR, McEvoy AC, Marsavela G, Calapre L, Meehan K, Ruhen O, Khattak MA, Meniawy TM, Long GV, Carlino MS, Menzies AM, Millward M, Ziman M, Gray ES. Detection of BRAF splicing variants in plasma-derived cell-free nucleic acids and extracellular vesicles of melanoma patients failing targeted therapy therapies. Oncotarget 2020; 11:4016-4027. [PMID: 33216826 PMCID: PMC7646833 DOI: 10.18632/oncotarget.27790] [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: 08/07/2020] [Accepted: 10/10/2020] [Indexed: 12/13/2022] Open
Abstract
The analysis of plasma circulating tumour nucleic acids provides a non-invasive approach to assess disease burden and the genetic evolution of tumours in response to therapy. BRAF splicing variants are known to confer melanoma resistance to BRAF inhibitors. We developed a test to screen cell-free RNA (cfRNA) for the presence of BRAF splicing variants. Custom droplet digital PCR assays were designed for the detection of BRAF splicing variants p61, p55, p48 and p41 and then validated using RNA from cell lines carrying these variants. Evaluation of plasma from patients with reported objective response to BRAF/MEK inhibition followed by disease progression was revealed by increased circulating tumour DNA (ctDNA) in 24 of 38 cases at the time of relapse. Circulating BRAF splicing variants were detected in cfRNA from 3 of these 38 patients; two patients carried the BRAF p61 variant and one the p55 variant. In all three cases the presence of the splicing variant was apparent only at the time of progressive disease. BRAF p61 was also detectable in plasma of one of four patients with confirmed BRAF splicing variants in their progressing tumours. Isolation and analysis of RNA from extracellular vesicles (EV) from resistant cell lines and patient plasma demonstrated that BRAF splicing variants are associated with EVs. These findings indicate that in addition to plasma ctDNA, RNA carried by EVs can provide important tumour specific information.
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Affiliation(s)
- Michael E. Clark
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Helen Rizos
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
- Westmead Institute for Cancer Research, The University of Sydney, Sydney, New South Wales, Australia
- Melanoma Institute Australia, Sydney, New South Wales, Australia
| | - Michelle R. Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Ashleigh C. McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Gabriela Marsavela
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, Chinese University of Hong Kong, Hong Kong
| | - Olivia Ruhen
- School of Biomedical Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Muhammad A. Khattak
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Tarek M. Meniawy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Mater Hospital, North Sydney, New South Wales, Australia
| | - Matteo S. Carlino
- Westmead Institute for Cancer Research, The University of Sydney, Sydney, New South Wales, Australia
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander M. Menzies
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Mater Hospital, North Sydney, New South Wales, Australia
| | - Michael Millward
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
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Mattox AK, Yan H, Bettegowda C. The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors. Neuro Oncol 2020; 21:1509-1518. [PMID: 31595305 PMCID: PMC6917400 DOI: 10.1093/neuonc/noz156] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cerebrospinal fluid (CSF) may be the best hope for minimally invasive diagnosis and treatment monitoring of central nervous system (CNS) malignancies. Discovery/validation of cell-free nucleic acid and protein biomarkers has the potential to revolutionize CNS cancer care, paving the way for presurgical evaluation, earlier detection of recurrence, and the selection of targeted therapies. While detection of mutations, changes in RNA and miRNA expression, epigenetic alterations, and elevations of protein levels have been detected in the CSF of patients with CNS tumors, most of these biomarkers remain unvalidated. In this review, we focus on the molecular changes that have been identified in a variety of CNS tumors and profile the approaches used to detect these alterations in clinical samples. We further emphasize the importance of systemic collection of CSF and the establishment of standardized collection protocols that will lead to better cross-study biomarker validation and hopefully FDA-approved clinical markers.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center, Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Monsellato I, Garibaldi E, Cassinotti E, Baldari L, Boni L, Elmore U, Delpini R, Rosati R, Perinotti R, Alongi F, Bertocchi E, Gori S, Ruffo G, Pernazza G, Pulighe F, De Nisco C, Morpurgo E, Contardo T, Mammano E, Perna F, Menegatti B, Coratti A, Buccianti P, Balestri R, Ceccarelli C, Cavaliere D, Solaini L, Ercolani G, Traverso E, Fusco V, Torri V, Orecchia S. Expression levels of circulating miRNAs as biomarkers during multimodal treatment of rectal cancer - TiMiSNAR-mirna: a substudy of the TiMiSNAR Trial (NCT03962088). Trials 2020; 21:678. [PMID: 32711544 PMCID: PMC7382047 DOI: 10.1186/s13063-020-04568-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 07/02/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Neoadjuvant chemoradiotherapy followed by surgery is the mainstay treatment for locally advanced rectal cancer, leading to significant decrease in tumor size (downsizing) and a shift towards earlier disease stage (downstaging). Extensive histopathological work-up of the tumor specimen after surgery including tumor regression grading and lymph node status helped to visualize individual tumor sensitivity to chemoradiotherapy, retrospectively. As the response to neoadjuvant chemoradiotherapy is heterogeneous, however, valid biomarkers are needed to monitor tumor response. A relevant number of studies aimed to identify molecular markers retrieved from tumor tissue while the relevance of blood-based biomarkers is less stringent assessed. MicroRNAs are currently under investigation to serve as blood-based biomarkers. To date, no screening approach to identify relevant miRNAs as biomarkers in blood of patients with rectal cancer was undertaken. The aim of the study is to investigate the role of circulating miRNAs as biomarkers in those patients included in the TiMiSNAR Trial (NCT03465982). This is a biomolecular substudy of TiMiSNAR Trial (NCT03962088). METHODS All included patients in the TiMiSNAR Trial are supposed to undergo blood collection at the time of diagnosis, after neoadjuvant treatment, after 1 month from surgery, and after adjuvant chemotherapy whenever indicated. DISCUSSION TiMiSNAR-MIRNA will evaluate the association of variation between preneoadjuvant and postneoadjuvant expression levels of miRNA with pathological complete response. Moreover, the study will evaluate the role of liquid biopsies in the monitoring of treatment, correlate changes in expression levels of miRNA following complete surgical resection with disease-free survival, and evaluate the relation between changes in miRNA during surveillance and tumor relapse. TRIAL REGISTRATION Clinicaltrials.gov NCT03962088 . Registered on 23 May 2019.
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Affiliation(s)
- Igor Monsellato
- Department of Surgery, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Via Venezia 16, 15121 Alessandria, Italy
| | - Elisabetta Garibaldi
- Department of Radiation Oncology, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Elisa Cassinotti
- Department of Surgery, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Ludovica Baldari
- Department of Surgery, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Luigi Boni
- Department of Surgery, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Ugo Elmore
- Ospedale San raffaele IRCCS, Milan, Italy
| | | | | | | | | | | | | | | | | | | | | | - Emilio Morpurgo
- Ospedale Civile Pietro Cosma, Camposampiero/Ospedale Sant’Antonio, Padova, Italy
| | - Tania Contardo
- Ospedale Civile Pietro Cosma, Camposampiero, Padova, Italy
| | - Enzo Mammano
- Ospedale Civile Pietro Cosma, Camposampiero/Ospedale Sant’Antonio, Padova, Italy
| | - Federico Perna
- Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | | | - Andrea Coratti
- Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | | | | | | | | | | | | | - Elena Traverso
- Department of Oncology, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Vittorio Fusco
- Department of Oncology, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Valter Torri
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sara Orecchia
- Department of Pathology, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
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Potential of Using Cell-Free DNA and miRNA in Breast Milk to Screen Early Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8126176. [PMID: 32714986 PMCID: PMC7354639 DOI: 10.1155/2020/8126176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
Objective An ideal sample source is critical for more reliable and sensitive early detection of nucleic acid changes associated with breast cancer. Breast milk (BM) is a good noninvasive origin for genetic testing of early breast cancer, but cells in BM are easily disintegrated. So we investigate here whether cell-free nucleic acid (cfNA) exists in BM in a more stable form and whether the quality of BM cfNA is good enough for genetic testing. Methods A self-designed qRT-PCR method was used to measure the existence and abundance of cfDNA. Quality of cfDNA and cfRNA were detected by capillary electrophoresis. Whole genome bisulfite sequencing and miRNA sequencing were used to explore the sources of cfDNA and cell-free miRNA in BM. The copy number analysis and z-test based on whole genome sequencing data were used to determine the integrity of genetic information in BM cfNA. Results We found that cell-free DNA and miRNA exist in the studied breast milk samples in a stable form that can tolerate incubation of BM at room temperature for at least 7 days. These cell-free nucleic acids come mainly from breast-derived cells and contain genetic information as good integrity as in BM cells. We further listed some candidate miRNAs as potential biomarkers for research of early breast cancer screening by analysis of previous reports and our data. Conclusions Our results suggest that cfDNA and cell-free miRNA in BM might be new noninvasive sample sources for finding early alterations of nucleic acid associated with the initiation and progression of breast cancer.
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Lolomadze EA, Kometova VV, Rodionov VV. Circulating RNA in blood plasma as diagnostic tool for clinical oncology. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
One of the key challenges facing today’s oncology is the discovery of early predictors of malignant neoplasms in patients’ biological samples. Liquid biopsy is a noninvasive diagnostic technique based on the detection and isolation of tumor cells, tumor-derived nucleic acid and exosomes circulating in the blood plasma of cancer patients. There is a plethora of research studies of circulating tumor DNA in patients with MN. The active proliferation of tumor cells occurs in the backdrop of altered gene expression. The presence of tissue-specific transcripts in the circulating RNA fraction suggests that levels of circulating RNA reflect the development of the primary tumor. We think that cell-free RNA circulating in the blood plasma is a promising molecular biomarker for early cancer detection.
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Affiliation(s)
- EA Lolomadze
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - VV Kometova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - VV Rodionov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
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Bottani M, Banfi G, Lombardi G. The Clinical Potential of Circulating miRNAs as Biomarkers: Present and Future Applications for Diagnosis and Prognosis of Age-Associated Bone Diseases. Biomolecules 2020; 10:E589. [PMID: 32290369 PMCID: PMC7226497 DOI: 10.3390/biom10040589] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/01/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Osteoporosis, related fracture/fragility, and osteoarthritis are age-related pathologies that, over recent years, have seen increasing incidence and prevalence due to population ageing. The diagnostic approaches to these pathologies suffer from limited sensitivity and specificity, also in monitoring the disease progression or treatment. For this reason, new biomarkers are desirable for improving the management of osteoporosis and osteoarthritis patients. The non-coding RNAs, called miRNAs, are key post-transcriptional factors in bone homeostasis, and promising circulating biomarkers for pathological conditions in which to perform a biopsy can be problematic. In fact, miRNAs can easily be detected in biological fluids (i.e., blood, serum, plasma) using methods with elevated sensitivity and specificity (RT-qPCR, microarray, and NGS). However, the analytical phases required for miRNAs' evaluation still present some practical issues that limit their use in clinical practice. This review reveals miRNAs' potential as circulating biomarkers for evaluating predisposition, diagnosis, and prognosis of osteoporosis (postmenopausal or idiopathic), bone fracture/fragility, and osteoarthritis, with a focus on pre-analytical, analytical, and post-analytical protocols used for their validation and thus on their clinical applicability. These evidences may support the definition of early diagnostic tools based on circulating miRNAs for bone diseases and osteoarthritis as well as for monitoring the effects of specific treatments.
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Affiliation(s)
- Michela Bottani
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Via Riccardo Galeazzi 4, 20161 Milano, Italy; (M.B.); (G.B.)
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Via Riccardo Galeazzi 4, 20161 Milano, Italy; (M.B.); (G.B.)
- Vita-Salute San Raffaele University, 20132 Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Via Riccardo Galeazzi 4, 20161 Milano, Italy; (M.B.); (G.B.)
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Królowej Jadwigi 27/39, 61-871 Poznań, Poland
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Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome. Cells 2020; 9:cells9040794. [PMID: 32224889 PMCID: PMC7226126 DOI: 10.3390/cells9040794] [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: 12/30/2019] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders with large heterogeneity at the clinical and molecular levels. As diagnostic procedures shift from bone marrow biopsies towards less invasive techniques, circulating small noncoding RNAs (sncRNAs) have become of particular interest as potential novel noninvasive biomarkers of the disease. We aimed to characterize the expression profiles of circulating sncRNAs of MDS patients and to search for specific RNAs applicable as potential biomarkers. We performed small RNA-seq in paired samples of total plasma and plasma-derived extracellular vesicles (EVs) obtained from 42 patients and 17 healthy controls and analyzed the data with respect to the stage of the disease, patient survival, response to azacitidine, mutational status, and RNA editing. Significantly higher amounts of RNA material and a striking imbalance in RNA content between plasma and EVs (more than 400 significantly deregulated sncRNAs) were found in MDS patients compared to healthy controls. Moreover, the RNA content of EV cargo was more homogeneous than that of total plasma, and different RNAs were deregulated in these two types of material. Differential expression analyses identified that many hematopoiesis-related miRNAs (e.g., miR-34a, miR-125a, and miR-150) were significantly increased in MDS and that miRNAs clustered on 14q32 were specifically increased in early MDS. Only low numbers of circulating sncRNAs were significantly associated with somatic mutations in the SF3B1 or DNMT3A genes. Survival analysis defined a signature of four sncRNAs (miR-1237-3p, U33, hsa_piR_019420, and miR-548av-5p measured in EVs) as the most significantly associated with overall survival (HR = 5.866, p < 0.001). In total plasma, we identified five circulating miRNAs (miR-423-5p, miR-126-3p, miR-151a-3p, miR-125a-5p, and miR-199a-3p) whose combined expression levels could predict the response to azacitidine treatment. In conclusion, our data demonstrate that circulating sncRNAs show specific patterns in MDS and that their expression changes during disease progression, providing a rationale for the potential clinical usefulness of circulating sncRNAs in MDS prognosis. However, monitoring sncRNA levels in total plasma or in the EV fraction does not reflect one another, instead, they seem to represent distinctive snapshots of the disease and the data should be interpreted circumspectly with respect to the type of material analyzed.
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Condrat CE, Thompson DC, Barbu MG, Bugnar OL, Boboc A, Cretoiu D, Suciu N, Cretoiu SM, Voinea SC. miRNAs as Biomarkers in Disease: Latest Findings Regarding Their Role in Diagnosis and Prognosis. Cells 2020; 9:E276. [PMID: 31979244 PMCID: PMC7072450 DOI: 10.3390/cells9020276] [Citation(s) in RCA: 637] [Impact Index Per Article: 159.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/14/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) represent a class of small, non-coding RNAs with the main roles of regulating mRNA through its degradation and adjusting protein levels. In recent years, extraordinary progress has been made in terms of identifying the origin and exact functions of miRNA, focusing on their potential use in both the research and the clinical field. This review aims at improving the current understanding of these molecules and their applicability in the medical field. A thorough analysis of the literature consulting resources available in online databases such as NCBI, PubMed, Medline, ScienceDirect, and UpToDate was performed. There is promising evidence that in spite of the lack of standardized protocols regarding the use of miRNAs in current clinical practice, they constitute a reliable tool for future use. These molecules meet most of the required criteria for being an ideal biomarker, such as accessibility, high specificity, and sensitivity. Despite present limitations, miRNAs as biomarkers for various conditions remain an impressive research field. As current techniques evolve, we anticipate that miRNAs will become a routine approach in the development of personalized patient profiles, thus permitting more specific therapeutic interventions.
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Affiliation(s)
- Carmen Elena Condrat
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
| | - Dana Claudia Thompson
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
| | - Madalina Gabriela Barbu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
| | - Oana Larisa Bugnar
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
| | - Andreea Boboc
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
| | - Dragos Cretoiu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
- Department of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania
| | - Nicolae Suciu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, 020395 Bucharest, Romania; (C.E.C.); (D.C.T.); (M.G.B.); (O.L.B.); (A.B.); (D.C.); (N.S.)
- Division of Obstetrics, Gynecology and Neonatology, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania
- Department of Obstetrics and Gynecology, Polizu Clinical Hospital, Alessandrescu-Rusescu National Institute for Mother and Child Health, 020395 Bucharest, Romania
| | - Sanda Maria Cretoiu
- Department of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania
| | - Silviu Cristian Voinea
- Department of Surgical Oncology, Prof. Dr. Alexandru Trestioreanu Oncology Institute, Carol Davila University of Medicine and Pharmacy, 252 Fundeni Rd., 022328 Bucharest, Romania;
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TERT promoter hotspot mutations and their relationship with TERT levels and telomere erosion in patients with head and neck squamous cell carcinoma. J Cancer Res Clin Oncol 2020; 146:381-389. [PMID: 31960186 DOI: 10.1007/s00432-020-03130-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/09/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE To evaluate the prevalence of two recurrent somatic mutations (-124 C>T and -146 C>T) within the promoter of the gene encoding telomerase reverse transcriptase (TERT) as well as their relationship with TERT level, telomeres length, and outcome in patients with head and neck squamous cell carcinomas (HNSCCs). METHODS We evaluate the prevalence of TERT promoter mutations, TERT levels, and telomere length in paired cancer tissue and adjacent mucosa (AM) in a series of HNSCCs. RESULTS Cancer tissue and AM specimens from 105 patients were analyzed. Telomere length and TERT mRNA levels were estimated using real-time polymerase chain reaction. TERT promoter mutations were assessed using Sanger sequencing. Out of 105 cases, 101 were considered suitable for the analysis. TERT promoter harbored mutations in 12 tumors (11.9%), with -124 C>T and -146 C>T accounting for 83.3% and 16.7% of the alterations, respectively. No mutations were detected in AM samples. The prevalence of TERT promoter mutations was significantly higher in oral cavity SCCs (10 out of 27 tumors; 37%), and telomere length in AM was shorter in patients with tumors carrying TERT promoter mutations than in patients with unmutated TERT promoter cancers (p = 0.023). TERT levels in tumor did not significantly differ according to the mutational status of TERT promoter. No significant association was found between TERT promoter status and overall survival. CONCLUSION TERT promoter mutations are most likely a late event in tumor development, occurring in a context of critically short telomeres, mostly in patients with oral cavity SCC. TERT levels, but not TERT promoter mutational status impact clinical outcome.
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Circulating Extracellular Vesicle MicroRNA as Diagnostic Biomarkers in Early Colorectal Cancer-A Review. Cancers (Basel) 2019; 12:cancers12010052. [PMID: 31878015 PMCID: PMC7016718 DOI: 10.3390/cancers12010052] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies in the developed world, with global deaths expected to double in the next decade. Disease stage at diagnosis is the single greatest prognostic indicator for long-term survival. Unfortunately, early stage CRC is often asymptomatic and diagnosis frequently occurs at an advanced stage, where long-term survival can be as low as 14%. Circulating microRNAs encapsulated in extracellular vesicles (EVs) have recently come to prominence as novel diagnostic markers for cancer. EV-miRNAs are dysregulated in the circulation of CRC patients compared to healthy controls, and several specific miRNA candidates have been posited as diagnostic markers, including miR-21, miR-23a, miR-1246, and miR-92a. This review outlines the current landscape of EV-miRNAs as potential diagnostic markers for CRC, with a specific focus on those able to detect early stage disease.
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Faraldi M, Sansoni V, Perego S, Gomarasca M, Kortas J, Ziemann E, Banfi G, Lombardi G. Study of the preanalytical variables affecting the measurement of clinically relevant free-circulating microRNAs: focus on sample matrix, platelet depletion, and storage conditions. Biochem Med (Zagreb) 2019; 30:010703. [PMID: 31839723 PMCID: PMC6904965 DOI: 10.11613/bm.2020.010703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023] Open
Abstract
Introduction Circulating microRNAs (miRNAs) are emerging as potential biomarkers. However, the lack of preanalytical and analytical standardization limits their use. The aim of this study was to determine the expression of different miRNAs in plasma according to different collection and storage conditions. Materials and methods Venous blood from 10 volunteers was collected in tubes spray-coated with dipotassium salt of ethylendiaminetetraacetic acid, either with (plasma-preparation tube, PPT) or without (K2EDTA) gel separator. Platelet-poor plasma (PPP) was also obtained from K2EDTA plasma. After storage under different conditions, miRNA-enriched total RNA was isolated from plasma and reverse transcribed. A panel of 179 miRNAs was assayed by quantitative polymerase chain reaction and the results were analysed by GenEx software. Detectability and stability of miRNAs were determined. Results The number of undetected miRNAs was: 18, 24, and 22 in PPT; 83, 43, and 20 in K2EDTA; and 76, 106, and 104 in PPP samples, for plasma immediately frozen at - 80°C and plasma stored for 24h at room temperature or 4°C, respectively. Circulating miRNA expression in PPT samples was not affected by storage delay or temperature, while the percentage of up- and down-regulated miRNA in K2EDTA and PPP samples ranged from 2%, and 1% to 7%, and 5%, respectively. Conclusions Sample matrix, temperature and delay in storage strongly influence the expression level of plasma miRNAs. Our results indicate PPT tubes as the most suitable matrix to improve total miRNA detectability and stability, independently of temperature.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia
| | - Veronica Sansoni
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia
| | - Silvia Perego
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia
| | - Jakub Kortas
- Department of Physical Culture, Gdańsk University of Physical Education & Sport, Gdańsk, Poland
| | - Ewa Ziemann
- Department of Athletics, Strength and Conditioning, Poznan University of Physical Education, Poznan, Poland
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia.,Università Vita-Salute San Raffaele, Milano, Italia
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto ortopedico Galeazzi, Milano, Italia.,Department of Physical Culture, Gdańsk University of Physical Education & Sport, Gdańsk, Poland
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Cacheux J, Bancaud A, Leichlé T, Cordelier P. Technological Challenges and Future Issues for the Detection of Circulating MicroRNAs in Patients With Cancer. Front Chem 2019; 7:815. [PMID: 31850308 PMCID: PMC6894013 DOI: 10.3389/fchem.2019.00815] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022] Open
Abstract
In the era of precision medicine, the success of clinical trials, notably for patients diagnosed with cancer, strongly relies on biomarkers with pristine clinical value but also on robust and versatile analytical technologies to ensure proper patients' stratification and treatment. In this review, we will first address whether plasmatic and salivary microRNAs can be considered as a reliable source of biomarkers for cancer diagnosis and prognosis. We will then discuss the pre-analytical steps preceding miRNA quantification (from isolation to purification), and how such process could be biased and time-consuming. Next, we will review the most recent tools derived from micro- and nano-technologies for microRNA detection available to date and how they may compete with current standards. This review will prioritize publications using relevant biological samples. The significance of various physical transduction schemes (mechanical, optical, electrical, etc.) for biological detection will be compared, and pros and cons of each method will be widely discussed. Finally, we will debate on how micro and nanotechnologies could widespread the use of biomarkers in modern medicine, to help manage patients with serious diseases such as cancer.
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Affiliation(s)
- Jean Cacheux
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.,Université Fédérale de Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, CRCT, Toulouse, France
| | | | | | - Pierre Cordelier
- Université Fédérale de Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, CRCT, Toulouse, France
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Predictive and prognostic significance of telomerase levels/telomere length in tissues and peripheral blood in head and neck squamous cell carcinoma. Sci Rep 2019; 9:17572. [PMID: 31772219 PMCID: PMC6879742 DOI: 10.1038/s41598-019-54028-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/05/2019] [Indexed: 01/09/2023] Open
Abstract
A growing body of evidence indicates that the expression of TERT, the catalytic subunit of telomerase, is a biological marker of progression in several cancers. We investigated the predictive and prognostic role of TERT levels and telomere length in tissues and peripheral blood in patients with head and neck squamous cell carcinoma (HNSCC). High TERT levels in cancer tissues were independently associated with worse response to therapy (odds ratio [OR]:6.26), regional failure (hazard ratio [HR]:5.75), progression (HR:2.12), and death (HR:3.53). Longer telomeres in the mucosa surrounding the tumor (SM) were independently associated with a lower risk of mucosal failure (HR:0.39). While telomere length in peripheral blood mononuclear cells (PBMC) significantly decreased with age, no correlation was found between age and telomere length in SM. No associations were found between TERT levels in plasma and telomere length in PBMC and the prognostic variables. High levels of TERT transcripts in cancer cells represent a reliable prognostic marker for identifying HNSCC patients with risk of progression. The altered relationship of telomere length to age in SM compared with PBMC suggests that in a subset of cases the phenotypically normal SM constitutes an acquired telomere-shortened epithelial field prone to genetic instability.
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Burns KE, Deane-Alder KD, Bellissima BL, Tingle MD. Circulating microRNA as biomarkers of clozapine-induced cardiotoxicity. Biomarkers 2019; 25:76-85. [PMID: 31722571 DOI: 10.1080/1354750x.2019.1693631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: This work investigated the utility of circulating microRNA (miRNA) as biomarkers of clozapine (CLZ)-induced cardiotoxicities: serious adverse events with an unusually high incidence in Australia and New Zealand.Methods: Global plasma miRNA expression was analysed by microarray in patients taking CLZ, to investigate differential expression between CLZ-induced cardiotoxicity cases (n = 6) and matched control patients (n = 12). The results were validated by RT-qPCR using a panel of 17 miRNA, and their expression was examined in both CLZ-naïve healthy volunteers (n = 12) and an expanded cohort of CLZ-taking patients (n = 21). Temporal changes were also examined in two healthy volunteers and two CLZ-induced cardiotoxicity patients.Results: No miRNA were differentially expressed between cases of CLZ-induced cardiotoxicity and control patients. Circulating levels of several miRNA were significantly altered in CLZ-taking patients compared to healthy volunteers, with miR-16-5p, miR-25-3p, miR-92a-3p, miR-320a-3p, and miR-486-3p upregulated and miR-22-3p, miR-126-3p, and miR-142-3p downregulated in the patients. Five of these (miR-16-5p, miR-22-3p, miR-92a-3p, miR-126-3p, miR-142-3p) were stably expressed over time in both CLZ-induced cardiotoxicity patients and CLZ-naïve healthy volunteers.Conclusions: Plasma miRNA are not useful biomarkers of CLZ-induced cardiotoxicity, however patients taking CLZ have significantly altered circulating miRNA compared to healthy volunteers.
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Affiliation(s)
- Kathryn E Burns
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Kieran D Deane-Alder
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Brandi L Bellissima
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Malcolm D Tingle
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
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Bottani M, Banfi G, Lombardi G. Perspectives on miRNAs as Epigenetic Markers in Osteoporosis and Bone Fracture Risk: A Step Forward in Personalized Diagnosis. Front Genet 2019; 10:1044. [PMID: 31737038 PMCID: PMC6831724 DOI: 10.3389/fgene.2019.01044] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Aging is associated with an increased incidence of age-related bone diseases. Current diagnostics (e.g., conventional radiology, biochemical markers), because limited in specificity and sensitivity, can distinguish between healthy or osteoporotic subjects but they are unable to discriminate among different underlying causes that lead to the same bone pathological condition (e.g., bone fracture risk). Among recent, more sensitive biomarkers, miRNAs — the non-coding RNAs involved in the epigenetic regulation of gene expression, have emerged as fundamental post-transcriptional modulators of bone development and homeostasis. Each identified miRNA carries out a specific role in osteoblast and osteoclast differentiation and functional pathways (osteomiRs). miRNAs bound to proteins or encapsulated in exosomes and/or microvesicles are released into the bloodstream and biological fluids where they can be detected and measured by highly sensitive and specific methods (e.g., quantitative PCR, next-generation sequencing). As such, miRNAs provide a prompt and easily accessible tool to determine the subject-specific epigenetic environment of a specific condition. Their use as biomarkers opens new frontiers in personalized medicine. While miRNAs circulating levels are lower than those found in the tissue/cell source, their quantification in biological fluids may be strategic in the diagnosis of diseases that affect tissues, such as bone, in which biopsy may be especially challenging. For a biomarker to be valuable in clinical practice and support medical decisions, it must be (easily) measurable, validated by independent studies, and strongly and significantly associated with a disease outcome. Currently, miRNAs analysis does not completely satisfy these criteria, however. Starting from in vitro and in vivo observations describing their biological role in bone cell development and metabolism, this review describes the potential use of bone-associated circulating miRNAs as biomarkers for determining predisposition, onset, and development of osteoporosis and bone fracture risk. Moreover, the review focuses on their clinical relevance and discusses the pre-analytical, analytical, and post-analytical issues in their measurement, which still limits their routine application. Taken together, research and clinical findings may be helpful for creating miRNA-based diagnostic tools in the diagnosis and treatment of bone diseases.
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Affiliation(s)
- Michela Bottani
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy
| | - Giuseppe Banfi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy.,Vita-Salute San Raffaele University, Milano, Italy
| | - Giovanni Lombardi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy.,Department of Physiology & Pharmacology, Gdańsk University of Physical Education & Sport, Gdańsk, Poland
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Abstract
Deregulation of microRNA expression has been shown to play an important role in human malignancies. The identification of circulating-free miRNAs in biofluids a decade ago led to great enthusiasm and motivation to develop non-invasive tests based on the expression of these small non-coding RNAs. Herein, we review the progress within the field of research for identifying circulating miRNA cancer biomarkers and discuss the advantages and challenges associated with this. We also discuss the methodological and analytical variables, which may influence the final miRNA quantification and the importance of standardizing pre-analytical, analytical, and post-analytical processes in order to enable a successful translation of the results from basic research into the clinics.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, The Bartholin Building, Bartholin Allé 6, 8000, Aarhus C, Denmark.,Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Azat M, Huojiahemaiti X, Gao R, Peng P. Long noncoding RNA MIAT: A potential role in the diagnosis and mediation of acute myocardial infarction. Mol Med Rep 2019; 20:5216-5222. [PMID: 31661125 DOI: 10.3892/mmr.2019.10768] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 07/19/2019] [Indexed: 11/06/2022] Open
Abstract
The long noncoding RNA myocardial infarction associated transcript (MIAT) has been shown to be a risk allele for myocardial infarction in a previous study. However, there is still controversy about whether MIAT can be used as a biomarker for acute myocardial infarction (AMI). Peripheral blood from patients with AMI and non‑AMI patients was collected to detect the expression levels of MIAT by reverse transcription‑quantitative PCR. Correlation analysis and receiver operating characteristic (ROC) curve analysis were performed to calculate the diagnostic value of MIAT. A rat AMI model was established to detect the expression of MIAT in plasma and cardiac samples. Neonatal rat cardiomyocytes were isolated and exposed to hypoxia, and MIAT small interfering RNAs were transfected into cells to test the expression levels of MIAT and to perform apoptosis‑related assays. The results showed that the plasma levels of MIAT were significantly increased in patients with AMI compared with non‑AMI patients. Correlation analysis showed that MIAT was positively associated with creatine kinase‑MB and cardiac troponin T (cTnT). ROC analysis indicated that MIAT had the same diagnostic value as cTnT. In addition, MIAT was expressed at low levels in the normal rat heart and was highly expressed in AMI hearts. Knockdown of MIAT significantly inhibited cardiomyocyte apoptosis. The present study demonstrated that MIAT may act as a novel potential biomarker for the diagnosis of AMI.
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Affiliation(s)
- Mayra Azat
- Department of Emergency Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Xiaokelaiti Huojiahemaiti
- Department of Emergency Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Ranran Gao
- Department of Emergency Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
| | - Peng Peng
- Department of Emergency Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830054, P.R. China
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Fang C, Li Y. Prospective applications of microRNAs in oral cancer. Oncol Lett 2019; 18:3974-3984. [PMID: 31579085 PMCID: PMC6757290 DOI: 10.3892/ol.2019.10751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 07/26/2019] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules that are generally encoded by endogenous genes and exert suppressive effects on post-transcriptional regulation of their target genes by translation repression or degradation of mRNA. This subsequently mediates activation or blocking of downstream signaling pathways associated with oral malignancies. Aberrant levels of certain miRNAs have been identified in cell experiments, clinical carcinomatous specimens, saliva, serum or plasma samples of patients with oral malignancies. miRNAs are associated with multiple aspects of oral cancer, including tumor growth, cellular proliferation, apoptosis, migration, invasion, metastasis, glycometabolism, radiosensitivity and chemosensitivity. miRNAs have the potential to be used in clinical applications as minimally invasive or non-invasive tools for early diagnosis and prognosis by the detection of serum, plasma and saliva levels, and may provide a new ancillary or additional reference index of traditional pathological grading and clinical staging. Furthermore, miRNAs may be used as prognostic biomarkers or targets for novel therapies for oral cancer.
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Affiliation(s)
- Chuan Fang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yadong Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Cheung KWE, Choi SYR, Lee LTC, Lee NLE, Tsang HF, Cheng YT, Cho WCS, Wong EYL, Wong SCC. The potential of circulating cell free RNA as a biomarker in cancer. Expert Rev Mol Diagn 2019; 19:579-590. [PMID: 31215265 DOI: 10.1080/14737159.2019.1633307] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ka Wan Emily Cheung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sin-yu Rachel Choi
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lok Ting Claire Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Nga Lam Ella Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Yin Tung Cheng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Elaine Yue Ling Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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50
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Cao W, Zhou D, Tang W, An H, Zhang Y. Discovery of plasma messenger RNA as novel biomarker for gastric cancer identified through bioinformatics analysis and clinical validation. PeerJ 2019; 7:e7025. [PMID: 31249732 PMCID: PMC6587939 DOI: 10.7717/peerj.7025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
Background Gastric cancer (GC) is the third leading cause of cancer-related death worldwide, partially due to the lack of effective screening strategies. Thus, there is a stringent need for non-invasive biomarkers to improve patient diagnostic efficiency in GC. Methods This study initially filtered messenger RNAs (mRNAs) as prospective biomarkers through bioinformatics analysis. Clinical validation was conducted using circulating mRNA in plasma from patients with GC. Relationships between expression levels of target genes and clinicopathological characteristics were calculated. Then, associations of these selected biomarkers with overall survival (OS) were analyzed using the Kaplan-Meier plotter online tool. Results Based on a comprehensive analysis of transcriptional expression profiles across 5 microarrays, top 3 over- and underexpressed mRNAs in GC were generated. Compared with normal controls, expression levels of collagen type VI alpha 3 chain (COL6A3), serpin family H member 1 (SERPINH1) and pleckstrin homology and RhoGEF domain containing G1 (PLEKHG1) were significantly upregulated in GC plasmas. Receiver-operating characteristic (ROC) curves on the diagnostic efficacy of plasma COL6A3, SERPINH1 and PLEKHG1 mRNAs in GC showed that the area under the ROC (AUC) was 0.720, 0.698 and 0.833, respectively. Combined, these three biomarkers showed an elevated AUC of 0.907. Interestingly, the higher COL6A3 level was significantly correlated with lymph node metastasis and poor prognosis in GC patients. High level of SERPINH1 mRNA expression was correlated with advanced age, poor differentiation, lower OS, and PLEKHG1 was also associated with poor OS in GC patients. Conclusion Our results suggested that circulating COL6A3, SERPINH1 and PLEKHG1 mRNAs could be putative noninvasive biomarkers for GC diagnosis and prognosis.
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Affiliation(s)
- Wei Cao
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Chinese Academy of Sciences, Xiamen, China
| | - Dan Zhou
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Chinese Academy of Sciences, Xiamen, China
| | - Weiwei Tang
- Department of Medical Oncology, Cancer Hospital, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China
| | - Hanxiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yun Zhang
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Chinese Academy of Sciences, Xiamen, China
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